[please keep denovoassembler-users cc'ed] Hello,
There are two dominant MPI implementations: Open-MPI and MPICH2. Most others are derived from these two. If you got a usage error, you are probably using MPICH2. With MPICH2, you can generate one log file per MPI rank with this command: mpiexec -np 64 \ -outfile-pattern Ray_test_08.%r.stdout \ -errfile-pattern Ray_test_08.%r.stderr \ Ray -k 21 -p \ /home/bio443/mtherkel/SRR131208_1.fastq \ /home/bio443/mtherkel/SRR131208_2.fastq \ -o Ray_test_08 Sébastien Wei-Jen Chang a écrit : > Hi Sebastien, > > I might have misunderstood you. I ran a line like this: > > mpiexec -np 64 -output-filename Ray_test_08 Ray -k 21 -p > /home/bio443/mtherkel/SRR131208_1.fastq > /home/bio443/mtherkel/SRR131208_2.fastq -o Ray_test_08 > > and received an error message (usage error). Did I put the > -output-filename wrongfully? > > Thanks, > > > WJ > > On Tue, Aug 14, 2012 at 11:24 AM, Sébastien Boisvert > <[email protected] <mailto:[email protected]>> > wrote: > > Hello Wei-Jen, > > > If you are using Open-MPI, you can use the command below to generate > one standard output file per MPI rank (there is 1 MPI rank per > processor core). > > mpiexec -n 64 \ > -output-filename Test21 \ > > Ray -k 21 \ > -o Test21 \ > -p SRR131208_1.fastq SRR131208_2.fastq > > You will get 64 standard output files named > Test21.1.00, Test21.1.01, ..., Test21.1.63. > > With this, it will be easier to find the problem. > > Also, you can compile Ray with > > make ASSERT=y DEBUG=y PREFIX=DebugBuild > make install > > To turn on runtime assertions. > ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Denovoassembler-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
