Anil Kumar wrote:
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
clust-id.xvg
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
problem.
Either don't use all of your structures to cluster, or get more memory
:-) Doubtless g_cluster has a -dt flag you can put to good use.
Mark
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