[mvapich-discuss] Error running test program after MVAPICH2-1.4.1 installation

[senthil.natesan at ndsu.edu]

Thanks Jonathan for your valuable time and suggestions. I tried the
wrapper script, but it doesn't seem to be fixing the problem
I get the following error:

/usr/bin/xauth:  error in locking authority file /home/senthil/.Xauthority
/usr/bin/xauth:  error in locking authority file /home/senthil/.Xauthority
pmemd-wrapper: line 2: pmemd: command not found
MPI process (rank: 1) terminated unexpectedly on compute-0-1.local
Exit code -5 signaled from compute-0-1
pmemd-wrapper: line 2: pmemd: command not found
pmemd-wrapper: line 2: pmemd: command not found
MPI process (rank: 0) terminated unexpectedly on compute-0-0.local
MPI process (rank: 2) terminated unexpectedly on compute-0-2.local
pmemd-wrapper: line 2: pmemd: command not found
MPI process (rank: 3) terminated unexpectedly on compute-0-3.local


I once again want to emphasize that the same command "pmemd" works well
with mpiexec.

thanks very much.

Senthil





> It looks like we're having problems with executing the command due to
> the extra options that need to be passed.  The error message indicates
> that it is trying to execute `pmemd -O -i min1.in -o min1.out -inf
> ...', instead of `pmemd'.  The problem seen in your first email seems
> to be resolved since `mpispawn' is now found but we'll look into this
> 2nd issue.  As a work around in the meantime, you should be able to
> create a script that simply calls the real binary with the needed
> options.
>
> Ex:
> #!/bin/sh
> # filename: pmemd-wrapper
> # permissions: 755
> pmemd -O -i min1.in -o min1.out -inf min1info -p C0101sol.prmtop -c
> C0101sol.inpcrd -r C0101solmin1.rst -ref C0101sol.inpcrd
>
> mpirun_rsh -np 4 -hostfile hostlist pmemd-wrapper
>
> On Sat, May 15, 2010 at 4:24 PM,  <senthil.natesan at ndsu.edu> wrote:
>>
>>> Jonathan Perkins wrote:
>>
>>> Just to check, did you install mvapich2 on all of the machines in the
>>> hostfile?
>>>
>>
>>
>> I installed mvapich2 on all compute nodes, but still I am getting the
>> following error.
>>
>>
>> mpirun_rsh -np 4 -hostfile  hostlist  pmemd -O -i min1.in -o min1.out
>> -inf
>> min1info -p C0101sol.prmtop -c C0101sol.inpcrd -r C0101sol    min1.rst
>> -ref C0101sol.inpcrd
>>
>> ****************************************
>> /usr/bin/xauth:  error in locking authority file
>> /home/senthil/.Xauthority
>> /usr/bin/xauth:  error in locking authority file
>> /home/senthil/.Xauthority
>> /usr/bin/xauth:  error in locking authority file
>> /home/senthil/.Xauthority
>> execv: No such file or directory
>> pmemd -O -i min1.in -o min1.out -inf min1info -p C0101sol.prmtop -c
>> C0101sol.inpcrd -r C0101solmin1.rst -ref C0101sol.inpcrd
>> execv: No such file or directory
>> pmemd execv: No such file or directory
>> pmemd -O -i min1.in -o min1.out -inf min1info -p C0101sol.prmtop -c
>> C0101sol.inpcrd -r C0101solmin1.rst -ref C0101sol.inpcrd
>> execv: No such file or directory
>> pmemd -O -i min1.in -o min1.out -inf min1info -p C0101sol.prmtop -c
>> C0101sol.inpcrd -r C0101solmin1.rst -ref C0101sol.inpcrd
>> MPI process (rank: 1) terminated unexpectedly on compute-0-1.local
>> -O -i min1.in -o min1.out -inf min1info MPI process (rank: 2) terminated
>> unexpectedly on compute-0-2.local
>> -p Exit code -5 signaled from compute-0-1
>> C0101sol.prmtop MPI process (rank: 3) terminated unexpectedly on
>> compute-0-3.local
>> -c C0101sol.inpcrd -r C0101solmin1.rst -ref C0101sol.inpcrd
>> MPI process (rank: 0) terminated unexpectedly on compute-0-0.local
>>
>> *******************************************************
>>
>>
>> The same program runs fine with mpiexec (from mvapich2). The submitting
>> script as follows.
>>
>>
>> mpdboot -v -n 5 --ifhn=craycx1 -f mpd.hosts
>>
>> mpiexec -machinefile  hostlist -np 4  pmemd -O -i min1.in -o min1.out
>> -inf
>> min1info -p C0101sol.prmtop -c C0101sol    .inpcrd -r C0101solmin1.rst
>> -ref C0101sol.inpcrd
>>
>> mpdallexit
>>
>> Thanks in advance for your suggestions.
>>
>>
>> Senthil Natesan
>>
>>
>>
>> _______________________________________________
>> mvapich-discuss mailing list
>> mvapich-discuss at cse.ohio-state.edu
>> http://mail.cse.ohio-state.edu/mailman/listinfo/mvapich-discuss
>>
>>
>
>
>
> --
> Jonathan Perkins
>
>