If you want to run an individual Amber test in parallel you need to
set the DO_PARALLEL environment variable to whatever your MPI run
command should be, so:
DO_PARALLEL="mpirun -np 15" ./Run.pHremd
Make sure your AMBERHOME environment variable is also properly set.
Hope this helps,
-Dan
On Wed, Feb 17, 2016 at 7:53 AM, Elisa Pieri <elisa.pieri90.gmail.com> wrote:
> I'm not sure on how I should "run tests", I went to this directory
> /home/elisa/amber14/test/cnstph_remd/Explicit_pHREM and ran the command mpirun
> -np 16 Run.pHremd
>
> this is the result (repeated 16 times):
> [agachon:05491] [[29828,1],0] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> rml_oob_send.c at line 104
> [agachon:05491] [[29828,1],0] could not get route to [[INVALID],INVALID]
> [agachon:05491] [[29828,1],0] ORTE_ERROR_LOG: A message is attempting to be
> sent to a process whose contact information is unknown in file
> base/plm_base_proxy.c at line 81
>
>
> On Wed, Feb 17, 2016 at 3:34 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> where you able to run OTHER sander or pmemd multi core files ?
>>
>> Run some of them as found in the test directory of the amber
>> installation. That way we can figure out if this is a problem with
>> constant pH or if it is related to amber itself.
>>
>> Thanks
>> adrian
>>
>>
>> On 2/17/16 9:22 AM, Elisa Pieri wrote:
>> > Dear all,
>> >
>> > I'm experiencing problems running pH-REMD on my computer. I have these
>> > machine: Intel® Xeon(R) CPU E5-2623 v3 @ 3.00GHz × 16, and I ran
>> > simulations using pmemd.MPI with no problems (I have Amber14). Now I'm
>> > using this command:
>> >
>> > mpirun -np 16 pmemd.MPI -ng 8 -groupfile prova.grpfile &
>> >
>> > Unfortunately, I get this error:
>> >
>> > Running multipmemd version of pmemd Amber12
>> > Total processors = 16
>> > Number of groups = 8
>> >
>> >
>> --------------------------------------------------------------------------
>> > 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 12 with PID 4994 on
>> > node agachon exiting improperly. There are two reasons this could occur:
>> >
>> > 1. this process did not call "init" before exiting, but others in
>> > the job did. This can cause a job to hang indefinitely while it waits
>> > for all processes to call "init". By rule, if one process calls "init",
>> > then ALL processes must call "init" prior to termination.
>> >
>> > 2. this process called "init", but exited without calling "finalize".
>> > By rule, all processes that call "init" MUST call "finalize" prior to
>> > exiting or it will be considered an "abnormal termination"
>> >
>> > This may have caused other processes in the application to be
>> > terminated by signals sent by mpirun (as reported here).
>> >
>> --------------------------------------------------------------------------
>> > [agachon:04981] 7 more processes have sent help message help-mpi-api.txt
>> /
>> > mpi-abort
>> > [agachon:04981] Set MCA parameter "orte_base_help_aggregate" to 0 to see
>> > all help / error messages
>> >
>> > Can you help me?
>> >
>> > Elisa
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>> --
>> Dr. Adrian E. Roitberg
>> Professor.
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 17 2016 - 07:30:06 PST
