Hallo Anna :-)
we need a little more information to figure out whats wrong. MPI may fail
for reasons connected to your system or other ones.
Are output files produced? Do they contain error messages?
Did Amber12 pass the parallel test suite?
Did other parallel TI jobs run ok before?
Do you use the right MPI version (the one compiled with Amber) or the
pre-installed one?
Does it run on a single machine (with MPI, but no submission queue etc)
Can you run single CPU calculations (no TI) with both of your prmtops?
Your input file looks ok, just the scalpha parameter you set has no effect
when softcore (ifsc) is not on. Maybe your two endstate systems are not
identical in composition?
Kind Regards,
Thomas
On Thu, June 21, 2012 5:42 am, Anna Bauß wrote:
> I wanted to start a TI calculation in Amber 12, parallel istallation
> (with MPI) by using the command
>
> mpirun -np 2 sander.MPI -ng 2 -groupfile group_min_0.00
>
>
> I got the following error message:
>
>
> Running multisander version of sander Amber12
> Total processors = 2
> Number of groups = 2
>
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
> My group file looks the following:
>
> -O -i mdin_min_1qdb_515w_0.00 -o 1qdb_515w_min_0.00.out -p 1qdb_515w.prm
> -c 1qdb_515w.rst -r 1qdb_515w_min_0.00.rst -ref 1qdb_515w.rst -inf
> mdinfo_1qdb_515w
> -O -i mdin_min_1qdb_517w_0.00 -o 1qdb_517w_min_0.00.out -p 1qdb_517w.prm
> -c 1qdb_517w.rst -r 1qdb_517w_min_0.00.rst -ref 1qdb_517w.rst -inf
> mdinfo_1qdb_517w
> ~
>
>
> the input file looks as following:
>
> 200 steps of minimation
> &cntrl
> imin = 1, ntx = 1, irest = 0,
> ntpr = 100, ntwr = 100, ntwx = 0,
> ntf = 2, ntc = 2, cut = 9.0,
> ntr = 1, restraintmask = '1-2', restraint_wt = 1.0,
> ntmin = 2, ntb = 2, maxcyc = 200,
> ntp = 1, pres0 = 1.0, taup = 2,
> icfe = 1, clambda = 0.00,
> ifsc = 0,
> crgmask = '',
> scmask = '',
> scalpha = 0.6,
> &end
> ~
>
> The same process worked completely fine in Amber 10 and 11. We couldn't
> find any solution to this problem in Amber 12 and would highly
> appreciate any helpful comments.
>
> Thank you,
>
> Anna Bauß
>
> --
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 21 2012 - 04:30:02 PDT
