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! 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
