Hi All,
I am hoping to get some help troubleshooting a problem. I am using Ray-1.6.0 on
one of the TeraGrid resources, and having problems with a memory issue. I can
run Ray successfully with k=31, but not with K=41 or k=51 (I am trying k=21
right now).. When I try, I get "Critical exception: The system is out of
memory, returned NULL." usually during the "computing vertices" steps, I am
assembling a genome of size ~1Gb and have 384Gb of Illumina reads in 16
libraries.
I have tried running with more cores (as many as 512) to distribute memory
requirements over more cores and with less "wayness", which basically allocates
more RAM per process... When I look at RAM usage, it does not look like I max
out-- the most I have seen is ~9Gb, out of ~30Gb available per node.
Can you please help me troubleshoot this issue?
Command:
/work/01301/mmacmane/Ray-1.6.0/build/Ray -k 41 \
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/091223HHMI_Tg_hfs1_36PE_270_s_7_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/091223HHMI_Tg_hfs2_36PE_317_s_8_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/100503GA1_Tg_PJC1_76PE_334bp_s_3_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/100503GA1_Tg_PJC1_76PE_334bp_s_4_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/100503GA1_Tg_PJC1_76PE_334bp_s_5_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/100527GA2_Tg_PJC2_101PE_384bp_s_1_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/100527GA2_Tg_PJC2_101PE_384bp_s_2_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/100819GA2_Tg_PJC1_76PE_334bp_s_6_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/100820GA3_Tg_PJC2_101PE_384bp_s_3_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/110324HS1A_Tg_PJC09_100PE_455bp_s_7_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/110324HS1A_Tg_PJC10_100PE_526bp_s_8_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/110331HS2A_Tg_PJC11_100PE_923bp_s_5_12_sequence.fq.trimmed.fastq
\
-i
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/110331HS2A_Tg_PJC12_100PE_1213bp_s_6_12_sequence.fq.trimmed.fastq
\
-s
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/100506GA2_Tg_PJC2_101PE_384bp_s_8_sequence.fq.fastq
\
-s
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/110316HS3B_Tg_PJC11_100PE_923bp_s_5_sequence.fq.fastq
\
-s
/scratch/01301/mmacmane/spider_genome/clean.reads/ray.reads/110316HS3B_Tg_PJC12_100PE_1213bp_s_6_sequence.fq.fastq
\
-show-memory-usage -o /scratch/01301/mmacmane/spider.runs/Rayk41/k41
Thanks, Matt
____________________________________________
Matthew MacManes, Ph.D.
University of California- Berkeley
Museum of Vertebrate Zoology
Phone: 510-495-5833
Lab Website: http://ib.berkeley.edu/labs/lacey
Personal Website: http://macmanes.com/
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