Hey TomTom :)
here my answers to your questions:
> Are output files produced? YES
> Do they contain error messages? NO
> Did Amber12 pass the parallel test suite? YES
> Did other parallel TI jobs run ok before? NOT IN AMBER12
> Do you use the right MPI version (the one compiled with Amber) or the
pre-installed one?
We use Debian 604 with pre-installed open MPI 142
> Does it run on a single machine (with MPI, but no submission queue
etc) YES
> Can you run single CPU calculations (no TI) with both of your
prmtops? YES
> Maybe your two endstate systems are not identical in composition?
the files are identical, only whith different charge
distribution on one HEM-residue.
Thank you so much for helping me,
viele Grüße von Fabi :)
Anna
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
>>
>> --
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Thu Jun 21 2012 - 05:00:02 PDT
