On 06/01/14 05:48 PM, Emily Tung wrote: > Sébastien - > Used m2.4xlarge for metagenomic library assembly. This error showed up. Can > you take a look? In the meantime, I'm running again with cr1.8xlarge.
Maybe you ran out of memory since you are running on one node. > > Emily > > > ... > > Rank 4: assembler memory usage: 8438828 KiB > Rank 6 has 264600000 vertices > Rank 6: assembler memory usage: 8435052 KiB > Rank 7 has 264600000 vertices > Rank 7: assembler memory usage: 8489572 KiB > Rank 1 has 264600000 vertices > Rank 1: assembler memory usage: 8400776 KiB > Rank 2 has 264700000 vertices > Rank 2: assembler memory usage: 8503020 KiB > Rank 3 has 264700000 vertices > Rank 3: assembler memory usage: 8606628 KiB > Rank 5 has 264700000 vertices > Rank 5: assembler memory usage: 8559664 KiB > Rank 0 has 264700000 vertices > Rank 0: assembler memory usage: 8548052 KiB > -------------------------------------------------------------------------- > mpiexec noticed that process rank 3 with PID 105 on node dx__lxc_hVQLlYKF > exited on signal 9 (Killed). > -------------------------------------------------------------------------- > Traceback (most recent call last): > File > "/home/dnanexus/dx_app-B6gvJkV2kfb7Byjxk55Q010K_job-BF5Pz8Q0Z4b03jyvB5y00fX3__UfIf5", > line 21, in <module> > execfile(_code_filename) > File > "/home/dnanexus/dx_app-B6gvJkV2kfb7Byjxk55Q010K_job-BF5Pz8Q0Z4b03jyvB5y00fX3__UfIf5.code.py > > <http://dx_app-B6gvJkV2kfb7Byjxk55Q010K_job-BF5Pz8Q0Z4b03jyvB5y00fX3__UfIf5.code.py>", > line 121, in <module> > dxpy.run() > File > "/usr/share/dnanexus/lib/python2.7/site-packages/dxpy-v0.79.3-py2.7.egg/dxpy/utils/exec_utils.py", > line 123, in run > result = ENTRY_POINT_TABLE[job['function']](**job['input']) > File > "/home/dnanexus/dx_app-B6gvJkV2kfb7Byjxk55Q010K_job-BF5Pz8Q0Z4b03jyvB5y00fX3__UfIf5.code.py > > <http://dx_app-B6gvJkV2kfb7Byjxk55Q010K_job-BF5Pz8Q0Z4b03jyvB5y00fX3__UfIf5.code.py>", > line 104, in main > contigs = dxpy.upload_local_file("Output/Contigs.fasta"); > File > "/usr/share/dnanexus/lib/python2.7/site-packages/dxpy-v0.79.3-py2.7.egg/dxpy/bindings/dxfile_functions.py", > line 179, in upload_local_file > fd = file if filename is None else open(filename, 'rb') > IOError: [Errno 2] No such file or directory: 'Output/Contigs.fasta' > > -- > ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
