See my responses below.
On 16/04/13 06:16 PM, Marcelino Suzuki wrote:
> Hurrah it compiled, but could you please take a look at "HELP!" below
>
>
> Well, after I picked the intel compiler and added the -
> DMPICH_IGNORE_CXX_SEEK option in the Makefile of RayPlatform
>
> $(Q)$(MPICXX) $(CXXFLAGS) -DMPICH_IGNORE_CXX_SEEK -D
> RAYPLATFORM_VERSION=\"$(RAYPLATFORM_VERSION)\" -I. -c -o $@ $<
>
> and the Makefile of ray
>
> find . -name *Makefile* | xargs -i sed -i "s/mpicxx/mpicxx -
> DMPICH_IGNORE_CXX_SEEK/g" {}
>
> It did compile through.
>
>
>
> === HELP!
>
> I will tried to run jobs with the newly compiled 2.2.0 but
> unfortunately I still get the "Error, crambe/ already exists, change
> the -o parameter to another value." error
>
> I get two types of errors:
>
> Whenever I start one node with 9 cores it crashes after some 20
> minuts during assembly, so I am guessing it is some RAM issue,
> although I am "only" running 3.2 M sequences. I do get the "Error,
> crambe/ already exists, change the -o parameter to another value. "
> but it does not seem to affect it. Actually when I do individual
> outfiles per core, it only one of the files gets written to,
>
>
> When I spread among different nodes i.e. 4 nodes with 4 jobs per
You mean 4 MPI ranks per node, right ?
> node, the job cancels within a minute or so, and individual outfiles
> for most of cores have the folowing last lines:
>
> Enabling CorePlugin 'TaxonomyViewer'
> Enabling memory usage reporting.
> Error, crambe/ already exists, change the -o parameter to another value.
>
What is your file system ? And is it shared between your nodes ?
> Rank 0: assembler memory usage: 37992 KiB
> Rank 0: assembler memory usage: 103716 KiB
> Rank 0: Rank= 0 Size= 1 ProcessIdentifier= 28047
>
> Nodes (08,11) have no errors and finish by
>
> Rank 0 is loading sequence reads
> Rank 0 : partition is [0;3602181], 3602182 sequence reads
> Rank 0 is fetching file /scratch/suzukim/mira/CCB1a.fastq with lazy
> loading (please wait...)
> Rank 0 has 0 sequence reads
> Rank 0: assembler memory usage: 142416 KiB
> Rank 0 has 100000 sequence reads
> Rank 0: assembler memory usage: 142416 KiB
> Rank 0 has 200000 sequence reads
> Rank 0: assembler memory usage: 142416 KiB
>
> Nodes 09,10, have no errors and finish by
>
> Rank 0 is loading sequence reads
> Rank 0 : partition is [0;3602181], 3602182 sequence reads
> Rank 0 is fetching file /scratch/suzukim/mira/CCB1a.fastq with lazy
> loading (please wait...)
>
> Marcelino
>
> On Apr 16, 2013, at 10:14 PM, Sébastien Boisvert wrote:
>
>> To compile the git version:
>>
>>
>> git clone git://github.com/sebhtml/ray.git
>> git clone git://github.com/sebhtml/RayPlatform.git
>>
>> cd ray
>> make
>>
>> On 16/04/13 04:09 PM, Marcelino Suzuki wrote:
>>> Hello and thanks
>>>
>>> Just that you know, I am getting rhe same type of compilcation
>>> errors with other .cpp files as well (after I excluded Amos.cpp)
>>> code/
>>> plugin_CoverageGatherer/CoverageGatherer.cpp (at least, perhaps
>>> others)
>>>
>>> I I will wait for the new version, and will try in a different
>>> cluster where I compiled with gcc.
>>>
>>> Marcelino
>>>
>>> On Apr 16, 2013, at 10:00 PM, Sébastien Boisvert wrote:
>>>
>>>> Hello,
>>>>
>>>> v2.2.0 should be released soon. There is one ticket left.
>>>>
>>>> Otherwise, I don't think this issue is critical as it does not
>>>> prevent
>>>> assemblies for completing.
>>>>
>>>> On 16/04/13 03:35 PM, Marcelino Suzuki wrote:
>>>>> Hello again
>>>>>
>>>>> Well, I am not really know how to add the changes using git (other
>>>>> than editing the .cpp files from V2.1.0, which are not quite the
>>>>> same
>>>>> as the ones in the commit. I tried to clone the latest ray and
>>>>> RayPlatform, and after some tweaeking to use the intel compiler
>>>>> (suggested by my sys admin) and the compilation crashed at
>>>>> plugin_Amos.cpp. Maybe you can give me some pointers on how to fix
>>>>> 2.1.0 (which I was able to compile)
>>>>>
>>>>> Thanks
>>>>>
>>>>> commands
>>>>> cd
>>>>> git clone https://bitbucket.org/sebhtml/ray.git
>>>>> mv ray /work/OOBMECO/bin
>>>>> git clone https://bitbucket.org/sebhtml/rayplatform.git
>>>>> mv rayplatform/ /work/OOBMECO/bin
>>>>> cd /work/OOBMECO/bin/ray/
>>>>> source /opt/cluster/gcc-4.4.3/refresh.sh
>>>>> source /opt/cluster/compilers/intel/Compiler/
>>>>> 11.1/072/
>>>>> bin/iccvars.sh intel64
>>>>> source /opt/cluster/compilers/intel/impi/
>>>>> 4.0.0.028/
>>>>> bin64/mpivars.sh
>>>>> find . -name *Makefile* | xargs -i sed -i "s/
>>>>> mpicxx/
>>>>> mpicxx -DMPICH_IGNORE_CXX_SEEK/g" {}
>>>>>
>>>>> edited the RayPlatform Makefile and add
>>>>> -DMPICH_IGNORE_CXX_SEEK
>>>>>
>>>>> make PREFIX=$PWD
>>>>>
>>>>> ERROR:
>>>>>
>>>>> CXX code/plugin_Amos/Amos.o
>>>>> code/plugin_Amos/Amos.cpp: In member function â:
>>>>> code/plugin_Amos/Amos.cpp:239: error: expected primary-expression
>>>>> before â token
>>>>> code/plugin_Amos/Amos.cpp:239: error: â was not declared in this
>>>>> scope
>>>>> code/plugin_Amos/Amos.cpp:240: error: expected primary-expression
>>>>> before â token
>>>>> code/plugin_Amos/Amos.cpp:240: error: â was not declared in this
>>>>> scope
>>>>> make: *** [code/plugin_Amos/Amos.o] Error 1
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ===================================================================
>>>>> oOOOOo Marcelino Suzuki, Assoc.
>>>>> Professor,
>>>>> Intl. Chair, Platform Responsible
>>>>> oOOO Univ Pierre Marie Curie (Paris 6) -
>>>>> Observatoire Océanologique de Banyuls
>>>>> oOOOOOo. UMR 7621 - Laboratoire
>>>>> d'Océanographie Microbienne (LOMIC)
>>>>> .oOOOOOOOo. Marine Biodiversity and
>>>>> Biotechnology (bio2mar) Platform
>>>>> .oOOOOOOOOOoo. suz...@obs-banyuls.fr http://bit.ly/
>>>>> fq3nbE
>>>>> bio2mar.obs-banyuls.fr
>>>>> .oOOOOOOOOOOOooooo. Ave du Fontaulé, Banyuls-sur-Mer 66650,
>>>>> France
>>>>> +33(0)430192401
>>>>> 0000000000000000000000000000000000000000000000000000000000000000000000000000
>>>>>
>>>>> On Apr 16, 2013, at 3:40 PM, Sébastien Boisvert wrote:
>>>>>
>>>>>> On 15/04/13 04:40 PM, Marcelino Suzuki wrote:
>>>>>>> Hello and thanks for the answer.
>>>>>>>
>>>>>>> I did undestand that and the directory does not exist when I
>>>>>>> lauch
>>>>>>> the job. I do not get this error from the fist 4 cores, but
>>>>>>> after
>>>>>>> core 5, I get the error in the output from all cores. The
>>>>>>> weirdest
>>>>>>> is
>>>>>>> that I had these messages in the outfile of a run that completed,
>>>>>>> and
>>>>>>> that is why I was wondering if that is normal.
>>>>>>>
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>>
>>>>>> This is a race condition affecting version 2.1.0.
>>>>>>
>>>>>> It was fixed by this commit:
>>>>>>
>>>>>> commit 73ada528e1d17105e17df524fdb60bdd03b40560
>>>>>> Author: Sébastien Boisvert <sebastien.boisver...@ulaval.ca>
>>>>>> Date: Fri Feb 8 23:55:34 2013 -0500
>>>>>>
>>>>>> fix a race condition during directory probing
>>>>>> Resolves-bug: https://github.com/sebhtml/ray/issues/125
>>>>>> Signed-off-by: Sébastien Boisvert <sebastien.boisvert.
>>>>>> 3...@ulaval.ca>
>>>>>>
>>>>>>
>>>>>> https://bitbucket.org/sebhtml/ray/commits/73ada528e1d17105e17df524fdb60bdd03b40560
>>>>>>
>>>>>>
>>>>>> The upcoming v2.2.0 release will include this bug fix.
>>>>>>
>>>>>>
>>>>>> This bug was introduced by the mini-ranks code.
>>>>>>
>>>>>>
>>>>>> For example, if you are using a single machine with 32 cores,
>>>>>> you can use
>>>>>>
>>>>>> mpiexec -n 32 Ray ...
>>>>>>
>>>>>> or you can use
>>>>>>
>>>>>> mpiexec -n 4 Ray -mini-ranks-per-rank 7 ...
>>>>>>
>>>>>>
>>>>>> Mini-ranks are experimental, but they seems to work nicely on SMP
>>>>>> NUMA machines.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Marcelino
>>>>>>>
>>>>>>>
>>>>>>> On Apr 15, 2013, at 10:14 PM, Sébastien Boisvert wrote:
>>>>>>>
>>>>>>>> On 14/04/13 04:45 PM, Marcelino Suzuki wrote:
>>>>>>>>> Hello Sebastien
>>>>>>>>>
>>>>>>>>> I am having issues with assembling a 3.2 M read ion torrent
>>>>>>>>> dataset
>>>>>>>>> using Loadleveler for an cluster intel iDataplex, with the mpi
>>>>>>>>> job
>>>>>>>>> crashing during execution. It might be an issue with the
>>>>>>>>> cluster
>>>>>>>>> (I
>>>>>>>>> got this message from the system administrator: En ce moment
>>>>>>>>> on a
>>>>>>>>> des
>>>>>>>>> soucis de réseau IB et de baie de disque), but since I've
>>>>>>>>> seen a
>>>>>>>>> Error
>>>>>>>>> in the output files coming from some cores using the -output-
>>>>>>>>> filename
>>>>>>>>> option, and just want to make sure I am not missing some
>>>>>>>>> detail:
>>>>>>>>>
>>>>>>>>> Error, crambe/ already exists, change the -o parameter to
>>>>>>>>> another
>>>>>>>>> value
>>>>>>>>>
>>>>>>>>> crambe is my -o directory
>>>>>>>>>
>>>>>>>>> Is that normal behavior? I noticed I got the same errors in a
>>>>>>>>> outfile of the same assembly that did go through to the end.
>>>>>>>>
>>>>>>>> Ray will not overwrite an existing directory.
>>>>>>>>
>>>>>>>> You must change use another directory name.
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> Marcelino
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> =
>>>>>>>>> ===============================================================
>>>>>>>>> oOOOOo Marcelino Suzuki, Assoc.
>>>>>>>>> Professor,
>>>>>>>>> Intl. Chair, Platform Responsible
>>>>>>>>> oOOO Univ Pierre Marie Curie (Paris
>>>>>>>>> 6) -
>>>>>>>>> Observatoire Océanologique de Banyuls
>>>>>>>>> oOOOOOo. UMR 7621 - Laboratoire
>>>>>>>>> d'Océanographie Microbienne (LOMIC)
>>>>>>>>> .oOOOOOOOo. Marine Biodiversity and
>>>>>>>>> Biotechnology (bio2mar) Platform
>>>>>>>>> .oOOOOOOOOOoo. suz...@obs-banyuls.fr http://bit.ly/
>>>>>>>>> fq3nbE
>>>>>>>>> bio2mar.obs-banyuls.fr
>>>>>>>>> .oOOOOOOOOOOOooooo. Ave du Fontaulé, Banyuls-sur-Mer 66650,
>>>>>>>>> France
>>>>>>>>> +33(0)430192401
>>>>>>>>> 0000000000000000000000000000000000000000000000000000000000000000000000000000
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Precog is a next-generation analytics platform capable of
>>>>>>>>> advanced
>>>>>>>>> analytics on semi-structured data. The platform includes APIs
>>>>>>>>> for
>>>>>>>>> building
>>>>>>>>> apps and a phenomenal toolset for data science. Developers can
>>>>>>>>> use
>>>>>>>>> our toolset for easy data analysis & visualization. Get a free
>>>>>>>>> account!
>>>>>>>>> http://www2.precog.com/precogplatform/slashdotnewsletter
>>>>>>>>> _______________________________________________
>>>>>>>>> Denovoassembler-users mailing list
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>>>>>>>>> users
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Precog is a next-generation analytics platform capable of
>>>>>>>> advanced
>>>>>>>> analytics on semi-structured data. The platform includes APIs
>>>>>>>> for
>>>>>>>> building
>>>>>>>> apps and a phenomenal toolset for data science. Developers can
>>>>>>>> use
>>>>>>>> our toolset for easy data analysis & visualization. Get a free
>>>>>>>> account!
>>>>>>>> http://www2.precog.com/precogplatform/slashdotnewsletter
>>>>>>>> _______________________________________________
>>>>>>>> Denovoassembler-users mailing list
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>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
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