Re: [QE-users] MPI error in pw.x
99 > > c_bands.f90 > > pw.x 0040C014 electrons_scf_552 > > electrons.f90 > > pw.x 00408DBD electrons_146 > > electrons.f90 > > pw.x 0057582B run_pwscf_132 > > run_pwscf.f90 > > pw.x 00406AC5 MAIN__ 77 > > pwscf.f90 > > pw.x 0040695E Unknown Unknown Unknown > > libc.so.6 2ACB4C4B7445 Unknown Unknown > > Unknown > > pw.x 00406869 Unknown Unknown Unknown > > > > Sample output below > > > > Parallel version (MPI), running on16 processors > > > > MPI processes distributed on 1 nodes R & G space division: > > proc/nbgrp/npool/nimage = 16 > > > > Reading cobalt.scf Message from routine > > read_cards :DEPRECATED: no units specified in > > ATOMIC_POSITIONS card Message > > from routine read_cards : > > > > ATOMIC_POSITIONS: units set to alat > > > > Current dimensions of program PWSCF are: > > > > Max number of different atomic species (ntypx) = 10 > > > > Max number of k-points (npk) = 4 > > > > Max angular momentum in pseudopotentials (lmaxx) = 3 > > > > Presently no symmetry can be used with electric field > > > > > > file Co.pz-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 4S 3D renormalized > > > > > > Subspace diagonalization in iterative solution of the eigenvalue problem: > > > > one sub-group per band group will be used > > > > scalapack distributed-memory algorithm (size of sub-group: 2* 2 procs) > > > > > > Parallelization info > > > > > > > > sticks: dense smooth PW G-vecs:dense smooth PW > > > > Min 13 13 4 2449 2449 462 > > > > Max 14 14 5 2516 2516 527 > > > > Sum 221 221 693994539945 > > > > Many thanks, > > > > Alex Durie > > PhD student > > Open University > > United Kingdom > > ___ > > users mailing list > > users@lists.quantum-espresso.org > > https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > -- next part -- > An HTML attachment was scrubbed... > URL: > <http://lists.quantum-espresso.org/pipermail/users/attachments/20181209/d619524d/attachment-0001.html> > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] make problem under Debian9
On Mon, May 7, 2018 at 11:46 AM, Prokudaylo Sergey wrote: > Dear All, > > please see my log attached. I try to get espress at debian9 installed at > Oracle Virtual Machine. > ./configure passed with success. make just made no effect. what is wrong ? there is no "make" program installed. axel. > regards, Sergey. > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [Pw_forum] heating and cooling vc-md
On Mon, Oct 23, 2017 at 3:04 PM, Jalil Mahdizadeh wrote: > What we were discusting about (solid-solid phase transition probably). > well, it depends on the specifics of the system, and whether reaxff is applicable depends on whether there is a suitable and suitably reliable parameter set. nobody but yourself or somebody working on the same kind of problem can make a definite statement. you'll have to carefully study the literature, make tests and benchmarks and also study the thermodynamics of the processes that you are modeling. none of that is specific to QE, either. i've told you about as much as somebody with a general stat mech and MD background can tell you. axel. > -- > S. J. Mahdizadeh > > On Oct 23, 2017 10:29 PM, "Axel Kohlmeyer" wrote: > > > > On Mon, Oct 23, 2017 at 2:58 PM, Jalil Mahdizadeh < > saja.mahdiza...@gmail.com> wrote: > >> Thank you Axel. Hence, I'm thinking about ReaxFF based MD instead. What >> do you think? >> > > using reaxff to do what? > > axel. > > > >> -- >> S. J. Mahdizadeh >> >> On Oct 23, 2017 10:21 PM, "Axel Kohlmeyer" wrote: >> >> >> >> On Mon, Oct 23, 2017 at 2:31 PM, Jalil Mahdizadeh < >> saja.mahdiza...@gmail.com> wrote: >> >>> Thanks god. I was thinking I'm some kind of hollow man nobody can see >>> me. However, dear axel recently a group of magicians accomplished such a >>> "doomed project" successfully. >>> >> please note that you asked about "phase transition" without any >> particular detail of what kind of transition you are after. in the most >> general case one would assume a solid-liquid or liquid-gas transition. >> those are activated processes with a significant barrier and all the issues >> i mentioned. in fact, if somebody is after determining a melting point or >> similar this way, even classical MD will fail. >> >> if you look at the transition in the paper you quote, it is a solid-solid >> transition with rather minimal changes to the geometry and probably a very >> small activation barrier, if any. yet, those folks still used a very large >> supercell. that is quite telling. >> >> at any rate, my statement, that any temperature increase will be "rapid" >> for AIMD simulations still stands. >> >> axel. >> >> >> >> >>> PHYSICAL REVIEW B 96, 054111 (2017). >>> -- >>> S. J. Mahdizadeh >>> >>> On Oct 23, 2017 9:16 PM, "Axel Kohlmeyer" wrote: >>> >>>> >>>> >>>> On Mon, Oct 23, 2017 at 1:04 PM, Jalil Mahdizadeh < >>>> saja.mahdiza...@gmail.com> wrote: >>>> >>>>> Dear QE users, >>>>>> >>>>>> I'm going to perform some vc-md with gradually heating/cooling >>>>>> process until achieving phase transition temperature. Does any body know >>>>>> how to do heating/cooling process in vc-md? I know that only "rescaling" >>>>>> option is implemented for vc-md. Could Nobody help me? >>>>>> >>>>> >>>> i suppose nobody has replied, because nobody wanted to tell you that >>>> what you are asking about, is a doomed project. >>>> >>>> at the time scales accessible to DFT based MD simulation, >>>> heating/cooling will *always* be rapid. >>>> also, it is a good idea to stay away from phase transition >>>> temperatures, since there you will have very bad sampling of phase space >>>> and suffer from massive finite size effects. >>>> >>>> axel. >>>> >>>> >>>> >>>>> >>>>>> Cheers. >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> S. J. Mahdizadeh >>>>> >>>>> ___ >>>>> Pw_forum mailing list >>>>> Pw_forum@pwscf.org >>>>> http://pwscf.org/mailman/listinfo/pw_forum >>>>> >>>> >>>> >>>> >>>> -- >>>> Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 >>>> College of Science & Technology, Temple University, Philadelphia PA, USA >>>> International Centre f
Re: [Pw_forum] heating and cooling vc-md
On Mon, Oct 23, 2017 at 2:58 PM, Jalil Mahdizadeh wrote: > Thank you Axel. Hence, I'm thinking about ReaxFF based MD instead. What do > you think? > using reaxff to do what? axel. > -- > S. J. Mahdizadeh > > On Oct 23, 2017 10:21 PM, "Axel Kohlmeyer" wrote: > > > > On Mon, Oct 23, 2017 at 2:31 PM, Jalil Mahdizadeh < > saja.mahdiza...@gmail.com> wrote: > >> Thanks god. I was thinking I'm some kind of hollow man nobody can see >> me. However, dear axel recently a group of magicians accomplished such a >> "doomed project" successfully. >> > please note that you asked about "phase transition" without any > particular detail of what kind of transition you are after. in the most > general case one would assume a solid-liquid or liquid-gas transition. > those are activated processes with a significant barrier and all the issues > i mentioned. in fact, if somebody is after determining a melting point or > similar this way, even classical MD will fail. > > if you look at the transition in the paper you quote, it is a solid-solid > transition with rather minimal changes to the geometry and probably a very > small activation barrier, if any. yet, those folks still used a very large > supercell. that is quite telling. > > at any rate, my statement, that any temperature increase will be "rapid" > for AIMD simulations still stands. > > axel. > > > > >> PHYSICAL REVIEW B 96, 054111 (2017). >> -- >> S. J. Mahdizadeh >> >> On Oct 23, 2017 9:16 PM, "Axel Kohlmeyer" wrote: >> >>> >>> >>> On Mon, Oct 23, 2017 at 1:04 PM, Jalil Mahdizadeh < >>> saja.mahdiza...@gmail.com> wrote: >>> >>>> Dear QE users, >>>>> >>>>> I'm going to perform some vc-md with gradually heating/cooling process >>>>> until achieving phase transition temperature. Does any body know how to do >>>>> heating/cooling process in vc-md? I know that only "rescaling" option is >>>>> implemented for vc-md. Could Nobody help me? >>>>> >>>> >>> i suppose nobody has replied, because nobody wanted to tell you that >>> what you are asking about, is a doomed project. >>> >>> at the time scales accessible to DFT based MD simulation, >>> heating/cooling will *always* be rapid. >>> also, it is a good idea to stay away from phase transition >>> temperatures, since there you will have very bad sampling of phase space >>> and suffer from massive finite size effects. >>> >>> axel. >>> >>> >>> >>>> >>>>> Cheers. >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> S. J. Mahdizadeh >>>> >>>> _______ >>>> Pw_forum mailing list >>>> Pw_forum@pwscf.org >>>> http://pwscf.org/mailman/listinfo/pw_forum >>>> >>> >>> >>> >>> -- >>> Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 >>> College of Science & Technology, Temple University, Philadelphia PA, USA >>> International Centre for Theoretical Physics, Trieste. Italy. >>> >>> _______ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste. Italy. > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] heating and cooling vc-md
On Mon, Oct 23, 2017 at 2:31 PM, Jalil Mahdizadeh wrote: > Thanks god. I was thinking I'm some kind of hollow man nobody can see me. > However, dear axel recently a group of magicians accomplished such a > "doomed project" successfully. > please note that you asked about "phase transition" without any particular detail of what kind of transition you are after. in the most general case one would assume a solid-liquid or liquid-gas transition. those are activated processes with a significant barrier and all the issues i mentioned. in fact, if somebody is after determining a melting point or similar this way, even classical MD will fail. if you look at the transition in the paper you quote, it is a solid-solid transition with rather minimal changes to the geometry and probably a very small activation barrier, if any. yet, those folks still used a very large supercell. that is quite telling. at any rate, my statement, that any temperature increase will be "rapid" for AIMD simulations still stands. axel. > PHYSICAL REVIEW B 96, 054111 (2017). > ------ > S. J. Mahdizadeh > > On Oct 23, 2017 9:16 PM, "Axel Kohlmeyer" wrote: > >> >> >> On Mon, Oct 23, 2017 at 1:04 PM, Jalil Mahdizadeh < >> saja.mahdiza...@gmail.com> wrote: >> >>> Dear QE users, >>>> >>>> I'm going to perform some vc-md with gradually heating/cooling process >>>> until achieving phase transition temperature. Does any body know how to do >>>> heating/cooling process in vc-md? I know that only "rescaling" option is >>>> implemented for vc-md. Could Nobody help me? >>>> >>> >> i suppose nobody has replied, because nobody wanted to tell you that >> what you are asking about, is a doomed project. >> >> at the time scales accessible to DFT based MD simulation, heating/cooling >> will *always* be rapid. >> also, it is a good idea to stay away from phase transition temperatures, >> since there you will have very bad sampling of phase space and suffer from >> massive finite size effects. >> >> axel. >> >> >> >>> >>>> Cheers. >>>> >>>> >>>> >>> >>> >>> >>> -- >>> S. J. Mahdizadeh >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> >> -- >> Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste. Italy. >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] heating and cooling vc-md
On Mon, Oct 23, 2017 at 1:04 PM, Jalil Mahdizadeh wrote: > Dear QE users, >> >> I'm going to perform some vc-md with gradually heating/cooling process >> until achieving phase transition temperature. Does any body know how to do >> heating/cooling process in vc-md? I know that only "rescaling" option is >> implemented for vc-md. Could Nobody help me? >> > i suppose nobody has replied, because nobody wanted to tell you that what you are asking about, is a doomed project. at the time scales accessible to DFT based MD simulation, heating/cooling will *always* be rapid. also, it is a good idea to stay away from phase transition temperatures, since there you will have very bad sampling of phase space and suffer from massive finite size effects. axel. > >> Cheers. >> >> >> > > > > -- > S. J. Mahdizadeh > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] [QE-GPU] qe version and gpu model
On Tue, Sep 19, 2017 at 6:05 AM, Stefano Prina wrote: > Hi > > I'm looking for confirmation that qe-6.1 version has not already > released whit gpu support. > > Where should I look for this info ? ( http://www.quantum-espresso.org/ > news/gpgpu/ this poage is 2011 old 0: ) ) > > > I would compile qe-gpu for this gpu : > GP102 [GeForce GTX 1080 Ti] > > is this hw supported ? it should work, but you should not expect acceleration due to its extremely limited support for double precision operations. axel. > > where can i gater this info from official source ? > > > regards > stefano > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] psuedopotentials between atoms
On Mon, Jun 12, 2017 at 3:24 PM, SMITH, BRIGETTE wrote: > Hello, > I am an undergraduate student looking to find a way to calculate > Lennard-Jones potentials for Uranium for Molecular Dynamics simulations. I > am looking for the potentials between Uranium and Uranium, Uranium and > Nitrogen, Uranium and Hydrogen, etc. If anyone could direct me to an > example it would be sincerely appreciated. > brigette, sorry, if this is not the kind of answer that you want to hear, but what you are describing is work for experienced domain experts, not an undergraduate student. force-field parameterization is not a simple black box process, but can be quite tedious and complicated. even if you would have an example procedure for a given system, it may not be transferable for your target. especially classical potentials like lennard-jones are only applicable to specific compounds and usually not transferable to any combination of elements. uranium is a particularly difficult element, that cannot be simply mapped to a spherical point potential, but requires to include complex manybody interactions. hell, it is already difficult to build well transferable and ghost state free uranium pseudopotentials for quantum chemical calculations with plain DFT functionals. do you have somebody overseeing your work? you should talk to that person or have that person put you in contact with an expert and discuss your project. from your description it looks like it is rather ill-conceived. axel. > Thank you, > Brigette Smith > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Installing Quantum ESPRESSO on Windows
On Wed, Apr 26, 2017 at 7:49 AM, Wilbert James Futalan < wilbert.james.futa...@gmail.com> wrote: > Hi all! > > I understand that installing Quantum ESPRESSO on Windows has its cons, but > I would like to know if it's possible to install v. 6.0 in Windows. > > For the time being, I decided to install 5.3.0 because it's the latest > version with the Windows .exe installer. I also tried to install MPICH so I > can use multiple cores; unfortunately, its latest versions are in .tar.gz > format. I want to avoid installing v. 1.4 of MPICH ( > http://www.mpich.org/static/downloads/1.4.1p1/) . I have come up with two > possible solutions, but I do not know how to implement any of them: > > a) convert .tar.gz to .msi format. > > b) use Microsoft MPI v8 (https://www.microsoft.com/en- > us/download/details.aspx?id=54607). I suppose that the syntax would not > be > mpiexec -localonly # pw... but something else. > > Can anyone advise me what to do? > neither your option a) nor your option b) are practical. the .tar.gz packages you are talking about contain source code, not binaries. so you'd have to compile MPI for yourself. doing this is a highly non-trivial and complicated process and that is the main reason, why there are so few binary packages for MPI on windows. both, MPICH and OpenMPI have abandoned them, as it takes too much effort for too few active users. the Microsoft MPI package has the issue, that you need to use microsoft's compilers, but those lack a fortran compiler and thus are useless to compile QE. the "old" v1.4 binary version of MPICH is still providing all of the MPI that is required by QE, so why not use it? that package is also compatible with GNU compilers for windows (either Cygwin or MingGW) and for a native compilation on windows, probably having a Cygwin setup should be your best option. another option worth considering is to install the native linux client for windows (if you are running windows 10) and then compile/install an ubuntu linux executable. another option would be to install/use a linux virtual machine. that will most certainly make the compilation/installation part simpler, as you would not have to deal with linux/windows portability issues. as somebody who has build QE binaries for windows for several years, resolving the (often minor) portability issues, that almost always happen when new versions of QE are released, have been the major time drain and are the reason why there are no new packages. it just has become too much work for no more benefit (initially the motivation was to have binaries for tutorials where linux was not an option, but now virtual machines have become a viable alternative with *much* less overhead, so native windows executables are no longer a requirement). axel. > > Thank you. > -- > Jim F. > > > _______ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] QE version for windows
On Mon, Apr 3, 2017 at 9:08 AM, Paolo Giannozzi wrote: > It's not "abolished", but it depends upon the good will and time > availability of somebody who knows (or is willing to learn) how to do > it > yes, and the person who did this in the past, doesn't have the time to play catch-up with all the changes to QE to make it work reasonably on windows anymore. i think building QE from source directly using Cygwin is still supposed to work, but it requires a good understanding of a unix build environment *and* the incompatibilities of windows with unix as well as the restrictions of Cygwin. the existing windows installer packages, instead were built on Linux using cross-compilers. this avoids many of the windows specific issues of the build process, but requires a better understanding of the compilation process. on top of that, you have to learn and understand how to setup and deploy software using NSIS installers. i am happy to share my notes and scripts that worked for me on older versions of QE, but i will not hand them to people with limited knowledge and am not able in any way to support those and provide additional explanations. in short, if don't have the experience and skill to figure out on your own, how this kind stuff works, don't bother to ask me. axel. > > Paolo > > On Wed, Mar 29, 2017 at 9:27 AM, zhizhichangjiuye > wrote: > > Dear QE family, > > > > I am using the QE 5.3 for windows (binary packages). The QE is updating > but > > I did not see new versions for windows. > > I want to know whether the updating of windows is abolished or there > will be > > new windows versions in the future. > > > > Thank you. > > > > Dawei Wen > > Chemical engineering department > > Tohoku U. > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] CPMD
On Thu, Jan 5, 2017 at 11:39 PM, ashkan shekaari wrote: > Dear experts, > > > Once a CPMD simulation at zero pressure, constant volume, and at a finite > temperature (say, T=70 K) is performed (temperature is kept constant by > rescaling the nuclear degrees of freedom), what kind of MD (NVE, or, NPT) is > going to be used? neither. axel. > > > > > Regards, > Ashkan > > Ashkan Shekaari > Plasma Physics Research Center > Science and Research Branch > I A U, 14778-93855 Tehran, Iran. > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] (no subject)
On Thu, Oct 6, 2016 at 2:08 PM, stefano de gironcoli wrote: > don't really know anymore... Quantum ESPRESSO 6.0 has been just released. MS-MPI only supports MS Visual C++, which has no fortran support. axel > stefano > > > On 06/10/2016 20:01, Kanak Datta wrote: > > Dear researchers > > Can Quantum Espresso 3.0 can be run with mpi distribution provided by > microsoft i.e. MSMPI? In that case, will the command be the same? > > Best > Kanak > > -- > Kanak Datta > Lecturer > Department of Electrical and Electronic Engineering > Bangladesh University of Engineering and Technology > Dhaka-1205 > Website: https://sites.google.com/site/kanak0806085/home > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Parallel execution
On Wed, Oct 5, 2016 at 10:17 AM, Kanak Datta wrote: > Dear researchers > > I have been facing problem while running quantum espresso in parallel > format. I have been using the code: > > mpiexec -localonly -np 8 pw Si.scf.out i don't think that this exact command line could have ever worked. to the best of my knowledge, the -localonly flag is only available for windows, and then it *replaces* the -np flag and takes the number of processes as an argument. > The code seemed to work fine. However, when I run the same code now, I get > the following message: > > Unknown option: -localonly that means, either you installed a different MPI library, or are running on a different machine (using a different OS?). > I am trying to run espresso version 5.3 compatible to mpich2 64 bit. I think > the problem is with mpi. > > Can anyone help in this regard? has anyone else faced this issue before? > Apart from mpi, what else can be used to perform parallel execution on > windows platform? MPI is the thing and it works. it has little to do with windows, but with the application you use. axel. > > Please let me know at your earliest. > > -- > Kanak Datta > Lecturer > Department of Electrical and Electronic Engineering > Bangladesh University of Engineering and Technology > Dhaka-1205 > Website: https://sites.google.com/site/kanak0806085/home > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] [Pw_Forum] Parallel execution and configuration issues
On Mon, Sep 19, 2016 at 6:01 AM, Konrad Gruszka wrote: > Dear colleagues, > > I'm Writing to our community to clarify once and for all issues with > parallel pwscf execution. > > By lecture of PWSCF manual, I know that there are several levels of > parallelization, including FFTW and more. At the same time, I'm quite sure > that most of beginner QE users do not have complicated clusters, but are > rather starting with decent multicore PC's. > > There are two main parallel mechanisms (known to me) namely: MPI and > OpenMP. Because I'm using Ubuntu, there is free Hydra MPI software (mpich) as far as i know, ubuntu ships with *two* MPI package OpenMPI (not OpenMP) and MPICH and OpenMPI is the default MPI package. OpenMP is not a specific package, but a compiler feature (and included in GCC). > and also free OpenMP. From what I know (please correct me if this is wrong) > MPI software is used for parallelization within one multicore PC and OpenMP > is used to make parallelization between several PC's. that is incorrect. OpenMP is *restricted* to multi-core CPUs, because it is based on multi-threading. MPI (i.e. either OpenMPI or MPICH, but not both at the same time) can be used for intra-node or inter-node or a combination of both. in many cases, using only MPI is the most effective parallelization approach. only when you have many cores per node and communication contention become a performance limiting factor, you will run faster with MPI+OpenMP > So my reasoning is: because I have 2 multicore PCs (namely PC1: 6 cores 2 > threads, and PC2: 4 cores 2 threads, giving in overall PC1: 12 and PC2 8 > 'cores') on both PC1 and PC2 I've installed hydra MPI (for parallelization > within multicores) and on both there are OpenMP for communication between > PC1 and PC2 to act as 'cluster'. you seem to be confusing OpenMPI with OpenMP. for your system, an MPI-only configuration (using the default MPI, i.e. OpenMPI) should work well. no need to worry about the additional complications from OpenMP until you have a larger, more potent machine. > I've configured OpenMP so both machines sees one another and when I'm > starting some pw.x job using openmp on both machines i see that processors > are 100% busy. Problem is that in produced output files I can see several > repeats of pwscf output (just like several separate pwscf processes write > into one file at the same time). that is an indication of compiling executable without MPI support or with support for an MPI library *different* from the one used when launching the executable. > The QE was configured and compiled with --enable-openmp on both machines and > when I simply run pw.x on PC1 it writes: > > "Parallel version (MPI & OpenMP), running on 12 processor cores" > > I'm running job with this command: > > mpirun.openmp -np 20 pw.x -in job.in > job.out > > and as said before, both machines are occupied with this job (tested using > htop). > > Looking for help in this topic I often get to the truth 'please contact your > system administrator', but sadly I am the administrator! then look for somebody with experience in linux clusters. you definitely want somebody local to help you, that can look over your shoulder while you are doing things and explain stuff. this is really tricky to do over e-mail. these days it should not be difficult to find somebody, as using linux in parallel is ubiquitous in most computational science groups. there also is a *gazillion* of material available online including talk slides from workshops and courses and online courses and self-study material. HPC university has an aggregator for such material at: http://hpcuniversity.org/trainingMaterials/ axel. > > Could some one with a similar hardware configuration could comment here how > to achieve properly working cluster? > > Sincerely yours > > Konrad Gruszka > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] different computing cores lead to different results when calculating phonon spectrum by ph.x
;> However, when I using 128 computing cores, the corresponding results turn >> to be: >> >> ** >> freq (1) = -1.941478 [THz] = -64.760743 [cm-1] >> ( -0.00 0.00 -0.00 0.00 0.237504 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.237504 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.237504 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.237504 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.237504 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.237504 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.209612 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.209612 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.209612 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.209612 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.209612 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.209612 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.364201 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.364201 0.00 ) >> ( -0.00 0.00 -0.00 0.00 0.364201 0.00 ) >> freq (2) = -0.797967 [THz] = -26.617308 [cm-1] >> ( -0.217955 0.00 -0.132999 0.00 -0.00 0.00 ) >> ( -0.217955 0.00 -0.132999 0.00 -0.00 0.00 ) >> ( -0.212134 0.00 -0.133209 0.00 0.00 0.00 ) >> ( -0.212134 0.00 -0.133209 0.00 0.00 0.00 ) >> ( -0.215227 0.00 -0.138145 0.00 0.00 0.00 ) >> ( -0.215227 0.00 -0.138145 0.00 0.00 0.00 ) >> ( -0.230258 0.00 -0.129133 0.00 -0.00 0.00 ) >> ( -0.230258 0.00 -0.129133 0.00 -0.00 0.00 ) >> ( -0.205571 0.00 -0.130026 0.00 0.00 0.00 ) >> ( -0.205571 0.00 -0.130026 0.00 0.00 0.00 ) >> ( -0.218687 0.00 -0.150959 0.00 0.00 0.00 ) >> ( -0.218687 0.00 -0.150959 0.00 0.00 0.00 ) >> ( -0.228822 0.00 -0.140474 0.00 0.00 0.00 ) >> ( -0.224086 0.00 -0.140645 0.00 -0.00 0.00 ) >> ( -0.226602 0.00 -0.144661 0.00 -0.00 0.00 ) >> freq (3) = -0.797967 [THz] = -26.617308 [cm-1] >> ( -0.136570 0.00 0.212256 0.00 -0.00 0.00 ) >> ( -0.136570 0.00 0.212256 0.00 -0.00 0.00 ) >> ( -0.136360 0.00 0.218077 0.00 0.00 0.00 ) >> >> So, why do different computing cores lead to different results? Does >> someone encounter the same problems? >> >> By the way, is it reasonable for the negative frequency (such as freq ( >> 1) = -1.940214 [THz] = -64.718584 [cm-1]) ? >> >> >> (2) With different computing cores, I always get the phonon spectrum with >> small imaginary frequency no matter how I adjust the parameters suggested by >> other guys. >> >> So can someone give me some useful suggestions to eliminate the imaginary >> frequency? >> >> >> Thanks for your time, >> >> Xiaoming >> >> Department of Materials Science and Engineering, University of Utah >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] PWscf compilation error
On Mon, Jun 13, 2016 at 2:44 PM, udayagiri sai babu wrote: > OS version= centos 5.11 > arch = x86_64 > kernel = 2.6.18-410.el5 > I am running only ./configure with out any additional flags. PFA the > ./configure output. Thank you. centos 5.11 is from the stone ages. its fortran compiler is *way* outdated to be able to compile quantum espresso. axel. > > On Mon, Jun 13, 2016 at 8:42 PM, Máximo Ramírez > wrote: >> >> can you give more technical details of your computer like OS version, >> arch, kernel compiler. >> >> Whene you run ./configure you are using any other parameters or you are >> using qe internal libs? >> >> El 13/06/16 a las 05:00, Paolo Giannozzi escribió: >> > Would you mind reducing the size of your fonts? it's a problem of YOUR >> > compiler on YOUR machine, not of Quantum ESPRESSO. The line: >> >USE, intrinsic :: iso_c_binding >> > is a perfectly legitimate line. LIkely you have an old compiler that >> > doesn't accept this relatively new (so to speak: 2003 standard, I >> > guess) syntax >> > ___ >> > Pw_forum mailing list >> > Pw_forum@pwscf.org >> > http://pwscf.org/mailman/listinfo/pw_forum >> >> -- >> >> Máximo Ramírez >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > Regards > U.Sai Babu > Research Scholar, > Deformation Mechanisms Modeling Group, > Materials Engineering Department, > IISc Bangalore, > India. > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] pw.x warning message : IEEE_DENORMAL - reg.,
On Mon, Jun 13, 2016 at 5:34 AM, Muthu V wrote: > Dear all > while o trying to use pw.x i'm getting the error message > > running the scf calculation...Note: The following floating-point exceptions > are signalling: IEEE_DENORMAL > done > > running the band-structure calculation for Si...Note: The following > floating-point exceptions are signalling: IEEE_DENORMAL > done > > how to solve this floating point error these are no errors. > > > thank you > > -- > Muthu V > Sri Paramakalyani College > Alwarkurichi, India > -- > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Unable to Successfully Install Parallel Version of QE on Windows
On Wed, Jun 1, 2016 at 1:06 PM, Suchit wrote: > Hi Axel, > > Good idea! QE-5.3.0 from the site you provided (after uninstalling the one > that I had installed from QE site) didn't work either. However, QE-5.2.1 > from both the alternate site as well as the QE download site successfully > runs an SCF calculation in parallel. All these tests were performed with the > 64-bit MPICH2 versions. thanks a lot. that is helpful. now i need to look for the problem, which is likely on the linux machine where those packages are compiled and assembled. :-( axel. > > Thanks, > --Suchit > > On Wed, Jun 1, 2016 at 8:55 AM, Axel Kohlmeyer wrote: >> >> On Wed, Jun 1, 2016 at 11:02 AM, Suchit wrote: >> > Hi Axel, >> > >> > Thank you for your response. I determined that the serial version is >> > installed by running an SCF calculation on Silicon, and looking at the >> > first >> > few lines of the output file, which reads either "Serial version" or >> > "Parallel version (MPI & OpenMP)" depending on which version is being >> > used. >> > I also ran "mpiexec -np 4 pw -i Si.scf.in > Si.scf.out," which performed >> > SCF >> > calculations in serial mode in 4 different processors. >> >> can you please try to uninstall the QE version on your windows >> partition and check against the binaries posted on the alternate >> download site here: >> >> http://rpm.lammps.org/qe4win/release/index.html >> >> please also make certain, that you have only one version, serial or >> parallel installed at the same time. >> >> > Now, however, I have finally decided to just perform QE research using a >> > Linux virtual machine which is actually working out pretty well, and the >> > parallel version is working. >> >> that is good for you, but i'd like to track down the origin of this, >> i.e. whether there is an issue with the installer packages or the >> binaries on qe-forge are mixed up. so in the interest of other QE >> users on windows, please make the test i suggested. >> >> thanks, >> axel. >> >> >> > Best Regards, >> > --Suchit >> >> >> >> -- >> Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste. Italy. > > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Unable to Successfully Install Parallel Version of QE on Windows
On Wed, Jun 1, 2016 at 11:02 AM, Suchit wrote: > Hi Axel, > > Thank you for your response. I determined that the serial version is > installed by running an SCF calculation on Silicon, and looking at the first > few lines of the output file, which reads either "Serial version" or > "Parallel version (MPI & OpenMP)" depending on which version is being used. > I also ran "mpiexec -np 4 pw -i Si.scf.in > Si.scf.out," which performed SCF > calculations in serial mode in 4 different processors. can you please try to uninstall the QE version on your windows partition and check against the binaries posted on the alternate download site here: http://rpm.lammps.org/qe4win/release/index.html please also make certain, that you have only one version, serial or parallel installed at the same time. > Now, however, I have finally decided to just perform QE research using a > Linux virtual machine which is actually working out pretty well, and the > parallel version is working. that is good for you, but i'd like to track down the origin of this, i.e. whether there is an issue with the installer packages or the binaries on qe-forge are mixed up. so in the interest of other QE users on windows, please make the test i suggested. thanks, axel. > Best Regards, > --Suchit -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Unable to Successfully Install Parallel Version of QE on Windows
On Tue, May 31, 2016 at 10:32 PM, Suchit wrote: > Dear All, > > I would like to get parallel version of the QE code working on Windows. I > first installed MPICH2 and integrated it into my system by following the > instructions in the document "QE-on-Windows.pdf," available in the QE > download page among the QE-5.3.0 related files. After installing MPICH2, I > installed "qe-5.3.0-64bit-mpich2.exe." Despite following the instructions in > the mentioned PDF file, it seems the QE installer is unable to detect the > presence of a parallel environment and only downloads the serial version of > the code. I just wanted to check if other researchers have successfully > installed the parallel version of QE for Windows and whether you could share > tips for successfully installing it? the installer doesn't download anything and it doesn't try to detect anything. the parallel version simply will not work without the mpich package installed. how did you determine that the version you have installed is the serial version? axel. > > Thank you. > > With Best Regards, > --Suchit > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Problem with QE-5.2.1 in building exx routines
On Tue, Feb 9, 2016 at 10:28 AM, Mahmoud Payami Shabestari wrote: > I went through all the "exx_*.f90" routines and it seems the problem was not > what I mentioned in my last post. However, whatever the cause of the error > is, it is in these routines (I do not know the exact reason). Maybe there is > some small programming error which is ignored by newer versions of > compilers?! if you get an "internal compiler error", the problem is with the specific compiler version. please note that intel 11.1 is six years old and its compliance with newer fortran standards is sub-par and their implementation has bugs. upgrading to a newer version of the compiler is the way to proceed, or you'll have to stick with older versions of QE or you have to place a strategic if statement to cause the code to abort and thus disable this feature and remove the offending code. mind you, the last of those approaches still leaves plenty of doubts about the compiler, as there may be other cases, where you do not get an internal compiler error, but just miscompiled code. in short, trying to fix code to accommodate an outdated compiler is a fool's errand. axel. > > > -Original Message- > From: Lorenzo Paulatto > To: PWSCF Forum > Date: Mon, 8 Feb 2016 13:23:30 +0100 > Subject: Re: [Pw_forum] Problem with QE-5.2.1 in building exx routines > > > On 8 Feb 2016 11:41 a.m., "Mahmoud Payami Shabestari" > wrote: >> >> Ciao Paolo, >> Thank you very much for your reply. >> As it is mentioned in the UG-5.3.0, "Also, compilers that do not support >> intrinsic calls flush, get_environment_variable,get_command_argument, >> command_argument_count are no longer supported since v.5.2.1.", the old >> compiler complains about "internal error" which most probably is due to the >> above-mentioned calls present in "exx_X.f90" routines in the CP package. > This is very unlikely, there are no calls to those intrinsic functions in > EXX, and even if there were, they wouldn't cause an internal compiler error. > Upgrade your compiler or ask your system administrator if you cannot. > For others there is no problem. >> Thank you again, >> mahmoud >> >>> >>> >>> Hi Mahmoud, it depends upon the kind of problem. If it is an "internal >>> compiler error", there is little that can be done. What does the old >>> compiler complain about exactly? Paolo >>> Dear QE users and developers, >>> >>> Kindly, I encountered with some problems in compiling the CP package >>> using Intel ifort-11.1.080. The problem is referred to some line in >>> exx_psi.f90. >>> However, using a newer version of Intel Compiler such as Compxe-2013, the >>> compilation proceeds without any problem. >>> Is there any simple solution other than moving to new versions of >>> compilers? >>> Any suggestions is highly appreciated. >>> >>> Mahmoud Payami >>> Theoretical and Computational Physics Group >>> AEOI, Tehran, Iran >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] accuracy of the energies printed to file
On Sat, Jan 30, 2016 at 3:38 PM, Małgorzata Wawrzyniak-Adamczewska wrote: > Hello Stefano, > > > > the problem is that i would like to study the band structure etc. around the > K point in graphene and graphene with adatoms with SO. With the accuracy of > order 10^-4 I think I will not be able to see some important details. on the other hand, i think it would be very advisable to do some sensitivity analysis with respect to what level of systematic and numerical accuracy is possible for the eigenvalue spectrum. chances are, that you may just be digging around in numerical noise or that any systematic differences may due to technicalities and not the underlying physics. i.e. (small) changes to cutoffs, grids, number of atoms, type of pseudopotentials, number of processors may cause changes of equal or greater magnitude and thus would then render findings questionable (to put it mildly). axel. > > Best wishes, > > > > Malgorzata Wawrzyniak-Adamczewska > > Adam Mickiewicz University, Poznan, Poland > > > > Message: 2 Date: Fri, 29 Jan 2016 14:13:33 +0100 From: stefano de gironcoli > Subject: Re: [Pw_forum] accuracy of the energies printed > to file To: pw_forum@pwscf.org Message-ID: <56ab657d.9000...@sissa.it> > Content-Type: text/plain; charset="utf-8" do you really need to print the > eigenvalues with 10^-7 eV accuracy ? stefano On 29/01/2016 14:08, Ma?gorzata > Wawrzyniak-Adamczewska wrote: > > Dear QE users and developers, I was wondering if there is a possibility to > increase the accuracy of the energies printed in the e.g. scf.out file or > bands.out file? I find the accuracy of D^-4: > --- > k = 0. 0. 0. ( 2289 PWs) bands (ev): -21.2789 -21.2789 -9.3618 > -9.3618 -4.7450 -4.7450 -4.7357 -4.7357 1.2876 1.2876 2.0573 2.0573 2.2604 > 2.2604 4.3273 4.3273 4.9921 4.9921 6.6656 6.6656 6.6734 6.6734 8.2476 8.2476 > 9.4082 9.4082 9.8358 9.8358 10.9914 10.9914 13.5952 13.5952 > - > and would like to increase it to D^-7. Thank you in advance, Malgorzata > Wawrzyniak > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Electrostatic Potential Map
On Fri, Jan 15, 2016 at 1:48 PM, Ari P Seitsonen wrote: > > Dear Reza, > > This is actually a question on the visualisation programs, not of > Quantum ESPRESSO. Yes, QE can produce the two cube files needed, then you > need to find a visualisation program that can do the mapping. I have once > upon a time used gOpenMol for that, but it is no longer maintained nor > possibly available anymore, I do not know if VMD can do it - there is at > least some discussion on the mailing list - > http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/ looks like > it. yes, VMD can do it, if the OpenGL support in the graphics driver is sufficiently capable. these days most of them are. axel. > Molekel, I do not know (and I cannot connect to 'http://molekel.cscs.ch/' > just now - is the project continued, does some one know?). > > If you do manage to do it, please let us know; Good Luck! > > Greetings, > >apsi > > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=- > Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/ > Ecole Normale Supérieure (ENS), Département de Chimie, Paris > Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935 > > > > On Fri, 15 Jan 2016, reza vatan wrote: > > Dear Lorenzo, >> >> Many thanks for your reply. >> >> I already have the cube file of my structure obtained from pp.x >> calculation. >> I want to visualize that cube file in a 3D picture with a color scale in >> such a way that each color represent the intensity of charge in that >> specific volume or area (something like the attached picture). I can plot >> a >> plane containing different color inside the cell by using VMD and xCrySDen >> to visualize that cube file but I can not plot the 3D charge density plot >> (which I think some people call it electrostatic potential map). >> >> My first question is if I'm able to get those 3D charge density plot using >> the cube file obtaining from pp.x calculations. >> And if yes, my second question is that: How can I do it. >> >> Many thanks in advances. >> >> Best, >> Reza >> >> On Fri, Jan 15, 2016 at 2:28 AM, Lorenzo Paulatto >> wrote: >> Dear Reza, >> I do not know exactly what you mean by electrostatic potential >> map, but I >> think this is something you can do with pp.x after the pw.x >> calculation is >> finished. Have a look at PP/Doc/INPUT_PP.html (it takes 10 >> minutes to read it) >> and you'll have an idea of the quantities you can plot (the >> total and hartree >> potentials among them) and how you can plot them (i.e. you can >> plot a plane >> inside the unit cell). Please come back to us if there is any >> detail you >> cannot understand. >> >> hth, kind regards >> >> On Thursday, January 14, 2016 11:04:47 PM reza vatan wrote: >> > Dear all, >> > >> > I just wanted to know if the Quantum Espresso has the ability >> to calculate >> > the electrostatic potential map of a structure. If yes how I >> can visualize >> > the resulted output files? >> > >> > Thanks in advances. >> > >> > Best, >> > Reza >> >> -- >> Dr. Lorenzo Paulatto >> IdR @ IMPMC -- CNRS & Université Paris 6 >> +33 (0)1 44 275 084 / skype: paulatz >> http://www.impmc.upmc.fr/~paulatto/ >> 23-24/4é16 Boîte courrier 115, >> 4 place Jussieu 75252 Paris Cédex 05 >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> >> >> >> > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] using all cores for processing
On Fri, Jan 15, 2016 at 4:33 AM, siddheshwar chopra wrote: > For more information, I installed 5.2.1 setup for windows. And got the > following error: > > Error while connecting to host, No connection could be made because the > target machine actively refused it. (10061) > Connect on sock (host=Matrix, port=8678) failed, exhaused all end points > Unable to connect to 'Matrix:8678', > sock error: Error = -1 this is a problem of your MPI configuration, or rather your firewall blocking MPI message passing to remote machines. this needs to be properly configured and you need to follow the MPI installation and configuration instructions specific to the MPI package that you installed. have you followed the instructions given here? http://rpm.lammps.org/qe4win.html since you are running on your local machine only, try: mpiexec -localonly 2 pw.x -in si.inp > si.out also, it is *very* unlikely that you'll get any speedup from hyperthreading, more likely the added processes will cause congestion on the memory bus and slow you down. axel. > > > I was running QE using the following command: > > mpiexec -np 4 pw.x > > Please help. > > Regards, > > On Fri, Jan 15, 2016 at 1:23 PM, siddheshwar chopra > wrote: >> >> Dear Users, >> I want to use the Windows version of Quantum Espresso. I have a 2 core (4 >> threads) system. How can I run program using all 4 threads? It doesn't work >> with qcenv_p.bat. What are the priminary packages needed for parallel >> execution? >> >> Regards, >> >> -- >> Dr. Siddheshwar chopra, >> M.Sc., Ph.D (Physics) >> Assistant Professor (Physics), >> Amity University, Noida, India. >> > > > > -- > Dr. Siddheshwar chopra, > M.Sc., Ph.D (Physics) > Assistant Professor (Physics), > Amity University, Noida, India. > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] relax does not converge after 100 iterations
-0.7870485578264509 -0.5268114277294700 > Si 0.6209657124110631 0.7870485578264510 -0.5268114277294700 > Si 0.6209657124110631 -0.7870485578264509 0.5268114277294700 > Si -0.6209657124110629 0.7870485578264510 0.5268114277294700 > Si -0.5268114277294699 -0.6209657124110630 -0.7870485578264509 > Si -0.5268114277294699 0.6209657124110630 0.7870485578264510 > Si 0.5268114277294701 0.6209657124110630 -0.7870485578264511 > Si 0.5268114277294701 -0.6209657124110630 0.7870485578264510 > Si -0.7870485578264510 -0.5268114277294700 -0.6209657124110629 > Si 0.7870485578264510 -0.5268114277294700 0.6209657124110630 > Si -0.7870485578264510 0.5268114277294700 0.6209657124110630 > Si 0.7870485578264510 0.5268114277294700 -0.6209657124110631 > Si -0.7870485578264510 -0.6209657124110630 -0.5268114277294700 > Si 0.7870485578264510 0.6209657124110630 -0.5268114277294700 > Si -0.7870485578264510 0.6209657124110630 0.5268114277294700 > Si 0.7870485578264510 -0.6209657124110630 0.5268114277294700 > Si -0.6209657124110629 -0.5268114277294700 -0.7870485578264509 > Si 0.6209657124110631 -0.5268114277294700 0.7870485578264510 > Si 0.6209657124110631 0.5268114277294700 -0.7870485578264511 > Si -0.6209657124110629 0.5268114277294700 0.7870485578264510 > Si -0.5268114277294699 -0.7870485578264509 -0.6209657124110629 > Si -0.5268114277294699 0.7870485578264510 0.6209657124110630 > Si 0.5268114277294701 -0.7870485578264509 0.6209657124110630 > Si 0.5268114277294701 0.7870485578264510 -0.6209657124110631 > Si -0.7200428553989950 -0.7200428553989949 -0.5738142830984929 > Si 0.7200428553989950 0.7200428553989950 -0.5738142830984930 > Si 0.7200428553989950 -0.7200428553989949 0.5738142830984930 > Si -0.7200428553989950 0.7200428553989950 0.5738142830984930 > Si -0.5738142830984930 -0.7200428553989949 -0.7200428553989949 > Si -0.5738142830984930 0.7200428553989950 0.7200428553989950 > Si 0.5738142830984930 0.7200428553989950 -0.7200428553989952 > Si 0.5738142830984930 -0.7200428553989949 0.7200428553989950 > Si -0.7200428553989950 -0.5738142830984929 -0.7200428553989949 > Si 0.7200428553989950 -0.5738142830984929 0.7200428553989950 > Si -0.7200428553989950 0.5738142830984930 0.7200428553989950 > Si 0.7200428553989950 0.5738142830984930 -0.7200428553989952 > Si -0.5712314265114920 -0.7207342829023089 -0.4287685734885080 > Si 0.5712314265114920 0.7207342829023090 -0.4287685734885079 > Si 0.5712314265114920 -0.7207342829023089 0.4287685734885080 > Si -0.5712314265114920 0.7207342829023090 0.4287685734885080 > Si -0.4287685734885080 -0.5712314265114920 -0.7207342829023088 > Si -0.4287685734885080 0.5712314265114920 0.7207342829023090 > Si 0.4287685734885080 0.5712314265114920 -0.7207342829023090 > Si 0.4287685734885080 -0.5712314265114920 0.7207342829023090 > Si -0.7207342829023090 -0.4287685734885079 -0.5712314265114918 > Si 0.7207342829023089 -0.4287685734885079 0.5712314265114920 > Si -0.7207342829023090 0.4287685734885079 0.5712314265114920 > Si 0.7207342829023089 0.4287685734885079 -0.5712314265114921 > Si -0.6457914352416989 -0.6457914352416990 -0.3542085647583010 > Si 0.6457914352416991 0.6457914352416990 -0.3542085647583009 > Si 0.6457914352416991 -0.6457914352416990 0.3542085647583010 > Si -0.6457914352416989 0.6457914352416990 0.3542085647583010 > Si -0.6461057118007110 -0.6461057118007110 -0.6461057118007110 > Si -0.5729028565543040 -0.5729028565543040 -0.5729028565543040 > Si 0.6461057118007110 0.6461057118007110 -0.6461057118007110 > Si 0.5729028565543040 0.5729028565543040 -0.5729028565543040 > Si 0.6461057118007110 -0.6461057118007110 0.6461057118007110 > Si 0.5729028565543040 -0.5729028565543040 0.5729028565543040 > Si -0.6461057118007110 0.6461057118007110 0.6461057118007110 > Si -0.5729028565543040 0.5729028565543040 0.5729028565543040 > Si -0.4999 -0.6439485686165939 -0.4999 > Si 0.5001 0.6439485686165940 -0.4999 > Si -0.4999 -0.4999 -0.6439485686165939 > Si -0.4999 0.5000 0.6439485686165940 > Si -0.6439485686165939 -0.4999 -0.4998 > Si 0.6439485686165941 -0.5000 0.5000 > CELL_PARAMETERS alat > 35.00.00.0 > 0.035.00.0 > 0.00.035.0 > K_POINTS crystal > 1 > 0.0 0.0 0.0 1.000 > > > -- &g
Re: [Pw_forum] pwscf generates duplicate k-points
On Thu, Dec 17, 2015 at 12:14 PM, Cohen, Ronald wrote: > The attached input gives duplicate k-points: > with > K_POINTS automatic > 2 2 2 0 0 0 > > number of k points=12 gaussian smearing, width (Ry)= 0.0020 >cart. coord. in units 2pi/alat > k(1) = ( 0.000 0.000 0.000), wk = 0.125 > k(2) = ( 0.000 0.000 -0.4859086), wk = 0.125 > k(3) = ( 0.000 -0.500 0.000), wk = 0.250 > k(4) = ( 0.000 -0.500 -0.4859086), wk = 0.250 > k(5) = ( -0.500 -0.500 0.000), wk = 0.125 > k(6) = ( -0.500 -0.500 -0.4859086), wk = 0.125 > k(7) = ( 0.000 0.000 0.000), wk = 0.125 > k(8) = ( 0.000 0.000 -0.4859086), wk = 0.125 > k(9) = ( 0.000 -0.500 0.000), wk = 0.250 > k( 10) = ( 0.000 -0.500 -0.4859086), wk = 0.250 > k( 11) = ( -0.500 -0.500 0.000), wk = 0.125 > k( 12) = ( -0.500 -0.500 -0.4859086), wk = 0.125 > with > K_POINTS automatic > 2 2 2 1 1 1 > > number of k points= 2 gaussian smearing, width (Ry)= 0.0020 >cart. coord. in units 2pi/alat > k(1) = ( 0.250 0.250 0.2429543), wk = 1.000 > k(2) = ( 0.250 0.250 0.2429543), wk = 1.000 > >cryst. coord. > k(1) = ( 0.250 0.250 0.250), wk = 1.000 > k(2) = ( 0.250 0.250 0.250), wk = 1.0 > > This is very sick! Hard to believe for something so simple. This why sick? one each for spin up and for spin down. > happens on two different machines and builds and versions. Is there a > fix? Thank you! > > > Ronald Cohen > > > > --- > Ronald Cohen > Geophysical Laboratory > Carnegie Institution > 5251 Broad Branch Rd., N.W. > Washington, D.C. 20015 > rco...@carnegiescience.edu > office: 202-478-8937 > skype: ronaldcohen > https://twitter.com/recohen3 > https://www.linkedin.com/profile/view?id=163327727 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] find thread and core number
On Thu, Dec 10, 2015 at 5:25 PM, mohammed shambakey wrote: > Hi > > when running pw.x on a multi-node cluster using OpenMP+MPI, is it possible > to record each thread id, running on which core, in which node? not without using special settings and special libraries. both MPI ranks and OpenMP thread-ids are by default 100% hardware agnostic and are assigned to individual cores based on the kernel scheduling algorithms, thus those can change quite rapidly. many MPI and OpenMP implementations allow to use OS-specific APIs to assign "affinity" of an MPI rank or a thread to specific cores (or rather provide an assignment pattern). axel. > > Regards > > -- > Mohammed > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] default parallelization and parallelization of bands.x
ik > Department of Physics > University of Konstanz > > Am Samstag, 05. Dezember 2015 02:37 CET, stefano de gironcoli > schrieb: > > > > > On 04/12/2015 22:53, Maxim Skripnik wrote: > > Hello, > > I'm a bit confused by the parallelization scheme of QE. First of all, I run > calculations on a cluster with usually 1 to 8 nodes, each of which has 16 > cores. There is a very good scaling of pw.x e.g. for structural relaxation > jobs. I do not specify any particular parallelization scheme as mentioned in > the documentation, i.e. I start the calculations with > mpirun -np 128 pw.x < job.pw > on 8 nodes, 16 cores each. According to the documentation ni=1, nk=1 and > nt=1. So in which respect are the calculations parallelized by default? Why > do the calculations scale so well without specifying ni, nk, nt, nd? > > R and G parallelization is performed. > wavefunctions' planewaves, density planewaves and slices of real space > objects are distributed across 128 processors. A report of how this is done > is given at the beginning of the output. > Did you had a look to it ? > > > Second question is, whether one can speed up bands.x calculations. Up to now > I start these this way: > mpirun -np 64 bands.x < job.bands > on 4 nodes, 16 cores each. Does it make sense to define nb for bands.x? If > yes, what would be reasonable values? > > expect no gain. band parallelization is not implemented in bands. > > stefano > > > > > > > > > The systems of interest consist of typically ~50 atoms with periodic > boundaries. > > Maxim Skripnik > Department of Physics > University of Konstanz > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] invalid flag
On Fri, Nov 20, 2015 at 6:07 PM, Hugo Siles wrote: > Hello, > > I have installed espresso-5.2.1 on fedora 22, with some minor difficulties, > but it has been installed, I run all the tests, and as far as I could see > all of them passed. > However when running one of the samples from the tutorials with the > following command: > pw.x Si.sample.out > I get the following message during execution: > > [hsiles@localhost exercise1]$ pw.x Si.sample.out > Note: The following floating-point exceptions are signalling: > IEEE_INVALID_FLAG IEEE_DENORMAL. > > There is an output file > > Does the message means any thing to worry about ?? yes and no. the messages by itself are harmless. either of the two signaled cases can happen in normal calculations. however, they also indicate that you may be subject to a significant performance penalty due to how the GNU C library and compilers manage your floating point unit. often the difference is rather small, but in pathological cases, the difference can be substantial. since you are running on a desktop machine, i would not worry too much. this is usually avoided by using, e.g. a custom math library (libm) and BLAS library and also a compiler that bypasses a lot of the "lets-be-as-correct-as-possible-even-if-it-doesn't-make-sense-for-most-people" nonsense the GNU people seem to love so much. axel. > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Getting_an_Error
On Fri, Nov 20, 2015 at 3:05 PM, Mofrad, Amir Mehdi (MU-Student)
wrote:
> I didn't quite understand what you said. I cut the content of my file and
> pasted it to another file. However, when I run it, it gives me the same
> error.
that can happen for example, if you create a file that is missing the
end-of-line character (if you are using a decent editor, this should
not happen, but ...). just try adding add a couple of empty lines at
the end.
other than that, if you are using a non-ASCII character set (e.g. when
using UTF-8 encoding or and/or native language support), sometimes
"funky" characters are inserted (e.g. different width spaces) to make
the text look "nicer". however, since those are not ASCII characters,
they are not recognized by text mode programs, despite looking
(mostly) the same as their ASCII counter part.
if that still doesn't make sense to you, i suggest you google around
and find out more about these issues.
axel.
>
>
> Amir M. Mofrad
>
> University of Missouri
>
>
>
>
> From: pw_forum-boun...@pwscf.org on behalf of
> Paolo Giannozzi
> Sent: Friday, November 20, 2015 1:42 PM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] Getting_an_Error
>
> Unexplained input errors are often a consequence of strange characters or of
> the presence of ^M characters in the file. Your input (taken with a cut and
> paste) works for me
>
> Paolo
>
> On Fri, Nov 20, 2015 at 7:50 PM, Mofrad, Amir Mehdi (MU-Student)
> wrote:
>>
>> Dear all quantum users and experts,
>>
>>
>> I'm trying to run an scf calculation on a zeolite but I'm not successful
>> because I keep getting the following error on my terminal which I don't know
>> what it is:
>>
>> At line 136 of file read_cards.f90
>>
>> Fortran runtime error: End of file
>>
>>
>> Here is my input file just in case you might need to take a look at:
>>
>>
>> &control
>> calculation='scf'
>> restart_mode='from_scratch'
>> prefix='SOD'
>> tstress=.true.
>> tprnfor=.true.
>> pseudo_dir='/global/espresso/pseudo/'
>> outdir='./scratch/'
>> verbosity='high'
>> etot_conv_thr=1e-8
>> forc_conv_thr=1e-7
>> wf_collect=.true.
>> /
>> &system
>> ibrav=0
>> nat=36
>> ntyp=2
>> ecutwfc=30
>> ecutrho=300
>> nbnd=100
>> /
>> &electrons
>> diagonalization='cg'
>> mixing_mode='plain'
>> mixing_beta=0.7
>> conv_thr=1e-10
>> /
>>
>> ATOMIC_SPECIES
>> Si 28.086 Si.pbe-n-rrkjus_psl.0.1.UPF
>> O 15.9994 O.pbe-n-rrkjus_psl.0.1.UPF
>>
>>
>> ATOMIC_POSITIONS bohr
>> O 4.223852 10.209245 16.553687
>> O 12.694549 1.738548 8.082990
>> O 16.194639 10.209245 16.553687
>> O 7.723942 1.738548 8.082990
>> O 16.194639 10.209245 4.582900
>> O 7.723942 1.738548 13.053597
>> O 4.223852 10.209245 4.582900
>> O 12.694549 1.738548 13.053597
>> O 16.194639 4.223852 10.568293
>> O 7.723942 12.694549 19.038991
>> O 16.194639 16.194639 10.568293
>> O 7.723942 7.723942 2.097596
>> O 4.223852 16.194639 10.568293
>> O 12.694549 7.723942 2.097596
>> O 4.223852 4.223852 10.568293
>> O 12.694549 12.694549 2.097596
>> O 10.209245 16.194639 4.582900
>> O 1.738548 7.723942 13.053597
>> O 10.209245 16.194639 16.553687
>> O 1.738548 7.723942 8.082990
>> O 10.209245 4.223852 16.553687
>> O 1.738548 12.694549 8.082990
>> O 10.209245 4.223852 4.582900
>> O 1.738548 12.694549 13.053597
>> Si 5.973897 10.209245 19.038991
>> Si 14.444594 1.738548 10.568293
>> Si 14.444594 10.209245 2.097596
>> Si 5.973897 1.738548 10.568293
>> Si 1.738548 5.973897 10.568293
>> Si 10.209245 14.444594 19.038991
>> Si 1.738548 14.444594 10.568293
>> Si 10.209245 5.973897 2.097596
>> Si 10.209245 1.738548 6.332945
>> Si 1.738548 10.209245 14.803642
>> Si 10.209245 1.738548 14.803642
>> Si 1.738548 10.209245 6.332945
>>
>> K_POINTS {automatic}
>> 9 9 9 0 0 0
>>
>> CELL_PARAMETERS angstrom
>> 8.848 0.000 0.000
>> 0.000 8.848 0.000
>> 0.000 0.000 8.848
>>
>>
>> Best,
>>
>>
>>
>> Amir M. Mofrad
>>
>> University of Missouri
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
>
> --
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
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Re: [Pw_forum] adding vacuum
On Mon, Nov 16, 2015 at 3:30 PM, Nicola Marzari wrote: > On 16/11/2015 21:17, Jaret Qi wrote: >> but that will cost time! > > you are right! just keep the 4 angstroms, no one will notice. > > (actually, skip the calculations altogether, and make up some > plausible numbers in your paper - that will be even faster). right! after all, we already know that the answer to the ultimate question about life, the universe and everything is 42. ;-) axel. > > nicola > >> >> >> >> On Monday, November 16, 2015 9:26 AM, Pascal Boulet >> wrote: >> >> >> Hello, >> >> 4 angstroms wide seems to be very small for the vacuum. As a rule of >> thumb you should use at least 2.5 times the thickness of your slab. This >> is what we observed in the calculations of semiconductor slabs. This has >> to be tested. >> >> Pascal >> >> Le 16 nov. 2015 à 16:40, Jaret Qi > <mailto:jare...@yahoo.com>> a écrit : >> >>> Hello all, >>> I am trying to minimize the interaction between my system and its >>> periodic images. To do so, I introduced a layer of vacuum along the >>> z-axis by increasing the lattice vector along the z-axis by 4A. At the >>> same time, I fixed it by using this parameter: cell_dofree='2Dxy', >>> But I have noticed atoms that are close to the vacuum move along the >>> z-axis and vacuum is decreasing, is this wrong or I should use >>> different cell_dofree? >>> note:relaxation still ongoing, not relaxed yet. >>> >>> >>> JARET, >>> ASU >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org <mailto:Pw_forum@pwscf.org> >>> http://pwscf.org/mailman/listinfo/pw_forum >> >> -- >> Pascal Boulet /- MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE/ >> Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie >> Niemen - 13013 Marseille >> Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 >> Site : http://allos.up.univ-mrs.fr/pascal - Email : >> pascal.bou...@univ-amu.fr <mailto:pascal.bou...@univ-amu.fr> >> /Afin de respecter l'environnement, merci de n'imprimer cet email que si >> nécessaire./ >> >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > -- > -- > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > Director, National Centre for Competence in Research NCCR MARVEL, EPFL > http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] need help to learn Quantum Espresso
On Wed, Oct 14, 2015 at 2:35 PM, rojib raj wrote: > hello, > i am a new user of Quantum Espresso.so i don't know everything about it. > i need a help. > I want to simulate large area graphene. Can i use "Periodic Boundary > Condition" to do it ? > don't do that right away. start with simpler problems. everybody makes mistakes initially, and thus you want to do them on a system that is so simple that you can spot them. if you start with your research project right away, you will never know whether a problem is a real problem or just due to you inexperience. > > And please suggest me some ways, how can i develop my skill in this > software ??? > read the documentation, practice with the extensive tutorial material, read/study suggested text books, find yourself a tutor or experienced colleague that is willing to discuss and/or study with you. axel. > > thanks in advance, > Rojib > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] INSTALL QE ON MAC PRO SIX CORE (INTEL XEON E5)
gt; iotk_base.f90(101): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(102): warning #5117: Bad # preprocessor line > > #ifdef __IOTK_COMPLEX1 > > -^ > > iotk_base.f90(100): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_REAL4 = __IOTK_REAL4 > > ---^ > > iotk_base.f90(104): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(105): warning #5117: Bad # preprocessor line > > #ifdef __IOTK_COMPLEX2 > > -^ > > iotk_base.f90(103): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_COMPLEX1 = __IOTK_COMPLEX1 > > -^ > > iotk_base.f90(107): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(108): warning #5117: Bad # preprocessor line > > #ifdef __IOTK_COMPLEX3 > > -^ > > iotk_base.f90(106): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_COMPLEX2 = __IOTK_COMPLEX2 > > -^ > > iotk_base.f90(110): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(111): warning #5117: Bad # preprocessor line > > #ifdef __IOTK_COMPLEX4 > > -^ > > iotk_base.f90(109): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_COMPLEX3 = __IOTK_COMPLEX3 > > -^ > > iotk_base.f90(113): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(114): warning #5117: Bad # preprocessor line > > #ifdef __IOTK_CHARACTER1 > > -^ > > iotk_base.f90(112): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_COMPLEX4 = __IOTK_COMPLEX4 > > -^ > > iotk_base.f90(116): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(117): warning #5117: Bad # preprocessor line > > #ifdef __IOTK_CHARACTER2 > > -^ > > iotk_base.f90(115): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_CHARACTER1 = __IOTK_CHARACTER1 > > -^ > > iotk_base.f90(119): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(120): warning #5117: Bad # preprocessor line > > #ifdef __IOTK_CHARACTER3 > > -^ > > iotk_base.f90(118): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_CHARACTER2 = __IOTK_CHARACTER2 > > -^ > > iotk_base.f90(122): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(123): warning #5117: Bad # preprocessor line > > #ifdef __IOTK_CHARACTER4 > > -^ > > iotk_base.f90(121): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_CHARACTER3 = __IOTK_CHARACTER3 > > -^ > > iotk_base.f90(125): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(124): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_CHARACTER4 = __IOTK_CHARACTER4 > > -^ > > iotk_base.f90(133): warning #5117: Bad # preprocessor line > > #ifdef __IOTK_STREAMS > > -^ > > iotk_base.f90(130): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_header_kind = __IOTK_HEADER_KIND > > ---^ > > iotk_base.f90(136): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_record_kind = __IOTK_RECORD_KIND > > -^ > > iotk_base.f90(139): warning #5117: Bad # preprocessor line > > #endif > > -^ > > iotk_base.f90(137): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_record_length = __IOTK_RECORD_LENGTH > > ---^ > > iotk_base.f90(143): error #5192: Lead underscore not allowed > > character, parameter :: iotk_newline = __IOTK_NEWLINE > > -^ > > iotk_base.f90(144): error #5192: Lead underscore not allowed > > character, parameter :: iotk_eos = __IOTK_EOS > > -^ > > iotk_base.f90(174): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_maxargs = __IOTK_MAXARGS > > ---^ > > iotk_base.f90(260): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_unitmin_def = __IOTK_UNITMIN > > ---^ > > iotk_base.f90(262): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_unitmax_def = __IOTK_UNITMAX > > ---^ > > iotk_base.f90(264): error #5192: Lead underscore not allowed > > integer, parameter :: iotk_error_unit_def = __IOTK_ERROR_UNIT > > --^ > > iotk_base.f90(266): catastrophic error: Too many errors, exiting > > compilation aborted for iotk_base.f90 (code 1) > > make[2]: *** [iotk_base.o] Error 1 > > make[1]: *** [libiotk] Error 2 > > make: *** [libiotk] Error 2 > > > > Sorry for the inconvenience. Regards > M. C. Reyna Méndez Camacho. > > > > From: lorenzo.paula...@impmc.upmc.fr > > To: pw_forum@pwscf.org > > Date: Mon, 7 Sep 2015 15:39:57 +0200 > > Subject: Re: [Pw_forum] INSTALL QE ON MAC PRO SIX CORE (INTEL XEON E5) > > > > > On Monday, September 07, 2015 08:00:48 AM reyna mendez camacho wrote: > > > Hi good day: > > > I am trying to install quantum espresso in a Mac Pro 2013, can you > > > recommend some tutorial or modifications to Intel XeonPhi brand ?, but > when > > > compiling files for errors in libiotk and iotk.f90. Thank you very much > > > > > > Reyna Méndez Camacho. > > > > Please be more specific. > > > > kind regards > > > > -- > > Dr. Lorenzo Paulatto > > IdR @ IMPMC -- CNRS & Université Paris 6 > > +33 (0)1 44 275 084 / skype: paulatz > > http://www.impmc.upmc.fr/~paulatto/ > > 23-24/4é16 Boîte courrier 115 > > 4 place Jussieu 75252 Paris Cédex 05 > > > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Displaying charge density difference
On Tue, Aug 25, 2015 at 10:33 AM, Ozan Dernek wrote: > Hi, > I want to display the difference of charge densities of a bimetallic > structure by using VMD. > this appears to be a VMD question and thus would be off-topic here, but should be posted to the VMD mailing list. > But the .cube file has only the charge density information. Is it possible > to obtain charge density difference by using weight flag or should I do > separate calculations ? (For both cases an explanation about how to do them > will be much appreciated.) > how can you compute a density difference, if you have only a density? what weight flag where and how would it be applied? it is difficult to explain something, if you provide incomplete information. axel. p.s.: you already tried your luck elsewhere and there is a pattern that you don't describe your problems very well, which hints at a lack of fundamental understanding. you are thus strongly advised to discuss this with your PI/adviser/supervisor or (senior) colleagues. mailing lists can provide advice to solve technical problems, but it is required that you can formulate your problem well. if not, it will be difficult to give meaningful advice, as any technically focused advice will likely exceed your understanding. > > Cheers, > Ozan > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] segmentation fault
On Fri, Aug 14, 2015 at 1:20 PM, Vishal Gupta wrote: > Sorry, I should've mentioned. > I asked them but they said there might be something wrong with the QE input > file. If that was the case, the file shouldn't have been running fine with 7 > processors but it is. Could there really be something wrong with the input > file ? sysadmins often say this, so they don't have to check it out, or when they don't know what they are doing. if they *know* that there is something wrong with the input, then they should at the very least tell you what it is. but i agree that if it works with less processors, it should work with more. unless you are using some very unusual settings when launching the job. more likely is that you are running out of memory on the machine or are hitting a stack size limit or something similar. your system manager(s) should be able to figure this out and/or advise you how to run that you are using less memory, or with a hybrid MPI plus OpenMP parallelization or whatever else is possible on the specific machine. in any case, it doesn't really sound like a QE problem. axel. > Sorry if I am asking stupid doubts but I am little new at this. > Vishal Gupta > B.Tech. 3rd year Mechanical > Indian Institute of Technology Ropar > Rupnagar (140001), Punjab, India. > Email :- vishal.gu...@iitrpr.ac.in > > On Fri, Aug 14, 2015 at 10:32 PM, Axel Kohlmeyer wrote: >> >> On Fri, Aug 14, 2015 at 12:58 PM, Vishal Gupta >> wrote: >> > I've been running an SCF calculation for a fee Ni system on High >> > performance >> > cluster. The job runs fine with processors 7 or less but it always leads >> > to >> > segmentation fault if the no of processors exceeds 7. >> > The job takes 4-5 days for the run. >> > Is there any way to increase the no of processors so that it doesn't >> > lead to >> > the error ? >> > mpirun noticed that process rank 0 with PID 6353 on node c7c exited on >> > signal 11 (Segmentation fault). >> > or excessive memory leakage. >> >> that is really a question your should ask the system manager(s) or >> user support people of the machine that you are running on. >> >> axel. >> >> >> > >> > Thank You >> > Vishal Gupta >> > B.Tech. 3rd year Mechanical >> > Indian Institute of Technology Ropar >> > Rupnagar (140001), Punjab, India. >> > Email :- vishal.gu...@iitrpr.ac.in >> > >> > ___ >> > Pw_forum mailing list >> > Pw_forum@pwscf.org >> > http://pwscf.org/mailman/listinfo/pw_forum >> >> >> >> -- >> Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste. Italy. >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] segmentation fault
On Fri, Aug 14, 2015 at 12:58 PM, Vishal Gupta wrote: > I've been running an SCF calculation for a fee Ni system on High performance > cluster. The job runs fine with processors 7 or less but it always leads to > segmentation fault if the no of processors exceeds 7. > The job takes 4-5 days for the run. > Is there any way to increase the no of processors so that it doesn't lead to > the error ? > mpirun noticed that process rank 0 with PID 6353 on node c7c exited on > signal 11 (Segmentation fault). > or excessive memory leakage. that is really a question your should ask the system manager(s) or user support people of the machine that you are running on. axel. > > Thank You > Vishal Gupta > B.Tech. 3rd year Mechanical > Indian Institute of Technology Ropar > Rupnagar (140001), Punjab, India. > Email :- vishal.gu...@iitrpr.ac.in > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Compilation crash with intel13
On Thu, Aug 13, 2015 at 2:01 PM, Samuel Poncé wrote: > Dear Axel, > > Intel 13 stands for the version of the intel compiler I've tested. It is i understood that. you asked for what the reason was, and for me the logical conclusion from your data would be that the intel 13 compiler was the problem. > actually intel 13.5.192 to be more accurate. > > Best, > > Samuel > > On 13 August 2015 at 14:13, Axel Kohlmeyer wrote: >> >> On Thu, Aug 13, 2015 at 9:08 AM, Samuel Poncé >> wrote: >> > Dear all, >> > >> > I've noticed that the latest trunk version of QE (r11674) does not >> > compile >> > on intel 13 >> > >> > The problematic routine is in PW/src >> > mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL >> > -D__FFTW3 >> > -D__MPI -D__PARA -D__SCALAPACK >> > -I/home/farmer/local/fftw3_intel13/include >> > -I../../iotk/src -I../../Modules -c force_lc.f90 >> > >> > force_lc.f90(20): error #6580: Name in only-list does not exist. >> > [ESM_FORCE_LC] >> > USE esm, ONLY : esm_force_lc, do_comp_esm, esm_bc >> > ^ >> > compilation aborted for force_lc.f90 (code 1) >> > >> > I've checked that the esm.mod and esm.o file existed and that the >> > esm_force_lc is indeed public and should be accepted >> > >> > The same version of QE with the same flags (mkl+external fftw 3.3.4) >> > does >> > compile without problem on intel 12 and intel 15. >> > >> > Any idea on what the problem might be? >> >> intel 13? >> >> > >> > Best, >> > >> > Samuel Ponce >> > >> > ___ >> > Pw_forum mailing list >> > Pw_forum@pwscf.org >> > http://pwscf.org/mailman/listinfo/pw_forum >> >> >> >> -- >> Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste. Italy. >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Compilation crash with intel13
On Thu, Aug 13, 2015 at 9:08 AM, Samuel Poncé wrote: > Dear all, > > I've noticed that the latest trunk version of QE (r11674) does not compile > on intel 13 > > The problematic routine is in PW/src > mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D__FFTW3 > -D__MPI -D__PARA -D__SCALAPACK -I/home/farmer/local/fftw3_intel13/include > -I../../iotk/src -I../../Modules -c force_lc.f90 > > force_lc.f90(20): error #6580: Name in only-list does not exist. > [ESM_FORCE_LC] > USE esm, ONLY : esm_force_lc, do_comp_esm, esm_bc > ^ > compilation aborted for force_lc.f90 (code 1) > > I've checked that the esm.mod and esm.o file existed and that the > esm_force_lc is indeed public and should be accepted > > The same version of QE with the same flags (mkl+external fftw 3.3.4) does > compile without problem on intel 12 and intel 15. > > Any idea on what the problem might be? intel 13? > > Best, > > Samuel Ponce > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Computer cluster Parallel run:-Reg
On Tue, Aug 11, 2015 at 7:01 AM, Suresh A wrote: > Respected Sir/Friends, > I have formed a PC beowulf cluster (X86_64 old PC's made > on 2007) and installed quantum espresso-5.2.0 in it. Now the cluster is > running very slowly than the single core i5 processor, DDR3 RAM with 1600MHZ > speed. The following is my observation in single core i5 processor and in > beowulf cluster for the titanium dioxide supercell of size 2x2x1. One more > thing is, in cluster every node has 2GB DDR2 RAM with speed 667 MHZ. for i5 > processor 8GB with 1600 HZ. > > total cpu time spent upto now is408.7 secs (for i5 CPU having > 1600MHZ) > > total cpu time spent upto now isit is keepon running more than 1 hour > (for one single processor in PC cluster) > > total cpu time spent upto now is1402 secs ( for -ni 10 -nk 10 in PC > cluster) > > > > Is this due to RAM speed, size or anything else? it is due to *everything*: clock rate, memory speed, memory architecture, processor architecture, processor cache size, disk caching efficiency, availability of SIMD instructions, compiler, libraries. the speed difference you quote seems quite normal for comparing a single core on current hardware versus 8 year old hardware. axel. > > Looking forward to your valuable suggestions > > With Regards, > A.Suresh, > Research Scholar, > Madurai Kamaraj University, > Madurai. > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Band structure calculation using Quantum ESPRESSO
On Aug 9, 2015 11:57 PM, "sapna bondwal" wrote: > > Dear all, > > I want to know the steps involved in the band structure calculation of small molecule, say SiH4 using QE. What are are the concerned executables? In which order they must be used to get a clear picture of the electronic structure and band gap.Please give some small example exercise to practice the step by step use of executables correctly. How should that be possible, when small molecules have no bands? Axel > > Thank you in advance. > > -- > > Sapna Bondwal > Research Scholar > IIT ROORKEE > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] error: tcp_peer_recv_connect_ack
6 >> C 7.30907 6.93029 3.56166 >> C 23.70057 2.93304 3.56166 >> C 6.56849 1.06421 9.09734 >> C 22.95999 5.06146 9.09734 >> C 23.51465 7.25282 6.17782 >> C 7.12315 3.25557 6.17782 >> C 24.25523 0.74168 0.64214 >> C 7.86373 4.73893 0.64214 >> C 21.16001 7.74028 6.99710 >> C 4.76851 3.74303 6.99710 >> C 21.90060 0.25422 1.46142 >> C 5.50910 4.25147 1.46142 >> C 21.00252 6.87857 5.99071 >> C 4.61102 2.88132 5.99071 >> C 21.74310 1.11593 0.45503 >> C 5.35160 5.11318 0.45503 >> C 27.41664 7.76370 5.98186 >> C 11.02514 3.76645 5.98186 >> C 28.15722 0.23080 0.44618 >> C 11.76572 4.22805 0.44618 >> H 27.59489 0.54455 5.42718 >> H 11.20339 4.54180 5.42718 >> H 26.85431 7.44995 10.96286 >> H 10.46280 3.45270 10.96286 >> H 28.18126 7.63147 6.56310 >> H 11.78976 3.63422 6.56310 >> H 28.92184 0.36303 1.02742 >> H 12.53034 4.36028 1.02742 >> C 27.26323 6.60922 5.13933 >> C 10.87173 2.61197 5.13933 >> C 26.52265 1.38528 10.67501 >> C 10.13115 5.38253 10.67501 >> H 27.61795 5.83339 5.59879 >> H 11.22645 1.83614 5.59879 >> H 28.35854 2.16111 0.06311 >> H 11.96704 6.15836 0.06311 >> H 27.78169 6.73853 4.33001 >> H 11.39019 2.74128 4.33001 >> H 27.04111 1.25597 9.86569 >> H 10.64961 5.25322 9.86569 >> C 13.44202 0.18298 1.85556 >> C 29.83352 4.18023 1.85556 >> C 12.70144 7.81152 7.39124 >> C 29.09294 3.81427 7.39124 >> H 13.72839 7.55876 1.16581 >> H 30.11989 3.56151 1.16581 >> H 12.98780 0.43574 6.70150 >> H 29.37930 4.43299 6.70150 >> H 14.02273 0.95930 1.82235 >> H 30.41423 4.95655 1.82235 >> H 13.28214 7.03520 7.35803 >> H 29.67364 3.03795 7.35803 >> C 13.55775 7.53144 3.17416 >> C 29.94925 3.53419 3.17416 >> C 12.81716 0.46306 8.70984 >> C 29.20866 4.46031 8.70984 >> H 13.68661 0.21518 3.85616 >> H 30.07811 4.21243 3.85616 >> H 12.94602 7.77932 9.39184 >> H 29.33752 3.78207 9.39184 >> H 14.33307 6.94883 3.18191 >> H 30.72457 2.95158 3.18191 >> H 13.59248 1.04567 8.71759 >> H 29.98398 5.04292 8.71759 >> K_POINTS automatic >> 1 2 2 0 0 0 >> >> >> Thanks and regards >> >> >> Stephan Ludwig >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] error: tcp_peer_recv_connect_ack
26 > F 13.26118 3.34243 10.76026 > F 30.47339 6.23106 5.35854 > F 14.08189 2.23381 5.35854 > F 29.73280 1.76344 10.89422 > F 13.34130 5.76069 10.89422 > F 29.96030 7.30601 3.28598 > F 13.56880 3.30876 3.28598 > F 29.21972 0.68849 8.82166 > F 12.82821 4.68574 8.82166 > F -0.26088 7.52461 5.52461 > F 16.13062 3.52736 5.52461 > F -1.00147 0.46989 11.06029 > F 15.39003 4.46714 11.06029 > C 4.77264 7.25965 3.40666 > C 21.16414 3.26240 3.40666 > C 4.03205 0.73485 8.94234 > C 20.42355 4.73210 8.94234 > C 7.12868 7.79932 2.56191 > C 23.52018 3.80207 2.56191 > C 6.38809 0.19518 8.09759 > C 22.77959 4.19243 8.09759 > C 24.86295 7.22306 5.97079 > C 8.47145 3.22581 5.97079 > C 25.60353 0.77144 0.43510 > C 9.21203 4.76869 0.43510 > C 18.61690 7.45190 6.77235 > C 2.22540 3.45465 6.77235 > C 19.35749 0.54260 1.23667 > C 2.96599 4.53985 1.23667 > C 11.00638 7.55584 2.60731 > C 27.39788 3.55859 2.60731 > C 10.26580 0.43866 8.14299 > C 26.65730 4.43591 8.14299 > C 9.65436 7.44215 2.72245 > C 26.04587 3.44490 2.72245 > C 8.91378 0.55235 8.25813 > C 25.30528 4.54960 8.25813 > C 16.66566 0.56358 7.82192 > C 0.27416 4.56083 7.82192 > C 17.40624 7.43092 2.28624 > C 1.01474 3.43367 2.28624 > H 17.33387 0.90270 8.42088 > H 0.94237 4.89995 8.42088 > H 18.07446 7.09180 2.88520 > H 1.68295 3.09455 2.88520 > H 15.99844 0.08734 8.32234 > H -0.39307 4.08459 8.32234 > H 16.73902 7.90716 2.78666 > H 0.34752 3.90991 2.78666 > H 16.25380 1.29452 7.35581 > H -0.13770 5.29177 7.35581 > H 16.99438 6.69998 1.82013 > H 0.60288 2.70273 1.82013 > C 2.84149 6.31548 4.62008 > C 19.23299 2.31823 4.62008 > C 2.10091 1.67902 10.15576 > C 18.49241 5.67627 10.15576 > H 3.50975 5.72019 4.96440 > H 19.90125 1.72294 4.96440 > H 2.76917 2.27431 10.50008 > H 19.16067 6.27156 10.50008 > H 2.12009 5.80314 4.23922 > H 18.51159 1.80589 4.23922 > H 1.37951 2.19136 9.77491 > H 17.77101 6.18861 9.77491 > H 2.4 6.86149 5.33308 > H 18.89149 2.86424 5.33308 > H 1.75941 1.13301 10.86876 > H 18.15091 5.13026 10.86876 > C 16.35379 6.90785 5.93536 > C -0.03771 2.91060 5.93536 > C 17.09438 1.08665 0.39968 > C 0.70288 5.08390 0.39968 > H 16.84589 6.32182 5.35300 > H 0.45439 2.32457 5.35300 > H 16.10531 1.67268 10.88868 > H -0.28619 5.66993 10.88868 > H 15.86389 7.54510 5.40947 > H -0.52761 3.54785 5.40947 > H 15.12331 0.44940 10.94515 > H -1.26819 4.44665 10.94515 > H 15.74245 6.39404 6.46678 > H -0.64905 2.39679 6.46678 > H 16.48303 1.60046 0.93110 > H 0.09153 5.59771 0.93110 > C 17.30660 7.62854 6.82992 > C 0.91510 3.63129 6.82992 > C 18.04719 0.36596 1.29424 > C 1.65569 4.36321 1.29424 > C 3.44486 7.19037 3.56498 > C 19.83636 3.19312 3.56498 > C 2.70427 0.80413 9.10066 > C 19.09577 4.80138 9.10066 > C 7.30907 6.93029 3.56166 > C 23.70057 2.93304 3.56166 > C 6.56849 1.06421 9.09734 > C 22.95999 5.06146 9.09734 > C 23.51465 7.25282 6.17782 > C 7.12315 3.25557 6.17782 > C 24.25523 0.74168 0.64214 > C 7.86373 4.73893 0.64214 > C 21.16001 7.74028 6.99710 > C 4.76851 3.74303 6.99710 > C 21.90060 0.25422 1.46142 > C 5.50910 4.25147 1.46142 > C 21.00252 6.87857 5.99071 > C 4.61102 2.88132 5.99071 > C 21.74310 1.11593 0.45503 > C 5.35160 5.11318 0.45503 > C 27.41664 7.76370 5.98186 > C 11.02514 3.76645 5.98186 > C 28.15722 0.23080 0.44618 > C 11.76572 4.22805 0.44618 > H 27.59489 0.54455 5.42718 > H 11.20339 4.54180 5.42718 > H 26.85431 7.44995 10.96286 > H 10.46280 3.45270 10.96286 > H 28.18126 7.63147 6.56310 > H 11.78976 3.63422 6.56310 > H 28.92184 0.36303 1.02742 > H 12.53034 4.36028 1.02742 > C 27.26323 6.60922 5.13933 > C 10.87173 2.61197 5.13933 > C 26.52265 1.38528 10.67501 > C 10.13115 5.38253 10.67501 > H 27.61795 5.83339 5.59879 > H 11.22645 1.83614 5.59879 > H 28.35854 2.16111 0.06311 > H 11.96704 6.15836 0.06311 > H 27.78169 6.73853 4.33001 > H 11.39019 2.74128 4.33001 > H 27.04111 1.25597 9.86569 > H 10.64961 5.25322 9.86569 > C 13.44202 0.18298 1.85556 > C 29.83352 4.18023 1.85556 > C 12.70144 7.81152 7.39124 > C 29.09294 3.81427 7.39124 > H 13.72839 7.55876 1.16581 > H 30.11989 3.56151 1.16581 > H 12.98780 0.43574 6.70150 > H 29.37930 4.43299 6.70150 > H 14.02273 0.95930 1.82235 > H 30.41423 4.95655 1.82235 > H 13.28214 7.03520 7.35803 > H 29.67364 3.03795 7.35803 > C 13.55775 7.53144 3.17416 > C 29.94925 3.53419 3.17416 > C 12.81716 0.46306 8.70984 > C 29.20866 4.46031 8.70984 > H 13.68661 0.21518 3.85616 > H 30.07811 4.21243 3.85616 > H 12.94602 7.77932 9.39184 > H 29.33752 3.78207 9.39184 > H 14.33307 6.94883 3.18191 > H 30.72457 2.95158 3.18191 > H 13.59248 1.04567 8.71759 > H 29.98398 5.04292 8.71759 > K_POINTS automatic > 1 2 2 0 0 0 > > > Thanks and regards > > > Stephan Ludwig > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] pw2wannier90.x in windows version
On Mon, Jul 27, 2015 at 10:25 AM, Khalid Ibne Masood Khalid wrote: > Dear Researchers, > 1. I am trying to run wannier90 in windows, for that I have to run > pw2wannier90.x. I have completed scf, nscf and wannier90 -pp calculation, > but when I try to run pw2wannier90 it shows error. > my input file: > > &inputpp > outdir='./outdir' > prefix='AGNR' > seedname = 'AGNR' > write_mmn = true > write_amn = true > write_unk = false > wan_mode = 'standalone' > / > > and the output file: > > Error in routine pw2wannier90 (1): > reading inputpp namelist > > I have run the almost same code in linux without any complain. How can I get > rid of this problem? by correcting your input. your name list is using incorrect syntax for the following three entries. > write_mmn = true > write_amn = true > write_unk = false > > 2. Also, I would like to know whether wannier90.x can be run in parallel > mode in windows. have you tried it? axel. > > Thanks in advance. > Khalid Ibne Masood > M.Sc student > BUET > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] charge analysis
On Mon, Jul 27, 2015 at 3:17 AM, Jure Varlec wrote: > Dear Raj kamal, > > In order to calculate Bader charges, you need to do three steps: > > - Do an scf calculation using pw.x. > - Use pp.x to extract the charge density and put it into a CUBE file. > Use the same prefix and outdir as for pw.x and use iflag = 3 and > output_format = 6 to generate the CUBE file. please note that this procedure is missing the contributions from the core electrons of the pseudopotentials and thus the results may be off or completely bogus. this is a particular concern for intercalation compounds. axel. > - Use the program linked below to compute Bader or Vornoi charges. > > http://theory.cm.utexas.edu/henkelman/code/bader/ > > Regards, > > Jure Varlec > National Institute of Chemistry > Ljubljana > > > On Sat, 25 Jul 2015 06:18:51 +0530 > Raj kamal wrote: > >> dear QE experts, >> i need to calculate badar charge or charge >> analysis calculation for my lithium intercalated graphene system .i >> tried lot to learn about this i couldnt much info .kindly please >> anyone send me clear description of input and output of any system of >> charge analysis.thanks in advance. >> > > _______ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] no scf started for huge system
4589 6.32182 5.35300 > H 0.45439 2.32457 5.35300 > H 16.10531 1.67268 10.88868 > H -0.28619 5.66993 10.88868 > H 15.86389 7.54510 5.40947 > H -0.52761 3.54785 5.40947 > H 15.12331 0.44940 10.94515 > H -1.26819 4.44665 10.94515 > H 15.74245 6.39404 6.46678 > H -0.64905 2.39679 6.46678 > H 16.48303 1.60046 0.93110 > H 0.09153 5.59771 0.93110 > C 17.30660 7.62854 6.82992 > C 0.91510 3.63129 6.82992 > C 18.04719 0.36596 1.29424 > C 1.65569 4.36321 1.29424 > C 3.44486 7.19037 3.56498 > C 19.83636 3.19312 3.56498 > C 2.70427 0.80413 9.10066 > C 19.09577 4.80138 9.10066 > C 7.30907 6.93029 3.56166 > C 23.70057 2.93304 3.56166 > C 6.56849 1.06421 9.09734 > C 22.95999 5.06146 9.09734 > C 23.51465 7.25282 6.17782 > C 7.12315 3.25557 6.17782 > C 24.25523 0.74168 0.64214 > C 7.86373 4.73893 0.64214 > C 21.16001 7.74028 6.99710 > C 4.76851 3.74303 6.99710 > C 21.90060 0.25422 1.46142 > C 5.50910 4.25147 1.46142 > C 21.00252 6.87857 5.99071 > C 4.61102 2.88132 5.99071 > C 21.74310 1.11593 0.45503 > C 5.35160 5.11318 0.45503 > C 27.41664 7.76370 5.98186 > C 11.02514 3.76645 5.98186 > C 28.15722 0.23080 0.44618 > C 11.76572 4.22805 0.44618 > H 27.59489 0.54455 5.42718 > H 11.20339 4.54180 5.42718 > H 26.85431 7.44995 10.96286 > H 10.46280 3.45270 10.96286 > H 28.18126 7.63147 6.56310 > H 11.78976 3.63422 6.56310 > H 28.92184 0.36303 1.02742 > H 12.53034 4.36028 1.02742 > C 27.26323 6.60922 5.13933 > C 10.87173 2.61197 5.13933 > C 26.52265 1.38528 10.67501 > C 10.13115 5.38253 10.67501 > H 27.61795 5.83339 5.59879 > H 11.22645 1.83614 5.59879 > H 28.35854 2.16111 0.06311 > H 11.96704 6.15836 0.06311 > H 27.78169 6.73853 4.33001 > H 11.39019 2.74128 4.33001 > H 27.04111 1.25597 9.86569 > H 10.64961 5.25322 9.86569 > C 13.44202 0.18298 1.85556 > C 29.83352 4.18023 1.85556 > C 12.70144 7.81152 7.39124 > C 29.09294 3.81427 7.39124 > H 13.72839 7.55876 1.16581 > H 30.11989 3.56151 1.16581 > H 12.98780 0.43574 6.70150 > H 29.37930 4.43299 6.70150 > H 14.02273 0.95930 1.82235 > H 30.41423 4.95655 1.82235 > H 13.28214 7.03520 7.35803 > H 29.67364 3.03795 7.35803 > C 13.55775 7.53144 3.17416 > C 29.94925 3.53419 3.17416 > C 12.81716 0.46306 8.70984 > C 29.20866 4.46031 8.70984 > H 13.68661 0.21518 3.85616 > H 30.07811 4.21243 3.85616 > H 12.94602 7.77932 9.39184 > H 29.33752 3.78207 9.39184 > H 14.33307 6.94883 3.18191 > H 30.72457 2.95158 3.18191 > H 13.59248 1.04567 8.71759 > H 29.98398 5.04292 8.71759 > K_POINTS automatic > 1 2 2 0 0 0 > > > Has anybody made similar experiences? Any ideas how to come at least to a > scf calculation? > > Does anybody know any tricks and hints for huge systems? > > > Thanks and regards > > > Stephan > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] question about hybridized atoms
On Tue, Jun 16, 2015 at 11:14 AM, yelena wrote: > Thank you for the answer. > So structure like in Zhang et al. PNAS 2015 112 (8) 2372-2377 can't be > modeled like that? i don't know. i have not read that paper and i don't care. > Maybe I didn't understand a way this structure is made. that is why i suggested that you rather talk to somebody local and look for somebody with sufficient experience in quantum mechanical computations. axel. > Thank you! > > > On 2015-06-16 16:53, Axel Kohlmeyer wrote: >> On Tue, Jun 16, 2015 at 10:47 AM, yelena wrote: >>> Dear All, >>> I wanted to model structure with sp2 and sp3-hybridized carbon >>> atoms. >>> So to do that, i need to put 2 types of carbons in my pw input, lets >> >> no you don't. in quantum mechanical calculations hybridization is not >> an input parameter but an interpretation of the result. >> >>> call them C1 and C2s. And there I have to add information about >>> hybrid >>> orbitals. I am not sure how to do that. Can anyone offer me some >>> advice >>> or point me in direction to find answer. >> >> find somebody local that know a little bit about quantum chemistry >> and >> have that person explain this to you. or just talk to your adviser. >> >> axel. >> >>> Thank you! >>> PhD Student >>> J. Pesic >>> Center for Solid State and New Materials >>> Institute of Physics Belgrade,Serbia >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum > > -- > Institute of Physics Belgrade > Pregrevica 118, 11080 Belgrade, Serbia > http://www.ipb.ac.rs/ > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] question about hybridized atoms
On Tue, Jun 16, 2015 at 10:47 AM, yelena wrote: > Dear All, > I wanted to model structure with sp2 and sp3-hybridized carbon atoms. > So to do that, i need to put 2 types of carbons in my pw input, lets no you don't. in quantum mechanical calculations hybridization is not an input parameter but an interpretation of the result. > call them C1 and C2s. And there I have to add information about hybrid > orbitals. I am not sure how to do that. Can anyone offer me some advice > or point me in direction to find answer. find somebody local that know a little bit about quantum chemistry and have that person explain this to you. or just talk to your adviser. axel. > Thank you! > PhD Student > J. Pesic > Center for Solid State and New Materials > Institute of Physics Belgrade,Serbia > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] access forum from China
On Jun 9, 2015 12:36 AM, "Andrea Floris" wrote: > > Dear all, > > I am supervising two Chinese MSc students, using QE. > They work at the Wuhan University, China. > > From their location, they are unable to access the forum > at the site > > http://www.mail-archive.com/pw_forum@pwscf.org/ This is by means the authoritative location. The mailing list is hosted and archived on qe-forge.org. If you go to the quantum espresso homepage you will see. Google is your friend... ;-) Axel > > As I see many students/scientists working from China and using the forum, > I 'd like to ask if there is an alternative possibility to access this forum and other > QE documents from China and in particular from the Wuhan region. > > Thanks for your help. > > Kind Regards > > Andrea Floris > > > -- > Dr Andrea Floris > Associate Researcher > C/Albert Einstein, 48 > 01510 Miñano (Alava) Spain > Phone +34 632 780 680 > Email an.flo...@gmail.com, andrea.flo...@kcl.ac.uk > / > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] quantum_espresso 5.1.2 installation problem
On Mon, Jun 8, 2015 at 2:58 PM, Paolo Giannozzi wrote: > The Open64 compiler doesn't accept what all other compilers think is a valid > syntax (not sure what the standard says). what is valid also depends on the version of the standard that is supported. my guess is that open64 only supports fortran up to fortran 95, whereas most other compilers can handle fortran 2003 (and some fortran 2008) these days. axel. > Try to replace the line >REAL(DP), PARAMETER :: fact(0:8) = > REAL((/1,1,2,6,24,120,720,5040,40320/),DP) > with >REAL(DP), PARAMETER :: fact(0:8) = > (/1_dp,1_dp,2_dp,6_dp,24_dp,120_dp,720_dp,5040_dp,40320_dp/) > or whatever syntax your compiler digests. Please report if you manage to > compile and produce valid QE executables > > Paoolo > > On Mon, Jun 8, 2015 at 2:36 PM, mohammed shambakey > wrote: >> >> Hi >> >> It is my first time to use quantum_espresso. I'm trying to install it on >> an hpc with redhat enterprise 6 and the following modules: >> >> gcc/4.8.1 >> blas/open64/64/1 >> mvapich2/open64/64/1.9 >> slurm/2.5.7 >> fftw3/openmpi/open64/64/3.3.3 >> blacs/openmpi/open64/64/1.1patch03 >> open64/4.5.2.1 >> mpich/ge/open64/64/3.0.4 >> scalapack/open64/64/1.8.0 >> >> configuration ends successfully, but "make all" gives me the following >> error: >> >> " >> module xdm_module >>^ >> openf95-855 openf90: ERROR XDM_MODULE, File = xdm_dispersion.f90, Line = >> 11, Column = 8 >> The compiler has detected errors in module "XDM_MODULE". No module >> information file will be created for this module. >> >> REAL(DP), PARAMETER :: fact(0:8) = >> REAL((/1,1,2,6,24,120,720,5040,40320/),DP) >> ^ >> openf95-587 openf90: ERROR XDM_MODULE, File = xdm_dispersion.f90, Line = >> 71, Column = 38 >> The initialization expression must be a constant to be used with >> PARAMETER assignment for object "FACT". >> >> openf95: Open64 Fortran Version 4.5.2.1 (f14) Mon Jun 8, 2015 11:19:18 >> openf95: 940 source lines >> openf95: 2 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) >> openf95: "explain openf95-message number" gives more information about >> each message >> make[2]: *** [xdm_dispersion.o] Error 2 >> make[1]: *** [pw] Error 1 >> make: *** [pw] Error 1 >> " >> >> Thanks >> >> -- >> Mohammed >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > hone +39-0432-558216, fax +39-0432-558222 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Pw_forum Digest, Vol 95, Issue 6
On Mon, Jun 8, 2015 at 8:49 AM, Amreen Bano wrote: > Dear all, >I am a new user, and i want to calculate the optical spectra using TDDFT. > I have done SCF calculation at gamma but when i run the Lanczos.x file an > error messege occured says: as a new user, you should first pay a little attention to mailing list etiquette. if you want to start a new discussion, please do *not* reply to a previous e-mail but start a new e-mail and give it a meaningful subject line. it is particularly rude to reply to a digested e-mail in the way you did, since you are sending now the *entire* digest to *everybody* again. thanks for your understanding, axel. -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] How to deal with the error (bad termination exit code: 9) in phonon calculation?
On Thu, May 28, 2015 at 7:22 AM, liyinc...@gmail.com wrote: > I was using mpich2 to run parallel version of pw.x and ph.x. I think this > error information was generated by my mpich2. In this case, where could I > reach the real error information? you have to talk to the people that operate the machine that you are running on. i have seen this kind of termination most often when people submitted a calculation to a batch system without reserving a suitable amount of wall time and then the calculation was forcibly terminated by the batch system. you should see that in the batch system outputs that correspond to your calculation, if that is what happened to you. axel. > > Best Regards, > Dr. Yin Li > Department of Biophysics,Medical School, University of Pecs, > No.12 Szigeti Street, Pecs, H-7624, HUNGARY > Phone: +36-72-535271/36271 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Does QE generate random structures?
On May 20, 2015 12:52 AM, "reza vatan" wrote: > > Dear QE users, > > I want to create a thin amorphous Si layer on the top of a crystalline silicon terminated with (100) plane. Does any one knows if QE has that ability. If no, is there any free software for generating those amorphous structure? Have you looked through the published literature and checked what others have done for this? I would probably try to use a classical MD code that supports a potential like tersoff create just a thicker structure and then melt the top layer while keeping the rest immobile. Then transfer this geometry to qe and continue equilibration there. Relaxing a random structure in QE will likely require _much_ more computational effort. Axel > > Any comment and suggestion would be highly appreciated. > > Best, > Reza > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Generate proton in Quantum Espresso
On Thu, May 14, 2015 at 9:06 AM, Leong Jun Xing wrote: > To whom it may concern > > My name is Leong. Currently I am using Quantum Espresso to calculate proton > diffusion through graphene. > > 1. I would like to know how to generate a proton in the scf input file? just remove an electron. whether you do get an isolated proton or something else as a consequence depends on quantum mechanics. > 2. Besides, if there is a proton in the system (with positive 1 charge), is > that it is compulsory to create jellium background to neutral the system > since the system is periodic? you cannot avoid it. in fact, this is not created, but rather having a non-neutral system would make the lattice sum that is used when computing the electrostatic interactions diverge. since this divergence is due to a single term that has no positional dependence, it is just ignored and _that_ will have the same effect as having a homogeneous background charge. > Wish to receive your reply soon. > > > Thank you. > > > Best regards > Leong > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] how to install QE linking with libxc
ce to `xc_f90_func_end_' > ../../flib/flib.a(metagga.o): In function `tpsscxc_': > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:57: > undefined reference to `xc_f90_func_init_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:59: > undefined reference to `xc_f90_mgga_exc_vxc_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:60: > undefined reference to `xc_f90_func_end_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:68: > undefined reference to `xc_f90_func_init_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:70: > undefined reference to `xc_f90_mgga_exc_vxc_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:71: > undefined reference to `xc_f90_func_end_' > ../../flib/flib.a(metagga.o): In function `tb09cxc_': > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:1415: > undefined reference to `xc_f90_func_init_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:1417: > undefined reference to `xc_f90_mgga_vxc_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:1418: > undefined reference to `xc_f90_func_end_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:1428: > undefined reference to `xc_f90_func_init_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:1430: > undefined reference to `xc_f90_mgga_exc_vxc_' > /home/plgong/Soft/Package/ESPRESSO_TAR_GZ/espresso-5.1.2/flib/metagga.f90:1431: > undefined reference to `xc_f90_func_end_' > collect2: ld returned 1 exit status > > Best wishes > PL Gong > > > > -- > > > Addr: Institute of Solid State Physics, Chinese Academy of > Sciences, Hefei, Anhui 230031, China > Tel: +86-551-65591591(office), 18756086113(cell phone) > Email: plg...@theory.issp.ac.cn > > > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Compilation Error With ICC
On Wed, Mar 25, 2015 at 4:23 PM, Cameron Foss wrote: > Hello, > > I am trying to install Quantum-Espresso on the parallel machine MGHPCC. I am > trying to use intel compilers to do so (ie ifort, icc, and icpc). Note I > have installed and tested the serial version to confirm that the issues I am > seeing are not coming from the cluster environment itself. > > I've load the necessary modules containing these compilers: > > [cf79a@ghpcc06 espresso-5.1]$ which ifort > /share/pkg/intel/composer_xe_2013_sp1.0.080/bin/intel64/ifort > [cf79a@ghpcc06 espresso-5.1]$ which icc > /share/pkg/intel/composer_xe_2013_sp1.0.080/bin/intel64/icc > [cf79a@ghpcc06 espresso-5.1]$ which icpc > /share/pkg/intel/composer_xe_2013_sp1.0.080/bin/intel64/icpc > > however when I run ./configure --enable-parallel I get the following error > (NOTE: I get the same error when just running ./configure: > setting CC... icc > checking how to run the C preprocessor... icc -E > configure: error: in `/home/cf79a/ESPRESSO-PAR/espresso-5.1': > configure: error: C preprocessor "icc -E" fails sanity check > > and in the config.log file it states ac_cv_env_CPP_value=icc > however when I explicitly set CPP via export > CPP=/share/pkg/intel/composer_xe_2013_sp1.0.080/bin/intel64/icpc > > I now get this error: > setting CC... icc > checking how to run the C preprocessor... > /share/pkg/intel/composer_xe_2013_sp1.0.080/bin/intel64/icpc > configure: error: in `/home/cf79a/ESPRESSO-PAR/espresso-5.1/install': > configure: error: C preprocessor > "/share/pkg/intel/composer_xe_2013_sp1.0.080/bin/intel64/icpc" fails sanity > check > > It sets CC to icc but when checking the C preprocessor it references the > icpc compiler. > > Any idea's as to fix this issue? or perhaps why it is happening? most likely there is something not fully working with the installation of the intel compiler package. i have composer_xe_2013_sp1.1.106 on my desktop machine here and configure works fine. you should check the config.log file to see what kind of error message you get. axel. > > Best, > Cameron > > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] TiO2 nanotube builder?
On Tue, Mar 17, 2015 at 5:44 PM, Amin Torabi wrote: > Let's say I know the xyz coordinates of the atoms in bulk anatase TiO2, and > I want to roll a sheet of it into a nanotube. How do I find the xyz > coordinates of the nanotube? > > Can someone guide me through this? this is a rather basic geometry/trigonometry exercise. basically you have to solve the problem: how do you compute the x and y coordinate of a point on a circle from its angle? consider a suitably sized rectangular sheet, e.g. in the x-z plane. z coordinates remain unchanged. the length of the rectangle in x-direction L_x becomes the radius of the resulting tube and thus the original x-coordinate now corresponds to an angle of 2*pi*x/L_x. from that you can compute the x and y position on the circle. any y-coordinates, i.e. from atoms that are above or below that base plane, would then correspond to positions on a circle with larger or smaller radius. if this is still too confusing, search the web for examples of how people construct carbon nanotube coordinates from a sheet of graphene. its the same thing. axel. > > Thanks! > > -- > ** > Amin Torabi > Ph.D. Candidate > Department of Chemistry > University of Western Ontario > ** > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Workshop on Accelerated High-Performance Computing in Computational Sciences at ICTP, Trieste
The Abdus Salam International Centre for Theoretical Physics is organizing a two week Workshop on Accelerated High-Performance Computing in Computational Sciences to be held at ICTP (Trieste, Italy) from May 25th to June 5th, 2015. Deadline for applications is on: 15-03-2015 For more details, please see: http://indico.ictp.it/event/a14302/ -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] [Pw-forum] Cygwin - Make pw Error
On Mon, Feb 2, 2015 at 2:27 PM, hossein daneshpajooh wrote: > I know, but I have added all packages related to pthread, still not working! > and if problem is from libiotk I don't know how to solve it. > Now dear Paolo what do you suggest to try? the -pthread flag is obviously not supported with your version of gfortran (or may never have been). the error message indicates this very clearly, as paolo already noted. you have to get rid of it somehow. axel. > > > >> > >gfortran -g -pthread -o iotk_print_kinds.x iotk_print_kinds.o >> > libiotk.a >> > >gfortran: error: unrecognized command line option ‘-pthread’ >> >> > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Making Doc for PW
On Mon, Feb 2, 2015 at 10:46 AM, Reza Behjatmanesh-Ardakani
wrote:
> Dear Users
> I have installed packages needed for making Doc such as
> texlive-latex
> latex2html
> xhtml2fo-style-xsl
> ocaml-fileutils
> ocaml-fileutils-devel
> tcl
> tcl-devel
> .
> .
> .
> For some packages such as atomic, everything is good, but for some others
> such as PW, only pdf file is generated, and there is not html for input
> guide. In this case, I get following error:
>
>
> PWD: /home/espresso-5.1.1/PW/Doc:
>
>
> [root@Astek Doc]# make doc
> ../../dev-tools/helpdoc INPUT_PW.def
> can't find package fileutil
> while executing
> "package require fileutil"
the fileutil package is part of tcllib. not all linux distributions
include it in the Tcl package.
axel.
> (file
> "/home/espresso-5.1.1/dev-tools/helpdoc.d/../../PWgui-5.1/lib/Guib-0.5.1/lib/tclUtils.tcl"
> line 41)
> invoked from within
> "source
> /home/espresso-5.1.1/dev-tools/helpdoc.d/../../PWgui-5.1/lib/Guib-0.5.1/lib/tclUtils.tcl"
> ("package ifneeded tclu 0.9" script)
> invoked from within
> "package require tclu 0.9"
> (file "/home/espresso-5.1.1/dev-tools/helpdoc.d/helpdoc.tcl" line 25)
> invoked from within
> "source [file join $sourcedir helpdoc.tcl]"
> (file "../../dev-tools/helpdoc" line 8)
> make: *** [INPUT_PW.html] Error 1
>
> ==
>
> With the Best Regards
>
>Reza Behjatmanesh-Ardakani
>Associate Professor of Physical Chemistry
>Address:
>Department of Chemistry,
>School of Science,
>Payame Noor University (PNU),
>Ardakan,
>Yazd,
>Iran.
>E-mails:
> 1- reza_b_...@yahoo.com (preferred),
> 2- behjatman...@pnu.ac.ir,
> 3- reza.b@gmail.com.
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
___
Pw_forum mailing list
Pw_forum@pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] converter for XYZ file of B.O MD.
On Mon, Jan 19, 2015 at 12:54 AM, FF_解析セ_奥野幸洋 wrote: > Dear PWSCF users and developer. > > I'm now try to calculate Born Oppenheimer molecular dynamics. > I want to see the trajectory of molecular dynamics of pw.x > by using VMD. > > Are there any converter script for pw.x output file to XYZ file > (not only the initial or final, but the all the trajectory of atomic > positions) for viewing VMD software? the .xyz file format is a bad choice, since it doesn't contain the box information and thus prohibits using periodic copies of the data in VMD. you should instead use the pwo2xsf.sh script to generate an .xsf file format animation and visualize it with VMD. .xsf is a file format supported by VMD and the converter script is part of the QE distribution. axel > > Sincerely, > > Yukihiro Okuno > > -- > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Basis sets (plane wave)
On Dec 30, 2014 5:54 AM, "Sadegh Ghaderzadeh" wrote: > > Dear QE users, > > I have a simple question. How can I find the file(s) containing basis sets (plane waves)? I mean, where is the file in the installation directory? There is/are no such file(s). There is no need. The basis sets are uniquely defined by the energy cutoff. Axel. > > Thank in advance > > Sadegh Ghaderzadeh > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] How to find the energy of the particular bond for all the nstep = 3000 in one go
On Dec 23, 2014 9:46 PM, "YousafMasood" wrote: > > Dear Members > > Kindly guide How to find the energy of the particular bond for all the nstep in one go in a MD calculation. Particular Bond energy can be find easily for a single structure. But if we want to calculate bond energy (example: C-OH) in a compound under external effects after each time interval "dt" in one go then what will be the possible method ? What you are looking for only exists in classical force field calculations, due to how they are constructed. DFT only cares about and considers the total energy of the entire system. Axel > Best wishes > Masood > UNIST, Republic of Korea > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] parallel version for Windows
On Sun, Dec 7, 2014 at 11:08 AM, David Foster wrote: > Dear Axel > > Thanks for your effort for providing the windows version. Until now, I ran > the linux version which had been compiled with ifort, intelmpi, icc on a > cluster of > > CentOs6.5. I downloaded windows version last day, and did according your user > guide (installing mpich2, ...). > > I ran sample input for a SMP system with 16 core. It was interesting and > very simple. However, I have a question: > > Is it possible to use HPC tools to run the program through a windows cluster. > What should I do? i wouldn't know. i don't use windows (except for an occasional quick test whether the installer packages still do what they are supposed to do or to debug a reported issue) and don't compile on windows. the QE windows packages are built on a linux machine using a cross compiler. you most certainly would have to compile a version yourself that uses the same MPI library than what is used on the cluster. that MPI library is most likely compiled against the microsoft compilers, so you'd have to compile QE natively on that machine, which is likely a significant porting and debugging effort. the MS compilers are known to be quite idiosyncratic. in short, it is likely easier to convince folks to put linux on that cluster. axel. > > Regards > > David Foster > > Ph.D. Student of Chemistry > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] [Q-e-developers] Not able to subscribe the mailing list
On Fri, Nov 28, 2014 at 6:45 AM, Paolo Giannozzi wrote: > @yahoo.com e-mail? the following post gives a quite technical > explanation of what is happening and why, but the title says > it all: http://jrl.guru/Email/yahoobomb.html > I asked a few months ago our system administrator if there is > a simple solution, but apparently there isn't any. I don't know FYI, on vmd-l and namd-l the following workaround has been established: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23598.html i.e. email addresses in the From: list originating at yahoo.com will be changed by the mailing list processor. axel. > if things have meanwhile evolved. > > Paolo > > On Fri, 2014-11-28 at 10:29 +, Masood Yousaf wrote: >> Dear Members, >> >> >> Might be this is not the right forum. Sorry for sending this email. I >> am trying to subscribe the QE forum. Trying 3 of my email IDs for the >> last two weeks. After completing the registration, the message appears >> that I will receive a message soon but I never got the message. I did >> wait for more than a week. Checked my spam but didnt find anything. >> Kindly guide/help me , how can I subscribe the mailing list. >> >> >> Best Regards >> Masood >> Postdoctoral Research Fellow >> >> >> >> >> UNIST 50, Ulsan, 689-798, Republic of Korea >> >> ___ >> Q-e-developers mailing list >> q-e-develop...@qe-forge.org >> http://qe-forge.org/mailman/listinfo/q-e-developers > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] the first version of pwscf
On Fri, Nov 28, 2014 at 10:14 AM, Reza Behjatmanesh-Ardakani wrote: > Dear Developers, > I need the first or at least the simplest version of pwscf for educational > purposes. if you want a simple version, particularly for teaching purposes, it is probably best to write one yourself and use the current version as a template. > The following link has previous versions: > > http://www.quantum-espresso.org/previous-versions/ > > But, it is not possible to download versions from pw.1.0.0 to pw.1.3.0. please keep in mind that early development versions often are riddled with problems, inconsistent programming, outdated programming styles and lack of documentation. neither of that is something that you want to expose people to that are in the process of learning. you may want to check out the material from the multiple recent QE developer workshops. that may be much more suitable for your need and provide the necessary information. axel. > > With the Best Regards > >Reza Behjatmanesh-Ardakani >Associate Professor of Physical Chemistry >Address: >Department of Chemistry, >School of Science, >Payame Noor University (PNU), >Ardakan, >Yazd, >Iran. >E-mails: > 1- reza_b_...@yahoo.com (preferred), > 2- behjatman...@pnu.ac.ir, > 3- reza.b@gmail.com. > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] QHA Compile: Using gfortran instead of ifort
On Fri, Nov 28, 2014 at 1:23 AM, W2AGZ wrote: > Alex, thanks for your quick and wise response! > > I did a cursory pass through of the source code, matdyn.f90 and lambda.f90, > used in QHA (matdyn) and the general phonon packages within QE, and didn't i don't understand this statement. the two files you mention are part of the standard build and compile fine with gfortran. when people complain about QHA not being compiled with gfortran, they usually refer to the files in the QHA package and they quote error messages that indicated such illegal coding. > find any obvious uses of floating point loop variables. Frankly, I can't > imagine why such assignments would ever be done! On the other hand, most of the time, this would happen "unintentionally" through with implicit variable declarations. the files in the QHA packages have this in spades: [akohlmey@zero QHA]$ find ./ -name \*.f90 -or -name \*.f -or -name *.h | xargs grep -i implicit ./SRC/Partial_phonon_DOS.f90: implicit real*8(a-h,o-z) ./SRC/Ghost_DOS.f90: implicit real*8(a-h,o-z) ./SRC/Atom_projected_properties.f90: implicit none ./SRC/F_QHA.f90: implicit none ./SRC/Mean_square_displacement.f90: implicit none ./Debye/Debye.f90:! implicit none ./Debye/Debye.f90: implicit real*8(a-h,o-z) ./Debye/Debye_T.f: implicit real*8(a-h,o-z) ./Phonon_DOS/parameters.h:implicit real*8(a-h,o-z) they are also full of other things that were accepted programming style when i learned fortran, but are in dire need of refactoring into modern fortran (now here is a self-contradicting description. ;-) ) these days. > occasionally posted on the forum are reports of NaN errors embedded in > phonon calculation output. I wonder if such result from the "very bad" > programming practices you describe. there are plenty possible reasons for NaNs. using floating point math for loops can lead to too few or too many loop iterations. that would more likely lead to slightly different results, not likely to NaNs (unless there is some rounding error involved leading to negative numbers when positive numbers are required (e.g. when taking a logarithm or a square root). > Hope to see you at the March Meeting upcoming in San Antonio. *very* unlikely. axel. > -Paul > -Original Message- > From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On > Behalf Of Axel Kohlmeyer > Sent: Thursday, November 27, 2014 6:24 AM > To: PWSCF Forum > Subject: Re: [Pw_forum] QHA Compile: Using gfortran instead of ifort > > On Wed, Nov 26, 2014 at 11:27 PM, W2AGZ wrote: >> To the Community: >> >> >> >> I believe I may have raised this question in the far distant past. >> >> >> >> It appears that under QE-5.1.1, it is still necessary to compile the >> source code within QHA using ifort. Are any in the QE community aware >> of a QHA package compile-able with gfortran, or object code resulting >> from such? Is there an equivalent to QHA somewhere within the QE >> package (or outside!) capable of yielding similar results such as, e.g., > Debye temperatures? >> >> >> >> As always, thanks for any advice/guidance. > > for the most part it seems as if all it needs is somebody with a little bit > to time to sit down and replace the loops using floating point variables > with the equivalent using integral loop variables. > > using floating point loop variables is very, *very*, *VERY* bad programming > style (due to limitations of floating point math) and as of the last decade > removed from the fortran standard. > > not really rocket science... > > axel. > >> >> >> >> Paul Michael Grant, PhD >> >> Physicist and Science Writer >> >> Senior Life Fellow, American Physical Society >> >> Fellow, Institute of Physics, United Kingdom >> >> w2...@w2agz.com >> >> http://www.w2agz.com >> >> >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of > Science & Technology, Temple University, Philadelphia PA, USA International > Centre for Theoretical Physics, Trieste. Italy. > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] QHA Compile: Using gfortran instead of ifort
On Wed, Nov 26, 2014 at 11:27 PM, W2AGZ wrote: > To the Community: > > > > I believe I may have raised this question in the far distant past. > > > > It appears that under QE-5.1.1, it is still necessary to compile the source > code within QHA using ifort. Are any in the QE community aware of a QHA > package compile-able with gfortran, or object code resulting from such? Is > there an equivalent to QHA somewhere within the QE package (or outside!) > capable of yielding similar results such as, e.g., Debye temperatures? > > > > As always, thanks for any advice/guidance. for the most part it seems as if all it needs is somebody with a little bit to time to sit down and replace the loops using floating point variables with the equivalent using integral loop variables. using floating point loop variables is very, *very*, *VERY* bad programming style (due to limitations of floating point math) and as of the last decade removed from the fortran standard. not really rocket science... axel. > > > > Paul Michael Grant, PhD > > Physicist and Science Writer > > Senior Life Fellow, American Physical Society > > Fellow, Institute of Physics, United Kingdom > > w2...@w2agz.com > > http://www.w2agz.com > > > > > > > _______ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohl...@gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] QHA compilation
On Nov 20, 2014 2:41 AM, "PRATIK DAS" wrote: > > Dear everybody, > I want to compile QHA package in Quantum espresso. I have only gfortran installed. So I modified the make files and replace ifort by gfortran. Now when I ran the Compile script, it is giving me the following error. Can anyone help me out of this problem. Actually I'm a newbie in linux. The first issue can be solved by deleting the -static flag in the makefile. The second issue requires correcting the fortan code that is violating the fortran standard as indicated by the error messages. Axel. > > Thanking you in advance. > > Pratik Kumar Das > JRF, > Jadavpur University > Kolkata-700032 > INDIA > > [pratik@localhost QHA]$ ./Compile > gfortran -O3 -c tetra.f > gfortran -O3 -c k_brillouin.f > gfortran -O3 -c generate_tetra.f > gfortran -O3 -c det3.f > gfortran -O3 -c det4.f > gfortran -static -o tetra.x tetra.o k_brillouin.o generate_tetra.o det3.o det4.o > /usr/bin/ld: cannot find -lgfortran > /usr/bin/ld: cannot find -lm > /usr/bin/ld: cannot find -lquadmath > /usr/bin/ld: cannot find -lm > /usr/bin/ld: cannot find -lc > collect2: error: ld returned 1 exit status > make: *** [tetra] Error 1 > gfortran -O3 -c Debye.f90 > Debye.f90:144.8: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: Loop variable at (1) must be integer > Debye.f90:144.11: > > do T = T_low_start, T_low, T_low_delta >1 > Warning: Deleted feature: Start expression in DO loop at (1) must be integer > Debye.f90:144.24: > > do T = T_low_start, T_low, T_low_delta > 1 > Warning: Deleted feature: End expression in DO loop at (1) must be integer > Debye.f90:144.31: > > do T = T_low_start, T_low, T_low_delta >1 > Warning: Deleted feature: Step expression in DO loop at (1) must be integer > Debye.f90:177.4: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: Loop variable at (1) must be integer > Debye.f90:177.7: > > do T = T_low+5, T_high, T_high_delta >1 > Warning: Deleted feature: Start expression in DO loop at (1) must be integer > Debye.f90:177.16: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: End expression in DO loop at (1) must be integer > Debye.f90:177.24: > > do T = T_low+5, T_high, T_high_delta > 1 > Warning: Deleted feature: Step expression in DO loop at (1) must be integer > gfortran -O3 -c Debye_T.f > gfortran -O3 -c debye3.f > gfortran -O3 -c cheval.f > gfortran -O3 -c d1mach.f > gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o > /usr/bin/ld: cannot find -lgfortran > /usr/bin/ld: cannot find -lm > /usr/bin/ld: cannot find -lquadmath > /usr/bin/ld: cannot find -lm > /usr/bin/ld: cannot find -lc > collect2: error: ld returned 1 exit status > make: *** [Debye_x] Error 1 > gfortran -FR -c Mean_square_displacement.f90 > Mean_square_displacement.f90:162.7: > > do T=T_start,T_end,T_delta >1 > Warning: Deleted feature: Loop variable at (1) must be integer > gfortran -static -o Mean_square_displacement.x Mean_square_displacement.o > /usr/bin/ld: cannot find -lgfortran > /usr/bin/ld: cannot find -lm > /usr/bin/ld: cannot find -lquadmath > /usr/bin/ld: cannot find -lm > /usr/bin/ld: cannot find -lc > collect2: error: ld returned 1 exit status > make: *** [MSD] Error 1 > ln: failed to create symbolic link ‘tetra.x’: File exists > ln: failed to create symbolic link ‘phonon_dos.x’: File exists > ln: failed to create symbolic link ‘Debye.x’: File exists > ln: failed to create symbolic link ‘Atom_projected_properties.x’: File exists > ln: failed to create symbolic link ‘F_QHA.x’: File exists > ln: failed to create symbolic link ‘Ghost_DOS.x’: File exists > ln: failed to create symbolic link ‘Partial_phonon_DOS.x’: File exists > ln: failed to create symbolic link ‘Mean_square_displacement.x’: File exists > ln: failed to create symbolic link ‘atom_info.x’: File exists > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Not running on parallel mode
please make sure that the mpirun command you use is the one that matches the MPI library used during compilation. if you use the mpirun from MPICH on executables compiled with OpenMPI or vice versa, you get exactly the effect you are seeing. axel. On Tue, Oct 7, 2014 at 9:15 AM, mohaddeseh abbasnejad wrote: > Dear Layla, > > Thanks for your reply. > Still the problem exists! > I have attached the output file. > > Yours, > Mohaddeseh > > On Tue, Oct 7, 2014 at 4:37 PM, Layla Martin-Samos > wrote: >> >> hi, try >> >> mpirun -np 16 pw.x -in input > output >> >> cheers >> >> Layla >> >> 2014-10-07 15:01 GMT+02:00 mohaddeseh abbasnejad : >>> >>> >>> Dear PWscf users, >>> >>> I have installed Quantum ESPRESSO package (ver. 5.1) on our system >>> (having 16 cores). During the installation, it detected the parallel >>> environment successfully. However, when I run the program on parallel (I use >>> the following command: >>> mpirun -n 16 pw.x -in input > output ), it only runs on single mode and >>> the output will be printed n time (n: the number of cores I define in >>> parallel). >>> Would you please guide me what the problem is? >>> Thanks in advance. >>> >>> Regards, >>> Mohaddeseh >>> -- >>> - >>> >>> Mohaddeseh Abbasnejad, >>> Room No. 323, Department of Physics, >>> University of Tehran, North Karegar Ave., >>> Tehran, P.O. Box: 14395-547- IRAN >>> Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 >>> Cellphone: +98 917 731 7514 >>> E-Mail: m.abbasnejad at gmail.com >>> Website: http://physics.ut.ac.ir >>> >>> - >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > - > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +98 917 731 7514 > E-Mail: m.abbasnejad at gmail.com > Website: http://physics.ut.ac.ir > > - > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] High symmetry points
On Oct 1, 2014 3:58 AM, "Winfred Mulwa" wrote: > > Dear all, > Its trivial but i want to understand what we mean by points of high symmetry along the Brillouin zone . It is trivial and a question you should discuss with your adviser, who will likely point out a text book to you, where you will find the insight you seek. Axel > KInd regards > Mulwa Winfred. > D Phil Student, Computational Material Science Group, > University of the Free State - QwaQwa, > South Africa. > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20141001/77ba1c03/attachment.html
[Pw_forum] why do we need to relax the atomic coordinates obtained from cif file
On Sun, Sep 21, 2014 at 1:44 PM, janardhan H.L. wrote: > Dear all, > > I am an experimentalist wanted to use QE for obtaining DOS and band > structure. As I was recently got introduced to QE and also most of the > theory, I have a small question. I searched in PW archives and didnt find > the answer looking for. My question is as follows, > > While solving a crystal structure we take lots of parameter and refine the > crystal structure to at most accuracy. If we take this atomic coordinates > for QE scf calculation does it affect the results obtained? yes. > If yes why, and relaxing the atomic positions may result in different > coordinates which may be different from the input file which may not give > the similar XRD patterns. Hence by relaxing the atomic coordinates from cif > file and using for further calculations may not match to experimental > results. Please comment on this. there are assumptions in *both*, your DFT calculations and your x-ray diffraction pattern refinement. your "most accurate" results may not that be as accurate on a absolute scale, they are for the most part *consistent* with the model that you use to refine your crystal structure. the same is true for DFT calculations and wanting a geometry that is *consistent* with the model is usually desirable. using the unoptimized coordinates may result in a wavefunction that is "squeezed" into a situation that it doesn't really want to be and then will "act funny". in general, the differences in relative geometries are fairly small, since in both cases a lot of error cancellation is happening. if you cannot get a good agreement between the experimental results and the DFT calculation, that is usually an indication that something is going badly wrong (or that you may be on the brink of a nobel prize worthy discovery) HTH, axel. > > > > with respectful regards > > Janardhan H L > Research Fellow > Poornaprajna Institute of Scientific Research > Bangalore India > www.ppisr.res.in > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] QE-GPU: compilation error with Espresso 5.1
On Wed, Sep 10, 2014 at 9:37 AM, Axel Kohlmeyer wrote: > On Wed, Sep 10, 2014 at 9:35 AM, Filippo Spiga > wrote: >> Dear Mauro, >> >> On Sep 8, 2014, at 9:47 AM, Mauro Sgroi >> wrote: >>> I'm using now gcc 4.4 wih the internal blas/lapack libraries, just to >>> reduce the complexity of the problem. >> >> Bus still, Intel MKL will give you best performance. It is worth the >> complexity, give it a try! >> >> >>> I modified GPU/install/make_phiGEMM.inc to link with -lgfortran to solve >>> some undefined reference errors. >>> But now the compilation stops with an undefined reference to `main'. >> >> uhm I will look at this, I do not see any problem on my local machine but I >> will double-check again. > > that would happen, if gcc is used as linker instead of gfortran (which > would also explain the need of adding -lgfortran) or when you try to link a shared library without the -shared flag. > > axel. > > >> F >> >> -- >> Mr. Filippo SPIGA, M.Sc. >> http://filippospiga.info ~ skype: filippo.spiga >> >> ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert >> >> * >> Disclaimer: "Please note this message and any attachments are CONFIDENTIAL >> and may be privileged or otherwise protected from disclosure. The contents >> are not to be disclosed to anyone other than the addressee. Unauthorized >> recipients are requested to preserve this confidentiality and to advise the >> sender immediately of any error in transmission." >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > College of Science & Technology, Temple University, Philadelphia PA, USA > International Centre for Theoretical Physics, Trieste. Italy. -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] QE-GPU: compilation error with Espresso 5.1
On Wed, Sep 10, 2014 at 9:35 AM, Filippo Spiga wrote: > Dear Mauro, > > On Sep 8, 2014, at 9:47 AM, Mauro Sgroi > wrote: >> I'm using now gcc 4.4 wih the internal blas/lapack libraries, just to reduce >> the complexity of the problem. > > Bus still, Intel MKL will give you best performance. It is worth the > complexity, give it a try! > > >> I modified GPU/install/make_phiGEMM.inc to link with -lgfortran to solve >> some undefined reference errors. >> But now the compilation stops with an undefined reference to `main'. > > uhm I will look at this, I do not see any problem on my local machine but I > will double-check again. that would happen, if gcc is used as linker instead of gfortran (which would also explain the need of adding -lgfortran) axel. > F > > -- > Mr. Filippo SPIGA, M.Sc. > http://filippospiga.info ~ skype: filippo.spiga > > ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert > > * > Disclaimer: "Please note this message and any attachments are CONFIDENTIAL > and may be privileged or otherwise protected from disclosure. The contents > are not to be disclosed to anyone other than the addressee. Unauthorized > recipients are requested to preserve this confidentiality and to advise the > sender immediately of any error in transmission." > > > > _______ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Looking for testers (again) for QE-5.1 binaries for windows
On Fri, Sep 5, 2014 at 10:43 AM, ehsan targholi wrote: > Thank you for the good explanation. Your explanation was perfect. I > realized. What do I need to do? please send me the download link. If like i said before. i will set the URL when it is ready. i am still looking for more volunteers. specifically people with a good technical knowledge of windows, that can specifically review the packaging and installation setup. the core of my windows expertise dates back to the times of windows 3.1 before i transitioned to linux in the late 1990s. > possible, please tell me step by step process. My computer knowledge is not > very good. i have no time to teach you that and there are likely *lots* of people right where you are, that can train and advise you better in person than i could do via e-mail. > > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Looking for testers (again) for QE-5.1 binaries for windows
On Thu, Sep 4, 2014 at 10:34 PM, ehsan targholi wrote: > I'm confused. Your order is that espresso must be implemented in virtualbox? no. i don't say this anywhere. what i say is that executables compiled with the intel compiler and linked to the intel MKL are currently faster on x86 machines than executables compiled with the GNU compiler. how much faster depends on a few factors. but the matter of the fact is that the windows executables are compiled with the GNU compilers. i do all my work on Linux and since there are the mingw cross-compilers i can not only compile native linux programs but also executables for windows. i am doing this for other projects as well. this is a *much* easier way to compile executables for windows for a package like QE. building native executables with a native compiler (cygwin is a bit of a hybrid) would have been much more effort. > I have worked with this software. and the loss of efficiency is very high. then you did something wrong. with the proper settings and reasonable hardware, the cost of the virtual machine is only a few percent performance. i am regularly running linux on linux virtual machines (to build RPM packages for different linux distributions) and they work just fine and efficient. > Efficiency is very important in my work. In any case, I am willing to then running on windows is probably not the best choice. like i said, the main purpose for providing windows binaries is to give people the opportunity to run QE calculations where it is not easy or possible to use linux (e.g. when teaching a class in a computer lab) or to help people to make tests before they run calculations on a more capable machine. windows is convenient for a lot of things, but it is not as well suited for high-performance as linux. axel. > cooperate with you to test its performance. > > > > best regards > > > On Thu, Sep 4, 2014 at 11:19 PM, Axel Kohlmeyer wrote: >> >> On Thu, Sep 4, 2014 at 8:19 PM, siddheshwar chopra >> wrote: >> > Dear Sir, >> > I willing to run QE on my Windows xp (with 2 GB RAM and dual core 2.7 >> > GHz >> > cpu) and windows 7 (with 2GB RAM and i3 2.2 GHz ) machines.. >> > Sir I would be glad if you could clarify one doubt.. Is will there be >> > any >> > DEGRADATION of QE performance on windows, as compared to linux? >> > I have used cygwin and virtualbox and found severe performance >> > degradations. >> >> the executables are compiled with a mingw cross-compiler on a linux >> machine. so the performance should be equivalent to what you achieve >> with gfortran and gcc on a linux box. compared to cygwin it is likely >> a bit faster. at least that is what people found with a different >> package. >> >> there are a few things where windows is better than linux and some >> other things where it is worse. it depends a lot on the specific >> windows version. with numerical codes like QE, often the compiler and >> optimized BLAS/LAPACK libraries is the biggest impact. with virtual >> machines, the problem is often the limited amount of RAM. if you care >> about performance, obtain an academic license for the intel compilers >> with MKL and run on a linux machine. it is well worth the money (often >> cheaper than the equivalent CPU upgrade) >> >> the primary motivation to provide windows binaries is to make QE more >> accessible for classrooms and tutorials and for people that want to >> run tests on their own machine (not everybody runs linux on their >> laptops) before sending larger versions of the same calculation to a >> cluster or a supercomputer. so the best performance is not the highest >> priority. >> >> if you are able to make properly documented comparative benchmarks, >> i'd be happy to get to know pass that information on to other users in >> the documentation of the windows port. >> >> >> >> >> > I would eagerly wait for your mail regarding the download links. >> > >> > Kind Regards, >> > >> > On 04-Sep-2014 11:27 pm, "Axel Kohlmeyer" wrote: >> >> >> >> On Thu, Sep 4, 2014 at 7:52 PM, ehsan targholi >> >> wrote: >> >> > Hi >> >> > Dear axel >> >> > It's a very interesting idea. I'm interested to running it in Windows >> >> > and in >> >> > parallel version. What should I do? >> >> >> >> just wait for my e-mail telling you where to find the temporary >> >> repository and the installer packages. >> >> >> >> what kind/version of windows are you running and how much RAM and h
[Pw_forum] Looking for testers (again) for QE-5.1 binaries for windows
On Thu, Sep 4, 2014 at 8:19 PM, siddheshwar chopra wrote: > Dear Sir, > I willing to run QE on my Windows xp (with 2 GB RAM and dual core 2.7 GHz > cpu) and windows 7 (with 2GB RAM and i3 2.2 GHz ) machines.. > Sir I would be glad if you could clarify one doubt.. Is will there be any > DEGRADATION of QE performance on windows, as compared to linux? > I have used cygwin and virtualbox and found severe performance degradations. the executables are compiled with a mingw cross-compiler on a linux machine. so the performance should be equivalent to what you achieve with gfortran and gcc on a linux box. compared to cygwin it is likely a bit faster. at least that is what people found with a different package. there are a few things where windows is better than linux and some other things where it is worse. it depends a lot on the specific windows version. with numerical codes like QE, often the compiler and optimized BLAS/LAPACK libraries is the biggest impact. with virtual machines, the problem is often the limited amount of RAM. if you care about performance, obtain an academic license for the intel compilers with MKL and run on a linux machine. it is well worth the money (often cheaper than the equivalent CPU upgrade) the primary motivation to provide windows binaries is to make QE more accessible for classrooms and tutorials and for people that want to run tests on their own machine (not everybody runs linux on their laptops) before sending larger versions of the same calculation to a cluster or a supercomputer. so the best performance is not the highest priority. if you are able to make properly documented comparative benchmarks, i'd be happy to get to know pass that information on to other users in the documentation of the windows port. > I would eagerly wait for your mail regarding the download links. > > Kind Regards, > > On 04-Sep-2014 11:27 pm, "Axel Kohlmeyer" wrote: >> >> On Thu, Sep 4, 2014 at 7:52 PM, ehsan targholi wrote: >> > Hi >> > Dear axel >> > It's a very interesting idea. I'm interested to running it in Windows >> > and in >> > parallel version. What should I do? >> >> just wait for my e-mail telling you where to find the temporary >> repository and the installer packages. >> >> what kind/version of windows are you running and how much RAM and how >> many CPU cores do you have? >> >> > >> > >> > best regards >> > E.Targholi >> > >> > >> > >> > On Thu, Sep 4, 2014 at 9:14 PM, Axel Kohlmeyer >> > wrote: >> >> >> >> hi everybody, >> >> >> >> following up on my previous request last fall, i am looking again for >> >> folks that are interested to run quantum espresso on windows? >> >> >> >> last fall some of you helped to improve the development version of QE >> >> so it can be compiled and run on windows machine (in serial and >> >> parallel). now i finally found the time to update this to the recent >> >> release 5.1 and built a new set of packages. before we unleash those >> >> to the general audience, and particularly inexperienced QE noobies, i >> >> want to make certain that everything works reasonably well. >> >> >> >> i only have very limited access to windows (on a virtual machine) and >> >> practice with it (the compilation is done with a cross compiler on >> >> linux) and thus cannot test very thoroughly (and don't have the time), >> >> so it seem just logical to farm this out to the QE community. >> >> >> >> if you are still interested, please contact me off-list with a short >> >> description of what kind of setup you are willing to test on (CPU, >> >> windows version, 32-bit or 64-bit, MPI or serial or both). i will then >> >> point you to a webpage with some instructions and a link to a >> >> repository where you can download the new packages as soon as they are >> >> available. >> >> >> >> thanks, >> >> axel. >> >> >> >> -- >> >> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 >> >> College of Science & Technology, Temple University, Philadelphia PA, >> >> USA >> >> International Centre for Theoretical Physics, Trieste. Italy. >> >> ___ >> >> Pw_forum mailing list >> >> Pw_forum at pwscf.org >> >> http://pwscf.org/mailman/listinfo/pw_forum >> > >> > >> > >> >
[Pw_forum] Looking for testers (again) for QE-5.1 binaries for windows
On Thu, Sep 4, 2014 at 7:52 PM, ehsan targholi wrote: > Hi > Dear axel > It's a very interesting idea. I'm interested to running it in Windows and in > parallel version. What should I do? just wait for my e-mail telling you where to find the temporary repository and the installer packages. what kind/version of windows are you running and how much RAM and how many CPU cores do you have? > > > best regards > E.Targholi > > > > On Thu, Sep 4, 2014 at 9:14 PM, Axel Kohlmeyer wrote: >> >> hi everybody, >> >> following up on my previous request last fall, i am looking again for >> folks that are interested to run quantum espresso on windows? >> >> last fall some of you helped to improve the development version of QE >> so it can be compiled and run on windows machine (in serial and >> parallel). now i finally found the time to update this to the recent >> release 5.1 and built a new set of packages. before we unleash those >> to the general audience, and particularly inexperienced QE noobies, i >> want to make certain that everything works reasonably well. >> >> i only have very limited access to windows (on a virtual machine) and >> practice with it (the compilation is done with a cross compiler on >> linux) and thus cannot test very thoroughly (and don't have the time), >> so it seem just logical to farm this out to the QE community. >> >> if you are still interested, please contact me off-list with a short >> description of what kind of setup you are willing to test on (CPU, >> windows version, 32-bit or 64-bit, MPI or serial or both). i will then >> point you to a webpage with some instructions and a link to a >> repository where you can download the new packages as soon as they are >> available. >> >> thanks, >> axel. >> >> -- >> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 >> College of Science & Technology, Temple University, Philadelphia PA, USA >> International Centre for Theoretical Physics, Trieste. Italy. >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Looking for testers (again) for QE-5.1 binaries for windows
hi everybody, following up on my previous request last fall, i am looking again for folks that are interested to run quantum espresso on windows? last fall some of you helped to improve the development version of QE so it can be compiled and run on windows machine (in serial and parallel). now i finally found the time to update this to the recent release 5.1 and built a new set of packages. before we unleash those to the general audience, and particularly inexperienced QE noobies, i want to make certain that everything works reasonably well. i only have very limited access to windows (on a virtual machine) and practice with it (the compilation is done with a cross compiler on linux) and thus cannot test very thoroughly (and don't have the time), so it seem just logical to farm this out to the QE community. if you are still interested, please contact me off-list with a short description of what kind of setup you are willing to test on (CPU, windows version, 32-bit or 64-bit, MPI or serial or both). i will then point you to a webpage with some instructions and a link to a repository where you can download the new packages as soon as they are available. thanks, axel. -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] How to show more digits in the results?
On Mon, Sep 1, 2014 at 2:32 PM, Mike Marchywka wrote: [...] >> For that, you do _not_ need more digits for exactly the reason I gave >> you. If you output more digits, you are just adding random numbers. >> Literally. > > I suppose in general there could be offset problems with energies and you are > adding > some large fixed amount to a small change of interest. Or, you could want to > examine that would only make matters worse, since in that case you lose additional digits of precision due to the lower "density" of floating point numbers at large absolute values. > the numerical issues. what would be the point of computing a number with a significantly large systematic error with extreme numerical precision? not to mention that only because we treat atom cores as point particles, we can specify their positions with high precision. aiming to do accurate calculations is commendable, but one has to put things into perspective and be able to tell numerical precision from actual accuracy of the calculation. a lot of calculations we do look much more precise than what their accuracy is. axel. >> >>> >>> Please let me know if you or anyone know how to change the code >> showing more digits in pw.x. >> >> Many people know (including me). But why should anybody tell you, if >> what you want is a stupid thing? Have you talked about this with your >> adviser? >> >> In general, please spent a little time learning about the systematic >> errors of DFT, the numerical precision of floating point numbers, the >> accuracy of a self-consistent calculation and error propagation. >> >> You should quickly see the folly of your request. >> >>> Best regards >>> Haibei >>> >>> >>> On Sun, Aug 31, 2014 at 1:51 PM, Axel Kohlmeyer >> mailto:akohlmey at gmail.com>> wrote: >>>> >>>> >>>> On Aug 30, 2014 10:57 PM, "Haibei Huang" >> mailto:haibeih at student.unimelb.edu.au>> >> wrote: >>>>> >>>>> Dear All, >>>>> >>>>> I am aware of that the QE will only show at most 8 digits after >> the decimal point in the output file, while more digits are needed in >> my calculation. >>>>> >>>>> Could any of you provide a way to increase the number digits after >> the decimal point? >>>> >>>> What is the point of using more digits, when the error is larger? >> You could just add random digits and have the same effect. >>>> >>>>> >>>>> Thanks for your time! >>>>> Looking forward to your reply! >>>>> Regards >>>>> Haibei >>>>> >>>>> >>>>> ___ >>>>> Pw_forum mailing list >>>>> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org> >>>>> http://pwscf.org/mailman/listinfo/pw_forum >>>> >>>> >>>> ___ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org> >>>> http://pwscf.org/mailman/listinfo/pw_forum >>> >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org> >>> http://pwscf.org/mailman/listinfo/pw_forum >> >> ___ Pw_forum mailing list >> Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] How to show more digits in the results?
On Sep 1, 2014 1:16 AM, "Haibei Huang" wrote: > > Dear Axel, > > Thanks for your reply. > > The truth is that I was trying to diagonalize a matrix made of a serials of Energies obtained by pw.x, while some of elements in the matrix is quite small (e.g. 10^-7 or 10-^8). Thus, I would like to know how many digits I could trust in Energies. Or at least I should keep the Energies and these small elements in the same scale, say 10^-8. For that, you do _not_ need more digits for exactly the reason I gave you. If you output more digits, you are just adding random numbers. Literally. > > Please let me know if you or anyone know how to change the code showing more digits in pw.x. Many people know (including me). But why should anybody tell you, if what you want is a stupid thing? Have you talked about this with your adviser? In general, please spent a little time learning about the systematic errors of DFT, the numerical precision of floating point numbers, the accuracy of a self-consistent calculation and error propagation. You should quickly see the folly of your request. > Best regards > Haibei > > > On Sun, Aug 31, 2014 at 1:51 PM, Axel Kohlmeyer wrote: >> >> >> On Aug 30, 2014 10:57 PM, "Haibei Huang" wrote: >> > >> > Dear All, >> > >> > I am aware of that the QE will only show at most 8 digits after the decimal point in the output file, while more digits are needed in my calculation. >> > >> > Could any of you provide a way to increase the number digits after the decimal point? >> >> What is the point of using more digits, when the error is larger? You could just add random digits and have the same effect. >> >> > >> > Thanks for your time! >> > Looking forward to your reply! >> > Regards >> > Haibei >> > >> > >> > ___ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://pwscf.org/mailman/listinfo/pw_forum >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140831/d1ddc683/attachment.html
[Pw_forum] How to show more digits in the results?
On Aug 30, 2014 10:57 PM, "Haibei Huang" wrote: > > Dear All, > > I am aware of that the QE will only show at most 8 digits after the decimal point in the output file, while more digits are needed in my calculation. > > Could any of you provide a way to increase the number digits after the decimal point? What is the point of using more digits, when the error is larger? You could just add random digits and have the same effect. > > Thanks for your time! > Looking forward to your reply! > Regards > Haibei > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140831/ea90d056/attachment.html
[Pw_forum] running PWSCF on IB-based cluster
On Sat, Aug 30, 2014 at 4:44 AM, ?? wrote:
> Dear Paolo,
>
> Thanks a lot for your quick response! We are using intel compiler and
> openmpi. Actually, someone else configured our cluster, and I had to use
> mpirun with option "bind-to-core" to run a job over more than one nodes. If
i seriously doubt that. rather you should discuss this with the person
that configured the cluster and get an answer that is consistent with
the existing configuration.
> I do not use "--bind-to-core" option, the job will be submitted to only one
> node with np processors. There was no problem to run other program with
> "--bind-to-core" option except QE, for which I got "processor affinity
> failure". That's why I posted my question on pw_forum. Thanks again for your
this explanation doesn't make sense. the bind-to-core option does
nothing like that. and it has definitely nothing to do with QE
it sounds more like you do not provide a suitable hostfile. please
spend some time going over the OpenMPI documentation, compile a simple
MPI test program and experiment with that how to run properly on your
cluster. if you have further problems, you should post to the OpenMPI
mailing list, or bug your provider again.
axel.
> reply!
>
> Best,
>
> Xing
>
>
>> --
>> ???: "Paolo Giannozzi"
>> : 2014?8?29? ???
>> ???: "PWSCF Forum"
>> ??:
>> ??: Re: [Pw_forum] running PWSCF on IB-based cluster
>
>>
>> QE knows nothing about which processor is on which node.
>> It must be related to the MPI libraries ("openmpi" and
>> "intel mpi" are different, by the way, and one should
>> be careful not to mix up the two) and to how MPI is
>> started on your machine
>>
>> P.
>>
>> On Fri, 2014-08-29 at 17:53 +0800, ?? wrote:
>> >
>> > Dear QE community,
>> >
>> > We have an infini-band based cluster with 8 computing nodes and each
>> > nodes contains 16 cores. I compiled QE package on this cluster
>> > successfully with compiler mpif90 (openmpi intel compiler) and there
>> > was no problem to run pw.x on one node with 16 processors. However,
>> > when I tried to use two nodes (that is, -np 32), I met "processor
>> > affinity failure". It says, "an attempt to set processor affinity has
>> > failed - please check to ensure that your system supports such
>> > functionality. If so, then this is probably something that should be
>> > reported to the OMPI developers". Actually, there is no such problem
>> > when I run other program. I am wondering if someone else met the
>> > similar question before? And please give me any hint which may help me
>> > on this problem! Thanks in advance!
>> >
>> > Best,
>> >
>> > Xing
>> >
>> >
>> >
>> >
>> >
>> >
>> > ___
>> > Pw_forum mailing list
>> > Pw_forum at pwscf.org
>> > http://pwscf.org/mailman/listinfo/pw_forum
>>
>> --
>> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Help with running QE on supercomputer
On Fri, Aug 29, 2014 at 4:10 PM, Cameron Foss wrote: > Hello all, > > I am using TACC's supercomputer GORDON to do some phonon dispersion > calculations for silicon. However, i am having trouble getting my batch > scripts working, I keep getting this error: > > [gcn-7-16.sdsc.edu:mpirun_rsh][child_handler] Error in init phase, aborting! > (0/1 mpispawn connections) gordon is not hosted by TACC, but by SDSC. > > GORDON system details: > > Does anyone know what may be the issue here? you should contact the local user support of that machine. they should know best. axel. > > here is the script file: > #!/bin/sh > #PBS -N silconPH > #PBS -l nodes=4:ppn=16:native > #PBS -l walltime=00:15:00 > #PBS -q normal > #PBS -o si.scf.out > #PBS -A sef101 > #PBS -m bea > #PBS -M cjfoss at umass.edu > ### > > cd $PBS_O_WORKDIR > > #module swap mvapich2_ib openmpi_ib > export ESPRESSO_HOME=$HOME/espresso-5.1 > export ESPRESSO_TMPDIR=$PBS_O_WORKDIR > export ESPRESSO_PSEUDO=$ESPRESSO_HOME/pseudo > > #export OMP_NUM_THREAD = 32 > > mpirun_rsh -np $PBS_NP -hostfile $PBS_NODEFILE $ESPRESSO_HOME/bin/pw.x < > si.scf.in > > Best, > Cameron > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Pw_forum Digest, Vol 85, Issue 22
On Thu, Aug 28, 2014 at 2:50 PM, Chukwu Jonathan wrote: > My calculation is QE and I am using it to solve problems on Molecular > Dynamics (MD). Please do we have anyone working on MD to put me through? that is far too generic a question to help you with. how to run an MD is not explained in a few words. please keep in mind that a mailing list is no replacement for an adviser, textbooks or a tutorial. specific QE tutorial materials are available here: http://www.quantum-espresso.org/tutorials/ there also is the documentation and FAQ. axel. > Thank you > > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Point Charges for Molecular Dynamics
On Sun, Aug 10, 2014 at 11:46 PM, Kevin Schmidt wrote: > Hello PWSCF Forum, > > First time caller, long time listener. I am working with a group using > Quantum Espresso to extract two-body interatomic potentials (IP) for an > ionic crystal system (metal borides, to be exact). These potentials will > then be put to use in molecular dynamics software (DL-Poly). From my > understanding with MD, most software nowadays typically employs > electrostatics as a separate potential from the heteronuclear IP's. In it always has been like that for all cases where "full" (i.e. not screened) electrostatics are assumed. however, you have to have a good look at methodologies for force field parameterization. simply computing a point charge distribution from some QM density and dropping them into an MD force field is highly unlikely to work. parameterizing a classical force field is a substantial amount of work and having some initial guess for the charge distribution is only the beginning. a lot depends on what you are going to do with your model and whether it will be combined with other elements from an existing force field. you mention ionic crystals, so that would typically require a many-body method with dynamic charges via some charge equilibration system or some bond order constraint system for achieve good accuracy. if you stick to a simpler model with fixed charges, you will have to spend a signficant amount of time validating your choice of parameters, since very often adjustments need to be made to make the parameterization able to reproduce some known experimental properties (and remember, also DFT calculations do not always reproduce those accurately). > order to (1) get the correct heteronuclear IP and (2) simulate a "realistic" > electrostatic environment in MD, it would be best to have the right point > charges for the system. After browsing through the forum and user guides, I but there is the problem. what are the "right" charges. there are multiple recipes to map the total density distribution to individual point charges at the location of the atoms, but this will have errors since it is often quite ambiguous how to do this projection. for force field parameterization often methods trying to reproduce the electrostatic potential are used. > noticed that PP.x (plot_num = 0) has the ability to output charge density > distributions. The output I received had, depending on which plot type > used, five or six columns, of which I am assuming are related to charge > values on a grid. Is this correct, and if so, how do I find the > corresponding grid? > > My idea was to integrate the charge density in a Wigner-Seitz cell around > each ion to get point charges for use in electrostatics. I'm not sure if > there's a better way to accomplish this goal; this was my attempt. I there are multiple methods available. some are even implemented in Q-E. however, before you continue, please read up on force field parameterization and do not waste any time on doing Q-E calculations before you know what you need to do. > apologize if I have overlooked a thread, please notify me so. Thanks in > advance and I look forward to your advice. > > P.S. The output I received for a model system is given below for a > specified "filplot", plot_num = 0. > > > 72 72 72 72 72 72 4 2 > 17. 0. 0. 0. > 0. 0. > 1191.5371196339 12.00 80.00 0 >1 La 11.00 >2 B 3.00 >1 0.00.00.01 >2 0.00.50.52 >3 0.50.00.52 >4 0.50.50.02 > 3.434814311E-01 3.431749032E-01 3.422272391E-01 3.405249826E-01 > 3.378906730E-01 > 3.341004832E-01 3.288993448E-01 3.220354913E-01 3.132873382E-01 > 3.024951442E-01 > 2.895821234E-01 2.745777240E-01 2.576219405E-01 2.389737928E-01 > 2.190001080E-01 > 1.981636489E-01 1.769910061E-01 1.560378501E-01 1.358452121E-01 > 1.168975755E-01 > 9.959052347E-02 8.420256729E-02 7.088392771E-02 5.965905586E-02 > 5.043519819E-02 > . more values > > -- > Kevin Schmidt > Chemical Engineering Department > University of Nevada, Reno, USA > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] SATA vs SAS
On Aug 8, 2014 1:23 PM, "Eduardo Menendez" wrote: > > Hi, > Thanks for the replies to my question. Some answers were devoted to solid state devices (SSD), but I had asked about SAS (Serial attached SCSI) in comparison to SATA disks. I know that SAS are better for high I/O load. The point is how critical ist that for QE. > > I have to choice between (better CPU with SATA) vs (worse CPU with SAS). > > > I have the feeling (from the times of IDE hard disks), that under heavy I/O load (using swap memory), the use of CPU drops to 1% and calculations are impractical. I guess it is still true, i.e., heavy I/O are to be avoided in ab initio calculations. There is no simple answer to your choice that is always valid. Many other factors can have a big impact, bigger than SAS vs sata. E.g. High capacity disks have higher throughput. Thus your approach is not very useful. You need to find what the weakest point in your configuration is. That can be ram, cpu clock or type, disk, whether to add an SSD or not, a dedicated scratch disk. And more. > > > > > > Eduardo Menendez Proupin > Departamento de Fisica, Facultad de Ciencias, Universidad de Chile > URL: http://www.gnm.cl/emenendez > > ?Science may be described as the art of systematic oversimplification.? Karl Popper > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140808/5cd463c8/attachment.html
[Pw_forum] SATA vs SAS
On Thu, Aug 7, 2014 at 6:56 AM, siddheshwar chopra wrote: > Dear Sir, > Oh I am sorry... I think I didn't mention correctly.. I said "write times".. > It is actually "number of write times". Ofcourse these are very fast..But > their life is shorter than the normal HDDs... > Yes budget is what is the final verdict.. :-) not only that. but also, how much time you save, i.e. how much value you attribute to your own time. if an SSD will wear out and become unusable, you can easily replace it at the fraction of the cost of the entire machine, and then - provided an SSD scratch does significantly improve your calculation run times - you have a faster machine all the time. please also note that SSD performance varies a lot and also the amount of guaranteed writes. axel. > > Regards, > > > On Thu, Aug 7, 2014 at 4:18 PM, Carlo Nervi wrote: >> >> I'm not an expert, and maybe my infos are old, but I think you are wrong. >> Certain SSD have degraded performances, however the best SSD have much >> faster access I/O time than than the best HDD. at least for medium >> workstation. Cost for Gb is of course much higher for SSD, but in this case >> I would go only for a working directory to be placed on a SSD partition (128 >> Gb could be enough). I do not know how is the situation for high-end >> enterprise solutions or supercomputers, but in this case i suspect that the >> special HDDs are not connected via simple SATA or SAS, and in these cases >> very probably they are much faster (again at much hgher prices) due several >> optimized performances (independent memory cache, for example). >> >> In other words, it depend how much is your budget... >> Cheers, >> Carlo >> >> >> >> 2014-08-07 11:42 GMT+02:00 siddheshwar chopra : >>> >>> Dear Sir, >>> I just want to participate in this good discussion. I read somewhere that >>> Solid State Hard Disk has LESSER write times than a normal HDD. Yes >>> undoubtedly it is the fastest we have in the market with low power >>> consumption and zero mechanical failure risk, but at the cost of shorter >>> lives and more money. >>> Any comments welcome.. >>> >>> Regards, >>> >>> >>> On Thu, Aug 7, 2014 at 2:16 PM, Carlo Nervi wrote: >>>> >>>> My two cents: even though there are differences between SAS and SATA, >>>> they are not so huge. >>>> From this point of view I guess that a fast Solid State Hard Disk would >>>> make the difference on the I/O. >>>> >>>> >>>> >>>> 2014-08-07 10:06 GMT+02:00 Paolo Giannozzi : >>>> >>>>> On Wed, 2014-08-06 at 18:15 -0400, Eduardo Menendez wrote: >>>>> >>>>> > Is it critical to use SAS disks (compared to SATA) for good >>>>> > performance of Quantum ESPRESSO? >>>>> >>>>> I guess it depends upon the amount of I/O you plan to do >>>>> >>>>> Paolo >>>>> >>>>> -- >>>>> Paolo Giannozzi, Dept. Chemistry&Physics&Environment, >>>>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >>>>> Phone +39-0432-558216, fax +39-0432-558222 >>>>> >>>>> ___ >>>>> Pw_forum mailing list >>>>> Pw_forum at pwscf.org >>>>> http://pwscf.org/mailman/listinfo/pw_forum >>>> >>>> >>>> >>>> >>>> -- >>>> >>>> >>>> Prof. Carlo Nervi carlo.nervi at unito.it Tel:+39 0116707507/8 >>>> Fax: +39 0116707855 - Dipartimento di Chimica, via >>>> P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.it/ >>>> >>>> >>>> ___ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://pwscf.org/mailman/listinfo/pw_forum >>> >>> >>> >>> >>> -- >>> Dr. Siddheshwar chopra, >>> M.Sc., Ph.D (Physics) >>> Assistant Professor (Physics), >>> Amity University, Noida, India. >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >> >> >> >> >> -- >> >> >> Prof. Carlo Nervi carlo.nervi at unito.it Tel:+39 0116707507/8 >> Fax: +39 0116707855 - Dipartimento di Chimica, via >> P. Giuria 7, 10125 Torino, Italy.http://lem.ch.unito.it/ >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > Dr. Siddheshwar chopra, > M.Sc., Ph.D (Physics) > Assistant Professor (Physics), > Amity University, Noida, India. > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] espresso-4.0.3 Compilation Issues
On Thu, Jul 24, 2014 at 4:18 PM, W2AGZ wrote: > My Linux box (running kubuntu) successfully, and has for years, run QE 4.3.2 > and 5.0.1 without issue. However, an attempt to compile 4.0.3, with all > necessary packages installed and after a successful ./configure, running a > simple make pw gives, after dozens of lines of messages, abends with the > following: > > > > mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW > -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW > -I../PH -c read_upf_v1.f90 > > mpif90 -O3 -x f95-cpp-input -D__GFORTRAN -D__FFTW -D__USE_INTERNAL_FFTW > -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW > -I../PH -c read_upf_v2.f90 > > read_upf_v2.f90:437.16-34: > > > > ALLOCATE( upf%nn(upf%nwfc), upf%nn(upf%nwfc), & > >1 2 > > Error: Allocate-object at (1) also appears at (2) > > make[1]: *** [read_upf_v2.o] Error 1 > > make[1]: Leaving directory `/home/pmpgrant/Desktop/espresso-4.0.3/Modules' > > make: *** [mods] Error 2 > > pmpgrant at w2agz-hp9280:~/Desktop/espresso-4.0.3$ ^C > > pmpgrant at w2agz-hp9280:~/Desktop/espresso-4.0.3$ > > > > Once more, as far as I can tell, all the packages (gfortran, lapack, etc.) > are available. Sounds like some bizarre conflict between 4.0.3 and kubuntu > may exist! paul, this can be fixed by simply reading the error message and acting upon it. there is an obvious bug in that line of code in that the same array is allocated twice in the same statement. while this was apparently silently(?) skipped over by more forgiving compilers, gfortran comes down hard on it and requires you to remove one of the two. if i am not mistaken, this report and fix has been posted to this very list already a few times. compiling a very old version of QE with gfortran is asking for trouble. old versions of gfortran are buggy or incomplete and new versions are very demanding in terms of standard compliance (often more than the average scientific software developer is ready to handle). axel. > > > > Thanks in advance for any advice. > > > > Paul Grant > > IBM RSM/Manager Emeritus > > W2AGZ Technologies > > www.w2agz.com > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] QE on Xeon Phi
On Mon, Jul 14, 2014 at 9:34 AM, Eduardo Menendez wrote: > Thank you Axel. Your advise rises another doubt. Can we get the maximum > performance from a highly clocked CPU? > I used to consider that the the fastest CPUs were too fast for the memory > access, resulting in bottlenecks. Of couse it depends on cache size. your concern is justified, but the situation is more complex these days. highly clocked CPUs have less cores and thus receive a larger share of the available memory bandwidth and the highest clocked inter-CPU and memory bus is only available for a subset of the CPUs. now you have an optimization problem that has to consider the strong scaling (or lack thereof) of the code in question as an additional input parameter. to give an example: we purchased at the same time dual socket nodes that had the same mainboard, but either 2x 3.5GHz quad-core or 2x 2.8GHz hex-core. the 3.5GHz was the fastest clock available at the time. for classical MD, i get better performance out of the 12-core nodes, for plane-wave DFT i get about the same performance out of both, for CP2k i get better performance with the 8-core (in fact, CP2k runs fastest on the 12-core with using only 8 cores). now, the cost of the 2.8GHz CPUs is significantly lower, so that is why we procured the majority of the cluster with those. but we do have applications that scale less than CP2k or are serial, but require high per-core memory bandwidth, so we got a few of the 3.5GHz ones, too (and since they are already expensive we filled them with RAM as much as it doesn't result in underclocking of the memory bus; and in turn we put "only" 1GB/core into the 12-core nodes). so it all boils down to finding the right balance and adjusting it to the application mix that you are running. last time i checked the intel spec sheets, it looked as if the best deal was to be had for CPUs with the second largest number of CPU cores and as high a clock as required to have the full memory bus speed. that will also keep the heat in check, as the highest clocked CPUs usually have a much higher TDP (>50% more) and that is just a much larger demand on cooling and power and will incur additional indirect costs as well. HTH, axel. > >>Stick with the cpu. For QE you should be best off with intel. Also you are >> likely to >get the best price/performance ratio with CPUs that have less >> than the maximum >number of cpu cores and a higher clock instead. > > > Eduardo Menendez Proupin > Departamento de Fisica, Facultad de Ciencias, Universidad de Chile > URL: http://www.gnm.cl/emenendez > > ?Science may be described as the art of systematic oversimplification.? Karl > Popper > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] QE on Xeon Phi
Stick with the cpu. For QE you should be best off with intel. Also you are likely to get the best price/performance ratio with CPUs that have less than the maximum number of cpu cores and a higher clock instead. Axel. On Jul 11, 2014 7:45 PM, "Eduardo Menendez" wrote: > > Dear fellows, > > I need to know if it is worth to buy Xeon coprocessors for use with Quantum ESPRESSO. I need make a choice between more CPU or less CPU+coprocessor, and even to choose between few Intel cores vs not-so-few AMD Opterons. Searching in the Web I have found these implemntatios of QE on Xeon Phi: > (1) a Quantum ESPRESSO modified for Xeon Phi, by Fabio Affinito, and > (2) an instructions for instalation of standard Quantum ESPRESSO with some automagic use of Xeon Phi by the MKL. Here is the site > https://software.intel.com/en-us/articles/quantum-espresso-for-intel-xeon-phi-coprocessor > > Is the choice (1) available and mature enough for a general use, or at least for > using PWscf for calculations of defects in supercells containg a multiple of 64 atoms? > Is choice (2) effcient? I see a benchmark in that site that, if I interpret correctly, it indicates only a 12% improvement. Hence I think this automagic choice is not worth enough. Am I wrong? > > Choice 2 needs installing MPSS (Manycore Platform Software Stacks) and Intel MPI. Does choice (1) also require these components? > > MPSS is supported for Red Hat and SUSE. Is there any good experience with Debian or Ubuntu? > > At this point I feel rather conservative :-( . If not warmed by enthusiastic praise of coprocessors, or GPU, I will keep looking for as many CPU cores as possible. > > > Cheers, > > > Eduardo Menendez Proupin > Departamento de Fisica, Facultad de Ciencias, Universidad de Chile > URL: http://www.gnm.cl/emenendez > > ?Science may be described as the art of systematic oversimplification.? Karl Popper > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140712/149f0368/attachment.html
[Pw_forum] job doesnot complete for CP md
lume: 1000.01000.0 (AU) > > > initialize : 1.31s CPU 2.19s WALL ( 1 calls) > main_loop: 3.68s CPU 4.66s WALL ( 109 calls) > > Called by main_loop: > move_electro : 3.60s CPU 4.35s WALL ( 109 calls) > ortho: 0.05s CPU 0.08s WALL ( 110 calls) > updatc : 0.01s CPU 0.01s WALL ( 110 calls) > strucf : 0.00s CPU 0.00s WALL ( 1 calls) > calbec : 0.00s CPU 0.00s WALL ( 111 calls) > > Called by move_electrons: > rhoofr : 0.50s CPU 0.92s WALL ( 110 calls) > vofrho : 2.40s CPU 3.02s WALL ( 110 calls) > dforce : 0.09s CPU 0.12s WALL ( 220 calls) > calphi : 0.00s CPU 0.02s WALL ( 110 calls) > newd : 0.63s CPU 0.64s WALL ( 110 calls) > > Called by ortho: > ortho_iter : 0.01s CPU 0.01s WALL ( 110 calls) > rsg : 0.01s CPU 0.02s WALL ( 110 calls) > rhoset : 0.01s CPU 0.02s WALL ( 110 calls) > sigset : 0.00s CPU 0.00s WALL ( 110 calls) > tauset : 0.00s CPU 0.00s WALL ( 110 calls) > > Small boxes: > rhov : 0.26s CPU 0.35s WALL ( 110 calls) > fftb : 0.43s CPU 0.43s WALL (4512 calls) > > Low-level routines: > prefor : 0.00s CPU 0.00s WALL ( 110 calls) > nlsm1: 0.02s CPU 0.02s WALL ( 331 calls) > fft : 1.20s CPU 1.81s WALL ( 990 calls) > ffts : 0.09s CPU 0.17s WALL ( 220 calls) > fftw : 0.12s CPU 0.25s WALL ( 660 calls) > fft_scatter : 0.89s CPU 1.41s WALL (1870 calls) > betagx : 0.69s CPU 0.69s WALL ( 1 calls) > qradx: 0.37s CPU 0.39s WALL ( 1 calls) > gram : 0.00s CPU 0.00s WALL ( 1 calls) > nlinit : 1.25s CPU 1.36s WALL ( 1 calls) > init_dim : 0.01s CPU 0.03s WALL ( 1 calls) > newnlinit: 0.13s CPU 0.15s WALL ( 1 calls) > from_scratch : 0.04s CPU 0.48s WALL ( 1 calls) > ortho_iter : 0.01s CPU 0.01s WALL ( 110 calls) > > > CP : 5.22s CPU 7.68s WALL > > >This run was terminated on: 15:37:49 27Jun2014 > > =--= >JOB DONE. > =--= > -- > Thanks > Ravi > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] A "relax" input runs on CPU (pw.x) but not on CPU-GPU (pw-gpu.x)
On Mon, Jun 23, 2014 at 11:59 AM, David Foster wrote: > Dear Axel > I have some questions in this topic, too. Suppose we use a poor DP floating > point performance GTX cards for QE-GPU. Does the codes in > GPU technology of nVIDIA (such as CUDA and ...) change the DP of QE to SP > automatically? or program ended with error. neither. if the CUDA (or OpenCL or OpenACC kernel) requests double precision, it *will* use the available double precision units. only if you compile for extremely old architecture (1.0 and older IIRC), the double instructions/data will be silently truncated to single precision. i would suggest to make a real-world test to confirm this. e.g. the force kernels in the GPU package of the LAMMPS classical MD code can be compiled in all-SP, mixed-P and all-DP and then you could run that executable on different hardware and see how the relative performance and accuracy changes. > If it changes DP to SP automatically, users might get wrong results without > any attention. > > How about a full SP GPU card for full DP code? Does code run on it? all SP GPUs are *very* old and i doubt that you can compile QE for those. older GPU architectures require to program (complicated) workarounds due to limitations of the architecture. since they also are slower than newer cards, it is not worth to implement those. current consumer cards *do* have double precision floating point support, but usually at a DP:SP ratio of 1:10 rather than the 1:3 present in (kepler based) tesla cards (fermi even has 1:2). as has been explained many times before. GPU support for QE is a niche solution. it helps to push calculations farther, especially on workstation-like machines and large machines with GPUs, where being able to utilize the GPUs is a prerequisite condition to get access. particularly with the recent improvements to the CPUs and the increase in the number of CPU cores and improvements in vector instructions, it is currently often better to invest effort and money into a better CPU based solution than including GPUs. learning how to compil/test/use GPU acceleration would be most useful, if you plan to work on improving the GPU support and adding new features. in general, the problem with GPUs is that they are not as general purpose as people are made to believe. on the contrary, GPUs are very extreme and thus require "extreme" programming that puts consideration for the architecture first and physics second (i.e. the opposite of what is common in scientific computing). that doesn't mean that it is useless, since most tricks and strategies that are a necessity for GPUs (because they are so extreme) will also be beneficial for multi-threaded and vectorized. in fact, i personally have mostly abandoned GPU programming, in favor of adding multi-threading and vectorization to code, but my multi-thread programming is heavily influenced by what i learned from trying to program GPUs, and these makes the code much better than what i wrote before. HTH, axel. > > Regards > > David Foster > > Ph.D. Student of Chemistry > > ---- > On Sat, 6/21/14, Axel Kohlmeyer wrote: > > Subject: Re: [Pw_forum] A "relax" input runs on CPU (pw.x) but not on > CPU-GPU (pw-gpu.x) > To: "PWSCF Forum" > Date: Saturday, June 21, 2014, 2:20 AM > > On Sat, Jun 21, 2014 at 4:20 AM, Reza > Behjatmanesh-Ardakani > > wrote: > > Dear Axel > > This was just a proposal. If I am right, Terachem code > can use gaming cards for GPU calculations (I saw some of its > authors' papers). > > yes, but terachem was written from ground up with new > algorithms to > avoid loss of precision. in quantum mechanics this is > important, since > a lot of calculations depend on comparing large numbers of > equal sign > and magnitude and looking at the difference. about the only > part of a > plane wave DFT calculation that is "conservative" in terms > of > precision without a massive redesign are the FFTs. the loss > of > precision is fairly small when replacing double precision > FFTs with > single precision ones. for the many 3d-FFTs required, this > is > particularly beneficial when trying to scale out via MPI, as > this > reduces the amount of bytes that need to be sent and copied > around in > half and also reduces the strain on memory bandwidth. > > > As you know, the main problem of GTX cards comes back > to two important things. One, single precision, and the > other lack of ECC. > > ECC is a lesser issue. and it is not a problem of single > precision, > but lack of performance with double precision due to having > only a > fraction of double precision units. another issue is the > lack of RAM. > also you
[Pw_forum] A "relax" input runs on CPU (pw.x) but not on CPU-GPU (pw-gpu.x)
On Sun, Jun 22, 2014 at 3:12 AM, Reza Behjatmanesh-Ardakani wrote: > Dear Axel > Thank you. It was very helpful for me. > As you said some new GTX cards have good DP floating point performance such > as GTX Ti Black or GTX Ti Z that for both DP is 1/3 of SP. > They are much cheaper than Tesla cards. > I am not sure that Ti Black or Ti Z has ECC. no it hasn't. > Quadro K6000 has it. well, the quadro is practically a tesla with all graphics features enabled. ...at a price. > Thanks again. > > With the Best Regards > >Reza Behjatmanesh-Ardakani >Associate Professor of Physical Chemistry >Address: >Department of Chemistry, >School of Science, >Payame Noor University (PNU), >Ardakan, >Yazd, >Iran. >E-mails: > 1- reza_b_m_a at yahoo.com (preferred), > 2- behjatmanesh at pnu.ac.ir, > 3- reza.b.m.a at gmail.com. > > > On Sat, 6/21/14, Axel Kohlmeyer wrote: > > Subject: Re: [Pw_forum] A "relax" input runs on CPU (pw.x) but not on > CPU-GPU (pw-gpu.x) > To: "PWSCF Forum" > Date: Saturday, June 21, 2014, 1:50 PM > > On Sat, Jun 21, 2014 at 4:20 AM, Reza > Behjatmanesh-Ardakani > > wrote: > > Dear Axel > > This was just a proposal. If I am right, Terachem code > can use gaming cards for GPU calculations (I saw some of its > authors' papers). > > yes, but terachem was written from ground up with new > algorithms to > avoid loss of precision. in quantum mechanics this is > important, since > a lot of calculations depend on comparing large numbers of > equal sign > and magnitude and looking at the difference. about the only > part of a > plane wave DFT calculation that is "conservative" in terms > of > precision without a massive redesign are the FFTs. the loss > of > precision is fairly small when replacing double precision > FFTs with > single precision ones. for the many 3d-FFTs required, this > is > particularly beneficial when trying to scale out via MPI, as > this > reduces the amount of bytes that need to be sent and copied > around in > half and also reduces the strain on memory bandwidth. > > > As you know, the main problem of GTX cards comes back > to two important things. One, single precision, and the > other lack of ECC. > > ECC is a lesser issue. and it is not a problem of single > precision, > but lack of performance with double precision due to having > only a > fraction of double precision units. another issue is the > lack of RAM. > also you have to distinguish between different GTX cards. a > few of the > most high-end consumer cards *do* have the full set of > double > precision units and a large amount of RAM. > > ECC is mostly relevant for people running a large number of > GPUs in a > supercomputer environment. > > > > > It is not necessary to write a stand alone code. We can > test the QE-GPU with both TESLA and/or GTX and QE (cpu > only), and compare the outputs. > > but it is pointless to run on a hardware that is not > competitive. > you'll have a hard time already to get a 2x speedup from > using a top > level tesla card vs. an all CPU run on a decent machine. > what would be > the point of having the GPU _decelerate_ your calculation? > > in general, a lot of the GPU stuff is hype and > misinformation. the > following is a bit old, but still worth a read: > > http://www.hpcwire.com/2011/12/13/ten_ways_to_fool_the_masses_when_giving_performance_results_on_gpus/ > > as a consequence of a very smart and successful PR strategy, > there is > now the impression that *any* kind of GPU will result in a > *massive* > speedup. even people with a laptop GPU with 2 SMs, no memory > bandwidth > are now expecting 100x speedups and more. however, except > for a few > corner cases and applications that are very well represented > on GPUs > (not very complex) and badly on a CPU, you will often get > more like a > 2x-5x speedup in a "best effort" comparison of a well > equipped host > with a high-end GPU. in part, this situation has become > worse with > some choices made by nvidia hardware and software engineers. > while 5 > years back, the difference between a consumer and a > computing GPU was > small, the consumer models have been systematically > "downgraded" (via > removing previously supported management features in the > driver and > having consumer cards be based on a simplified design that > mostly > makes them mid-level
[Pw_forum] A "relax" input runs on CPU (pw.x) but not on CPU-GPU (pw-gpu.x)
, the output may be not reproducible. > However, I think due to the nature of SCF algorithm, the code can be used at > least when you have memory corruption due to bad/overheated memory, no SCF algorithm will save you. if you go back 10 years when CPUs didn't have all those power management and automatic self-protection and also memory modules in desktop were often of very low quality, people experienced a lot of problems. "signal 11" and "segmentation fault" were a common topic in many mailing lists on scientific (or other) software that caused a high CPU load. but the indication of broken memory was usually a crash due to a segfault or bad data corruption leading to a massive change in numbers and often NaNs. once you have a single NaN in your data, it will spread like a highly infective virus and render the calculation invalid. a well set up consumer level GPU will run as reliable as a tesla or better, only you cannot tell since the nvidia tools will not show you. the main issue is performance and available memory. > for VC-RELAX, RELAX, and SCF types of calculations with GTX cards. Of course, > it should be tested. Thank you for your interest. you are not making much sense here either. but if it makes you feel better to do those tests, don't let me discourage you. sometimes people learn the best this way. axel. > With the Best Regards > >Reza Behjatmanesh-Ardakani >Associate Professor of Physical Chemistry >Address: >Department of Chemistry, >School of Science, >Payame Noor University (PNU), >Ardakan, >Yazd, >Iran. >E-mails: > 1- reza_b_m_a at yahoo.com (preferred), > 2- behjatmanesh at pnu.ac.ir, > 3- reza.b.m.a at gmail.com. > > > On Fri, 6/20/14, Axel Kohlmeyer wrote: > > Subject: Re: [Pw_forum] A "relax" input runs on CPU (pw.x) but not on > CPU-GPU (pw-gpu.x) > To: "PWSCF Forum" > Date: Friday, June 20, 2014, 2:19 PM > > On Fri, Jun 20, 2014 at 4:22 AM, Reza > Behjatmanesh-Ardakani > > wrote: > > Dear Filippo > > > > Due to the nature of QE which is iterative, I think > lack of ECC and even double precision floating point in > gaming cards (GTX) comparing to tesla cards > > > > is not serious problem for QE-GPU. Some authors have > checked this for AMBER molecular dynamics simulation code. > See following site: > > classical MD is a very different animal than what you do > with QE. > errors due to single precision to some properties in > classical MD are > huge with all single precision calculations. to compute a > force from a > distance will not be much affected, but summing up the force > can > already be a problem. "good" classical MD codes usually > employ a mixed > precision approach, where only the accuracy insensitive > parts are done > in single precision. for very large system, even double > precision can > show significant floating point truncation errors. usually > you are > dependent on error cancellation, too, i.e. when you study a > simple > homogenous system (as it is quite common in those tests). > > > > > > http://www.hpcwire.com/2014/03/13/ecc-performance-price-worth-gpus > > > > > > and see the following paper: > > > > > > > www.rosswalker.co.uk/papers/2014_03_ECC_AMBER_Paper_10.1002_cpe.3232.pdf > > > > > > > > I encourage the users of QE-GPU to test it for QE, and > report the difference on the site. > > it is a waste of time and effort. people have done DFT and > HF in > (partial) single precision before and only if you write a > new code > from scratch and have an extremely skilled programmer, you > will > succeed. have a look at the terachem software out of the > group of todd > martinez for example. > > axel. > > > PS: to be able to test the results for GTX and TESLA, > it is needed QE-GPU code to be run on GTX :-) > > > > > > With the Best Regards > > > >Reza Behjatmanesh-Ardakani > >Associate Professor of Physical Chemistry > >Address: > >Department of Chemistry, > >School of Science, > >Payame Noor University (PNU), > >Ardakan, > >Yazd, > >Iran. > >E-mails: > > 1- reza_b_m_a at yahoo.com > (preferred), > > 2- behjatmanesh at pnu.ac.ir, > > 3- reza.b.m.a at gmail.com. > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pws
[Pw_forum] A "relax" input runs on CPU (pw.x) but not on CPU-GPU (pw-gpu.x)
On Fri, Jun 20, 2014 at 4:22 AM, Reza Behjatmanesh-Ardakani wrote: > Dear Filippo > > Due to the nature of QE which is iterative, I think lack of ECC and even > double precision floating point in gaming cards (GTX) comparing to tesla cards > > is not serious problem for QE-GPU. Some authors have checked this for AMBER > molecular dynamics simulation code. See following site: classical MD is a very different animal than what you do with QE. errors due to single precision to some properties in classical MD are huge with all single precision calculations. to compute a force from a distance will not be much affected, but summing up the force can already be a problem. "good" classical MD codes usually employ a mixed precision approach, where only the accuracy insensitive parts are done in single precision. for very large system, even double precision can show significant floating point truncation errors. usually you are dependent on error cancellation, too, i.e. when you study a simple homogenous system (as it is quite common in those tests). > > http://www.hpcwire.com/2014/03/13/ecc-performance-price-worth-gpus > > > and see the following paper: > > > www.rosswalker.co.uk/papers/2014_03_ECC_AMBER_Paper_10.1002_cpe.3232.pdf > > > > I encourage the users of QE-GPU to test it for QE, and report the difference > on the site. it is a waste of time and effort. people have done DFT and HF in (partial) single precision before and only if you write a new code from scratch and have an extremely skilled programmer, you will succeed. have a look at the terachem software out of the group of todd martinez for example. axel. > PS: to be able to test the results for GTX and TESLA, it is needed QE-GPU > code to be run on GTX :-) > > > With the Best Regards > >Reza Behjatmanesh-Ardakani >Associate Professor of Physical Chemistry >Address: >Department of Chemistry, >School of Science, >Payame Noor University (PNU), >Ardakan, >Yazd, >Iran. >E-mails: > 1- reza_b_m_a at yahoo.com (preferred), > 2- behjatmanesh at pnu.ac.ir, > 3- reza.b.m.a at gmail.com. > _______ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] Installing QE-5.0.3 with ifort- iotk error- reg.,
r library containing mpi_init... (cached) -lmpi > > > > *checking for library containing pdgemr2d... nochecking for library > containing pdgemr2d... nochecking for library containing pdgemr2d... > nochecking for library containing pdgemr2d... no* > setting DFLAGS... -D__INTEL -D__FFTW3 -D__MPI -D__PARA > setting IFLAGS... -I../include > setting FDFLAGS... $(DFLAGS) > checking for ranlib... ranlib > setting RANLIB... ranlib > checking for wget... wget -O > setting WGET... wget -O > configure: creating ./config.status > config.status: creating include/fft_defs.h > config.status: creating make.sys > config.status: creating configure.msg > config.status: creating install/make_wannier90.sys > config.status: creating install/make_blas.inc > config.status: creating install/make_lapack.inc > config.status: creating include/c_defs.h > config.status: include/c_defs.h is unchanged > > ESPRESSO can take advantage of several optimized numerical libraries > (essl, fftw, mkl...). This configure script attempts to find them, > but may fail if they have been installed in non-standard locations. > If a required library is not found, the local copy will be compiled. > > The following libraries have been found: > BLAS_LIBS=/opt/intel/mkl/lib/intel64/ > LAPACK_LIBS=/opt/intel/mkl/lib/intel64/ > /opt/intel/composer_xe_2013_sp1.3.174/mkl/lib/intel64/ > FFT_LIBS= -lfftw3 > MPI_LIBS=-lmpi > Please check if this is what you expect. > > If any libraries are missing, you may specify a list of directories > to search and retry, as follows: > ./configure LIBDIRS="list of directories, separated by spaces" > > Parallel environment detected successfully.\ > Configured for compilation of parallel executables. > > For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex). > > configure: success > > whether this configuration is correct? > > there are lot of "NOs" i understood first few. but whether *pdgemr2d *are > needed for ifort > *? since some NOs are * > > > > *checking for library containing pdgemr2d... nochecking for library > containing pdgemr2d... nochecking for library containing pdgemr2d... no > checking for library containing pdgemr2d... no*. > > Second Question: > finally i hit make all and it ended with error. > > *slave2 at slave2:~/espresso$ make all* > test -d bin || mkdir bin > cd install ; make -f extlibs_makefile libiotk > make[1]: Entering directory `/home/slave2/espresso/install' > if test ! -d ../S3DE; then \ > (gzip -dc ../archive/iotk-1.2.beta.tar.gz | (cd ../; tar -xvf -)) ; \ > if test -e Makefile_iotk; then \ > (cp Makefile_iotk ../S3DE/iotk/src/Makefile); fi; \ > if test -e iotk_config.h; then \ > (cp iotk_config.h ../S3DE/iotk/include/iotk_config.h); fi; fi > cd ../S3DE/iotk/src; make lib+util; > make[2]: Entering directory `/home/slave2/espresso/S3DE/iotk/src' > ifort -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 > -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -I../include -c > iotk_error.f90 > iotk_error.f90(473): error #5102: Cannot open include file 'mpif.h' > include 'mpif.h' > --^ > iotk_error.f90(499): error #6404: This name does not have a type, and must > have an explicit type. [MPI_COMM_WORLD] > call MPI_Abort(MPI_COMM_WORLD,1,ierrx) > -^ > compilation aborted for iotk_error.f90 (code 1) > make[2]: *** [iotk_error.o] Error 1 > make[2]: Leaving directory `/home/slave2/espresso/S3DE/iotk/src' > make[1]: *** [libiotk] Error 2 > make[1]: Leaving directory `/home/slave2/espresso/install' > make: *** [libiotk] Error 2 > slave2 at slave2:~/espresso$ > > How to resolve this problem > > thank you in advance > > * > > *Muthu.V ?Project Fellow ?Madurai Kamaraj University* > > * > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140611/1bd98e3c/attachment.html
[Pw_forum] Problem with Installing Quantum Espresso 5.1.
On Tue, Jun 10, 2014 at 5:02 PM, Paolo Giannozzi wrote: > On Tue, 2014-06-10 at 20:05 +, Goytia, Michael wrote: > > > > "if 'make' is not a typo you can use command-not-to found to look up > > packages that contain it like this, cnf make" > > > what am I doing wrong in the installation > > apparently your computer has no "make" utility installed. > Usually "make" is present on any unix of unix-like machine. > ? > > ?no, paolo. not an?ymore. most linux distributions now install a desktop environment by default without any support for software development. those packages will have to be installed in addition to the default system. axel. > Are you trying to install QE on a coffee machine ... ? > > P. > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140610/dddab0a0/attachment.html
[Pw_forum] Using Intel Fortran, C++ complier- parallel, serial versions - reg.,
On Jun 7, 2014 8:10 PM, "Paolo Giannozzi" wrote: > > Well, it's trivial if you know (or figure out) how to convince > mpif90 to use the fortran compiler you want and not the one it > thinks you want. With openmpi it is possible to select a > fortran compiler at run time with variable OMPI_FC or something > like this. Not sure if it is possible with other MPI implementations. You cannot with mpich based ones. They contain fortran code. That is why centers always compile n+1 permutations of mpi libs. > > Paolo > > On Sat, 2014-06-07 at 11:26 -0400, Axel Kohlmeyer wrote: > > > > On Jun 7, 2014 4:02 PM, "Filippo Spiga" > > wrote: > > > > > > Dear Muthu, > > > > > > On Jun 4, 2014, at 5:42 PM, Muthu V > > wrote: > > > > but if i try with mpich2 > > > > > > Try MVAPICH2 (http://mvapich.cse.ohio-state.edu/overview/mvapich2/) > > or Open MPI (http://www.open-mpi.org/). > > > > > > Got nothing to do with the mpi library per se, but which fortran > > compiler it uses. The output of the configure script is > > self-explanatory. > > > > Trivial to fix. > > > > Axel > > > > > > > F > > > > > > -- > > > Mr. Filippo SPIGA, M.Sc. > > > http://www.linkedin.com/in/filippospiga ~ skype: filippo.spiga > > > > > > ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert > > > > > > * > > > Disclaimer: "Please note this message and any attachments are > > CONFIDENTIAL and may be privileged or otherwise protected from > > disclosure. The contents are not to be disclosed to anyone other than > > the addressee. Unauthorized recipients are requested to preserve this > > confidentiality and to advise the sender immediately of any error in > > transmission." > > > > > > > > > > > > ___ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://pwscf.org/mailman/listinfo/pw_forum > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140607/d83f81ae/attachment.html
[Pw_forum] Using Intel Fortran, C++ complier- parallel, serial versions - reg.,
On Jun 7, 2014 4:02 PM, "Filippo Spiga" wrote: > > Dear Muthu, > > On Jun 4, 2014, at 5:42 PM, Muthu V wrote: > > but if i try with mpich2 > > Try MVAPICH2 (http://mvapich.cse.ohio-state.edu/overview/mvapich2/) or Open MPI (http://www.open-mpi.org/). Got nothing to do with the mpi library per se, but which fortran compiler it uses. The output of the configure script is self-explanatory. Trivial to fix. Axel > F > > -- > Mr. Filippo SPIGA, M.Sc. > http://www.linkedin.com/in/filippospiga ~ skype: filippo.spiga > > ?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert > > * > Disclaimer: "Please note this message and any attachments are CONFIDENTIAL and may be privileged or otherwise protected from disclosure. The contents are not to be disclosed to anyone other than the addressee. Unauthorized recipients are requested to preserve this confidentiality and to advise the sender immediately of any error in transmission." > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140607/040694ca/attachment.html
[Pw_forum] Compiling error in ubuntu
On Thu, Jun 5, 2014 at 4:29 AM, zafar rasheed wrote: > Sorry for it. Yes Unmodified comile well but when I modify Tabd.f90 and > Set_hubbard_l.f90 for S,Te,and Se then this error appears. > ?... and what is the only applicable conclusion to that?? the modifications to tabd.f90 are wrong! fix them. the code in this file is *trivial* to read and understand. this is not a Q-E problem but a case of PEBCAC. axel. > > > hubbard_occ = 2.d0 >1 > Error: Symbol 'hubbard_occ' at (1) has no IMPLICIT type > make[2]: *** [tabd.o] Error 1 > make[2]: Leaving directory `/home/zafar/espresso-5.1/PW/src' > make[1]: *** [pw] Error 1 > make[1]: Leaving directory `/home/zafar/espresso-5.1/PW' > make: *** [pw] Error 1 > > Muhammad Zafar > PhD Scholar > Department of Physics > The Islamia University of Bahawalpur,Pakistan > > > On Wednesday, June 4, 2014 4:05 PM, Paolo Giannozzi < > paolo.giannozzi at uniud.it> wrote: > > > In your extremely confusing message, a > fundamental piece of information is missing: > * does the unmodified code compile? > > There is no "occ_loc" variable, by the way > > P > > On Wed, 2014-06-04 at 08:01 -0700, zafar rasheed wrote: > > Dear All > > I want to install espresso-5.1 by doing some setting in hubbard_l.f90 > > and tabd.f90 > > changes in tabd.f90 > > > > CASE( 'S' ) > > > > >occ_loc = 4.d0 > > ! > > CASE( 'Se' ) > >occ_loc = 4.d0 > > ! > > CASE( 'Te' ) > >occ_loc = 4.d0 > > ! > > CASE( 'H' ) > >hubbard_occ = 1.d0 > > ! > > CASE( 'Ga', 'In' ) > >hubbard_occ = 10.d0 > > > > > > and changes in set_hubbard_l.f90 > > > > > > CASE( 'C', 'N', 'O','S','Se','Te' ) > >! > >hubbard_l = 1 > > > > but whe I compile it following error appears. Please help me solve > > this problem. I compile it with ubuntu 11.10 but fails with ubuntu > > 13.10 having gfortran-4.2 compiler. > > > > > > > > > > gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW > > -I../../iotk/src -I../../Modules -c symmetrize_at.f90 > > gfortran -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW > > -I../../iotk/src -I../../Modules -c tabd.f90 > > tabd.f90:100.19: > > > >hubbard_occ = 2.d0 > >1 > > Error: Symbol 'hubbard_occ' at (1) has no IMPLICIT type > > make[2]: *** [tabd.o] Error 1 > > make[2]: Leaving directory `/home/zafar/espresso-5.1/PW/src' > > make[1]: *** [pw] Error 1 > > make[1]: Leaving directory `/home/zafar/espresso-5.1/PW' > > make: *** [pw] Error 1 > > > > > > > > Muhammad Zafar > > PhD Scholar > > Department of Physics > > The Islamia University of Bahawalpur,Pakistan > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140605/eff20cc9/attachment.html
