Sebastien,
Okay, if I'm reading the output correctly, this should be the memory
allocation in KiB (is that bits or bytes? Or Kibibytes? I'm not sure) for
each rank (which should basically be each processor, right?). Reads
allocated to each rank were 32868106.
Rank-KiB
0-3008256
1-2074124
2-1926640
3-1926636
4-1926640
5-1926636
6-1074460
7-1926636
8-1926636
9-1926640
10-1910248
11-1074460
12-1926640
13-1926640
14-1926640
15-1926640
16-1074460
17-1926640
18-1926640
19-1910248
Rough estimate adds up to around 40GB, right?
Cheers,
Nate
On Mon, Sep 23, 2013 at 9:36 AM, Sébastien Boisvert <
sebastien.boisver...@ulaval.ca> wrote:
> On 22/09/13 10:13 PM, Nathaniel Jue wrote:
>
>> Hi Sebastien,
>>
>> By job.log, I assume you mean the stout. I tried grepping "BloomFilter"
>> in both that output and all the files created in the output directory. The
>> only instances of the term BloomFilter occurred in the test error example I
>> sent you earlier, which occurs right after loading all the reads. Do you
>> think this is a too many reads issue or something else? If so, any
>> suggestions on how to deal with that?
>>
>
> (Please use the list.)
>
> I would be informative to get the number of bits that the Bloom filter is
> trying to allocate
> -- this is the information that can be found in the standard output.
>
>
>> Regards,
>> Nate
>>
>>
>> On Sep 20, 2013 5:19 PM, "Sébastien Boisvert" <
>> sebastien.boisver...@ulaval.ca <mailto:sebastien.boisver...@ulaval.ca>>
>> wrote:
>>
>> On 20/09/13 05:06 PM, Nathaniel Jue wrote:
>>
>> 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
>>
>>
>> So you are getting this with the git version of Ray. Strange.
>>
>> ...
>>
>> ------------------------------__------------------------------__--------------
>>
>> 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]
>>
>>
>> You don't need to patch the code since the git repository includes
>> these
>> patches already.
>>
>> These patches are to be applied on Ray 2.2.0.
>>
>> 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?
>>
>>
>>
>> The number of bytes for the Bloom filter depends on the number of
>> reads, mostly.
>> I think it is a bug in Ray that occurs when you have too many reads
>> and not enough ranks.
>>
>> Can you search for BloomFilter in your log ?
>>
>> You can do that with this command:
>>
>> grep BloomFilter job.log
>>
>>
>>
>> Regards,
>> Nate
>>
>>
>>
>
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