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 *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> 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/
------------------------------------------------------------------------------
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
