Yes, the Machine is a 64bit, sparc, solaris. Any setting could be done for using the required memory?
################################################################## Message: 3 Date: Thu, 11 Jan 2007 10:57:56 +0100 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] RAM MEMORY USAGE FOR g_cluster/g_rms To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed [EMAIL PROTECTED] wrote: > Dear GMX users, > > I am facing Memory problem while running g_cluster and g_rms (for RMSD > matrix) > calculations. The output of g_rms command is as follows. > ##################################################################### > Building RMSD matrix, 50001x50001 elements > element 9040; time 9040.00 Fatal error: calloc for rmsd_mat[i] > (nelem=50001, elsize=4, file g_rms.c, line 575): Not enough space > ##################################################################### > > But I am sure that the available physical RAM memory is sufficient (> 50 Giga > Bytes) for calculations, but somehow the program is unable to utilize the > memory. Below is the output of "top" command in our server, which tells about > the available RAM. There could be an issue with the memory allocation. Is this a 64 bit machine? Otherwise, you will not be able to allocate more than 2 or 4 Gb at a time, and you need 10 Gb. Note that the calculation will take a long time too.... A simple workaround is to use fewer structures. > > ##################################################################### > load averages: 0.11, 1.46, 2.59; up 8+01:16:22 17:25:28 > 194 processes: 193 sleeping, 1 on cpu > CPU states: 98.9% idle, 0.0% user, 1.1% kernel, 0.0% iowait, 0.0% swap > Memory: 64G phys mem, 53G free mem, 16G swap, 16G free swap > ##################################################################### > > IS there any way to make the program to utilize all the available RAM? > > Thanking you, > > Sridhar Acharya > > > _______________________________________________ > 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
