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

[David van der Spoel]

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
> 
> 
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-- 
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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