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sebhtml / ray

Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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likely a bug when 0 nucleotides are generated in contigs #85

Closed sebhtml closed 12 years ago

sebhtml commented 12 years ago

likely a bug when 0 nucleotides are generated in contigs

(it pauses after scaffolding)

sebhtml commented 12 years ago

seems to be a problem with 1024 cores:

Rank 0 computing contig abundances [4573/4575] [82/82] Rank 0 computing contig abundances [4574/4575] [1/84] Rank 0 computing contig abundances [4574/4575] [84/84] Rank 0 computing contig abundances [4575/4575] [1/82] Rank 0 computing contig abundances [4575/4575] [82/82] [IO] Input/output operations for coverage XML objects: 1 / bufferSize: 16777216 bytes

sebhtml commented 12 years ago

For Jay Flatley sample with 512:

these folks are not doing anything and therefore never send their control message to their master...

[boisver1@ip03 JayFlatley]$ tail -n1 Jay-genome-2012-09-27-512-degree-21.1.1.*|grep -v Jay|grep -v XML|grep Rank Rank 75: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 103: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 229: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 251: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 255: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 295: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 315: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 319: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 365: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 380: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 383: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 419: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 487: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 507: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES Rank 511: starting SlaveMode= call_RAY_SLAVE_MODE_CONTIG_BIOLOGICAL_ABUNDANCES

sebhtml commented 12 years ago

This was a race condition fixed in d8a8d737481d657ad8979e025eecacb9f400f3b1