Hi,
I've run into a bit of an issue with Ray (v2.3.0-devel) and was wondering
if you might be able to give me some advice/help. I keep on getting this
error message when I try to run Ray with all of my data with the following
command (the ellipse represents the first two lines of the error being
repeat 29 more time for each processor or all 30 processors in total).
There is quite a bit data in the analysis (2 runs of MiSeq data and 2 lanes
of HiSeq):
>mpiexec -n 20 Ray -k 31 -p
/data2/reads/illumina/limulus/GRL1397_S1_L001.left.rept.corr.fasta
/data2/reads/illumina/limulus/GRL1397_S1_L001.right.rept.corr.fasta -p
/data2/reads/illumina/limulus/GRL1402_errorCorrect/GRL1402.left.2.rept.corr.fasta
/data2/reads/illumina/limulus/GRL1402_errorCorrect/GRL1402.right.rept.corr.fasta
-s /data2/reads/illumina/limulus/GRL1397_S1_L001.up.rept.corr.fasta -s
/data2/reads/illumina/limulus/GRL1402_errorCorrect/GRL1402.up.rept.corr.fasta
-p
/data2/reads/illumina/limulus/8871_CGATGT_L003_errorCorrect/8871_CGATGT_L003.left.2.rept.corr.fasta
/data2/reads/illumina/limulus/8871_CGATGT_L003_errorCorrect/8871_CGATGT_L003.right.rept.corr.fasta
-p
/data2/reads/illumina/limulus/8871_CGATGT_L004_errorCorrect/8871_CGATGT_L004.left.2.rept.corr.fasta
/data2/reads/illumina/limulus/8871_CGATGT_L004_errorCorrect/8871_CGATGT_L004.right.rept.corr.fasta
-s
/data2/reads/illumina/limulus/8871_CGATGT_L003_errorCorrect/8871_CGATGT_L003.up.rept.corr.fasta
-s
/data2/reads/illumina/limulus/8871_CGATGT_L004_errorCorrect/8871_CGATGT_L004.up.rept.corr.fasta
-o limulus_ray_IlluminaOnly
Subsequent error message:
Critical exception: The system is out of memory, returned NULL.
Requested -109661072 bytes of type RAY_MALLOC_TYPE_BLOOM_FILTER
...
--------------------------------------------------------------------------
mpiexec has exited due to process rank 8 with PID 22018 on
node redqueen exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
--------------------------------------------------------------------------
I did look in the Ray mailing list, installed the development version of
the program and Ray Platform and found discussion on a patch which I tried
to apply to program. When I did that, I get this:
patching file code/VerticesExtractor/VerticesExtractor.cpp
patching file code/VerticesExtractor/VerticesExtractor.h
Reversed (or previously applied) patch detected! Assume -R? [n]
which I have to respond "y" to in order to patch the program. Even after
patching, though, the program still gives me these error. I will also add
that when I tried an assembly with just the MiSeq data, the program was
able to finish the assembly with the same 20 processors indicates.
I am using our supercomputer to do this assembly with consists of 48
Intel(R) Xeon(R) X7542 CPUs @ 2.67GHz (I think each as 6 cores, if I
remember right; I'm not the hardware guy so not sure about that) with
something like 500GB of RAM (again, I think).
Do you have any thoughts or insight into what might be going on? Mpi or ray
issue?
Regards,
Nate
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