Re: [Denovoassembler-users] Error after reinstall. Removed libmpichcxx.so.1.2 but now no memory not running correctly

[Pier-Luc Plante]

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> wrote: Hello Rick, you could try the devel 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> 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 http://www.ocgy.ubc.ca/~suttle/ -- 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/ -- 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/

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