Thank you so much for your response,
here is the detailed information;
Hardware: Two intel Nehalem processors total 8 physical 16 logical cores
OS: Ubuntu Karmic Koala with gcc4.4.1 and gfortran.
Parallelization: OpenMPI 1.4
I applied all bugfixes, AmberTools installation and tests were fine
just two minor failures. Amber serial installation was also fine and
there was just 4 rounding-off type failures. As already discussed at
different times i created a symbolic link from /bin/bash to /bin/sh.
Parallel installation was fine again. Parallel tests gave me same
failures with serial test when i used 2 processors. After that i tried
with 4 and 8 processors, unfortunately in both cases tests stalled at
different tests. I mean results are totally not reproducible. At once
they stalled at Run.cap, next time at Run.tip4p_nve another time at
Run.dip and so on...I have two locally installed OpenMPI versions as
OpenMPI1.4 and OpenMPI1.2.8 such that i linked their lib and bin
folders to PATH and LD_PATH manually in my .bashrc file, i tried both,
nothing has changed. Also i was using PCGAMESS in parallel mode before
and even if i used it with 8 processors it worked just fine. As a last
piece of information i had from all above stalled processes, they are
all belong to sander.MPI. One last thing to say i cancelled all PIMD
tests because i wouldn't use them and what i explained above for all
the other tests.
thank you so much
peker milas
On Thu, May 20, 2010 at 3:56 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> This doesn't provide much information helpful for debugging. What are your
> system specs (OS, compilers, etc.)? What test is it specifically failing on
> (or stalling on)? Did the serial tests pass? Have you applied all bug
> fixes? The more details we have regarding system setup, the better chance
> someone will be able to help.
>
> All the best,
> Jason
>
> On Thu, May 20, 2010 at 3:19 PM, peker milas <pekermilas.gmail.com> wrote:
>
>> Dear Amber user and developers,
>>
>> My parallel (with openmpi1.4) Amber10 installation has a strange
>> problem. Let me try to explain it briefly, if run parallel tests with
>> only 2 processors (mpirun -np 2) everything goes fine except a couple
>> of failures. If i run them with 4 or more than 4 processors (mpirun
>> -np 4) it stalls in an arbitrary test. My computer has 8 physical cpu
>> s and it has shared memory parallelization. I used it for other
>> programs and there was no problem. So, really need help about this
>> number of processor issue and any will be greatly appreciated.
>>
>> thank you so much
>> peker milas
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu May 20 2010 - 13:30:03 PDT
