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 >>>>>>> Denovoassembler-users@lists.sourceforge.net >>>>>>> https://lists.sourceforge.net/lists/listinfo/denovoassembler- >>>>>>> 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 >>>>>> Denovoassembler-users@lists.sourceforge.net >>>>>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-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 Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
