It is ok now. I found from the sys admin here that they are having some memory issues with the cluster. The node I was running on has 2GB.
Thnx sandeep -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Friday, March 03, 2006 1:14 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] "Cannot allocate memory" by grompp Sandeep Somani wrote: > Hi > > I am testing a fresh gmx3.3 installation on a new dual opteron cluster > running redhat linux. > > Did the standard pdb2gmx -> energy minimization -> position restrained (PR) > MD and everything was fine. > > But next when I did grompp for production run, got the following: > " > ------------------------------------------------------- > Program grompp_d, VERSION 3.3 > Source code file: smalloc.c, line: 113 > > Fatal error: > calloc for pairs->param (nelem=664225, elsize=152, file topio.c, line 125) this corresponds to 100 Mb . How much does your computer have? > ------------------------------------------------------- > > "Is This the Right Room for an Argument ?" (Monty Python) > : Cannot allocate memory > " > > To trouble shoot I tried repeating the successful PR run and strangely > enough got the same error with grompp. > > Suddenly grompp broke down or something went wrong with the cluster here. > > I am clueless. Looking fwd to some pointers .. > > Regards > Sandeep > > > --- > Graduate Student > Gilson Laboratory > Center for Advanced Research in Biotechnology > University of Maryland Biotechnology Institute > 9600 Gudelsky Drive > Rockville, MD 20850 > > www.chemicalphysics.umd.edu/~ssomani > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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 [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
