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 Thu Jun 21 2012 - 03:00:03 PDT
