mpiexec -n 10 Ray -k 55 -i ILreads.fastq -o Test55k
I can't get the dev Ray to work.
Errors -
make: *** RayPlatform: No such file or directory. Stop.
make: *** [RayPlatform/libRayPlatform.a] Error 2
On Thu, Jul 4, 2013 at 3:55 PM, Pier-Luc Plante <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> 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/
>
>
>
>
--
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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