Which MPI library are you using ?
On 02/22/2013 07:34 AM, James Vincent wrote: > Here are the last 50 lines : > > -bash-4.1$ tail -50 out.run > > OPERATION_incrementReferences operations: 32762 > OPERATION_decrementReferences operations: 32386 > > OPERATION_purgeVirtualColor operations: 1567 > ********************************************************** > > Rank 25: assembler memory usage: 138560 KiB > Rank 31 biological abundances 3210 [1/1] [1752/2254] [4/7] > Rank 31 RAY_SLAVE_MODE_ADD_COLORS processed files: 43/56 > Rank 31 RAY_SLAVE_MODE_ADD_COLORS processed sequences in file: 3/7 > Rank 31 RAY_SLAVE_MODE_ADD_COLORS total processed sequences: 81/107 > Rank 31 RAY_SLAVE_MODE_ADD_COLORS processed k-mers for current > sequence: 2341425/0 > Rank 31 RAY_SLAVE_MODE_ADD_COLORS total processed k-mers: 149500000 > Speed RAY_SLAVE_MODE_ADD_COLORS 20803 units/second > > ********************************************************** > Coloring summary > Number of virtual colors: 232 > Number of real colors: 3444 > > Keys in index: 230 > Observed collisions when populating the index: 0 > COLOR_NAMESPACE_MULTIPLIER= 10000000000000000 > > Operations > > OPERATION_getVirtualColorFrom operations: 35380 > > OPERATION_IN_PLACE_ONE_REFERENCE: 31951 > OPERATION_NO_VIRTUAL_COLOR_HAS_HASH_CREATION operations: 1730 > OPERATION_VIRTUAL_COLOR_HAS_COLORS_FETCH operations: 1506 > OPERATION_NO_VIRTUAL_COLOR_HAS_COLORS_CREATION operations: 193 > > OPERATION_createVirtualColorFrom operations: 1923 > > OPERATION_allocateVirtualColorHandle operations: 1923 > OPERATION_NEW_FROM_EMPTY operations: 1692 > OPERATION_NEW_FROM_SCRATCH operations: 231 > > OPERATION_applyHashOperation operations: 37303 > OPERATION_getHash operations: 0 > > OPERATION_incrementReferences operations: 35380 > OPERATION_decrementReferences operations: 34985 > > OPERATION_purgeVirtualColor operations: 1693 > ********************************************************** > > Rank 31: assembler memory usage: 139452 KiB > > On Fri, Feb 22, 2013 at 7:13 AM, Sébastien Boisvert > <[email protected]> wrote: >> What's the last thing reported in stdout ? >> >> On 02/22/2013 06:23 AM, jjv5 wrote: >>> Hello, >>> >>> I am running ray meta on a shared memory machine with 40 cores and 1TB >>> memory. One very small job with 25K reads finished and gave various >>> taxonomic outputs. Jobs with slightly >>> more input seem to never finish. The output log just stops but there >>> are no errors indicated. Where might one start to look to determine >>> where a job has gone wrong? >>> >>> The command I use is below. There are 100,000 paired reads. >>> >>> mpiexec -n 40 $RAY -o $OUTDIR -p $LEFT $RIGHT -k 31 \ >>> -search $NCBIDIR/NCBI-Finished-Bacterial-Genomes \ >>> -with-taxonomy $NCBIDIR/Genome-to-Taxon.tsv >>> $NCBIDIR/TreeOfLife-Edges.tsv $NCBIDIR/Taxon-Names.tsv >>> >>> ------------------------------------------------------------------------------ >>> Everyone hates slow websites. So do we. >>> Make your web apps faster with AppDynamics >>> Download AppDynamics Lite for free today: >>> http://p.sf.net/sfu/appdyn_d2d_feb >>> _______________________________________________ >>> Denovoassembler-users mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users >>> >> >> >> ------------------------------------------------------------------------------ >> Everyone hates slow websites. So do we. >> Make your web apps faster with AppDynamics >> Download AppDynamics Lite for free today: >> http://p.sf.net/sfu/appdyn_d2d_feb >> _______________________________________________ >> Denovoassembler-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
