[maker-devel] MPI

[Carson Holt]

The problem is the actual MPICH2 installation.  You may be missing prerequisites or you may not have compiled with the necessary shared library flags (-enable-shared). You may also be compiling on one machine that has certain libraries installed then running on another that doesn’t have access to those libraries (this can happen if running on a cluster).  Try reinstalling MPICH2 or switching to OpenMPI.

If you decide to use OpenMPI, he following is from the INSTALL file that should be included with MAKER —>

If using OpenMPI, make sure to set LD_PRELOAD to the location of libmpi.so before even trying to install MAKER. It must also be set before running MAKER (or any program that uses OpenMPI's shared libraries), so it's best just to add it to your ~/.bash_profile. (i.e. export LD_PRELOAD=/location/of/openmpi/lib/libmpi.so).


1.  Say yes to the 'configure for MPI' question when running 'perl Build.PL’ in step 1 of the EASY INSTALL.

2.  Give path to 'mpicc'. Note to make sure you do not give the path to ‘mpicc' from another MPI flavor that might be installed on your system.

3.  Give path to the folder containing 'mpi,h'. Note to make sure you do not give the path to a folder from another MPI flavor that might be installed on your system. Mixing MPI flavors for 'mpicc' and 'mpi.h' will cause failures. Make sure to read and confirm the auto-detected paths.

4.  Finish installation according to steps 2-4 of the EASY INSTALL

Note: For OpenMPI you may also want to set OMPI_MCA_mpi_warn_on_fork=0 in your ~/.bash_profile to turn off certain nonfatal warnings.

Note: If jobs hang or freeze when using mpiexec under OpenMPI try adding the '-mca btl ^openib' flag to mpiexec command when running MAKER.

        Example: mpiexec -mca btl ^openib -n 20 maker

Thanks,
Carson


> On Nov 5, 2015, at 12:16 AM, Anna Nyiri <dancsi90 at gmail.com> wrote:
> 
> Hi,
> 
> I tried to use MAKER with MPICH2, but I got an error message:
> "/molbio/bin/danna/mpich2-install/bin/hydra_pmi_proxy: error while loading shared libraries: libtorque.so.2: cannot open shared object file: No such file or directory"
> 
> The attached file contains the shell sctipt, which I used. Is this script correct?
> 
> The script should contain MPICH module. But I can't find it on my computer. Where can I find this module?
> 
> Thanks for your help,
> Anna Nyiri
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