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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 > > >>> _______________________________________________ > > >>> gmx-users mailing list gmx-users@gromacs.org > > >>> http://www.gromacs.org/mailman/listinfo/gmx-users > > >>> Please search the archive at http://www.gromacs.org/search before > > >>> posting! > > >>> Please don't post (un)subscribe requests to the list. Use the > > >>> www interface or send it to [EMAIL PROTECTED] > > >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > >> > > >> -- > > >> 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 > > >> [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > >> _______________________________________________ > > >> gmx-users mailing list gmx-users@gromacs.org > > >> http://www.gromacs.org/mailman/listinfo/gmx-users > > >> Please search the archive at http://www.gromacs.org/search before > > >> posting! > > >> Please don't post (un)subscribe requests to the list. Use the > > >> www interface or send it to [EMAIL PROTECTED] > > >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > >> > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > 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 > > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > _______________________________________________ gmx-users mailing list gmx-users@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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