Hi Wei-Jen, 1.
It seems that you are using mpiexec 0.83 from https://www.osc.edu/~djohnson/mpiexec/#Download This mpiexec flavor does not seem to have the option I told you to use. In the source code of mpiexec 0.83, there is this: #if 0 /* No this doesn't work, but if I don't check it in I'll forget where I put it. */ fprintf(stderr, " -output <prefix> : send process output to separate files\n"); #endif So the feature is in the source code, but is not activated. 2. To change the k-mer length, use -k <value> (for 31, use -k 31). For a k-mer length longer than 31, you need to compile Ray with MAXKMERLENGTH=<maximum> (for -k 55, you need to compile with MAXKMERLENGTH=64. Wei-Jen Chang a écrit : > Hi Sebastien, > > It still did not work. Below is the message I received. I have asked our > administrator to take a look. Maybe he has a better idea how to deal > with it. > > Btw, I want to ask how to increase the kmer limit in Ray? I know the > default number is 21. > > Thanks, > > WJ > > Usage: mpiexec [<args>] <executable> [<exe args>]... > or: mpiexec [<args>] -config[=]<file> > or: mpiexec [<args>] -server > -n <numproc> : use only some of the allocated processors > Default behavior allocates one process per allocated processor. > -verbose : be verbose about mpiexec operation > -nostdin : do not listen to stdin, allowing process to go into background > -allstdin : send stdin to all processes (default just proc #0) > -nostdout : do not redirect stdout/stderr, but let pbs accumulate it > -comm (gm|mx|p4|ib|rai|pmi|lam|shmem|emp|portals|none) : choose MPI > (default m > pich2-pmi) > -mpich-p4-[no-]shmem : for MPICH/P4, specify if the library was > compiled with shared memory support (default > yes) > -pernode : allocate only one process per compute node > -npernode <nprocs> : allocate no more than <nprocs> processes per > compute node > -nolocal : do not run any MPI processes on the local node > -transform-hostname[=]<sed expression> : use alternate names for MPI > -transform-hostname-program[=]<executable> : use this script or program > to generate alternate names > -tv : debug using totalview (ensure it is in your path) > -kill : kill other processes if any one process exits > -config[=]<file> : use heterogenous node specification file ("-" for > stdin) > -server : do not run any tasks, just serve other concurrent mpiexec > clients > -version : show version information > Version 0.83, configure options: '--with-pbs' '--with-default-comm=pmi' > > > On Wed, Aug 15, 2012 at 11:02 AM, Sébastien Boisvert > <sebastien.boisver...@ulaval.ca <mailto:sebastien.boisver...@ulaval.ca>> > wrote: > > [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 > <Sebastien.Boisvert.3@ulaval.__ca > <mailto:sebastien.boisver...@ulaval.ca> > <mailto:Sebastien.Boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>> > > 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. > > > > > > -- > Associate Professor of Biology > Hamilton College > Clinton, NY 13323 > (315) 859-4296 ------------------------------------------------------------------------------ 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. 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