Hello,
I recently started using Ray in an attempt to assemble a metatranscriptome.
I have tried multiple assemblies and repeatedly get a segmentation fault.
The fault happens after contigs are written and the AMOS file is
generated, however I don't think Ray gets to the scaffolding stage or any
downstream plugins (gene ontology, etc...). Below is my RayCommand.txt
file and the last few lines of stdout showing the segfault.
RayCommand.txt
###################################
mpiexec -n 25 Ray \ # This was also run with "--mca btl
^sm" and the same segfault
-p \
TAH-19.1_rejected_reads.fastq \
TAH-19.2_rejected_reads.fastq \
-p \
TAH-20.1_rejected_reads.fastq \
TAH-20.2_rejected_reads.fastq \
-p \
TAH-21.1_rejected_reads.fastq \
TAH-21.2_rejected_reads.fastq \
-p \
TAH-22.1_rejected_reads.fastq \
TAH-22.2_rejected_reads.fastq \
-p \
TAH-23.1_rejected_reads.fastq \
TAH-23.2_rejected_reads.fastq \
-p \
TAH-24.1_rejected_reads.fastq \
TAH-24.2_rejected_reads.fastq \
-o \
ray_assembly_new \
-show-memory-usage \
-write-contig-paths \
-amos \
-search \
/dbase/Ray/EMBL_CDS_Sequences \
-gene-ontology \
/dbase/Ray/OntologyTerms.txt \
/dbase/Ray/Annotations.txt
###################################
STDOUT
####################################
Rank 0 objectName: 20 => peakCoverage: 125 blockSize: 1305
Rank 0 objectName: 0 => peakCoverage: 192 blockSize: 1538
Rank 0 objectName: 12 => peakCoverage: 37 blockSize: 1486
Rank 0 objectName: 19 => peakCoverage: 107 blockSize: 1490
Rank 0 objectName: 16 => peakCoverage: 82 blockSize: 1880
[metatron:01941] *** Process received signal ***
[metatron:01941] Signal: Segmentation fault (11)
[metatron:01941] Signal code: Address not mapped (1)
[metatron:01941] Failing at address: 0xb0c68
[metatron:01941] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)
[0x7f8cd6851cb0]
[metatron:01941] [ 1] Ray(_ZNK4Read6lengthEv+0) [0x549160]
[metatron:01941] [ 2]
Ray(_ZN16MessageProcessor33call_RAY_MPI_TAG_GET_READ_MARKERSEP7Message+0x88)
[0x4b8208]
[metatron:01941] [ 3] Ray(_ZN11ComputeCore10runVanillaEv+0xb4) [0x5867c4]
[metatron:01941] [ 4] Ray(_ZN11ComputeCore3runEv+0x89) [0x58c019]
[metatron:01941] [ 5] Ray(_ZN7Machine5startEv+0x1876) [0x46d056]
[metatron:01941] [ 6] Ray(_ZN11RankProcessI7MachineE3runEv+0x9f) [0x46a6df]
[metatron:01941] [ 7] Ray(main+0xc7) [0x465477]
[metatron:01941] [ 8]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed) [0x7f8cd64a476d]
[metatron:01941] [ 9] Ray() [0x466a81]
[metatron:01941] *** End of error message ***
[metatron][[32923,1],0][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],4][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],8][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],9][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],12][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],14][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],23][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],2][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],21][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],1][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],3][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],5][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],6][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],7][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],10][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],11][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],13][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],15][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],17][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],18][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],19][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],20][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
[metatron][[32923,1],22][../../../../../../ompi/mca/btl/tcp/btl_tcp_frag.c:216:mca_btl_tcp_frag_recv]
mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
--------------------------------------------------------------------------
mpiexec noticed that process rank 24 with PID 1941 on node metatron exited
on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
####################################################
Any help?
Thanks,
-Cedar
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