Re: [Wien] Installation with MPI and GNU compilers

2018-04-04 Thread Laurence Marks 
I confess to being rather doubtful that gfortran+... is comparable to
ifort+... for Intel cpu, it might be for AMD. While the mkl vector
libraries are useful in a few codes such as aim, they are minor for the
main lapw[0-2].

On Wed, Apr 4, 2018, 10:55 Pavel Ondračka  wrote:

> Rui Costa píše v St 04. 04. 2018 v 14:21 +0100:
> > I will see what I can do about the Intel compilers. I've had a
> > question about this, supposedly the intel compilers are the fastest
> > [
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2D=DwIGaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=_NY1hgzBYHxYTFCc6OKMrgmlmLPdt3b__vsdXAoQC14=M8g1ileELz5aImqKU7vYPAV3_-54VZ7qLYURtbQMg2o=
> > archive.com/wien@zeus.theochem.tuwien.ac.at/msg13021.html], but how
> > much faster are they than the others? I expect this to vary from case
> > to case but on average, how much faster are they?
>
> In fact the compiler (e.g. ifort vs gfortran) hardly makes a difference
> . The important part are the algebra libraries. The opensource OpenBLAS
> should be almost identical to Intels MKL (see
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive=DwIGaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=_NY1hgzBYHxYTFCc6OKMrgmlmLPdt3b__vsdXAoQC14=7D6kz5IB8jHQBz1mDaZyKAY1Qi7mPGB6quKsNFRB0o4=.
> com/wien@zeus.theochem.tuwien.ac.at/msg15106.html
> 
> for comparison of
> OenBLAS vs MKL). However in this old benchmark the opensource stack is
> still quite slower since the MKL also provides the VML library for
> vectorized math functions, which did not had any open source
> alternative for a long time. Recently there is the libmvec library
> which provides such functions (you need recent glibc), but there is no
> official Wien2k support for this. However it is actually quite easy to
> get it working (see
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuw=DwIGaQ=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0=_NY1hgzBYHxYTFCc6OKMrgmlmLPdt3b__vsdXAoQC14=rdruSPlbzu87Wc6ZNL7iE8pWopEi2yuuvJSnKEzGxTQ=
> ien.ac.at/msg16159.html ).
> Hence if you use the gfortran + OpenBLAS + libmvec the performance is
> virtually identical to ifort + MKL + VML. The setup is somewhat more
> difficult though.
>
> Best regards
> Pavel
>
> > My objective is not to do simulations with mpi in the computer that
> > I'm trying to install but to figure out how to install wien2k with
> > mpi and then give some guidelines to the IT technician. I spent two
> > weeks telling them that the simulations were not running because the
> > packages were not compiled and in the end everything was poorly
> > installed.
> >
> > Thank you for your help.
> >
> > Best regards,
> > Rui Costa.
> >
>
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Re: [Wien] Installation with MPI and GNU compilers

2018-04-04 Thread Pavel Ondračka 
Rui Costa píše v St 04. 04. 2018 v 14:21 +0100:
> I will see what I can do about the Intel compilers. I've had a
> question about this, supposedly the intel compilers are the fastest
> [https://www.mail-
> archive.com/wien@zeus.theochem.tuwien.ac.at/msg13021.html], but how
> much faster are they than the others? I expect this to vary from case
> to case but on average, how much faster are they?

In fact the compiler (e.g. ifort vs gfortran) hardly makes a difference
. The important part are the algebra libraries. The opensource OpenBLAS
should be almost identical to Intels MKL (see https://www.mail-archive.
com/wien@zeus.theochem.tuwien.ac.at/msg15106.html for comparison of
OenBLAS vs MKL). However in this old benchmark the opensource stack is
still quite slower since the MKL also provides the VML library for
vectorized math functions, which did not had any open source
alternative for a long time. Recently there is the libmvec library
which provides such functions (you need recent glibc), but there is no
official Wien2k support for this. However it is actually quite easy to
get it working (see https://www.mail-archive.com/wien@zeus.theochem.tuw
ien.ac.at/msg16159.html ).
Hence if you use the gfortran + OpenBLAS + libmvec the performance is
virtually identical to ifort + MKL + VML. The setup is somewhat more
difficult though.

Best regards
Pavel

> My objective is not to do simulations with mpi in the computer that
> I'm trying to install but to figure out how to install wien2k with
> mpi and then give some guidelines to the IT technician. I spent two
> weeks telling them that the simulations were not running because the
> packages were not compiled and in the end everything was poorly
> installed.
> 
> Thank you for your help.
> 
> Best regards,
> Rui Costa.
> 

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Re: [Wien] Installation with MPI and GNU compilers

2018-04-04 Thread Rui Costa 
I will see what I can do about the Intel compilers. I've had a question
about this, supposedly the intel compilers are the fastest [
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13021.html],
but how much faster are they than the others? I expect this to vary from
case to case but on average, how much faster are they?

My objective is not to do simulations with mpi in the computer that I'm
trying to install but to figure out how to install wien2k with mpi and then
give some guidelines to the IT technician. I spent two weeks telling them
that the simulations were not running because the packages were not
compiled and in the end everything was poorly installed.

Thank you for your help.

Best regards,
Rui Costa.

On 4 April 2018 at 04:48, Gavin Abo  wrote:

> Some comments:
>
> I haven't seen many mailing list posts about using a gfortran-based mpi.
> That is probably because the clusters used for mpi are likely systems that
> cost something like $100k to $1 millon.  Those systems usually seem to be
> running Intel MPI.  So companies, computing centers, and universities for
> example likely have no problem paying say $1,499 for Cluster Edition for
> C/C++ and Fortran [ https://software.intel.com/en-
> us/articles/academic-pricing ].
>
> How much I get paid to help you: $0
>
> How much the IT Support Technician at your organization likely gets paid
> to help you: average pay of about $52k per year according to glassdoor [
> https://www.glassdoor.com/Salaries/it-support-
> technician-salary-SRCH_KO0,21.htm ]
>
> Meaning, please try asking your clusters IT department or helpdesk first
> for help with this if you have one.
>
> I assume your using at least a GB-network cluster [
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13632.html
> , https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.
> at/msg09334.html ] as mpi is usually useless with a single multi-core
> personal computer [ https://www.mail-archive.com/
> wien@zeus.theochem.tuwien.ac.at/msg05470.html ,
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg07371.html
> ].
>
> If you plan to use Bandstructure in w2web of WIEN2k 17.1, a "At line 75 of
> file modules_tmp_.F (unit = 5, file = 'ubuntu.in1c')" error can occur with
> gfortran when the "x lapw1 -band" button is clicked, so you may want to
> apply band.pl and scf.pl [ https://www.mail-archive.com/
> wien@zeus.theochem.tuwien.ac.at/msg16069.html ] or band.patch and
> scf.patch [ https://github.com/gsabo/WIEN2k-Patches/tree/master/17.1 ].
> There are some other patches that might also be helpful for gfortran [
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17175.html
> ].  However, I currently don't have files (SRC_symmetry and x_lapw) to fix
> the gfortran error with "x dstart" if you use the init_lapw command, but
> you could probably get them from Prof. Blaha or make the changes yourself
> following the instructions given before [ https://www.mail-archive.com/
> wien@zeus.theochem.tuwien.ac.at/msg16674.html ].
>
> Yes, it usually better to have only one MPI implementation and one BLAS
> library.  However, it should not be a problem as long as you can keep them
> from mixing and conflicting with each other.  As I recall, all mpi is
> somewhat equal [ https://www.mail-archive.com/
> wien@zeus.theochem.tuwien.ac.at/msg09557.html ], though openmpi might be
> easy to compile [ https://www.mail-archive.com/
> wien@zeus.theochem.tuwien.ac.at/msg07343.html ].
>
> The libfftw3 and libfftw3_mpi of FFTW 3.x.x [
> http://www.fftw.org/download.html ] are what you need to use.  The
> liblfftw3xf and libfftw3xf_gnu (or libfftw3x_cdft.a) files if I recall
> correctly would be located or generated in the interfaces directory of an
> Intel ifort/mkl installation [ https://www.mail-archive.com/
> wien@zeus.theochem.tuwien.ac.at/msg07333.html ].  The mkl interface to
> fftw3xf I think still does not work with mpi (only for serial compilation)
> [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.
> at/msg06959.html ].
> Sorry, I currently don't have answers to your other questions, but I think
> you are headed in the right direction.
>
>
> On 4/3/2018 2:02 PM, Rui Costa wrote:
>
> Dear wien2k users,
>
> I'm trying to install wien2k_17.1 with mpi, fftw and elpa using the GNU
> compilers. I must say that I'm not an expert in linking and compiling the
> packages, so probably some things will be wrong.
>
> I'm using Ubuntu 16.04 LTS and have installed:
> - BLAS: OpenBlas-0.2.20 which is in /opt/OpenBLAS and the libblas3 (shared
> version) and libblas-dev (static version) of netlib using synaptic package
> manager which is in /usr/lib;
> - LAPACK: liblapack3 (shared version) and libpalack-dev (static version)
> of netlib using synaptic package manager which is in /usr/lib;
> - BLACS: libblacs-mpi-dev and libblacs-openmpi1 of netlib using synaptic
> package manager which is in /usr/lib
> - ScaLAPACK:

Re: [Wien] construction of super cell for AFM calculation

2018-04-04 Thread Peter Blaha 

Simply numbering equivalent atoms with the same number does not work.

You have to group at least one or two atoms together (with a certain 
multiplicity, typically you would do this for the magnetic ions). Maybe 
it is easier for you if you rename the spin-up atoms as Fe and the 
spin-dn atoms as Co, then do the symmetry. (After symmetry has been 
done, rename the atoms back to AA_1 and _2. The rest of the atoms leave 
unchanged. sgroup should then find the spacegroup under these 
restrictions and group all other atoms properly.


Regards

Am 03.04.2018 um 08:19 schrieb Krishnaveni. S:

Dear Wien 2k users,

I am working on full Heusler alloys. To compare optimized energy in 
nonmagnetic, ferromagnetic and antiferromagnetic states, I constructed 
supercell of 2x2x2. As there is no doping or vacuum creation, I just 
named the position of atoms as atom1, atom2 etc(explained in user 
guide). As 32 atomic positions generated (i.e 16 for Iridium,8 for 
manganese and 8 for Aluminum) every attempt of naming the atoms as Ir1, 
Ir2 for various positions as well as for Mn and Al, it ends with 32 
atoms with space group 1-p1or with 16 atoms of space group R3m. But my 
target is to land up with 4 iridium atoms ,2 Manganese and2 Aluminum 
atoms. How can I achieve this? Some help in this appreciated . Thanks 
all in advance.


**//___^
**//___^
--
Thanks and regards

Krishnaveni Parthasarathy
8939675012


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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
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