On 12/11/13 02:41 PM, Tyx, Robert (CDC/ONDIEH/NCEH) wrote: > Hello, thanks for taking a look at this again... > > No, not a single core... We have OpenMPI set to use a hostfile which > specifies the nodes and processors per node. We specified 4 nodes, 4 > processors each node, so 16 ranks total.
Hi, In your initial message [1], there were some debugging messages (like "received RAY_MPI_TAG_SEARCH_ELEMENTS_REPLY, resuming work"). These were removed. You ran Ray 2.2.0 (which should work). Can you try with newer Ray 2.3.0 just to see if it solves the problem ? Otherwise, I would need a stack trace for your run with Ray 2.2.0. Let me know if you need information on how to generate a stack trace. --- [1]http://comments.gmane.org/gmane.science.biology.ray-genome-assembler/665 > > Thanks, > Robert > > -----Original Message----- > From: Sébastien Boisvert [mailto:sebastien.boisver...@ulaval.ca] > Sent: Monday, November 11, 2013 2:34 PM > To: Tyx, Robert (CDC/ONDIEH/NCEH) > Cc: denovoassembler-users@lists.sourceforge.net > Subject: Re: [Denovoassembler-users] error in running Ray with > communities...need help > > On 08/11/13 03:02 PM, Tyx, Robert (CDC/ONDIEH/NCEH) wrote: >> Hello, >> The command was >> >> mpiexec --hostfile /home/openmpi-1.6.5/hosts.txt Ray -s >> navy/XXXX_Meta_Small.fastq -o /home/rayOutputMPI_again/ -search >> scripts/NCBI-Taxonomy/NCBI-taxonomy/NCBI-Finished-Bacterial-Genomes/ >> -with-taxonomy scripts/NCBI-Taxonomy/NCBI-taxonomy/Genome-to-Taxon.tsv >> scripts/NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv >> scripts/NCBI-Taxonomy/Tax NCBI-taxonomy/Taxon-Names.tsv > > > I don't see the number of MPI ranks in your command. Are you running your > test on one single computing core ? > > > /home/rayOutputMPI_again/ is inside /home. Does the user that run Ray have > the rights to create that directory? > > >> >> Thanks, >> -Robert >> > ------------------------------------------------------------------------------ CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments & Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
