[gmx-users] RAM MEMORY USAGE FOR g_cluster/g_rms

[sridhar at cdfd.org.in]

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 <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] RAM MEMORY USAGE FOR g_cluster/g_rms
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <45A60A24.50707 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

sridhar at cdfd.org.in 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    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php