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
