This looks like a possible problem with file system rather than amber. can
you create files in the test directory? meaning can you create (using vi,
etc) a file called rem.out.000? Do the other test cases pass ok? does it
work if you run it outside of PBS?
On 2/18/07, Daniel Oehme <oehmes4.gmail.com> wrote:
>
> Hi all,
>
> I am having trouble getting the first exchange to proceed when running
> the rem_water tests on a newly compiled parallel version of Amber 9. I
> am getting the following errors output to an error file after the
> first stage of MD has been completed, and there is also nothing output
> to the remlog file.
>
> Unit 6 Error on OPEN: ./rem.out.000
>
> Unit 6 Error on OPEN: ./rem.out.001
> [0] MPI Abort by user Aborting program !
> [1] MPI Abort by user Aborting program !
> [0] Aborting program!
> [1] Aborting program!
> mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 192.168.2.45,
> killing all.
> mpiexec: Warning: tasks 0-1 died with signal 6 (Aborted).
>
> The job was run on two processors using the command
> '/usr/local/bin/mpiexec -np 2 /usr/local/amber9/exe/sander.MPI -O -ng
> 2 -groupfile groupfile' in a pbs-script.
>
> The cluster I am using has Power5 cpus with SUSE as the OS.
>
> Thanks in advance for your help.
>
> Daniel Oehme
> PhD Student
> La Trobe University
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Received on Wed Feb 21 2007 - 06:07:27 PST
