[gmx-users] Problem of memory allocation while doing g_cluster

Anil Kumar anil at chem.iitb.ac.in
Tue Mar 20 07:37:53 CET 2007

Hi All,

I am in need of kind help from any of gmx user regarding the memory
allocatin which i was facing while doing g_cluster.

I was trying to do clustering of 33000 strucutres and more of octa-alanine
(having 61 lines per pdb).

Command i used was: -

echo 4 4 | g_cluster_mpi -f total.pdb -s full*.tpr -g clu_total.log -cl
clu.pdb -fit -av -method gromos -cutoff 0.15 -ntr -tr totaltrans -clid

Note:-(Total no. of line in total.pdb = 2013000),

Error message: -

Last frame      32999 time 167995.016
Allocated 11088000 bytes for frames
Read 33000 frames from trajectory 168000.pdb
Fatal error: calloc for m[i] (nelem=33000, elsize=4, file matio.c, line
63): Cannot allocate memory

What i understood was it is problem in generating array of array (two
dimensional array) that's why it crashed
Since i have no backgroud of computer science i am not able to fix this

Any help !!

Thanks in advance
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ANIL KUMAR(Research Scholar),
Bio-Organic Lab No-336(2nd Floor),
Dept. of Chemistry,I.I.T.Bombay,Powai,
Ph. No.-022-25764780(Lab)
Hostel#1,Room#297,IIT Bombay,Powai,
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