ADL: Compiling & running parallel autodock

Prashant S. Khodade prashant.khodade at gmail.com
Thu May 28 07:19:37 PDT 2009


Hi Steve,

libmpi_cxx.so.0 is a shared library. Just see in which directory this
file is present. Once you know the directory put it in the
LD_LIBRARY_PATH variable.

To illustrate further, executable will search for required files in
directories listed in LD_LIBRARY_PATH variable. You can see contents
of this variable from shell by echo $LD_LIBRARY_PATH and set it
according to your shell command. In your environment, probably
LD_LIBRARY_PATH variable is not set or does not contain directory
containing libmpi_cxx.so.0.

Following url http://users.actcom.co.il/~choo/lupg/tutorials/libraries/unix-c-libraries.html
contains nice tutorial about shared library which might be useful.

Let me know if this solves the problem. Also let me know what other
errors you are getting, I would happy to help.

Regards,
Prashant

On Wed, May 27, 2009 at 8:29 PM, Steven Platt <Steven.Platt at hpa.org.uk> wrote:
> Hi again,
>
> Following Prashants advice (below) I have tried to compile Autodock for MPI by doing the following
> *       cd to autodock-4.0.1 source directory
> *       ./configure
> *       Edit Prashants MPI makefile for my system, and replaced all occurrences of gcc/g++ with mpicc/mpiCC
> *       Replace default autodock makefile, main.cc & main.h with MPI versions provided
> *       make
>
> which gives a few warnings...
> main.cc: In function âvoid ParallelInitialization(int, char**, int*, int*)â:
> main.cc:137: warning: unused variable âmpi_finishtâ
> main.cc:138: warning: unused variable âmpi_totaltâ
> main.cc:157: warning: unused variable âstatus1â
> mv -f .deps/main.Tpo .deps/main.Po
> mpiCC -Wall -O3     -o autodock4 main.o libad.a -lm
>
> So it appears to compile without too many complaints...
>
> The executable's then moved to the apps area of our Condor (v7.0.5) cluster. Our parallel cluster definitely works with other apps (Clustal, BLAST, etc), but running this compilation of MPI Autodock gives me a lot of the following errors (1 for each node it's trying to run on) and the job dies.
>
> /share/apps/autodock4: error while loading shared libraries: libmpi_cxx.so.0: cannot open shared object file: No such file or directory
>
> I'm not a C programmer by trade so I'm not sure what's going on or where to start looking for answers. Any pointers will be appreciated.
>
> Thanks
>
> Steve
>
> Dr Steven Platt
> Statistics, Modelling and Bioinformatics
> Health Protection Agency
> Centre for Infections
> 61 Colindale Avenue
> London
> NW9 5EQ
> www.hpa.org.uk/bioinformatics
>
> ------------------------------------------
>
> All,
>
> http://proline.physics.iisc.ernet.in/autodock/ has not been updated yet for AutoDock 4.0.1. I am attaching main.cc, main.h and Makefile for 4.0.1 with this email.
>
> Steve,
>
> Thank you for attaching output of make. I can suggest following things:
> 1) Instead of g++, use MPI compiler.
> 2) Specify location of mpi.h in your include path. If you use MPI compiler it will not be necessary to do this step.
>
> Let me know if it works.
>
> Cheers,
> Prashant
>
>
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