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.boisver...@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
