[maker-devel] openmpi instantly chokes on maker

[Carson Holt]

Hi Justin,

You need to set LD_PRELOAD to the proper location and add the '-mca btl ^openib’ flag to your command line.


The 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 Dec 27, 2014, at 7:59 PM, Justin Peyton <cognitiveshrapnel at gmail.com> wrote:
> 
> I am working on getting maker running on a system running ubuntu 14.04. I have installed maker and it runs great on a small but real data set. When I try it with openmpi with the exact same inputs, however, I get the below error almost instantly. 
> 
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> [molybdenum:23241] *** Process received signal ***
> [molybdenum:23241] Signal: Segmentation fault (11)
> [molybdenum:23241] Signal code: Address not mapped (1)
> [molybdenum:23241] Failing at address: 0x50c
> [molybdenum:23241] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7f99bd0e8c30]
> [molybdenum:23241] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f99bd5155a2]
> [molybdenum:23241] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7f99bd0e8c30]
> [molybdenum:23241] [ 3] /lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f99bd19fbad]
> [molybdenum:23241] [ 4] /usr/local/openmpi/lib/libopen-pal.so.6(+0x72156)[0x7f99bcbcc156]
> [molybdenum:23241] [ 5] /usr/local/openmpi/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0x13b)[0x7f99bcbc34bb]
> [molybdenum:23241] [ 6] /usr/local/openmpi/lib/libopen-rte.so.7(+0x3897e)[0x7f99bce6e97e]
> [molybdenum:23241] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f99bc944182]
> [molybdenum:23241] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f99bd1acefd]
> [molybdenum:23241] *** End of error message ***
> SIGTERM received
> SIGTERM received
> SIGTERM received
> SIGTERM received
> SIGTERM received
> [molybdenum:23252] *** Process received signal ***
> [molybdenum:23252] Signal: Segmentation fault (11)
> [molybdenum:23252] Signal code: Address not mapped (1)
> [molybdenum:23252] Failing at address: 0x50c
> [molybdenum:23252] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7fb191b31c30]
> [molybdenum:23252] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7fb191f5e5a2]
> [molybdenum:23252] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7fb191b31c30]
> [molybdenum:23252] [ 3] /lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7fb191be8bad]
> [molybdenum:23252] [ 4] /usr/local/openmpi/lib/libopen-pal.so.6(+0x72156)[0x7fb191615156]
> [molybdenum:23252] [ 5] /usr/local/openmpi/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0x13b)[0x7fb19160c4bb]
> [molybdenum:23252] [ 6] /usr/local/openmpi/lib/libopen-rte.so.7(+0x3897e)[0x7fb1918b797e]
> [molybdenum:23252] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7fb19138d182]
> [molybdenum:23252] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7fb191bf5efd]
> [molybdenum:23252] *** End of error message ***
> SIGTERM received
> --------------------------------------------------------------------------
> mpiexec noticed that process rank 2 with PID 23241 on node molybdenum exited on signal 11 (Segmentation fault).
> 
> 
> I have tried reinstalling both maker and openmpi. I have tried two different versions of both maker and openmpi. I am curenlty working with maker 2.31.6 and openmpi 1.8.3 because I have had those work together on another system. I have triple checked that LD_PRELOAD is properly set. I have a feeling that I am pissing something small. I appreciate all the help.
> 
> Justin Peyton
> The Ohio State University
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> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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