Hi, Frank
How many molecules are there in your system? What kind of simulation are
you running? Can you upload your input file?
Guanglei
S. Frank Yan wrote:
> Hi all,
>
> I ran many test cases. When single CPU is used (mpirun -np 1), sander
> runs fine. But when two CPUs are used, sander hangs right before:
>
> | Atom division among processors:
> | 0 1271
>
> Only the sentence:
>
> Number of triangulated 3-point waters found: 0
>
> is in the output file.
>
> The processes go on though without any additional output and it doesn't
> stop. Any idea what might have caused this problem?
>
> Thanks,
> Frank
>
>
>
>
>>-----Original Message-----
>>From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On
>
> Behalf
>
>>Of Carlos Simmerling
>>Sent: Wednesday, February 23, 2005 5:05 AM
>>To: amber.scripps.edu
>>Subject: Re: AMBER: mpirun sander8 problem
>>
>>does the mpi code work for a single processor? are you sure that the
>>input you are using works properly? mpi runs do not always give the
>>proper error message if the error occurs on a cpu other than the
>
> master.
>
>>S. Frank Yan wrote:
>>
>>
>>>Hi,
>>>
>>>I was able to recompile MPI using gcc and ifort with ch_shmem and
>>>compiled sander8 on a 2-CPU Linux box. I tested it with the dhfr
>>>testing case. The program runs in parallel but it stops spitting out
>>>output after "3. ATOMIC COORDINATES AND VELOCITIES... " section. I
>
> can
>
>>>see the CPU usage is around 100% for both CPUs, but sander seems to
>
> be
>
>>>stuck in a loop. Using mpirun -v yields "running ../../exe/sander on
>
> 2
>
>>>LINUX smp processors". Does anyone have the same experience like
>
> this?
>
>>>Thanks a lot.
>>>Frank
>>>
>>>
>>>
>>>
>>
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>
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Received on Thu Feb 24 2005 - 16:53:01 PST
