[gmx-users] Gromacs on IBM cluster

[Marius Retegan]

Dear GMX users,
I would like to give some feedback about my "experience" regarding the
compilation of Gromacs 3.3.1 on the IBM cluster using the IBM
compilers. Since I was unable to test a compilation with gcc, because
gcc is not instaled, I've decided to recompile Gromacs with the IBM
compilers using this this compilation script where I've disabled the
optimizations for xlc_r and xlf_r.
=====================================
export CC='xlc_r'
export F77='xlf_r'
export FFLAGS='-O0 -q64'
export CFLAGS='-O0 -q64'
export AR='ar -X 64'
export LDFLAGS='-L/p5cecic/home/mretegan/software/fftw2_64/lib'
export CPPFLAGS='-I/p5cecic/home/mretegan/software/fftw2_64/include'
#export FFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict'
#export CFLAGS='-O2 -qarch=pwr5 -qtune=pwr5 -qmaxmem=-1 -qstrict'


./configure --enable-double --with-qmmm-cpmd  --with-fft=fftw2
--prefix=/p5cecic/home/mretegan/software/gromacs_64_fftw2
====================================
With the new binaries I don't have problems when running grompp. Also
I've also tested the binaries with the Gromacs tests found on the
Wiki. All test have passed. So I think it's a good idea to disable all
optimization when compiling on a IBM machine, and if everything runs
smoothly start using optimizations for the compilers and test again.

With respect
Marius Retegan

On Oct 31, 2007 4:36 PM, Marius Retegan <marius.s.retegan at gmail.com> wrote:
> I have aprox. 81000 atoms. The system worked on a Itanium 2 cluster.
> On the IBM machine I've used the IBM compilers.
> I'm going to give it a try with gcc.
> Thank you
> Marius Retegan
>
>
> On 10/31/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> > Marius Retegan wrote:
> > > 32 Gb on each node of the cluster.
> > > Maybe I should add that I've also ran CPMD and cp2k jobs on the
> > > cluster but I've never had memory problems.
> > > Marius Retegan
> > It could still be too little, since this is the additional memory. What
> > kind of system are you using, how many atoms? Does a small water box
> > work? There have been problems with compilation on IBM machines as well,
> > in particular when using IBM compilers. Recompiling with gcc resolves that.
> >
> > >
> > > On 10/30/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> > >> Marius Retegan wrote:
> > >>> Dear Gromacs users
> > >>>
> > >>> I'm having some troubles running grompp on a IBM cluster P575 with AIX
> > >>> 5.3 installed.
> > >>> This is the error message that I'm getting:
> > >>> ====================================================
> > >>> processing coordinates...
> > >>> double-checking input for internal consistency...
> > >>> renumbering atomtypes...
> > >>> -------------------------------------------------------
> > >>> Program grompp_d, VERSION 3.3.1
> > >>> Source code file: smalloc.c, line: 113
> > >>>
> > >>> Fatal error:
> > >>> calloc for nbsnew (nelem=677329, elsize=148, file grompp.c, line 723)
> > >> This says it wants one Gb of RAM. How much do you have?
> > >> You can run grompp on a machine with a lot of memory and the mdrun on
> > >> your cluster.
> > >>> -------------------------------------------------------
> > >>>
> > >>> "I'm An Oakman" (Pulp Fiction)
> > >>> : Not enough space
> > >>> ====================================================
> > >>> While digging into the archive I've managed to find this post
> > >>> http://www.gromacs.org/pipermail/gmx-users/2006-February/020066.html,
> > >>> which basically says that there is not enough memory for the job. My
> > >>> job is lunched with LoadLeveler where I can define the @resources =
> > >>> ConsumableMemory (value), but if this is not defined in the
> > >>> LoadLeveler script, I think that the program should thake as much
> > >>> memory as it requires.
> > >>> So my question is why does Gromacs, a program renowned for low memory
> > >>> requirements, give this error message?
> > >>>
> > >>> Thank you
> > >>> Marius Retegan
> > >>> _______________________________________________
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> > >>
> > >> --
> > >> David.
> > >> ________________________________________________________________________
> > >> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > >> Dept. of Cell and Molecular Biology, Uppsala University.
> > >> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > >> phone:  46 18 471 4205          fax: 46 18 511 755
> > >> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >> _______________________________________________
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> > >>
> > > _______________________________________________
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> >
> >
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>