[Denovoassembler-users] Ray Assembler Chunk Size Error Problem

Boisvert, Sebastien

2015-05-29 16:48:59 UTC

This is a bug in version 2.3.1.

Can you try a previous version ?

________________________________
From: Zain A Alvi [***@student.shu.edu]
Sent: Friday, May 08, 2015 7:21 AM
To: denovoassembler-***@lists.sourceforge.net
Subject: [Denovoassembler-users] Ray Assembler Chunk Size Error Problem

Dear Ray Developers and Fellow Users,

I am a graduate student at Seton Hall University and I have been trying to run Ray Assembler 2.3.1. I am trying to assemble 275 paired end Illumina reads that I have interleaved together. Previously I was successfully ran the interleaved files at the Kmer value 137. I compiled latest Ray version at Max Kmer size of 600 (technically 599).

That code was:

mpiexec -n 30 Ray -k 137 -i interleaved.fastq -o Ray_K137

Now if I try a smaller Kmer value, I am running into a weird error Chunk Size error.

I have tried:

mpiexec -n 10 Ray -k 51 -i interleaved.fastq -o Ray_K51_try3

and

mpiexec -n 30 Ray -k 51 -i interleaved.fastq -o Ray_K51_try3

All these have caused the same Chunk Size error. I even tried it without mpiexec enabled. I still was returned with the error below.

Rank 0 : VirtualCommunicator (service provided by VirtualCommunicator): 2957916 virtual messages generated 115295 real messages (3.89785%)
Rank 0 freed 549453824 bytes from the path memory pool (chunks: 131)
Rank 0: gossiping generated 0 messages (gossips: 0 ---> 0)
Critical exception: The length of the requested memory exceeds the CHUNK_SIZE: 36423920 > 33554432
Ray: RayPlatform/memory/MyAllocator.cpp:97: void* MyAllocator::allocate(int): Assertion `false' failed.
[BioLinux301:05209] *** Process received signal ***
[BioLinux301:05209] Signal: Aborted (6)
[BioLinux301:05209] Signal code: (-6)
[BioLinux301:05209] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f4a34d27340]
[BioLinux301:05209] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x39) [0x7f4a34987bb9]
[BioLinux301:05209] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x148) [0x7f4a3498afc8]
[BioLinux301:05209] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2fa76) [0x7f4a34980a76]
[BioLinux301:05209] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x2fb22) [0x7f4a34980b22]
[BioLinux301:05209] [ 5] Ray() [0x533b50]
[BioLinux301:05209] [ 6] Ray() [0x4f7552]
[BioLinux301:05209] [ 7] Ray() [0x551768]
[BioLinux301:05209] [ 8] Ray() [0x5550ab]
[BioLinux301:05209] [ 9] Ray() [0x5562ea]
[BioLinux301:05209] [10] Ray() [0x413379]
[BioLinux301:05209] [11] Ray() [0x40c5bf]
[BioLinux301:05209] [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f4a34972ec5]
[BioLinux301:05209] [13] Ray() [0x40e0cf]
[BioLinux301:05209] *** End of error message ***
zsh: abort Ray -k 51 -i interleaved.fastq -o Ray_K51_try3

I am running this on BioLinux 8 Workstation that 32 threads (16 cores) and specs are: Intel Xeon E5-2640v2 2 Ghz with 128 GB of RAM.

I would really appreciate on how proceed on how to rectify this error to occur again.

Sincerely,

Zaiin