From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Mon Apr 04 2005 - 15:21:38 CDT
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
> ************************************************
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:38 CST