[Wien] trying to install WIEN2k on Ubuntu 12.04 64-bit
Peter Blaha
pblaha at theochem.tuwien.ac.at
Fri Feb 22 21:05:51 CET 2013
No. Please read the UG about parallelization. k-point parallelization is
done via scripts.
Am 22.02.2013 20:28, schrieb Long Zhang:
> Thank you for the information.
> I think I had wrong idea about k-point parallel. If it doesn't use
> OpenMP then it's perfectly fine for me. I'll drop the idea of
> finegrained parallel in this installation.
>
> Just want to confirm, for using k-point parallel only, MPICH2 is still
> required, is that right?
>
> Thanks.
> Long
>
>
>
>
> On Fri, Feb 22, 2013 at 11:04 AM, Laurence Marks
> <L-marks at northwestern.edu <mailto:L-marks at northwestern.edu>> wrote:
>
> As Peter said, the simplest approach is just k-point parallel which
> does not need OpenMP. The rate limiting steps are lapack calls which
> the Intel mkl is good for.
>
> Whether mpi is good for a small cluster such as you have in not so
> clear. Peter has benchmarked the mpi version and his conclusion is
> that it is not useful; I have benchmarked on my cluster and I have
> consistently found the mpi versions to be faster than the Intel
> threading. I suspect that it really depends upon many details specific
> to the systems, for instance cross-core optimizations, network and
> memory speed....
>
> Not a complete answer, but for certain the simplest approach is to
> just use k-point parallel.
>
> On Fri, Feb 22, 2013 at 9:55 AM, Long Zhang <lzhang6789 at gmail.com
> <mailto:lzhang6789 at gmail.com>> wrote:
> >
> > That's true I agree. If the k-point parallel version does not
> need mpi, then
> > it's OpenMP I suppose (please correct me if it's not). But I
> really don't
> > want to run OpenMP because it will mess my other applications up.
> >
> > I am building it on a small server of 2 Opteron 12-core cpus.
> It's just a
> > dual-cpu system, not a cluster. I am not sure if I can gain
> enough speed-up
> > by using 24 cores. Anyway if I want a little k-point parallel,
> can I choice
> > to use mpi? or there is no such choice at all?
> >
> > Thank you very much.
> > Long
> >
> >
> > On Fri, Feb 22, 2013 at 3:07 AM, Peter Blaha
> <pblaha at theochem.tuwien.ac.at <mailto:pblaha at theochem.tuwien.ac.at>>
> > wrote:
> >>
> >> I keep saying this all the time:
> >>
> >> The mpi-parallel version needs special hardware !
> >>
> >> It is not of much use on a single quadcore-cpu.
> >> A cluster needs a fast network like infiniband.
> >>
> >> Only then the installation of the mpi-version make sense.
> >>
> >> We have a k-point parallel version, which does not need mpi, but is
> >> perfect for a small cluster with a common NFS filesystem.
> >>
> >>
> >> Am 22.02.2013 06:20, schrieb Long Zhang:
> >>>
> >>>
> >>> Hello,
> >>>
> >>> I am trying to install the current version 12.1 on Ubuntu 12.04
> >>> (64-bit). I met some problem related to mpi, can someone please
> give me
> >>> some hint? Thanks in advance.
> >>>
> >>> The situation is like this, on a freshly installed Ubuntu 12.04
> 64bit, I
> >>> installed current version Intel Fortran Composer XE 2013.2.146, and
> >>> installed MPICH2 and FFTW3 via Ubuntu Software Center.
> >>>
> >>> Before run the siteconfig_lapw, I checked
> >>> which ifort
> >>> /opt/intel/composer_xe_2013.2.146/bin/intel64/ifort
> >>> which mpif90
> >>> /usr/bin/mpif90
> >>>
> >>> and did the following 3 lines in the terminal
> >>> source /opt/intel/composer_xe_2013.2.146/bin/compilervars.sh
> intel64
> >>> export
> >>>
> >>>
> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/composer_xe_2013.2.146/mkl/lib/intel64
> >>> export MKLROOT=/opt/intel/composer_xe_2013.2.146/mkl/
> >>>
> >>> Then I run the siteconfig_lapw, and selected system as
> "ifort12+mkl"
> >>> (the first one), selected compilers as "ifort" and "cc", selected
> >>> "finegrained parallel" and "mpif90", and got error message like
> this:
> >>>
> >>> ----------------------------------------------- cut1
> >>> -----------------------------------------------
> >>> Compile time errors (if any) were:
> >>> SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1
> >>> SRC_hf/compile.msg:make: *** [rp] Error 2
> >>> SRC_hf/compile.msg:make[1]: *** [modules.o] Error 1
> >>> SRC_hf/compile.msg:make: *** [cp] Error 2
> >>> SRC_lapw0/compile.msg:make[1]: *** [modules.o] Error 1
> >>> SRC_lapw0/compile.msg:make: *** [para] Error 2
> >>> SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1
> >>> SRC_lapw1/compile.msg:make: *** [rp] Error 2
> >>> SRC_lapw1/compile.msg:make[1]: *** [modules.o] Error 1
> >>> SRC_lapw1/compile.msg:make: *** [cp] Error 2
> >>> SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1
> >>> SRC_lapw2/compile.msg:make: *** [rp] Error 2
> >>> SRC_lapw2/compile.msg:make[1]: *** [modules.o] Error 1
> >>> SRC_lapw2/compile.msg:make: *** [cp] Error 2
> >>> ----------------------------------------------- cut1
> >>> -----------------------------------------------
> >>>
> >>> I looked into SRC_lapw1/compile.msg, and the detailed error is:
> >>>
> >>> ----------------------------------------------- cut2
> >>> -----------------------------------------------
> >>> mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3
> >>> -traceback -DParallel -c modules_tmp_.F
> >>>
> >>>
> --------------------------------------------------------------------------
> >>> The Open MPI wrapper compiler was unable to find the specified
> compiler
> >>> gfortran in your PATH.
> >>>
> >>> Note that this compiler was either specified at configure time
> or in
> >>> one of several possible environment variables.
> >>>
> >>>
> --------------------------------------------------------------------------
> >>> make[1]: *** [modules.o] Error 1
> >>> make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1'
> >>> make: *** [rp] Error 2
> >>> ----------------------------------------------- cut2
> >>> -----------------------------------------------
> >>>
> >>> It seems OpenMPI was invoked and it looked for gfortran. I
> don't have
> >>> gfortran installed at all, but I found I have openmpi
> installed. I then
> >>> used Ubuntu Software Center to search openmpi and uninstalled
> related
> >>> packages. I restarted the system and repeated the siteconfig_lapw.
> >>> However I still get error message, not same but similar, it
> still looks
> >>> for gfortran, for examplethe SRC_lapw1/compile.msg shows:
> >>>
> >>>
> >>> ----------------------------------------------- cut3
> >>> -----------------------------------------------
> >>> mpif90 -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -DFFTW3
> >>> -traceback -DParallel -c modules_tmp_.F
> >>> /usr/bin/mpif90: line 370: gfortran: command not found
> >>> make[1]: *** [modules.o] Error 127
> >>> make[1]: Leaving directory `/home/lzhang200/wien2k/SRC_lapw1'
> >>> make: *** [rp] Error 2
> >>> ----------------------------------------------- cut3
> >>> -----------------------------------------------
> >>>
> >>> I did not specify to use gfortran anywhere in the setupof
> >>> siteconfig_lapw, I don't see why mpif90 keeps looking for it.
> How can I
> >>> fix this problem? Thanks a lot.
> >>>
> >>> Regards,
> >>> Long Zhang
> >>>
> >>>
> >>> _______________________________________________
> >>> Wien mailing list
> >>> Wien at zeus.theochem.tuwien.ac.at
> <mailto:Wien at zeus.theochem.tuwien.ac.at>
> >>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> >>>
> >>
> >> --
> >> Peter Blaha
> >> Inst.Materials Chemistry
> >> TU Vienna
> >> Getreidemarkt 9
> >> A-1060 Vienna
> >> Austria
> >> +43-1-5880115671 <tel:%2B43-1-5880115671>
> >>
> >> _______________________________________________
> >> Wien mailing list
> >> Wien at zeus.theochem.tuwien.ac.at
> <mailto:Wien at zeus.theochem.tuwien.ac.at>
> >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> >
> >
>
>
>
> --
> Professor Laurence Marks
> Department of Materials Science and Engineering
> Northwestern University
> www.numis.northwestern.edu <http://www.numis.northwestern.edu>
> 1-847-491-3996 <tel:1-847-491-3996>
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought"
> Albert Szent-Gyorgi
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--
Peter Blaha
Inst.Materials Chemistry
TU Vienna
Getreidemarkt 9
A-1060 Vienna
Austria
+43-1-5880115671
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