AMBER Archive (2009)

Subject: [AMBER] RE: pmemd parallel

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 14 2009 - 07:24:06 CDT

Hi Jun,

> Dear Ross,
> I did test for pmemd parallel. We want to run pmemd parallel on a 8
> processor linux computer.
>
> amber10/test> setenv DO_PARALLEL "mpiexec -n 8"
> amber10/test> make test.pmemd
> export TESTsander='../../exe/pmemd'; cd 4096wat && ./Run.pure_wat
> diffing mdout.pure_wat.save with mdout.pure_wat
> possible FAILURE: check mdout.pure_wat.dif
> ==============================================================
> export TESTsander='../../exe/pmemd'; cd 4096wat &&
> ./Run.pure_wat_nmr_temp_reg
> diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp
> possible FAILURE: check mdout.pure_wat_nmr_temp.dif
> ==============================================================
...
...
> How to run pmemd parallel on a 8 processor machine? Is there a problem
> for our pmemd?

This should work fine. Are you sure your DO_PARALLEL command is correct for
your mpi? Did you check the dif files to see what they say? I suspect there
is an error such as some mpi demon is not running or you also need to
provide a node list, or you don't have passwordless ssh/rsh access etc.
Taking a look inside the 4096wat test directory at mdout.pure_wat and
mdout.pure_wat.dif would be a good start to find out what is going wrong.

Also check you can run some MPI tests - most mpi installations come with
their own test directory.

All the best
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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