[gmx-users] Zdock

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jan 13 21:45:11 CET 2008

Siavoush Dastmalchi wrote:
> Hi There,
> I know this is not related to GMX, but was wondering if any one has any experience with mpi enabled zdock on linux based cluster. Specifically, I am trying to use zdock2.3_linux_mpi version on a cluster of Opteron 2212 CPUs. It looks like the application works on all nods but can not write out the results into the output file. This does not happen when I use non-mpi version (zdock3.0_linux_p3) on a single processor. Here is the error that I get:
> $ sort: open failed: +6: No such file or directory
> [2]-  
> Also the content of the generated output file is like this (comparing to content of the output file for zdock3.0_linux_p3 program, nothing has been written to it):
> 105     1.2
> 0.000000        0.000000        0.000000
> 1CGI_r_m.pdb    23.552  26.554  22.589
> 1CGI_l_m_bl.pdb 43.446  33.312  33.288

Try other MPI programs to see whether the problem is specific to zdock 
or your MPI/cluster/whatever setup.


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