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

[Mark Abraham]

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