Hello,
I am recently using Ray meta for metagenome assembly. And I used different
kmer-size (from 31 to 81), it worked always fine, but this time it crashed in
halfway, and its not because run out the memory. The error message I got is
like this:
[m119:26639] *** Process received signal ***
[m119:26639] Signal: Segmentation fault (11)
[m119:26639] Signal code: Address not mapped (1)
[m119:26639] Failing at address: 0x88
[m119:26639] [ 0] /lib64/libpthread.so.0(+0xf710)[0x2abfc26ed710]
[m119:26639] [ 1]
/opt/openmpi/1.7.5gcc4.4/lib/openmpi/mca_oob_tcp.so(+0xbd48)[0x2abfc4c37d48]
[m119:26639] [ 2]
/opt/openmpi/1.7.5gcc4.4/lib/openmpi/mca_oob_tcp.so(mca_oob_tcp_peer_recv_connect_ack+0x87)[0x2abfc4c37fb7]
[m119:26639] [ 3]
/opt/openmpi/1.7.5gcc4.4/lib/openmpi/mca_oob_tcp.so(+0x7c20)[0x2abfc4c33c20]
[m119:26639] [ 4]
/opt/openmpi/1.7.5gcc4.4/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0x8bc)[0x2abfc2f709dc]
[m119:26639] [ 5]
/opt/openmpi/1.7.5gcc4.4/lib/libopen-rte.so.7(+0x38b1e)[0x2abfc2cc8b1e]
[m119:26639] [ 6] /lib64/libpthread.so.0(+0x79d1)[0x2abfc26e59d1]
[m119:26639] [ 7] /lib64/libc.so.6(clone+0x6d)[0x2abfc29e49dd]
[m119:26639] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 1 with PID 26639 on node m119 exited on
signal 11 (Segmentation fault).
--------------------------------------------------------------------------
slurmstepd: _slurm_cgroup_destroy: problem deleting step cgroup path
/cgroup/freezer/slurm/uid_44133/job_4258126/step_batch: Device or resource busy
The following command is what I used. Does anyone have any idea why it crashed?
for k in `seq 31 10 81`; do
mpiexec -n 32 Ray -k $k -p qtrim1.fastq qtrim2.fastq -o out_$k
I also have another problem using the above command. When I was running Ray, I
got weird log file sometimes, like below. Those lines start with Rank are not
supposed to appear there, because normally the log file should start from Ray
LICENSE part. I checked everything, but this did not happen to all samples or
all kmer size, only happen to one or two kmer size. I am really wondering why
it happened, and I am a bit worried about the results, I cannot be certain if
it was misassembled. Do you think its something to do with my command? Thanks
in advance!
Rank 1: assembler memory usage: 34460 KiB
Rank 2: assembler memory usage: 34464 KiB
Rank 4: assembler memory usage: 34460 KiB
Rank 5: assembler memory usage: 34464 KiB
Rank 6: assembler memory usage: 34388 KiB
Rank 7: assembler memory usage: 34388 KiB
Rank 9: assembler memory usage: 34388 KiB
Rank 10: assembler memory usage: 34388 KiB
Rank 11: assembler memory usage: 34460 KiB
Rank 12: assembler memory usage: 34388 KiB
Rank 13: assembler memory usage: 34388 KiB
Rank 15: assembler memory usage: 34460 KiB
Rank 3: assembler memory usage: 34464 KiB
**************************************************
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it
under certain conditions; see "LICENSE.txt" for details.
**************************************************
Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert
Centre de recherche en infectiologie de l'Université Laval
Project funded by the Canadian Institutes of Health Research (Doctoral award
200902CGM-2
Best
Xiaofen
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