[gmx-users] Re-compile Gromacs Program?

[Mark Abraham]

On 08/03/11, Chih-Ying Lin  <chihying2008 at gmail.com> wrote:
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> Hi
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> I found the Gromacs Program could not do the parallel computing since the staff of the compter center in my school upgraded the intel compiler to v 12, and rebuilt the mpich build with intel. I requested them to recompile the Gromacs Program but they rejected and they answered that the updated intel compiler is not the issue for the failure of running the parallel computing of Gromacs Program.
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> I listed the bounced-back of summited job to the computer center.
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> Warning: no access to tty (Bad file desc-riptor).
> Thus no job control in this shell.
> /usr/bin/xmgrace: No such file or directory.
> /usr/usc/mpich/default/mx-intel/setup.csh: line 30: syntax error: unexpected end of file
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> /usr/usc/gromacs/default/setup.csh: line 19: syntax error: unexpected end of file
> /usr/usc/intel/default/setup.csh: line 24: syntax error: unexpected end of file
> mpiexec_hpc1982: cannot connect to local mpd (/tmp/10429754.hpc-pbs.usc.edu/mpd2.console_hpc1982_chihying(http://10429754.hpc-pbs.usc.edu/mpd2.console_hpc1982_chihying)); possible causes:
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>   1. no mpd is running on this host
>   2. an mpd is running but was started without a "console" (-n option)
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> How does the problem happen?
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The way you are configuring your execution environment does not match reality. xmgrace is not found, and somehow all of those setup.csh files have problems. Then the MPI environment cannot set up.

This issue has nothing to do with GROMACS or the compilers. You need to find out how to configure the environment correctly for this system. If GROMACS ran previously in parallel, then either you've changed your environment configuration somehow, or the admins have changed the execution environment somehow.

Find and match the example scripts.

Mark
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