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Hi all,<br>
<br>
I am no expert for MPI so maybe this is something very trivial or
maybe not caused by MAKER at all but I'd be glad to have your
thoughts on this. I installed MAKER 2.31.8 with MPI support (openMPI
1.8.1) on our cluster. <br>
<br>
I ran maker with the options attached and the command in bsub_maker,
and I _think_ it worked fine. Here is the last output of maker:<br>
<br>
<blockquote><small>running exonerate search.<br>
#--------- command -------------#<br>
Widget::exonerate::protein2genome:<br>
/gpfs/fs1/cluster/Apps/bioinf/maker/2.31.8/exe/exonerate/bin/exonerate
-q /project/molgen/workbench_Florian/riparius_MAKER_v2/tmp_fil<br>
es/maker_yZhQlA/49/sp%7CQ4JHE0%7CXB36_ORYSJ.for.114901-115619.49.fasta
-t /project/molgen/workbench_Florian/riparius_MAKER_v2/tmp_fil<br>
es/maker_yZhQlA/49/scaffold299_size115619.114901-115619.49.fasta
-Q protein -T dna -m protein2genome --softmasktarget --percent
20 -<br>
-showcigar >
/project/molgen/workbench_Florian/riparius_MAKER_v2/tmp_files/maker_yZhQlA/49/scaffold299_size115619.114901-115619.sp%7<br>
CQ4JHE0%7CXB36_ORYSJ.p.exonerate<br>
#-------------------------------#<br>
cleaning blastx...<br>
in cluster::shadow_cluster...<br>
...finished clustering.<br>
in cluster::shadow_cluster...<br>
...finished clustering.<br>
cleaning clusters....<br>
total clusters:37 now processing 0<br>
...processing 0 of 11<br>
...processing 1 of 11<br>
...processing 2 of 11<br>
...processing 3 of 11<br>
...<br>
...processing 174 of 177<br>
...processing 175 of 177<br>
...processing 176 of 177<br>
flattening protein clusters<br>
prepare section files<br>
<br>
Maker is now finished!!!<br>
<br>
Start_time: 1454700985<br>
End_time: 1455023070<br>
Elapsed: 322085</small><br>
</blockquote>
<br>
but my cluster job didnt finish here, instead I got the following
errors until my runtime limit of 5 days was reached:<br>
<br>
<blockquote><small>Argument "ALRM" isn't numeric in exit at
/home/fdolze/perl5/lib/perl5/x86_64-linux-thread-multi/forks.pm
line 2184.</small><br>
<small>SIGTERM received</small><br>
<small>Argument "ALRM" isn't numeric in exit at
/home/fdolze/perl5/lib/perl5/x86_64-linux-thread-multi/forks.pm
line 2184.</small><br>
<small>SIGTERM received</small><br>
<small>Perl exited with active threads:</small><br>
<small> 1 running and unjoined</small><br>
<small> 0 finished and unjoined</small><br>
<small> 0 running and detached</small><br>
<small>SIGTERM received</small><br>
<small>Perl exited with active threads:</small><br>
<small> 1 running and unjoined</small><br>
<small> 0 finished and unjoined</small><br>
<small> 0 running and detached</small><br>
<small>SIGTERM received</small><br>
<small>Perl exited with active threads:</small><br>
<small> 1 running and unjoined</small><br>
<small> 0 finished and unjoined</small><br>
<small> 0 running and detached</small><br>
<small>SIGTERM received</small><br>
<small>SIGTERM received</small><br>
<small>Perl exited with active threads:</small><br>
<small> 1 running and unjoined</small><br>
<small> 0 finished and unjoined</small><br>
<small> 0 running and detached</small><br>
<small>SIGTERM received</small><br>
<small>Perl exited with active threads:</small><br>
<small> 1 running and unjoined</small><br>
<small> 0 finished and unjoined</small><br>
<small> 0 running and detached</small><br>
<small>SIGTERM received</small><br>
<small>Perl exited with active threads:</small><br>
<small> 1 running and unjoined</small><br>
<small> 0 finished and unjoined</small><br>
<small> 0 running and detached</small><br>
<small>Argument "ALRM" isn't numeric in exit at
/home/fdolze/perl5/lib/perl5/x86_64-linux-thread-multi/forks.pm
line 2184.</small><br>
<small>SIGTERM received</small><br>
<small>SIGTERM received</small><br>
<small>Perl exited with active threads:</small><br>
<small> 1 running and unjoined</small><br>
<small> 0 finished and unjoined</small><br>
<small> 0 running and detached</small><br>
<small>Argument "ALRM" isn't numeric in exit at
/home/fdolze/perl5/lib/perl5/x86_64-linux-thread-multi/forks.pm
line 2184.</small><br>
<small>Argument "ALRM" isn't numeric in exit at
/home/fdolze/perl5/lib/perl5/x86_64-linux-thread-multi/forks.pm
line 2184.</small><br>
<small>SIGTERM received</small><br>
<small>SIGTERM received</small><br>
<small>SIGTERM received</small><br>
<small>SIGTERM received</small><br>
<small>Perl exited with active threads:</small><br>
<small> 1 running and unjoined</small><br>
<small> 0 finished and unjoined</small><br>
<small> 0 running and detached</small><br>
<small>SIGTERM received<br>
</small><small>SIGTERM received</small><br>
<small>Perl exited with active threads:</small><br>
<small> 1 running and unjoined</small><br>
<small> 0 finished and unjoined</small><br>
<small> 0 running and detached</small><br>
<small>Argument "ALRM" isn't numeric in exit at
/home/fdolze/perl5/lib/perl5/x86_64-linux-thread-multi/forks.pm
line 2184.</small><br>
<small>[a0238:09542] *** Process received signal ***</small><br>
<small>[a0238:09542] Signal: Segmentation fault (11)</small><br>
<small>[a0238:09542] Signal code: Address not mapped (1)</small><br>
<small>[a0238:09542] Failing at address: 0xa80</small><br>
<small>[a0238:09542] [ 0]
/lib64/libpthread.so.0(+0xf710)[0x2ba955727710]</small><br>
<small>[a0238:09542] [ 1]
/usr/lib64/perl5/CORE/libperl.so(Perl_csighandler+0x22)[0x2ba954715002]</small><br>
<small>[a0238:09542] [ 2]
/lib64/libpthread.so.0(+0xf710)[0x2ba955727710]</small><br>
<small>[a0238:09542] [ 3]
/lib64/libc.so.6(__poll+0x53)[0x2ba955a170d3]</small><br>
<small>[a0238:09542] [ 4]
/cluster/mpi/gcc_4.4.7/OpenMPI-1.8.1/lib/libopen-pal.so.6(+0x6cfca)[0x2ba955fb4fca]</small><br>
<small>[a0238:09542] [ 5]
/cluster/mpi/gcc_4.4.7/OpenMPI-1.8.1/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0x221)[0x2ba955fabf11]</small><br>
<small>[a0238:09542] [ 6]
/cluster/mpi/gcc_4.4.7/OpenMPI-1.8.1/lib/libopen-rte.so.7(+0x376ae)[0x2ba955d076ae]</small><br>
<small>[a0238:09542] [ 7]
/lib64/libpthread.so.0(+0x79d1)[0x2ba95571f9d1]</small><br>
<small>[a0238:09542] [ 8]
/lib64/libc.so.6(clone+0x6d)[0x2ba955a208fd]</small><br>
<small>[a0238:09542] *** End of error message ***</small><br>
<small>Argument "ALRM" isn't numeric in exit at
/home/fdolze/perl5/lib/perl5/x86_64-linux-thread-multi/forks.pm
line 2184.</small><br>
<small>SIGTERM received</small><br>
<small>SIGTERM received<br>
...<br>
</small></blockquote>
<br>
maybe someone experienced something similar before or can give me
some hint if this is caused by my setup or by maker.<br>
<br>
<br>
kind regards,<br>
Florian Dolze<br>
<br>
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