[Wien] Installation with MPI and GNU compilers

Wed Apr 4 15:21:47 CEST 2018

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 <gsabo at crimson.ua.edu> 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 at 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 at 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 at 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 at zeus.theochem.tuwien.ac.at/msg09557.html ], though openmpi might be
> easy to compile [ https://www.mail-archive.com/
> wien at 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 at 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: libscalapack-mpi-dev where I don't find the shared or static
> libraries, i.e., the libscalapack-mpi-dev.a or libscalapack-mpi-dev.so
> files, and libscalapack-openmpi1 using synaptic package manager which is
> in /usr/lib;
> - MPI: mpich-3.2.1 and it is installed in /usr/local/bin, /usr/local/lib
> and /usr/local/include and since I installed the openmpi version of BLACS
> and ScaLAPACK, I also have Openmpi and the binary files are at /usr/bin;
> - FFTW: fftw-3.3.7 and I installed this one from source files with the
> option ./configure --enable-mpi, and installed it in /usr/local/lib/ and
> /usr/lib/x86_64-linux-gnu;
> - ELPA: libelpa-dev and libelpa3 and installed these using the synaptic
> manager again.
>
>
> Questions:
> 1) I'm concerned that having two MPI implementations and two BLAS
> libraries might cause things to be compiled incorrectly. My idea was to
> install wien2k with MPICH since it seems to be the recommended one because
> there is almost no reference to OpenMPI, but on the other hand, the
> ScaLAPACK and BLACS libraries that I have use OpenMPI and I have tried
> installing these packages from source with MPICH but don't know how. Do you
> have any recommendation on which libraries and MPI to use?
>
> 2) In section 11.1.1 of the userguide it says:
>
> "in case you do not have icc installed, but use GNU-C (gcc) you must:
> – edit makefile, and remove -D_GNU from the line “ CC=gcc -D GNU” (to
> remove additional from the object names)
> – make libintel64 compiler=gnu"
>
> which makefile is this? None of the Makefiles in SRC_lapw0, 1 and 2 have
> that -D_GNU flag. It also says to add, in my case,  -DFFTW3 to FOPT and
> -lfftw3xf and -lfftw3xf_gnu to R_LIBS in the Makefiles of lapw0 and lapw2,
> but I don't have any library named liblfftw3xf or libfftw3xf_gnu, are these
> supposed to be libfftw3 or libfftw3_mpi that I do have?
>
> 3) In the configuration of the parallel options I gave the locations of
> the directories, I had to edit the variables ELPA_OPT and ELPA_LIBS in the
> Makefile of SRC_lapw1 because they were not pointing to the correct
> directories, but in the RP_LIBS it warns that since I'm using gfortran, I
> might need additional libraries (-lredist -ltools -lfblacs -lblacs -lmpi),
> but I don't have the first three libraries and have tried searching them
> but I can't find them. What libraries are these? Do they have different
> names?
>
>
> I'm sorry for the long post.
>
> Best regards,
> Rui Costa.
>
>
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