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-- Gustavo Seabra Professor Adjunto Departamento de Química Fundamental Universidade Federal de Pernambuco Fone: +55-81-2126-7417 On Thu, May 20, 2010 at 5:22 PM, peker milas <pekermilas.gmail.com> wrote: > 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu May 20 2010 - 14:00:04 PDT