[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:
> Hi.
> 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?
ldd mdrun_mpi
on the nodes. probably the mpi is not installed on the nodes.

> BR
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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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