AMBER Archive (2009)

Subject: Re: [AMBER] parallel run error

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Feb 17 2009 - 06:40:03 CST

the error message says that the file ended early in mdread.
this means your input file has a problem. you might want to try it
with a serial version of sander,
or see if the test cases work properly before making your own input.
it isn't clear if this is the DNA tutorial input or you made it yourself.

On Tue, Feb 17, 2009 at 3:19 AM, balaji nagarajan
<balaji_sethu_at_hotmail.com> wrote:
>
> dear amber ,
>
> I am trying to run minimization of dna as given in the tutorial
> when I gave the run in parallel its giving error
> ,I have used LAM for parallel installation .
> when i gave lamboot alll nodes are getting booted
> but when i run sander.MPI
> it gives
> as belo
> ---------------------------------------------
> At line 862 of file _mdread.f
> Fortran runtime error: End of file
> MPI_Recv: process in local group is dead (rank 1, comm 3)
> Rank (1, MPI_COMM_WORLD): Call stack within LAM:
> Rank (1, MPI_COMM_WORLD): - MPI_Recv()
> Rank (1, MPI_COMM_WORLD): - MPI_Bcast()
> MPI_Recv: process in local group is dead (rank 2, comm 3)
> Rank (2, MPI_COMM_WORLD): Call stack within LAM:
> Rank (2, MPI_COMM_WORLD): - MPI_Recv()
> Rank (2, MPI_COMM_WORLD): - MPI_Bcast()
> Rank (2, MPI_COMM_WORLD): - MPI_Bcast()
> Rank (2, MPI_COMM_WORLD): - main()
> MPI_Recv: process in local group is dead (rank 4, comm 3)
> Rank (4, MPI_COMM_WORLD): Call stack within LAM:
> Rank (4, MPI_COMM_WORLD): - MPI_Recv()
> Rank (4, MPI_COMM_WORLD): - MPI_Bcast()
> Rank (4, MPI_COMM_WORLD): - MPI_Bcast()
> Rank (4, MPI_COMM_WORLD): - main()
> Rank (1, MPI_COMM_WORLD): - MPI_Bcast()
> Rank (1, MPI_COMM_WORLD): - main()
> MPI_Recv: process in local group is dead (rank 3, comm 3)
> Rank (3, MPI_COMM_WORLD): Call stack within LAM:
> Rank (3, MPI_COMM_WORLD): - MPI_Recv()
> Rank (3, MPI_COMM_WORLD): - MPI_Bcast()
> Rank (3, MPI_COMM_WORLD): - MPI_Bcast()
> Rank (3, MPI_COMM_WORLD): - main()
> -----------------------------------------------------------------------------
> One of the processes started by mpirun has exited with a nonzero exit
> code. This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
>
> PID 2745 failed on node n0 (192.1.1.53) with exit status 2.
> ----------------------------------------------------------------------------
>
> how can i solve this
> thanks in advance
>
> balaji
> uom
>
>
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