[maker-devel] Segfault with OpenMPI

[Carson Holt]

I tried setting this up but there are a number of issues I run into.

First RepeatMasker is not being installed correctly. The configuration step should create these files (created by ./configure script during RepeatMasker setup) —>
RepeatMasker.lib
RepeatMasker.lib.nhr
RepeatMasker.lib.nin
RepeatMasker.lib.nsq
RepeatMaskerLib.embl

But they do not exist in the share directory.

Also MAKER needs access to the te_proteins file in …/maker/data, and because you have rearranged maker’s structure it can’t find it.


Then for the Segmentation fault, I have seen this a handful of times in the past where users install their own version of perl rather than using the system perl together with their own install of OpenMPI. The issue is some series of flags either in OpenMPi or perl (I’m not sure which). But one way around it is to disable the interpreter threads option when compiling and installing perl for yourself. Most system perl installs have interpreter threads enabled, so I’m not sure why some self-installs generate this segfault and never the system perl. Interestingly interpreter threads are turned off by default when you install perl manually as they are “officially discouraged". You actually have to enable it during the self-install process, and conda is enabling them on the manual install to match most system perls.

Another work around is don’t use OpenMPI. Try MPICH3.


—Carson





> On Sep 25, 2018, at 6:10 AM, Anthony Bretaudeau <anthony.bretaudeau at inria.fr> wrote:
> 
> Hi,
> 
> I've worked on the Bioconda recipe for Maker (https://github.com/bioconda/bioconda-recipes/tree/master/recipes/maker/ <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/maker/>). It works well, except when using it in MPI mode. I get this segfault error:
> 
> STATUS: Processing and indexing input FASTA files...
> [cl1n022:06306] *** Process received signal ***
> [cl1n022:06306] Signal: Segmentation fault (11)
> [cl1n022:06306] Signal code: Address not mapped (1)
> [cl1n022:06306] Failing at address: 0x514
> [cl1n022:06306] [ 0] /lib64/libpthread.so.0(+0xf6d0)[0x2b9ce51026d0]
> [cl1n022:06306] [ 1] /local/miniconda3/envs/maker-2.31.10/bin/perl(Perl_csighandler+0x1e)[0x4aad4e]
> [cl1n022:06306] [ 2] /lib64/libpthread.so.0(+0xf6d0)[0x2b9ce51026d0]
> [cl1n022:06306] [ 3] /lib64/libc.so.6(__poll+0x2d)[0x2b9ce5f5cf0d]
> [cl1n022:06306] [ 4] /local/miniconda3/envs/maker-2.31.10/perl/lib/auto/Parallel/Application/MPI/../../../../../../lib/./libopen-pal.so.40(+0x869e5)[0x2b9cf05859e5]
> [cl1n022:06306] [ 5] /local/miniconda3/envs/maker-2.31.10/perl/lib/auto/Parallel/Application/MPI/../../../../../../lib/./libopen-pal.so.40(opal_libevent2022_event_base_loop+0x242)[0x2b9cf057a73a]
> [cl1n022:06306] [ 6] /local/miniconda3/envs/maker-2.31.10/perl/lib/auto/Parallel/Application/MPI/../../../../../../lib/./libopen-pal.so.40(+0x384de)[0x2b9cf05374de]
> [cl1n022:06306] [ 7] /lib64/libpthread.so.0(+0x7e25)[0x2b9ce50fae25]
> [cl1n022:06306] [ 8] /lib64/libc.so.6(clone+0x6d)[0x2b9ce5f67bad]
> [cl1n022:06306] *** End of error message ***
> SIGTERM received
> SIGTERM received
> 
> 
> As mentioned in older posts, I've tried adding the LD_PRELOAD variable, or running mpirun with the "-mca btl ^openib" option, but it didn't help.
> 
> As this happens with the Bioconda package, I guess it should be pretty reproducible on other setups.
> 
> Bioconda's Maker package uses version 5.26.2 of Perl and version 3.1.2 of OpenMPI, and the OpenMPI recipe is on https://github.com/conda-forge/openmpi-feedstock/tree/master/recipe <https://github.com/conda-forge/openmpi-feedstock/tree/master/recipe>
> Any help would be highly appreciated!
> 
> Anthony Bretaudeau
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20181005/4825acd8/attachment-0002.html>