[Pw_forum] Problem with restart mode of calculation (Paolo Giannozzi)
Yes, I have set it up thereafter. But it still doesn`t work -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/dad3e27d/attachment.html
[Pw_forum] Fwd: problem with running ./run_all_examples in PHonon/examples folder
Dear all, I have a problem with running examples in the PHonon folder using ./run_all_examples command although the same command works well when doing it for PW examples. There must be something special with the way ph.x runs... I have Mac 10.8.5 and QE 5.0.2, which was installed without any errors just with couple warnings. The examples I was running are in its PHonon/examples folder. I would be grateful to you for your help. May be my installation of QE lacks something... Thank you Please see the beginning of my log below: alexey-sorokin:examples admin$ ./run_all_examples run_all_examples: starting /Applications/Quantum_ESPRESSO/espresso-5.0.2/PHonon/examples/example01 : starting This example shows how to use pw.x and ph.x to calculate phonon frequencies at Gamma and X for Si and C in the diamond structure and for fcc-Ni. executables directory: /Applications/Quantum_ESPRESSO/espresso-5.0.2/bin pseudo directory: /Applications/Quantum_ESPRESSO/espresso-5.0.2/pseudo temporary directory: /Users/admin/tmp checking that needed directories and files exist... done running pw.x as: /Applications/Quantum_ESPRESSO/espresso-5.0.2/bin/pw.x -nband 1 -ntg 1 running ph.x as: /Applications/Quantum_ESPRESSO/espresso-5.0.2/bin/ph.x -nband 1 -ntg 1 cleaning /Users/admin/tmp... done running the scf calculation for Si... done running the phonon calculation at Gamma for Si... Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x104991f92 #1 0x10499275e #2 0x7fff8b4e3909 #3 0x7fff90aabd15 #4 0x10343a3c4 #5 0x103486d78 #6 0x10343b353 #7 0x103445170 #8 0x1033edc3e #9 0x1033ce55e #10 0x1037eeb0e example01/run_example: line 140: 16360 Segmentation fault: 11 $PH_COMMAND < si.phG.in > si.phG.out done running the phonon calculation at X for Si... Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x105ad2f92 #1 0x105ad375e #2 0x7fff8b4e3909 #3 0x7fff90aabd15 #4 0x1045aba21 #5 0x104583901 #6 0x10450d5a6 #7 0x10492db0e example01/run_example: line 156: 16366 Segmentation fault: 11 $PH_COMMAND < si.phX.in > si.phX.out Error condition encountered during test: exit status = 139 Aborting -- Best regards, Anna Kuznetsova -- Best regards, Anna -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/976a27b3/attachment.html
[Pw_forum] single atom calculations
?Dear Quantum Espresso users, Is it possible to use Quantum Espresso to calculate the properties of a single atom from a certain element? It is my understanding that periodic boundary conditions need to be imposed. Would it be possible to create a sufficiently large unit cell containing a single atom of the desired element? Any clarifications on this issue would be greatly appreciated. Thanks, Adib Samin Adib Samin Graduate Fellow The Department of Aerospace and Mechanical Engineering The Ohio State University -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/9828b67f/attachment.html
[Pw_forum] how to restart NEB calculations
Hi can any one please guide me how can i restart neb calculation from last un-converged calculation? which files are necessary to restart the calculation. more over, how can i make the calculation converge faster because i am using 115 atoms so i will need enough time to converge. which parameters are needed to be changed for faster convergence. please have a look at neb.dat file restart_mode = 'from_scratch' , string_method = 'neb', nstep_path= 20, ds= 2.D0, opt_scheme= 'broyden', num_of_images = 7, k_max = 0.3D0, k_min = 0.2D0, CI_scheme = 'auto', path_thr = 0.1D0, / thanks Adnan PhD Chemistry UFJF Brazil -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/9ced6108/attachment.html
[Pw_forum] Finding bond order inside the crystal
Dear all, I am interested to find the bond order (Mayer or Wiberg type) in a molecule inside a crystal structure. Is it possible to do using Quantum espresso? Any help is highly appreciated. Thanking you. Pratik -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/80395f53/attachment.html
[Pw_forum] single atom calculations
Dear Adib Is it possible to use Quantum Espresso to calculate the properties of a single atom from a certain element? yes It is my understanding that periodic boundary conditions need to be imposed. Would it be possible to create a sufficiently large unit cell containing a single atom of the desired element? Yes, you must to use an enough big cubic cell, and may be you should read the tag "assume_isolated" in the QE manual. Best PhD. Arles V. Gil Rebaza IFLP - Argentina 2014-07-14 19:01 GMT-03:00 Samin, Adib J. : > ?Dear Quantum Espresso users, > > > Is it possible to use Quantum Espresso to calculate the properties of a > single atom from a certain element? > > It is my understanding that periodic boundary conditions need to be > imposed. > > Would it be possible to create a sufficiently large unit cell containing a > single atom of the desired element? > > Any clarifications on this issue would be greatly appreciated. > > > Thanks, > > Adib Samin > > > Adib Samin > > Graduate Fellow > > The Department of Aerospace and Mechanical Engineering > > The Ohio State University > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- ###-> Arles V. <-### -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/9ffd1f3a/attachment.html
[Pw_forum] PW.X WORKS ONCE AND NEXT TIME DOESN'T.. FOR THE SAME INPUT FILE..
Dear Siddheshwar, it is quite improbable that this error did not occur in your first run. You must have changed something between the two runs (and probably forgotten about it). In any case, in the input file you wrote 'ecutrho=' but did not specify any value. This for sure is (one of the possible) causes of the error. Best, Giovanni On 07/14/2014 02:01 PM, siddheshwar chopra wrote: > Dear Users, > I ran the pw.x successfully using 4 processors. But again when I am > running the same i/p file, I am getting this error: > > %% > Error in routine read_namelists (5010): > reading namelist system > > %% > > stopping ... > > === > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 1 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > === > > Please tell me how to resolve this issue. > > Regards, > > -- > *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 -- Giovanni Pizzi Post-doctoral Research Scientist EPFL STI IMX THEOS MXC 340 (B?timent MXC) Station 12 CH-1015 Lausanne (Switzerland) Phone: +41 21 69 31124 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/27594e49/attachment.html
[Pw_forum] Problem with restart mode of calculation (Paolo Giannozzi)
On Mon, 2014-07-14 at 22:19 +0700, Ganjar Kurniawan wrote: > Yes, I have set it up thereafter. But it still doesn`t work unless you produce a REPRODUCIBLE example, nothing can be done P. -- Paolo Giannozzi, Dept. Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] PW.X WORKS ONCE AND NEXT TIME DOESN'T.. FOR THE SAME INPUT FILE..
Dear Users, I ran the pw.x successfully using 4 processors. But again when I am running the same i/p file, I am getting this error: %% Error in routine read_namelists (5010): reading namelist system %% stopping ... === = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 1 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES === Please tell me how to resolve this issue. Regards, -- *Dr. Siddheshwar chopra,* *M.Sc., Ph.D (Physics)Assistant Professor (Physics),* *Amity University, Noida, India.* -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/b7f14135/attachment.html -- next part -- A non-text attachment was scrubbed... Name: graphene.scf20.in Type: application/octet-stream Size: 3676 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140714/b7f14135/attachment.obj -- next part -- A non-text attachment was scrubbed... Name: graphene.scf20.out Type: application/octet-stream Size: 71353 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140714/b7f14135/attachment-0001.obj
[Pw_forum] Band structure calculations
Dear all ! Could anyone give me some suggestion to calculate band structure for a Silicon(111) slab which I cut from a cubic crystal structure of silicon . Can any body tell me how to mention high symmetric k-points for band structure for the Si(111) slab. Thanks in advance S.Balaiah On Mon, Jul 7, 2014 at 4:28 PM, balu shanigaram wrote: > Dear all ! > Could anyone give me some suggestion to calculate band structure for a > Silicon(111) slab which I cut from a cubic crystal structure of silicon . > Can any body tell me how to mention high symmetric k-points for band > structure for the Si(111) slab. > > Thanks in advance > > S.Balaiah > > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/6f2b0936/attachment.html
[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
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. >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 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/a7e06ac8/attachment.html
[Pw_forum] PW.X WORKS ONCE AND NEXT TIME DOESN'T.. FOR THE SAME INPUT FILE..
Hi The file graphene.scf20.out is not showing any error message. On Mon, Jul 14, 2014 at 5:01 AM, siddheshwar chopra wrote: > Dear Users, > I ran the pw.x successfully using 4 processors. But again when I am > running the same i/p file, I am getting this error: > > > %% > Error in routine read_namelists (5010): > reading namelist system > > > %% > > stopping ... > > > === > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 1 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > === > > Please tell me how to resolve this issue. > > Regards, > > -- > *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 > -- With Best Regards, Dr. Sanjeev Kumar Gupta Fulbright Post-Doctoral Scholar Dept. of Physics Michigan Technological University 1400 Townsend Drive, Houghton MI 49931, USA -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/8be72241/attachment.html
