[maker-devel] Maker Execution Error

[Carson Holt]

Hi Jackie,

From the INSTALL file included with MAKER —>

    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


Also the following —>

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=/usr/local/openmpi/lib/libmpi.so).


The first one is the most likely.

Thanks,
Carson



> On Mar 28, 2016, at 8:38 AM, Atkins, Jacqueline (NIH/NIAID) [C] <jacqueline.atkins at nih.gov> wrote:
> 
> Hello,
> 
> I have recently installed Maker on RHEL 7/ Perl-5.16.3.  When I attempt to execute, I get the following error
> 
> $ mpiexec -n 4 maker -help
> 
> An MPI process has executed an operation involving a call to the
> "fork()" system call to create a child process.  Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your MPI job may hang, crash, or produce silent
> data corruption.  The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.  
> 
> The process that invoked fork was:
> 
>   Local host:          submit (PID 316)
>   MPI_COMM_WORLD rank: 2
> 
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
> [submit:122878] 3 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork
> [submit:122878] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
> [submit bin]$  mpiexec --version
> mpiexec (OpenRTE) 1.8.4
> 
> 
> I have a previous version of Maker installed that is using OpenMPI 1.3.3 and it is working fine.  I was wondering if you think this might be related to the version of OpenMPI?
> 
> Thank you in advance.
> Jackie
> 
> 

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