Hi All
I'm trying to install the parallel version of Amber11 (actually i'm trying to install the GPU version, but I haven't got that far yet).
I've got AmberTools compiling ok, some tests were not 100% ok but I've found mailing list posts where it indicates that those errors are expected (problems with pbsa tests). The Amber11 parallel compile appeared to work just fine, but in the testing process it says 6 tests failed - although I can only find two errors in the logs, dip and noesy. I'm kind of at a loss as to where to go from here. When I run the individual tests from the command line it returns "Program Error". I've included what I hope is the relevant sections of make test below.
I'm performing the tests with DO_PARALLEL set to mpirun -np 4
Please note I'm not a scientist, only a systems engineer so my understanding of how Amber11 works is fairly limited (but my understanding of automake is reasonable!)
I've not included much configuration info in the interests of keeping this short but if you need to know anything about the way I built things just let me know. Any advice on how I can fix these tests would be appreciated!
Thank You
Ali
Alison Lynton
Senior Systems Engineer
Curtin University of Technology | Curtin IT Services | Building 204 | Room 521
Telephone 08 9266 2986 | Facsimile 08 9266 1072
Email a.lynton.curtin.edu.au | Website www.curtin.edu.au
“CRICOS provider code 00301J”
cd rdc && ./Run.dip
--------------------------------------------------------------------------
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 15539 on
node cn1 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
./Run.dip: Program error
make[2]: [test.sander.BASIC] Error 1 (ignored)
cd noesy && ./Run.noesy
--------------------------------------------------------------------------
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 16239 on
node cn1 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
./Run.noesy: Program error
make[2]: [test.sander.BASIC] Error 1 (ignored)
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Received on Mon Jun 13 2011 - 01:00:02 PDT
