Re: [AMBER] amber installation test question

From: David Case <>
Date: Sat, 28 Jan 2017 10:01:15 -0500

On Fri, Jan 27, 2017, James Kress wrote:

> I installed Amber16 using OpenMPI 1.10.5 on RHEL 7.3 Workstation with no
> errors. I then ran the MPI tests with np=2 ( using export >
> DO_PARALLEL="mpirun -np 2").
> All went well until the Run.dhfr.noboxinfo test which hung.
> Is this expected?

No. Is the error with sander or with pmemd (or both)? Do you see the
"peek_ewald" error message in the mdout.dhfr.noboxinfo file?

This test exits with an error message, and it may be that the master
process is exiting but the second thread is not seeing the signal,
and is therefore hanging (even though mpi_abort is being called with
MPI_COMM_WORLD). This sort of behavior could be a serious problem in a
production code.

I think that most/all Amber testing with openmpi has used releases prior
to 1.10, so it's possible that there is something funny going on. We'll
have to see if someone here can reproduce the problem.

...thanks for the report....dac

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Received on Sat Jan 28 2017 - 07:30:03 PST
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