I have successfully compiled raxmlHPC-MPI-SSE3 on our head node without issue. However, when I try to submit a raxml job to the queue I get some errors I do not understand. Below is the batch script I used:
# Walltime Limit: hh:nn:ss
#PBS -l walltime=48:00:00
# Node Specification:
#PBS -l ncpus=4 -l nodes=1
# Queue
#PBS -q long
# supress email notification
#PBS -m n
# Job Name:
#PBS -N RAxML_test
# Keep output
#PBS -k oe
echo ------------------------------------------------------
echo PBS: qsub is running on $PBS_O_HOST
echo PBS: originating queue is $PBS_O_QUEUE
echo PBS: executing queue is $PBS_QUEUE
echo PBS: working directory is $PBS_O_WORKDIR
echo PBS: execution mode is $PBS_ENVIRONMENT
echo PBS: job identifier is $PBS_JOBID
echo PBS: job name is $PBS_JOBNAME
echo PBS: node file is $PBS_NODEFILE
echo PBS: current home directory is $PBS_O_HOME
echo PBS: PATH = $PBS_O_PATH
echo ------------------------------------------------------
cd $PBS_O_WORKDIR
mpiexec -n 4 raxmlHPC-MPI-SSE3 -f d -m PROTGAMMALG -N 100 -o Escherichia_coli_str__K_12_substr__MG1655_chromosome_NC_000913 -s /home/mike/raxml_test/Concatenated_AA_alignment.phy -n /home/mike/raxml_test/Concatenated_AA_alignment -q /home/mike/raxml_test/AA_raxml_parts.txt
raxmlHPC-MPI-SSE3: axml.c:4188: analyzeRunId: Assertion `0' failed.
[node041:18522] *** Process received signal ***
[node041:18522] Signal: Aborted (6)
[node041:18522] Signal code: (-6)
raxmlHPC-MPI-SSE3: axml.c:4188: analyzeRunId: Assertion `0' failed.
[node041:18521] *** Process received signal ***
[node041:18521] Signal: Aborted (6)
[node041:18521] Signal code: (-6)
[node041:18521] [ 0] /lib64/libpthread.so.0 [0x35ad40eb10]
[node041:18521] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x35acc30265]
[node041:18521] [ 2] /lib64/libc.so.6(abort+0x110) [0x35acc31d10]
[node041:18521] [ 3] /lib64/libc.so.6(__assert_fail+0xf6) [0x35acc296e6]
[node041:18521] [ 4] raxmlHPC-MPI-SSE3(main+0x1852) [0x415dc2]
[node041:18521] [ 5] /lib64/libc.so.6(__libc_start_main+0xf4) [0x35acc1d994]
[node041:18521] [ 6] raxmlHPC-MPI-SSE3 [0x404339]
[node041:18521] *** End of error message ***
[node041:18522] [ 0] /lib64/libpthread.so.0 [0x35ad40eb10]
[node041:18522] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x35acc30265]
[node041:18522] [ 2] /lib64/libc.so.6(abort+0x110) [0x35acc31d10]
[node041:18522] [ 3] /lib64/libc.so.6(__assert_fail+0xf6) [0x35acc296e6]
[node041:18522] [ 4] raxmlHPC-MPI-SSE3(main+0x1852) [0x415dc2]
[node041:18522] [ 5] /lib64/libc.so.6(__libc_start_main+0xf4) [0x35acc1d994]
[node041:18522] [ 6] raxmlHPC-MPI-SSE3 [0x404339]
[node041:18522] *** End of error message ***
raxmlHPC-MPI-SSE3: axml.c:4188: analyzeRunId: Assertion `0' failed.
[node041:18524] *** Process received signal ***
[node041:18524] Signal: Aborted (6)
[node041:18524] Signal code: (-6)
[node041:18524] [ 0] /lib64/libpthread.so.0 [0x35ad40eb10]
[node041:18524] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x35acc30265]
[node041:18524] [ 2] /lib64/libc.so.6(abort+0x110) [0x35acc31d10]
[node041:18524] [ 3] /lib64/libc.so.6(__assert_fail+0xf6) [0x35acc296e6]
[node041:18524] [ 4] raxmlHPC-MPI-SSE3(main+0x1852) [0x415dc2]
[node041:18524] [ 5] /lib64/libc.so.6(__libc_start_main+0xf4) [0x35acc1d994]
[node041:18524] [ 6] raxmlHPC-MPI-SSE3 [0x404339]
[node041:18524] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 1 with PID 18522 on node node041 exited on signal 6 (Aborted).
--------------------------------------------------------------------------
raxmlHPC-MPI-SSE3: axml.c:4188: analyzeRunId: Assertion `0' failed.
[node041:18523] *** Process received signal ***
[node041:18523] Signal: Aborted (6)
[node041:18523] Signal code: (-6)
[node041:18523] [ 0] /lib64/libpthread.so.0 [0x35ad40eb10]
[node041:18523] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x35acc30265]
[node041:18523] [ 2] /lib64/libc.so.6(abort+0x110) [0x35acc31d10]
[node041:18523] [ 3] /lib64/libc.so.6(__assert_fail+0xf6) [0x35acc296e6]
[node041:18523] [ 4] raxmlHPC-MPI-SSE3(main+0x1852) [0x415dc2]
[node041:18523] [ 5] /lib64/libc.so.6(__libc_start_main+0xf4) [0x35acc1d994]
[node041:18523] [ 6] raxmlHPC-MPI-SSE3 [0x404339]
[node041:18523] *** End of error message ***
I am currently discussing this with our cluster admin, currently neither of us can determine what is causing the issue. I get the same error regardless if I use either the RAxML v7.2.8 or the github version. Any ideas on what the issue may be?
-Thanks for any help in advance.