AMBER Archive (2007)

Subject: RE: AMBER: amber9: running parallel error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Apr 11 2007 - 08:43:19 CDT

Dear Khatcharin

The error you are seeing is coming from mpirun, not from sander.MPI. Have
you verified that your mpi implementation runs correctly, do the mpi test
cases work? Can you successfully rsh or ssh to the node (even the master
node) without a password? Also check that you have the correct daemon for
mpi running (either lamboot, mpd etc...) depending on your version of mpi
etc.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Khatcharin Siriwong
> Sent: Wednesday, April 11, 2007 01:08
> To: amber
> Subject: AMBER: amber9: running parallel error
>
> Dear All,
>
> Serial compilation and test.serial were fine for AMBER9 installation
> (using "ifort_ia32" (intel_fc_p_9.0.021 version). Also, parallel
> compilation was successed, but when I run sander.MPI with
> command
>
> setenv PARALLEL "mpirun -np 2 $AMBERHOME/exe/sander.MPI"
>
> $PARALLEL -O -i gbin -c md12.x -o mdout.dhfr
>
> I got error message
> **********
> p0_7004: p4_error: Child process exited while making connection
> to remote process on ch1: 0
> forrtl: error (69): process interrupted (SIGINT)
> p0_7004: (33.014300) net_send: could not write to fd=4, errno =
> 32
> **********
>
> This run was on master node, not client.
> Any suggestion to solve this problem?
>
> Note:
> System:
> Intel Xeon 2CPUs
> OS:
> SUSE Linux Enterprise Server 9 (Kernel 2.6)
> MPICH2:
> mpich-1.2.7p1 compiled by ifort (intel_fc_p_9.0.021 version)
> Compiling SANDER:
> ./configure -mpich2 -static ifort_ia32
> make clean
> make parallel
> (PATH for ifort, AMBERHOME and MPI_HOME were set)
>
> One more question, after parallel compilation, there was no
> executed file "pmemd" in $AMBERHOME/exe. What's wrong?
>
> Many thanks in advance.
>
> Regards,
> Khatcharin
>
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