<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">I tried setting this up but there are a number of issues I run into.<div class=""><br class=""></div><div class="">First RepeatMasker is not being installed correctly. The configuration step should create these files (created by ./configure script during RepeatMasker setup) —></div><div class=""><div class="">RepeatMasker.lib</div><div class="">RepeatMasker.lib.nhr</div><div class="">RepeatMasker.lib.nin</div><div class="">RepeatMasker.lib.nsq</div><div class="">RepeatMaskerLib.embl</div></div><div class=""><br class=""></div><div class="">But they do not exist in the share directory.</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Another work around is don’t use OpenMPI. Try MPICH3.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 25, 2018, at 6:10 AM, Anthony Bretaudeau <<a href="mailto:anthony.bretaudeau@inria.fr" class="">anthony.bretaudeau@inria.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="content-type" content="text/html; charset=UTF-8" class="">
<div bgcolor="#FFFFFF" text="#000000" class=""><p class="">Hi,</p><p class="">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 class="">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 class=""><br class="">
</p><p class="">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 class="">As this happens with the Bioconda package, I guess it should be
pretty reproducible on other setups.</p><p class="">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 class="">Any help would be highly appreciated!</p><p class="">Anthony Bretaudeau<br class="">
</p>
</div>
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