Re: problem running namd

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Apr 04 2005 - 15:26:06 CDT

Good comment. Why then work with dynamic libraries in the first place??

Brian

On Mon, 4 Apr 2005, Jerry Ebalunode wrote:

> One quick way to avoid problems with namd or other programs having being
> built and supported by different versions of intel compiler intel compiler
> and their runtime libraries is to simply link the intel libraries statically
> at the build time. This way your namd2 would not have problems with running
> on machines with variations of the runtime libraries.
>
> To do this use the flag " -static-libcxa "
>
>
> On Monday 04 April 2005 01:12 pm, Brian Bennion wrote:
> > The problem is most likely a difference in mpi libraries that namd2 was
> > compiled with and the ones used at runtime on the larger machine.
> >
> > I have this issue all the time with icc8.0 and icc8.1 compilations.
> >
> > If you cant compile against the current libs on the larger machine, then
> > try exporting your LD_LIBRARY_PATH in your batch script.
> >
> > regards
> > Brian
> >
> > On Mon, 4 Apr 2005, Michel Espinoza-Fonseca wrote:
> > > Hi all,
> > >
> > > I compiled NAMD on an Altix machine. The executable ran very well and
> > > perform very good. I was really excited about running namd in a bigger
> > > machine, but when I sent the job I got the following message:
> > >
> > > Charm++> MPI timer is synchronized!
> > > Info: NAMD 2.5 for Linux-ia64
> > > Info:
> > > Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> > > Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> > > Info:
> > > Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
> > > Info: in all publications reporting results obtained with NAMD.
> > > Info:
> > > Info: Based on Charm++/Converse 0143163 for mpi-linux-ia64-ifort-mpt-icc
> > > Info: Built Thu Mar 10 18:04:44 CST 2005 by espinoza on balt
> > > Info: Sending usage information to NAMD developers via UDP. Sent data
> > > is: Info: 1 NAMD 2.5 Linux-ia64 18 altix.msi.umn.edu espinoza
> > > ./namd2-altix: relocation error: ./namd2-altix: undefined symbol:
> > > _Locksyslock MPI: MPI_COMM_WORLD rank 0 has terminated without calling
> > > MPI_Finalize() MPI: aborting job
> > >
> > > And of course the job just crashed. I also executed it without a input
> > > file, in order to test the binary, and I got the same problem. Do you
> > > have any suggestions on how can I solve the problem? Do I need to
> > > recompile namd?
> > >
> > > Thank you very much!
> > > Peace
> > > Michel
> >
> > ************************************************
> > Brian Bennion, Ph.D.
> > Bioscience Directorate
> > Lawrence Livermore National Laboratory
> > P.O. Box 808, L-448 bennion1_at_llnl.gov
> > 7000 East Avenue phone: (925) 422-5722
> > Livermore, CA 94550 fax: (925) 424-6605
> > ************************************************
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605
************************************************

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