I am trying to run Ray for a while now on our Illumina data. It is run in
parallel mode and memory is not a constraint now because we have a cluster
with 16 X 16 GB memory in each node.
my Command:
mpiexec -n 64 Ray \
-k \
31 \
-disable-recycling \
-p \
/scratch/sucheta/tmp1.fastq \
/scratch/sucheta/tmp2.fastq \
-p \
/scratch/sucheta/lane1_1b.fq \
/scratch/sucheta/lane1_2b.fq \
-o \
rayTest
Content of NumberOfSequences.txt
Files: 4
FileNumber: 0
FilePath: /scratch/sucheta/tmp1.fastq
NumberOfSequences: 73013670
FirstSequence: 0
LastSequence: 73013669
FileNumber: 1
FilePath: /scratch/sucheta/tmp2.fastq
NumberOfSequences: 72339350
FirstSequence: 73013670
LastSequence: 145353019
FileNumber: 2
FilePath: /scratch/sucheta/lane1_1b.fq
NumberOfSequences: 0
FileNumber: 3
FilePath: /scratch/sucheta/lane1_2b.fq
NumberOfSequences: 0
Summary
NumberOfSequences: 145353020
FirstSequence: 0
LastSequence: 145353019
However, after running for a while Ray terminates: This is the last few
lines of STDOUT:
---
Speed RAY_SLAVE_MODE_EXTENSION 1183 units/second
Rank 9: assembler memory usage: 850432 KiB
Rank 9 is changing direction.
Rank 12: assembler memory usage: 826944 KiB
Rank 12 starts on seed 1200, length is 477, flow 0 [1200/6451]
Rank 12 starts on seed 1201, length is 476, flow 0 [1201/6451]
Rank 10 traversed 1273646 nucleotide symbols
Rank 10: assembler memory usage: 869460 KiB
Rank 10 starts on seed 534, length is 906, flow 0 [534/6579]
Rank 31 reached 2270 vertices from seed 491, flow 1
Speed RAY_SLAVE_MODE_EXTENSION 1174 units/second
Rank 31: assembler memory usage: 866768 KiB
Rank 31 is changing direction.
Rank 2 traversed 1910058 nucleotide symbols
Rank 2 reached 1269 vertices from seed 1007, flow 2
Speed RAY_SLAVE_MODE_EXTENSION 1435 units/second
Rank 2: assembler memory usage: 843432 KiB
Rank 2 (extension done) NumberOfFlows: 2
Rank 2 FlowedVertices: 0 576 1 1269 2 1269
Rank 2: assembler memory usage: 839332 KiB
Rank 2 starts on seed 1008, length is 576, flow 0 [1008/6537]
Terminated
---
It creates the following output files before crashing:
CoverageDistributionAnalysis.txt NumberOfSequences.txt
CoverageDistribution.txt ParallelPaths.txt
degreeDistribution.txt Plugins
ElapsedTime.txt RayCommand.txt
FilePartition.txt RayPlatform_Version.txt
GraphPartition.txt RayVersion.txt
LibraryData.xml Scheduling
LibraryStatistics.txt SeedLengthDistribution.txt
NetworkTest.txt SequencePartition.txt
Any help in this regard will be much appreciated!
--
Sucheta Tripathy, Ph.D
Scientist, Ramalingaswamy Fellow,
Indian Institute of Chemical Biology,
Kolkata, India.
https://sites.google.com/site/suchetalab/
https://twitter.com/tsucheta
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