On 04/07/13 07:02 PM, Rick White wrote: > mpiexec -n 10 Ray -k 55 -i ILreads.fastq -o Test55k
With this command, you are saying that Ray is only launching on 1 process. Is that correct ? > > I can't get the dev Ray to work. > > Errors - > make: *** RayPlatform: No such file or directory. Stop. > make: *** [RayPlatform/libRayPlatform.a] Error 2 > You also need to clone RayPlatform Usually: git clone https://github.com/sebhtml/ray.git git clone https://github.com/sebhtml/RayPlatform.git cd ray make > > > On Thu, Jul 4, 2013 at 3:55 PM, Pier-Luc Plante <pier-luc.plant...@ulaval.ca > <mailto:pier-luc.plant...@ulaval.ca>> wrote: > > Hello again, > What is the command you are using to launch Ray? > > Pier-Luc > Le 2013-07-04 18:51, Rick White a écrit : >> Hello again, >> >> I am confused on how to fix this problem in that it is not >> multi-threading any more? >> >> As I don't understand how it could stop all the sudden?? >> >> Did I do all the steps correctly? >> >> another error: >> Critical exception: The system is out of memory, returned NULL. >> Requested -24427520 bytes of type RAY_MALLOC_TYPE_BLOOM_FILTER >> >> -------------------------------------------------------------------------- >> mpiexec noticed that the job aborted, but has no info as to the process >> that caused that situation. >> >> Cheers >> Rick >> >> >> >> >> On Thu, Jul 4, 2013 at 3:45 PM, Pier-Luc Plante >> <pier-luc.plant...@ulaval.ca <mailto:pier-luc.plant...@ulaval.ca>> wrote: >> >> Hello Rick, >> you could try the /deve//l/ version of Ray. Sébastien is always >> working to improve the stability and the performances of Ray. A bug was >> fixed for a similar issue: >> >> https://github.com/sebhtml/ray/commit/3bf06597ed21c6d72cf172884aa1708f37828347 >> >> To download: >> git clone https://github.com/sebhtml/ray.git >> >> Pier-Luc >> >> >> Le 2013-07-04 18:26, Rick White a écrit : >>> Hello Pier-luc, >>> >>> >>> Normally, when I run the script I get more then one core running. >>> But, currently only one core is running at a time causing the error. Its >>> not threading correctly for some reason now. >>> >>> >>> 1) Ray-v2.2.0/ >>> 2) a.Ubuntu 12.04.2 LTS (GNU/Linux 3.2.0-48-generic x86_64) >>> b.server AMD opteron 2.0ghz (16cores) 128GB RAM >>> 3) Tested it with a 12 mb (100k reads) and 4 gb (10m reads). >>> >>> >>> Ray was running perfectly fine then it just stopped all the sudden >>> and had the first error >>> Ray: error while loading shared libraries: libmpichcxx.so.1.2: >>> cannot open shared object file: No such file or directory >>> >>> I removed everything then reinstalled >>> sudo apt-get install libcr-dev mpich2 >>> >>> Tried old and new mpi >>> 1.4.3 by sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev >>> 1.5.3 by sudo apt-get install -y autotools-dev g++ build-essential >>> openmpi1.5-bin openmpi1.5-doc libopenmpi1.5-dev >>> >>> Reinstalled Ray-v2.2.0 >>> make PREFIX=/usr/local/bin/ray-build >>> >>> Now nothing works with another error: >>> Critical exception: The system is out of memory, returned NULL. >>> Requested -54534904 bytes of type RAY_MALLOC_TYPE_BLOOM_FILTER >>> >>> HELP! >>> >>> >>> >>> >>> On Thu, Jul 4, 2013 at 3:04 PM, Pier-Luc Plante >>> <pier-luc.plant...@ulaval.ca <mailto:pier-luc.plant...@ulaval.ca>> wrote: >>> >>> Hi, >>> to help you we need a little more information. >>> Which version of Ray are you using? >>> What are your system specs? >>> What is the size of your sample? >>> >>> Pier-Luc >>> >>> Le 2013-07-04 17:36, Rick White a écrit : >>>> Hello again, >>>> >>>> Fun continues. The reinstall removed the libmpichcxx.so.1.2 >>>> error. >>>> But, now it isn't running correctly and is running out of >>>> memory >>>> >>>> error >>>> Critical exception: The system is out of memory, returned NULL. >>>> Requested -54534904 bytes of type RAY_MALLOC_TYPE_BLOOM_FILTER >>>> >>>> >>>> HELP! >>>> -- >>>> Richard Allen White III M.S. >>>> PhD Candidate - Suttle Lab >>>> Department of Microbiology & Immunology >>>> The University of British Columbia >>>> Vancouver, BC, Canada >>>> cell. 604-440-5150 <tel:604-440-5150> >>>> http://www.ocgy.ubc.ca/~suttle/ >>>> <http://www.ocgy.ubc.ca/%7Esuttle/> >>>> >>>> >>> >>> >>> >>> >>> -- >>> Richard Allen White III M.S. >>> PhD Candidate - Suttle Lab >>> Department of Microbiology & Immunology >>> The University of British Columbia >>> Vancouver, BC, Canada >>> cell. 604-440-5150 <tel:604-440-5150> >>> http://www.ocgy.ubc.ca/~suttle/ <http://www.ocgy.ubc.ca/%7Esuttle/> >>> >>> >> >> >> >> >> -- >> Richard Allen White III M.S. >> PhD Candidate - Suttle Lab >> Department of Microbiology & Immunology >> The University of British Columbia >> Vancouver, BC, Canada >> cell. 604-440-5150 <tel:604-440-5150> >> http://www.ocgy.ubc.ca/~suttle/ <http://www.ocgy.ubc.ca/%7Esuttle/> >> >> > > > > > -- > Richard Allen White III M.S. > PhD Candidate - Suttle Lab > Department of Microbiology & Immunology > The University of British Columbia > Vancouver, BC, Canada > cell. 604-440-5150 > http://www.ocgy.ubc.ca/~suttle/ <http://www.ocgy.ubc.ca/%7Esuttle/> > > ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
