[gmx-users] GDB Debugging - GROMACS(v-3.3.3) Application with OpenMPI(v-1.2.5/v-1.2.6)
David van der Spoel
spoel at xray.bmc.uu.se
Thu Apr 17 20:51:52 CEST 2008
Mukesh K Srivastava wrote:
> Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3)
> application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had
> properly configured OpenMPI with debug option and also configured
> Gromacs alongwith FFTW succesfully. I can perform p2bdbx_mpi,
> editconf_mpi, genbox_mpi, grompp_mpi compilation and finally mdrun_mpi
> without any error or warning messages. But while executing mdrun_mpi
> w.r.t mprun, I get libmpi.so.0 not found.
> I had tried with LD_LIBRARY_PATH, forcefully mentioning PATH &
> LD_LIBRARY_PATH in etc/bashrc file and also tried with providing
> softlink to libmpi.so.0, but everytime I get same error message of
> "libmpi.so.0" not found.
> I had check ldd and it's dependency of executable mdrun_mpi, checked
> it's symbol table content, and finally all lib's configured for 64 bit
> with ELF format but still getting same error of libmpi.so.0 not found
> while performing GDB serial debugging with single node.
> Note: I had performed GDB debugging for small MPI program(hello
> world) using OpenMPI(v1.2.5/v1.2.6) wthout GROMACS association succesfully.
> Any clue plz?
on the nodes. probably the mpi is not installed on the nodes.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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