AMBER: PMEMD MPI_Finalize() error

From: Mingfeng Yang <>
Date: Fri, 10 Feb 2006 09:50:59 -0500

I was trying to run PMEMD program against a system with 106335 atoms on
a sgi altix machine, which is based on itanium 64 CPU and Red Hat
Enterprise Linux AS 3. The program was compiled with ifc 9.0. The
system was first minimized for 2000 steps with sander. When I just began
to heat the system from 10K to 100K, pmemd crashed with the following

/ MPI: MPI_COMM_WORLD rank 0 has terminated without calling
    MPI: aborting job
    MPI: Received signal 11

/Looked through the mail archive, I found somebody was in similar
situation before, and he solve the problem by modifying flush() call in
sys.f. However, it seems amber8 already fix this problem, so I think the
reason behind my story would be different.

Interestingly, the same pmemd program runs well against another system
on the same machine. Can anyone help?


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Received on Sun Feb 12 2006 - 06:10:09 PST
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