Hey,
I still have the same problem whith my TI calculations. My interest in
the calculation ist the charge transfer from one to another residue. The
two pdb files are hence indentical exept the residue's charges. The
error messages I get immediately after starting the calculation are:
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.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 3734 on
node PC2-KOS19 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[PC2-KOS19:03733] 1 more process has sent help message help-mpi-api.txt
/ mpi-abort
[PC2-KOS19:03733] Set MCA parameter "orte_base_help_aggregate" to 0 to
see all help / error messages
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 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.
--------------------------------------------------------------------------
Running multisander version of sander Amber12
Total processors = 2
Number of groups = 2
Error opening unit 30: File "515_now_min_0.00.rst" is missing or
unreadable
Error opening unit 30: File "517_now_min_0.00.rst" is missing or
unreadable
--------------------------------------------------------------------------
mpirun has exited due to process rank 1 with PID 3739 on
node PC2-KOS19 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[PC2-KOS19:03737] 1 more process has sent help message help-mpi-api.txt
/ mpi-abort
[PC2-KOS19:03737] Set MCA parameter "orte_base_help_aggregate" to 0 to
see all help / error messages
To find the problem, we already tried the following:
Amber test runs - all successful
Old TI files which already ran successfully in Amber 10 - successful
Systemsize was checked by not adding a waterbox, didn't make any difference.
Every sytem for itself can be simulated and converges in a time window
of 0.5 ns.
TI with the same file for V0 and V1 as suggested by Tom results in the
same errors as TI with different files.
We have no idea what the reason for the MPI aborting is and would be
thankful for any helpful comments.
Best regards
Anna Bauß
Am 21.06.2012 11:42, schrieb Anna Bauß:
> 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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Received on Mon Jul 02 2012 - 03:00:02 PDT
