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<p>Hi,</p>
<p>I've worked on the Bioconda recipe for Maker
(<a class="moz-txt-link-freetext"
href="https://github.com/bioconda/bioconda-recipes/tree/master/recipes/maker/"
moz-do-not-send="true">https://github.com/bioconda/bioconda-recipes/tree/master/recipes/maker/</a>).
It works well, except when using it in MPI mode. I get this
segfault error:</p>
<pre>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
</pre>
<p><br>
</p>
<p>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.</p>
<p>As this happens with the Bioconda package, I guess it should be
pretty reproducible on other setups.</p>
<p>Bioconda's Maker package uses version 5.26.2 of Perl and version
3.1.2 of OpenMPI, and the OpenMPI recipe is on <a
class="moz-txt-link-freetext"
href="https://github.com/conda-forge/openmpi-feedstock/tree/master/recipe"
moz-do-not-send="true">https://github.com/conda-forge/openmpi-feedstock/tree/master/recipe</a></p>
<p>Any help would be highly appreciated!</p>
<p>Anthony Bretaudeau<br>
</p>
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