AMBER: sander.MPI vs MPICH2 problem!!!

From: Swarup Gupta <>
Date: Fri, 23 Mar 2007 19:33:44 -0700 (PDT)

I have installed the sander.MPI successfully. I am using MPICH2. It has been installed on a HP-cluster and Redhat linux is the operating system. The processors are Opteron. Each node has two processors.
  When I submit the sander.MPI job (say Job-1) from the master node to run it on one or more nodes to run the jobs on multiple processors I do not see to run the sander.MPI programs on any of the CPUs. Suppose I submit the job-1 from masternode to run on ‘node-1’, just after submission I see that python2.2 is running node-1 and also sander.MPI starts to run and then with a fraction of a seconds sander.MPI disappears (also python) and nothing more happens. But at the same time the job is not aborted from the master node. I do not get any output file created by sander. So I guess that sander is not actually executed and not even aborted. Does it imply that I have some problem with MPI? (the non-mpi version of sander runs perfectly on the same machine). The jobscript is OK since it works on another cluster.
  If I just run (without running with mpi) the command $AMBERHOME/exe/sander.MPI then it creates “mdout” and gives the following message:
  “[unset]: aborting job:
  application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0”
  In this case it creates an output file and I guess that amber installation is OK but there is some communication problem from MPICH2. If anybody has any idea please let me know.

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Received on Sun Mar 25 2007 - 06:07:54 PDT
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