Can you try without this: -mini-ranks-per-rank \ 12 \
________________________________________ From: Wilhelm, Roland [rwilh...@mail.ubc.ca] Sent: Friday, August 22, 2014 7:53 PM To: Boisvert, Sebastien Cc: denovoassembler-us...@lists.sf.net Subject: RE: RAY on Compute Canada server (Parallel) Thanks for the quick reply! I retried with your command and had the same "Segmentation Fault" error: "mpiexec noticed that process rank 0 with PID 31421 on node cn0744 exited on signal 11 (Segmentation fault)." The process did last longer before giving this error, so perhaps I'm overtaxing the available memory (StandardOutput attached). Thoughts? Thanks again, Roli ________________________________________ From: Boisvert, Sebastien [boisv...@anl.gov] Sent: Friday, August 22, 2014 5:13 AM To: Wilhelm, Roland Cc: denovoassembler-us...@lists.sf.net Subject: RE: RAY on Compute Canada server (Parallel) In the log file, it says: Error, /home/rwilhelm/ASSEMBLY// already exists, change the -o parameter to another value. Can you try with: mpiexec -n 48 /global/software/ray/ray230/Ray -o ~/ASSEMBLY-2 -i FILE.pe.fa -s FILE.se.fa > From: Wilhelm, Roland [rwilh...@mail.ubc.ca] > Sent: Friday, August 22, 2014 12:47 AM > To: Boisvert, Sebastien > Subject: RAY on Compute Canada server (Parallel) > > > > Good Morning Dr. Boisvert! > > I wouldn't be writing you if I didn't think this might require quick and easy > advice from someone with your know-how in the Canadian computer sphere. I am > using the Compute Canada server, "Parallel," > to run Ray meta b/c it supports Message Passing Interface (MPI). They have > Ray (v. 2.3.0) installed and I would like to perform a simple assembly with > one paired end file and one singleton file. But, if I've fooled you till now, > I am actually a bit of a novice with the nitty > gritty of parallel processing. I've tried reading the server's "QuickStart" > guide and your RAY manual, but still cannot get the assembly to go beyond the > first 20 seconds (the command is recognized and the software engages). > > > My instinct says that this command should work: > > mpiexec -n 4 /global/software/ray/ray230/Ray -mini-ranks-per-rank 12 -o > ~/ASSEMBLY/ -i FILE.pe.fa -s FILE.se.fa > > Because they write that : > > "Since there are 12 cores per node on Parallel, a ppn (processors per node) > parameter of 12 will request that all the processors on a node be used. Also, > it is recommended that you ask for 22-23 GB of memory per node > requested, using the mem parameter. So, a typical job submission on Lattice > would look like: > qsub -l nodes=4:ppn=12,mem=88gb,walltime=72:00:00 parallel_diffuse.pbs" > > So, I've tailored 4 nodes with 12 mini-ranks (processors?) in your command. I > get the following error: > > "mpiexec noticed that process rank 0 with PID 21923 on node cn0744 exited on > signal 11 (Segmentation fault)." > > Now, it might easily be a problem I should take to Compute Canada, but I > thought I'd try with you first. The complete Standard Output is in the > attached file. > > Thank you kindly for your time, > > Roli > > ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
