AMBER Archive (2009)

Subject: RE: [AMBER] reg.parallel run error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jan 22 2009 - 14:06:33 CST

Hi Balaji,

This looks like a problem with one of your input files - most like the
polyAT_wat_min1.rst file. Can you run this calculation okay in serial?

Are you running this across multiple nodes? If so do all nodes mount the
same file system in the same place and do they all have permission to read
and write to those files?

Also have you run the test cases? You should do this.

cd $AMBERHOME/test/
lamboot ...... options for lamboot .......
export DO_PARALLEL='mpirun -np 4'
make test.parallel

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of balaji nagarajan
> Sent: Thursday, January 22, 2009 10:41 AM
> To: amber forumnew
> Subject: [AMBER] reg.parallel run error
>
>
> Dear Ross .,
>
> thank you for your previous mail
> i got your sugesstions
>
> when i gave the run it is giving the following error
> i could not get it
> could you please let me know
> --------------------------------------------------------------------------
> -------------------------
> ERROR !
>
>
> mpirun -np 4 $AMBERHOME/exe/sander -O -i polyAT_wat_min2.in -o
> polyAT_wat_min2.out -p polyAT_wat.prmtop -c polyAT_wat_min1.rst -r
> polyAT_wat_min2.rst
> At line 2268 of file _ew_setup.f
> Fortran runtime error: Bad value during floating point read
> At line 2268 of file _ew_setup.f
> Fortran runtime error: Bad value during floating point read
> --------------------------------------------------------------------------
> ---
> It seems that [at least] one of the processes that was started with
> mpirun did not invoke MPI_INIT before quitting (it is possible that
> more than one process did not invoke MPI_INIT -- mpirun was only
> notified of the first one, which was on node n0).
>
> mpirun can *only* be used with MPI programs (i.e., programs that
> invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program
> to run non-MPI programs over the lambooted nodes.
> --------------------------------------------------------------------------
> ---
>
> regards
> balaji
> UOM
>
>
>
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