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

[sridhar at cdfd.org.in]

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.

#####################################################################
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