To summarize: It's running on one process because presumably your are mixing MPI versions and or you are mixing MPICH2 with Open-MPI.
A consequence of using one process is that all the reads will go on that process. There is a bug that will fire up (it's fixed in the devel, see https://github.com/sebhtml/ray/commit/3bf06597ed21c6d72cf172884aa1708f37828347 ). So to be safe, make sure that the mpicxx you are using to build Ray is from the same version and library than the mpiexec you use to launch the whole thing. Here is an example of coherent paths: $ module load mpi/openmpi/1.6.4_gcc $ type mpicxx mpicxx is /software/mpi/openmpi/1.6.4_gcc/bin/mpicxx $ type mpiexec mpiexec is /software/mpi/openmpi/1.6.4_gcc/bin/mpiexec $ ldd ~/git-clones/ray/Ray | grep mpi | grep -v compilers libmpi_cxx.so.1 => /software/mpi/openmpi/1.6.4_gcc/lib/libmpi_cxx.so.1 (0x00002b92ea712000) libmpi.so.1 => /software/mpi/openmpi/1.6.4_gcc/lib/libmpi.so.1 (0x00002b92ea92d000) On 05/07/13 02:57 PM, Rick White wrote: > Hello Sebastien, > > So, I tried to add it to my path its not working again. Like it was. > > SO, I put in my path using .bashrc to the folder where the Ray script is > (Ray-v.2.2.0) > > Now it does work but here is the version: non-dev > Ray version 2.2.0 > License for Ray: GNU General Public License version 3 > RayPlatform version: 1.1.1 > License for RayPlatform: GNU Lesser General Public License version 3 > > MAXKMERLENGTH: 150 > Maximum coverage depth stored by CoverageDepth: 4294967295 > MAXIMUM_MESSAGE_SIZE_IN_BYTES: 4000 bytes > FORCE_PACKING = n > ASSERT = n > HAVE_LIBZ = n > HAVE_LIBBZ2 = n > PROFILER_COLLECT = n > MINIRANKS = y > CLOCK_GETTIME = n > __linux__ = y > _MSC_VER = n > __GNUC__ = y > RAY_32_BITS = n > RAY_64_BITS = y > MPI standard version: MPI 2.2 > MPI library: MPICH2 1.4.1 > Compiler: GNU gcc/g++ 4.6.3 > MPI I/O: n > > > > > On Fri, Jul 5, 2013 at 11:14 AM, Sébastien Boisvert > <sebastien.boisver...@ulaval.ca <mailto:sebastien.boisver...@ulaval.ca>> > wrote: > > On 05/07/13 02:00 PM, Rick White wrote: > > Ray command not found or command. Even though its running right now > on 10 cores. > And, when I try to exe again I get: > mpiexec -n 2 Ray -k 55 -i KLMB10-2.extfrags.HiSeq.PhiR.__fastq -o Test > [proxy:0:0...@mesa.zoology.ubc.ca > <mailto:proxy%3a0%...@mesa.zoology.ubc.ca> > <mailto:proxy%3A0%3A0@mesa.__zoology.ubc.ca > <mailto:proxy%253a0%25...@mesa.zoology.ubc.ca>>] HYDU_create_process > (./utils/launch/launch.c:69): execvp error on file Ray (No such file or > directory) > [proxy:0:0...@mesa.zoology.ubc.ca > <mailto:proxy%3a0%...@mesa.zoology.ubc.ca> > <mailto:proxy%3A0%3A0@mesa.__zoology.ubc.ca > <mailto:proxy%253a0%25...@mesa.zoology.ubc.ca>>] HYDU_create_process > (./utils/launch/launch.c:69): execvp error on file Ray (No such file or > directory) > > > Where is located your Ray executable ? > > Apparently, it is not in your PATH. > > > > Weird?? > > > > On Fri, Jul 5, 2013 at 10:55 AM, Sébastien Boisvert > <sebastien.boisvert.3@ulaval.__ca <mailto:sebastien.boisver...@ulaval.ca> > <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>> wrote: > > On 05/07/13 01:46 PM, Rick White wrote: > > Idd Ray - Idd command not found > > > OK, then can you do this: > > > Ray -version > > > type mpiexec - mpiexec is /usr/bin/mpiexec > > When I removed openmpi then exe the script (Ray exe on > multithreads but the result assemblies are different from before) > I get this: > [mpie...@mesa.zoology.ubc.ca > <mailto:mpie...@mesa.zoology.ubc.ca> <mailto:mpiexec@mesa.zoology.__ubc.ca > <mailto:mpie...@mesa.zoology.ubc.ca>> <mailto:mpiexec@mesa.zoology. > <mailto:mpiexec@mesa.zoology.>____ubc.ca <http://ubc.ca> > <mailto:mpiexec@mesa.zoology.__ubc.ca <mailto:mpie...@mesa.zoology.ubc.ca>>>] > set_default_values (./ui/mpich/utils.c:1337): no executable provided > [mpie...@mesa.zoology.ubc.ca > <mailto:mpie...@mesa.zoology.ubc.ca> <mailto:mpiexec@mesa.zoology.__ubc.ca > <mailto:mpie...@mesa.zoology.ubc.ca>> <mailto:mpiexec@mesa.zoology. > <mailto:mpiexec@mesa.zoology.>____ubc.ca <http://ubc.ca> > <mailto:mpiexec@mesa.zoology.__ubc.ca <mailto:mpie...@mesa.zoology.ubc.ca>>>] > HYD_uii_mpx_get_parameters (./ui/mpich/utils.c:1510): setting default values > failed > > > Usage: ./mpiexec [global opts] [exec1 local opts] : [exec2 > local opts] : ... > Global options (passed to all executables): > > Before I got: > mpiexec (OpenRTE) 1.4.3 > > But, when I reload OpenRTE 1.4.3 or 1.5.3 it doesn't > multithread any more and runs out of memory. > > Cheers and many thanks > Rick > > > On Fri, Jul 5, 2013 at 10:37 AM, Sébastien Boisvert > <sebastien.boisvert.3@ulaval.____ca <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>> <mailto:sebastien.boisvert.3@ > <mailto:sebastien.boisvert.3@>____ulaval.ca <http://ulaval.ca> > <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>>> wrote: > > On 05/07/13 11:54 AM, Rick White wrote: > > Hello Sebastien, > > Yes, I believe we updated to ubuntu 12.04 and I had > it running on Ubuntu 11.04 or 10.04 before. > But, I have it running on ubuntu 12.04 on my new > laptop same commands. > > I have tried 1.4.1 & 1.5.1 > sudo apt-get install libopenmpi-dev openmpi-bin > openmpi-doc > sudo apt-get install -y autotools-dev g++ > build-essential openmpi1.5-bin openmpi1.5-doc libopenmpi1.5-dev > > either works still only fire up on a single MPI. > > I have also tried the development version you sent > me. > same problem only a single MPI fires up > > > > You are probably mixing different MPI libraries > together. > > Can you provide the output of these two commands: > > > > ldd Ray > > > type mpiexec > > > or I get the segmentation fault error. > > Even when I get the Ray platform up and running on > the Ray Dev version same problem. > > Still confused on how to fix it. > > Cheers and many thanks > Rick > > > > On Fri, Jul 5, 2013 at 6:16 AM, Sébastien Boisvert > <sebastien.boisvert.3@ulaval.______ca <mailto:sebastien.boisvert.3@ > <mailto:sebastien.boisvert.3@>____ulaval.ca <http://ulaval.ca> > <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>> <mailto:sebastien.boisvert.3@ > <mailto:sebastien.boisvert.3@> <mailto:sebastien.boisvert.3@ > <mailto:sebastien.boisvert.3@>>______ulaval.ca <http://ulaval.ca> > <http://ulaval.ca> <mailto:sebastien.boisvert.3@ > <mailto:sebastien.boisvert.3@>____ulaval.ca <http://ulaval.ca> > <mailto:sebastien.boisvert.3@__ulaval.ca > <mailto:sebastien.boisver...@ulaval.ca>>>>> wrote: > > On 04/07/13 04:29 PM, Rick White wrote: > > > > Hello Sebastien, (Ray users!) > > I had ray working quite well on our server > then all the sudden it stopped. Worked fine yesterday. > > I get this error > Ray: error while loading shared libraries: > libmpichcxx.so.1.2: cannot open shared object file: No such file or directory > > > This means that libmpichcxx.so.1.2 is no > longer available in your library path $LD_LIBRARY_PATH. > > Did you update your operating system ? > > > > I used sudo apt-get install install > libcr-dev mpich2 to get the new mpi libraries states up to date. > > > If you recompile Ray with your updated MPI > library, does that work for you ? > > I don't know what happened? > > Cheers and many thanks > Rick > -- > 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 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>>>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>>>>> > http://www.ocgy.ubc.ca/~________suttle/ > <http://www.ocgy.ubc.ca/~______suttle/> > <http://www.ocgy.ubc.ca/~______suttle/ <http://www.ocgy.ubc.ca/~____suttle/>> > <http://www.ocgy.ubc.ca/~______suttle/ <http://www.ocgy.ubc.ca/~____suttle/> > <http://www.ocgy.ubc.ca/~____suttle/ <http://www.ocgy.ubc.ca/~__suttle/>>> > <http://www.ocgy.ubc.ca/~______suttle/ <http://www.ocgy.ubc.ca/~____suttle/> > <http://www.ocgy.ubc.ca/~____suttle/ <http://www.ocgy.ubc.ca/~__suttle/>> > <http://www.ocgy.ubc.ca/~____suttle/ <http://www.ocgy.ubc.ca/~__suttle/> > <http://www.ocgy.ubc.ca/~__suttle/ <http://www.ocgy.ubc.ca/~suttle/>>>> > <http://www.ocgy.ubc.ca/%________7Esuttle/ > <http://www.ocgy.ubc.ca/%______7Esuttle/> > <http://www.ocgy.ubc.ca/%______7Esuttle/ > <http://www.ocgy.ubc.ca/%____7Esuttle/>> > <http://www.ocgy.ubc.ca/%______7Esuttle/ > <http://www.ocgy.ubc.ca/%____7Esuttle/> > <http://www.ocgy.ubc.ca/%____7Esuttle/ > <http://www.ocgy.ubc.ca/%__7Esuttle/>>> > <http://www.ocgy.ubc.ca/%______7Esuttle/ > <http://www.ocgy.ubc.ca/%____7Esuttle/> > <http://www.ocgy.ubc.ca/%____7Esuttle/ <http://www.ocgy.ubc.ca/%__7Esuttle/>> > <http://www.ocgy.ubc.ca/%____7Esuttle/ <http://www.ocgy.ubc.ca/%__7Esuttle/> > <http://www.ocgy.ubc.ca/%__7Esuttle/ <http://www.ocgy.ubc.ca/%7Esuttle/>>>>> > > > > > > > > > > -- > 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 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>>>> > http://www.ocgy.ubc.ca/~________suttle/ > <http://www.ocgy.ubc.ca/~______suttle/> > <http://www.ocgy.ubc.ca/~______suttle/ <http://www.ocgy.ubc.ca/~____suttle/>> > <http://www.ocgy.ubc.ca/~______suttle/ <http://www.ocgy.ubc.ca/~____suttle/> > <http://www.ocgy.ubc.ca/~____suttle/ <http://www.ocgy.ubc.ca/~__suttle/>>> > <http://www.ocgy.ubc.ca/~______suttle/ <http://www.ocgy.ubc.ca/~____suttle/> > <http://www.ocgy.ubc.ca/~____suttle/ <http://www.ocgy.ubc.ca/~__suttle/>> > <http://www.ocgy.ubc.ca/~____suttle/ <http://www.ocgy.ubc.ca/~__suttle/> > <http://www.ocgy.ubc.ca/~__suttle/ <http://www.ocgy.ubc.ca/~suttle/>>>> > <http://www.ocgy.ubc.ca/%________7Esuttle/ > <http://www.ocgy.ubc.ca/%______7Esuttle/> > <http://www.ocgy.ubc.ca/%______7Esuttle/ > <http://www.ocgy.ubc.ca/%____7Esuttle/>> > <http://www.ocgy.ubc.ca/%______7Esuttle/ > <http://www.ocgy.ubc.ca/%____7Esuttle/> > <http://www.ocgy.ubc.ca/%____7Esuttle/ > <http://www.ocgy.ubc.ca/%__7Esuttle/>>> > <http://www.ocgy.ubc.ca/%______7Esuttle/ > <http://www.ocgy.ubc.ca/%____7Esuttle/> > <http://www.ocgy.ubc.ca/%____7Esuttle/ <http://www.ocgy.ubc.ca/%__7Esuttle/>> > <http://www.ocgy.ubc.ca/%____7Esuttle/ <http://www.ocgy.ubc.ca/%__7Esuttle/> > <http://www.ocgy.ubc.ca/%__7Esuttle/ <http://www.ocgy.ubc.ca/%7Esuttle/>>>>> > > > > > > > > > > -- > 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 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>> <tel:604-440-5150 <tel:604-440-5150> > <tel:604-440-5150 <tel:604-440-5150>>> > http://www.ocgy.ubc.ca/~______suttle/ > <http://www.ocgy.ubc.ca/~____suttle/> <http://www.ocgy.ubc.ca/~____suttle/ > <http://www.ocgy.ubc.ca/~__suttle/>> <http://www.ocgy.ubc.ca/~____suttle/ > <http://www.ocgy.ubc.ca/~__suttle/> <http://www.ocgy.ubc.ca/~__suttle/ > <http://www.ocgy.ubc.ca/~suttle/>>> <http://www.ocgy.ubc.ca/%______7Esuttle/ > <http://www.ocgy.ubc.ca/%____7Esuttle/> > <http://www.ocgy.ubc.ca/%____7Esuttle/ <http://www.ocgy.ubc.ca/%__7Esuttle/>> > <http://www.ocgy.ubc.ca/%____7Esuttle/ <http://www.ocgy.ubc.ca/%__7Esuttle/> > <http://www.ocgy.ubc.ca/%__7Esuttle/ <http://www.ocgy.ubc.ca/%7Esuttle/>>>> > > > > > > > -- > 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 <tel:604-440-5150> <tel:604-440-5150 > <tel:604-440-5150>> > http://www.ocgy.ubc.ca/~____suttle/ > <http://www.ocgy.ubc.ca/~__suttle/> <http://www.ocgy.ubc.ca/~__suttle/ > <http://www.ocgy.ubc.ca/~suttle/>> <http://www.ocgy.ubc.ca/%____7Esuttle/ > <http://www.ocgy.ubc.ca/%__7Esuttle/> <http://www.ocgy.ubc.ca/%__7Esuttle/ > <http://www.ocgy.ubc.ca/%7Esuttle/>>> > > > > > > > -- > 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 <tel:604-440-5150> > http://www.ocgy.ubc.ca/~__suttle/ <http://www.ocgy.ubc.ca/~suttle/> > <http://www.ocgy.ubc.ca/%__7Esuttle/ <http://www.ocgy.ubc.ca/%7Esuttle/>> > > > > > > > -- > 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/ <http://www.ocgy.ubc.ca/%7Esuttle/> > > ------------------------------------------------------------------------------ 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
