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> 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 <sebastien.boisver...@ulaval.ca><mailto:
>> Sebastien.Boisvert.3@**ulaval.ca <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
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