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Old 04-26-2013, 03:22 AM   #1
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Location: Bangalore

Join Date: Apr 2013
Posts: 3
Default Ray : Segmentation fault (11)


I am trying to run Ray to do hybrid assembly of Illumina (paired end data) and Roche 454 data. I am running the program on server with 64 cores and 512GB RAM

I ran the sample data in Ray; which is working fine.
When I give my data, the program is producing Contigs.fasta output but, giving error before scaffolding.

I ran the following command
$ mpiexec -n 20 ray-build/Ray -k 31 -p mp_R1_trimmed_q20_p100_clipped.fastq mp_R2_trimmed_q20_p100_clipped.fastq -s 454.fastq -o kmer_31_out

After contig buildng program gave the following fault while scaffolding

*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x15b710
[ 0] /lib64/ [0x3dbd00f500]
[ 1] ray-build/Ray(_ZNK4Read6lengthEv+0) [0x50a9b0]
[ 2] ray-build/Ray(_ZN16MessageProcessor33call_RAY_MPI_TAG_GET_READ_MARKERSEP7Message+0x9f) [0x49c09f]
[ 3] ray-build/Ray(_ZN11ComputeCore10runVanillaEv+0x61) [0x532351]
[ 4] ray-build/Ray(_ZN11ComputeCore3runEv+0x6e) [0x53379e]
[ 5] ray-build/Ray(_ZN7Machine5startEv+0x1697) [0x4487a7]
[ 6] ray-build/Ray(main+0x3a) [0x443bba]
[ 7] /lib64/ [0x3dbc41ecdd]
[ 8] ray-build/Ray() [0x443a89]
*** End of error message ***
mpiexec noticed that process rank 19 with PID 21982 on node pragnya exited on signal 11 (Segmentation fault).

I tried to run the program with different number of ranks and kmers. But still stoping at scaffolding stage.

Can anyone please help
Nagesh is offline   Reply With Quote
Old 07-04-2013, 08:27 PM   #2
Location: BC

Join Date: Aug 2010
Posts: 18
Default Ray:segmentation fault (11)

So, a question as
I am having the same problem.
I think its an open mpi error.
Run Top - do you see if all 20 cores are running Ray?

In my case, only one is running causing the error.

Double check and get back to me?

raw937 is offline   Reply With Quote
Old 07-04-2013, 09:20 PM   #3
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Location: Bangalore

Join Date: Apr 2013
Posts: 3
Default RE : Ray : Segmentation fault (11)


As you suggested, it is an open mpi fault. But when I run the program I see 20 cores being used for initial period of about 1 hour. The program stops after the contig building. The contigs are not scaffolded because of this error
Nagesh is offline   Reply With Quote
Old 02-02-2017, 05:22 AM   #4
Location: Poland

Join Date: Apr 2012
Posts: 13

I have the same problem. Has anyone managed to solve it?

Interesting fact is that I have managed to finish many samples with the same machine, mpi, settings, comparable complexity and size... This one refuses to cooperate.

dorix is offline   Reply With Quote

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