Hello,
thanks for your reply and Now i am getting following errors.
thanks.
zuh.node01:~/Working/rehana_il2/sim_Cmplx_IL-2_test> mpirun -n 8 a.out
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
zuh.node01:~/Working/rehana_il2/sim_Cmplx_IL-2_test> mpirun -np 8 a.out
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file a.out (No such file or directory)
zuh.node01:~/Working/rehana_il2/sim_Cmplx_IL-2_test> mpirun -np 8 mpi.f90
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file mpi.f90 (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file mpi.f90 (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file mpi.f90 (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file mpi.f90 (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file mpi.f90 (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file mpi.f90 (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file mpi.f90 (No such file or directory)
[proxy:0:0.node01] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file mpi.f90 (No such file or directory)
zuh.node01:~/Working/rehana_il2/sim_Cmplx_IL-2_test>
Tarique
>________________________________
> From: Jason Swails <jason.swails.gmail.com>
>To: Syed Tarique Moin <tarisyed.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
>Sent: Tuesday, May 15, 2012 7:42 PM
>Subject: Re: [AMBER] mpi problem
>
>Run it the same way you ran sander.MPI on several nodes (using mpirun).
>
>On Tue, May 15, 2012 at 3:29 AM, Syed Tarique Moin <tarisyed.yahoo.com>wrote:
>
>> No, the given below program ran smoothly on a single now but I do not know
>> how to check across different nodes.
>>
>> Regards
>>
>>
>> Tarique
>>
>>
>>
>>
>> >________________________________
>> > From: Jason Swails <jason.swails.gmail.com>
>> >To: AMBER Mailing List <amber.ambermd.org>
>> >Sent: Tuesday, May 15, 2012 12:53 PM
>> >Subject: Re: [AMBER] mpi problem
>> >
>> >Is this problem unique to Amber, or do you get this kind of issue with any
>> >MPI program?
>> >
>> >My suggestion is to write a quick MPI program that does some basic
>> >collective communication and see if it works across different nodes. An
>> >example Fortran program is:
>> >
>> >program test_mpi
>> > implicit none
>> > include 'mpif.h'
>> > integer holder, ierr
>> > call mpi_init(ierr)
>> > holder = 1
>> > call mpi_bcast(holder, 1, mpi_integer, 0, mpi_comm_world, ierr)
>> > call mpi_finalize()
>> >end program test_mpi
>> >
>> >You can compile it with "mpif90 program_name.f90" Do you still get the
>> >same error with this program?
>> >
>> >On Mon, May 14, 2012 at 11:04 PM, Syed Tarique Moin <tarisyed.yahoo.com
>> >wrote:
>> >
>> >> Hello,
>> >>
>> >> I have compiled mpich2 and amber12 with intel compiler successfully.
>> When
>> >> I run the job with sander.MPI on single nodes with multicore it runs
>> >> without errors. But the same job run with multiple nodes is giving
>> >> following errors with mpirun and mpiexec.
>> >>
>> >> Kindly guide me.
>> >>
>> >> Thanks and Regards
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> mpiexec -np 8 -machinefile /etc/mpich/machines.LINUX
>> >> $AMBERHOME/bin/sander.MPI -O -i sim_cmplx_1000.in -o test.out -p
>> a.prmtop
>> >> -c sim_cmplx_1000_36.rst -r test.rst -x test.mdcrd -e test.mden &
>> >> [1] 4374
>> >> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>> >> Fatal error in PMPI_Barrier: Other MPI error, error stack:
>> >> PMPI_Barrier(425)...........: MPI_Barrier(MPI_COMM_WORLD) failed
>> >> MPIR_Barrier_impl(306)......:
>> >> MPIR_Bcast_impl(1321).......:
>> >> MPIR_Bcast_intra(1155)......:
>> >> MPIR_Bcast_binomial(213)....: Failure during collective
>> >> MPIR_Barrier_impl(292)......:
>> >> MPIR_Barrier_or_coll_fn(121):
>> >> MPIR_Barrier_intra(83)......:
>> >> dequeue_and_set_error(596)..: Communication error with rank 0
>> >>
>> >> [1]+ Exit 1 mpiexec -np 8 -machinefile
>> >> /etc/mpich/machines.LINUX $AMBERHOME/bin/sander.MPI -O -i
>> >> sim_cmplx_1000.in -o test.out -p a.prmtop
>> >>
>> >> -----------------------------------------------
>> >> -------------------------------------------
>> >> mpirun -np 8 -machinefile
>> >> /etc/mpich/machines.LINUX $AMBERHOME/bin/sander.MPI -O -i
>> >> sim_cmplx_1000.in -o test.out -p a.prmtop -c sim_cmplx_1000_36.rst -r
>> >> test.rst -x test.mdcrd -e test.mden &
>> >>
>> >>
>> >>
>> >> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>> >> Fatal error in PMPI_Barrier: Other MPI error, error stack:
>> >> PMPI_Barrier(425)...........: MPI_Barrier(MPI_COMM_WORLD) failed
>> >> MPIR_Barrier_impl(306)......:
>> >> MPIR_Bcast_impl(1321).......:
>> >> MPIR_Bcast_intra(1155)......:
>> >> MPIR_Bcast_binomial(213)....: Failure during collective
>> >> MPIR_Barrier_impl(292)......:
>> >> MPIR_Barrier_or_coll_fn(121):
>> >> MPIR_Barrier_intra(83)......:
>> >> dequeue_and_set_error(596)..: Communication error with rank 0
>> >>
>> >> -------------------------------------------------------------
>> >>
>> >>
>> >>
>> >> Syed Tarique Moin
>> >> Ph.D. Research Fellow,
>> >> International Center for Chemical and Biological Sciences,
>> >> University of Karachi
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>> >--
>> >Jason M. Swails
>> >Quantum Theory Project,
>> >University of Florida
>> >Ph.D. Candidate
>> >352-392-4032
>> >_______________________________________________
>> >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
>>
>
>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Tue May 15 2012 - 22:30:03 PDT
