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
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