On 05/07/13 03:09 PM, Rick White wrote: > When I reload the openMPI and add too my path still only on one core.
The output of "Ray -version" that you provided below says "MPI library: MPICH2 1.4.1". You can not run this executable with the mpiexec from Open-MPI (well, you can, but it won't work.). > Cheers > Rick > > > > On Fri, Jul 5, 2013 at 11:57 AM, Rick White <raw...@gmail.com > <mailto:raw...@gmail.com>> 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 <tel:604-440-5150> > http://www.ocgy.ubc.ca/~suttle/ <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
