>From the log: Rank 0: Assembler panic: no peak observed in the k-mer coverage distribution. Rank 0: to deal with the sequencing error rate, try to lower the k-mer length (-k)
What value did you use for the k-mer length (-k) ? > ________________________________________ > De : nicolasber...@gmail.com [nicolasber...@gmail.com] de la part de Nicolas > Balcazar [balca...@molgen.mpg.de] > Date d'envoi : 30 août 2011 18:50 > À : Sébastien Boisvert > Cc : denovoassembler-us...@lists.sf.net > Objet : Re: RE : RE : RE : RE : RAY just on LAM/MPI? > > ok, i tried that version, and now it already kind of crashes after "Step: > K-mer counting": > > *** > Step: K-mer counting > Date: Wed Aug 31 00:23:57 2011 > Elapsed time: 20 minutes, 14 seconds > Since beginning: 21 minutes, 1 seconds > *** > > Rank 0 has 3196286 k-mers (completed) > Rank 7 has 3200778 k-mers (completed) > Rank 4 has 3198066 k-mers (completed) > Rank 12 has 3202550 k-mers (completed) > Rank 17 has 3198102 k-mers (completed) > Rank 20 has 3195578 k-mers (completed) > Rank 5 has 3199300 k-mers (completed) > Rank 19 has 3202550 k-mers (completed) > Rank 14 has 3199560 k-mers (completed) > Rank 1 has 3202036 k-mers (completed) > Rank 18 has 3201140 k-mers (completed) > Rank 11 has 3196140 k-mers (completed) > Rank 21 has 3205276 k-mers (completed) > Rank 15 has 3197538 k-mers (completed) > Rank 6 has 3203614 k-mers (completed) > Rank 9 has 3199128 k-mers (completed) > Rank 13 has 3196418 k-mers (completed) > Rank 3 has 3202886 k-mers (completed) > Rank 10 has 3197264 k-mers (completed) > Rank 16 has 3198038 k-mers (completed) > Rank 8 has 3195012 k-mers (completed) > > > Rank 0: the minimum coverage is 2 > Rank 0: the peak coverage is 2 > Rank 0: Assembler panic: no peak observed in the k-mer coverage distribution. > Rank 0: to deal with the sequencing error rate, try to lower the k-mer length > (-k) > Rank 21: sent 297225 messages, received 297226 messages. > Rank 20: sent 299887 messages, received 299888 messages. > Rank 19: sent 300109 messages, received 300110 messages. > Rank 18: sent 299799 messages, received 299800 messages. > Rank 17: sent 299766 messages, received 299767 messages. > Rank 16: sent 299239 messages, received 299240 messages. > Rank 15: sent 298580 messages, received 298581 messages. > Rank 14: sent 300802 messages, received 300803 messages. > Rank 13: sent 297063 messages, received 297064 messages. > Rank 12: sent 298839 messages, received 298840 messages. > Rank 11: sent 296100 messages, received 296101 messages. > Rank 10: sent 364948 messages, received 364949 messages. > Rank 9: sent 438765 messages, received 438766 messages. > Rank 8: sent 488448 messages, received 488449 messages. > Rank 7: sent 518148 messages, received 518149 messages. > Rank 6: sent 442586 messages, received 442587 messages. > Rank 5: sent 485924 messages, received 485925 messages. > Rank 4: sent 526806 messages, received 526807 messages. > Rank 3: sent 553545 messages, received 553546 messages. > Rank 2: sent 567784 messages, received 567785 messages. > Rank 1: sent 491188 messages, received 491189 messages. > Rank 0: sent 547613 messages, received 547591 messages. > > > i tried feeding him more reads, but it doent seem to have any influence on > the errormessage " Assembler panic: no peak observed in the k-mer coverage > distribution" > what does this mean? > > THANKS! > Nicolas > > > > > 2011/8/30 Sébastien Boisvert > <sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>> > Can you try with the last development version: > > https://github.com/sebhtml/ray/zipball/master > > > > (don't forget to CC the list.) > >> ________________________________________ >> De : nicolasber...@gmail.com<mailto:nicolasber...@gmail.com> >> [nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>] de la part de >> Nicolas Balcazar [balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>] >> Date d'envoi : 30 août 2011 12:34 >> À : Sébastien Boisvert >> Objet : Re: RE : RE : RE : RAY just on LAM/MPI? >> >> Hi Sebastien, >> >> as always u were right, i was still using the wrong mpi version, because it >> was not in the beginning of my $PATH. Now i corrected that (and the rank >> nummeration started to work suddenly), but now i get the following (very >> long) error message: (im just working on one server with 32 cores) >> >> Rank 18 is creating seeds [1/416914] >> Rank 16 is creating seeds [1/418234] >> Rank 5 is creating seeds [1/418420] >> Rank 8 is creating seeds [1/417864] >> Rank 20 is creating seeds [1/417350] >> >> *** >> Step: Selection of optimal read markers >> Date: Tue Aug 30 17:53:31 2011 >> Elapsed time: 1 minutes, 59 seconds >> Since beginning: 36 minutes, 47 seconds >> *** >> >> Rank 0 is creating seeds [1/418150] >> Rank 21 is creating seeds [1/420012] >> Rank 10 is creating seeds [1/417898] >> Rank 13 is creating seeds [1/417902] >> Rank 14 is creating seeds [1/415496] >> Rank 17 is creating seeds [1/416416] >> Rank 2 is creating seeds [1/418206] >> Rank 3 is creating seeds [1/418230] >> Rank 9 is creating seeds [1/418582] >> Rank 19 is creating seeds [1/417974] >> [floccinaucinihilipilification:24139] *** Process received signal *** >> [floccinaucinihilipilification:24152] *** Process received signal *** >> [floccinaucinihilipilification:24152] Signal: Segmentation fault (11) >> [floccinaucinihilipilification:24152] Signal code: Address not mapped (1) >> [floccinaucinihilipilification:24152] Failing at address: (nil) >> [floccinaucinihilipilification:24154] *** Process received signal *** >> [floccinaucinihilipilification:24154] Signal: Segmentation fault (11) >> [floccinaucinihilipilification:24154] Signal code: Address not mapped (1) >> [floccinaucinihilipilification:24154] Failing at address: (nil) >> [floccinaucinihilipilification:24156] *** Process received signal *** >> [floccinaucinihilipilification:24156] Signal: Segmentation fault (11) >> [floccinaucinihilipilification:24156] Signal code: Address not mapped (1) >> [floccinaucinihilipilification:24156] Failing at address: (nil) >> [floccinaucinihilipilification:24139] Signal: Segmentation fault (11) >> [floccinaucinihilipilification:24139] Signal code: Address not mapped (1) >> [floccinaucinihilipilification:24139] Failing at address: (nil) >> [floccinaucinihilipilification:24152] [ 0] /lib/libpthread.so.0 >> [0x7fbbd4a51020] >> [floccinaucinihilipilification:24152] [ 1] >> Ray(_ZN11SeedingData12computeSeedsEv+0x27e) [0x4781ce] >> [floccinaucinihilipilification:24152] [ 2] >> Ray(_ZN7Machine10runVanillaEv+0x76) [0x4430e6] >> [floccinaucinihilipilification:24152] [ 3] Ray(_ZN7Machine5startEv+0xd27) >> [0x448f27] >> [floccinaucinihilipilification:24152] [ 4] Ray(main+0x3a) [0x496a8a] >> [floccinaucinihilipilification:24152] [ 5] >> /lib/libc.so.6(__libc_start_main+0xf4) [0x7fbbd481f4f4] >> [floccinaucinihilipilification:24152] [ 6] Ray(__gxx_personality_v0+0x1f9) >> [0x422ee9] >> [floccinaucinihilipilification:24152] *** End of error message *** >> ( [...some stuff several times...] ) >> [floccinaucinihilipilification:24151] *** Process received signal *** >> [floccinaucinihilipilification:24151] Signal: Segmentation fault (11) >> [floccinaucinihilipilification:24151] Signal code: Address not mapped (1) >> [floccinaucinihilipilification:24151] Failing at address: (nil) >> [floccinaucinihilipilification:24159] *** Process received signal *** >> [floccinaucinihilipilification:24159] Signal: Segmentation fault (11) >> [floccinaucinihilipilification:24159] Signal code: Address not mapped (1) >> [floccinaucinihilipilification:24159] Failing at address: (nil) >> [floccinaucinihilipilification:24151] [ 0] /lib/libpthread.so.0 >> [0x7fefb916a020] >> [floccinaucinihilipilification:24151] [ 1] >> Ray(_ZN11SeedingData12computeSeedsEv+0x27e) [0x4781ce] >> [floccinaucinihilipilification:24151] [ 2] >> Ray(_ZN7Machine10runVanillaEv+0x76) [0x4430e6] >> [floccinaucinihilipilification:24151] [ 3] Ray(_ZN7Machine5startEv+0xd27) >> [0x448f27] >> [floccinaucinihilipilification:24151] [ 4] Ray(main+0x3a) [0x496a8a] >> [floccinaucinihilipilification:24151] [ 5] >> /lib/libc.so.6(__libc_start_main+0xf4) [0x7fefb8f384f4] >> [floccinaucinihilipilification:24151] [ 6] Ray(__gxx_personality_v0+0x1f9) >> [0x422ee9] >> [floccinaucinihilipilification:24151] *** End of error message *** >> [floccinaucinihilipilification:24159] [ 0] /lib/libpthread.so.0 >> [0x7f301b2df020] >> [floccinaucinihilipilification:24159] [ 1] >> Ray(_ZN11SeedingData12computeSeedsEv+0x27e) [0x4781ce] >> [floccinaucinihilipilification:24159] [ 2] >> Ray(_ZN7Machine10runVanillaEv+0x76) [0x4430e6] >> [floccinaucinihilipilification:24159] [ 3] Ray(_ZN7Machine5startEv+0xd27) >> [0x448f27] >> [floccinaucinihilipilification:24159] [ 4] Ray(main+0x3a) [0x496a8a] >> [floccinaucinihilipilification:24159] [ 5] >> /lib/libc.so.6(__libc_start_main+0xf4) [0x7f301b0ad4f4] >> [floccinaucinihilipilification:24159] [ 6] Ray(__gxx_personality_v0+0x1f9) >> [0x422ee9] >> [floccinaucinihilipilification:24159] *** End of error message *** >> -------------------------------------------------------------------------- >> mpirun noticed that process rank 8 with PID 24147 on node >> floccinaucinihilipilification.molgen.mpg.de<http://floccinaucinihilipilification.molgen.mpg.de><http://floccinaucinihilipilification.molgen.mpg.de> >> exited on signal 11 (Segmentation fault). >> -------------------------------------------------------------------------- >> [floccinaucinihilipilification:24141] *** Process received signal *** >> [floccinaucinihilipilification:24141] Signal: Segmentation fault (11) >> [floccinaucinihilipilification:24141] Signal code: Address not mapped (1) >> [floccinaucinihilipilification:24141] Failing at address: (nil) >> [floccinaucinihilipilification:24141] [ 0] /lib/libpthread.so.0 >> [0x7fdd46816020] >> [floccinaucinihilipilification:24141] [ 1] >> Ray(_ZN11SeedingData12computeSeedsEv+0x27e) [0x4781ce] >> [floccinaucinihilipilification:24141] [ 2] >> Ray(_ZN7Machine10runVanillaEv+0x76) [0x4430e6] >> [floccinaucinihilipilification:24141] [ 3] Ray(_ZN7Machine5startEv+0xd27) >> [0x448f27] >> [floccinaucinihilipilification:24141] [ 4] Ray(main+0x3a) [0x496a8a] >> [floccinaucinihilipilification:24141] [ 5] >> /lib/libc.so.6(__libc_start_main+0xf4) [0x7fdd465e44f4] >> [floccinaucinihilipilification:24141] [ 6] Ray(__gxx_personality_v0+0x1f9) >> [0x422ee9] >> [floccinaucinihilipilification:24141] *** End of error message *** >> ( [crash/finish] ) >> >> >> is this a problem on the server's side? >> Also i noticed that the error always shows up at the "Step: Selection of >> optimal read markers" process.. >> I think we are getting close to making it work :) please bear with me >> thank you very much, >> Nicolas >> >> >> >> >> 2011/8/30 Sébastien Boisvert >> <sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>>> >> ______________________________________ >>> De : >>> nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>> >>> >>> [nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>>] >>> de la part de Nicolas Balcazar >>> [balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>>] >>> Date d'envoi : 30 août 2011 00:03 >>> À : Sébastien Boisvert >>> Objet : Re: RE : RE : RAY just on LAM/MPI? >>> >>> Hi Sébastien >>> >>> i installed openmpi and with that Ray started to work perfectly! :) thanks >>> for the advice! >>> But now maybe u can help me out again: After 13h of computation Ray >>> suddenly stopped. Maybe i ran out of memory (130GB) but if so, >> >> >> There is an option called -show-memory-usage. >> >> If you run out of memory, your whole system becomes unstable and the linux >> kernel will give its out-of-memory killer (OOM killer) >> full authority. >> >> >> >>> i would have expected another kind of error message. Here how i started Ray >>> and the lines with the error message (in red): >>> >>> balcazar@floccinaucinihilipilification:/project/nicolas/run_RAY> mpirun -np >>> 25 Ray -k 101 -p ../data_solexa/C_GCCAAT_L001_R1_001.fastq >>> ../data_solexa/C_GCCAAT_L001_R2_001.fastq -s >>> ../data_454/sff/GFHVXCR01.RL2.sff -s ../data_454/sff/GFHVXCR02.RL2.sff -o >>> bal-Ray-SolAnd454-test2 | tee log_assembly_RAY_test2.txt >>> >> >> 1. You are not using Open-MPI at all. >> >> "You can use the "lamexec" program" from the log. lamexec is a program in >> LAM/MPI, not Open-MPI. >> >> >> 2. Why do you have only log lines for rank 0 ? >> >> >> >> >>> Rank 0 is selecting optimal read markers [850001/8725982] >>> Rank 0 is selecting optimal read markers [860001/8725982] >>> Rank 0 is purging edges [41350001/51238092] >>> Rank 0 is selecting optimal read markers [8725982/8725982] (completed) >>> Rank 0: peak number of workers: 186, maximum: 30000 >>> Rank 0: VirtualCommunicator: 302522250 pushed messages generated 2452837 >>> virtual messages (0.810796%) >>> >>> *** >>> Step: Selection of optimal read markers >>> Date: Tue Aug 30 04:17:16 2011 >>> Elapsed time: 23 minutes, 53 seconds >>> Since beginning: 13 hours, 22 minutes, 13 seconds >>> *** >>> >>> Rank 0 is creating seeds [1/51238092] >>> Rank 0 is purging edges [39300001/51238092] >>> Rank 0 is selecting optimal read markers [870001/8725982] >>> Rank 0 is selecting optimal read markers [880001/8725982] >>> Rank 0 is selecting optimal read markers [890001/8725982] >>> [floccinaucinihilipilification:11454] *** Process received signal *** >>> Rank 0 is selecting optimal read markers [900001/8725982] >>> Rank 0 is purging edges [41400001/51238092] >>> Rank 0 is purging edges [39350001/51238092] >>> Rank 0 is selecting optimal read markers [910001/8725982] >>> [floccinaucinihilipilification:11454] Signal: Segmentation fault (11) >>> [floccinaucinihilipilification:11454] Signal code: Address not mapped (1) >>> [floccinaucinihilipilification:11454] Failing at address: (nil) >>> Rank 0 is selecting optimal read markers [920001/8725982] >>> Rank 0 is selecting optimal read markers [930001/8725982] >>> Rank 0 is selecting optimal read markers [940001/8725982] >>> Rank 0 is purging edges [41450001/51238092] >>> Rank 0 is selecting optimal read markers [950001/8725982] >>> Rank 0 is purging edges [39400001/51238092] >>> Rank 0 is selecting optimal read markers [960001/8725982] >>> Rank 0 is selecting optimal read markers [970001/8725982] >>> Rank 0 is selecting optimal read markers [980001/8725982] >>> Rank 0 is selecting optimal read markers [990001/8725982] >>> Rank 0 is selecting optimal read markers [1000001/8725982] >>> Rank 0 is purging edges [41500001/51238092] >>> Rank 0 is purging edges [39450001/51238092] >>> Rank 0 is selecting optimal read markers [1010001/8725982] >>> Rank 0 is selecting optimal read markers [1020001/8725982] >>> Rank 0 is selecting optimal read markers [1030001/8725982] >>> Rank 0 is selecting optimal read markers [1040001/8725982] >>> Rank 0 has 31000000 vertices >>> Rank 0 is selecting optimal read markers [1050001/8725982] >>> Rank 0 is purging edges [41550001/51238092] >>> Rank 0 is selecting optimal read markers [1060001/8725982] >>> Rank 0 is purging edges [39500001/51238092] >>> Rank 0 is selecting optimal read markers [1070001/8725982] >>> Rank 0 is selecting optimal read markers [1080001/8725982] >>> Rank 0 is selecting optimal read markers [1090001/8725982] >>> Rank 0 is selecting optimal read markers [1100001/8725982] >>> Rank 0 is selecting optimal read markers [1110001/8725982] >>> Rank 0 is purging edges [41600001/51238092] >>> Rank 0 is purging edges [39550001/51238092] >>> Rank 0 is selecting optimal read markers [1120001/8725982] >>> Rank 0 is selecting optimal read markers [1130001/8725982] >>> Rank 0 is selecting optimal read markers [1140001/8725982] >>> Rank 0 is selecting optimal read markers [1150001/8725982] >>> Rank 0 is selecting optimal read markers [1160001/8725982] >>> Rank 0 is purging edges [41650001/51238092] >>> Rank 0 is selecting optimal read markers [1170001/8725982] >>> Rank 0 is purging edges [39600001/51238092] >>> [floccinaucinihilipilification:11454] [ 0] /lib/libpthread.so.0 >>> [0x7fd87790c020] >>> [floccinaucinihilipilification:11454] [ 1] >>> Ray(_ZN11SeedingData12computeSeedsEv+0x27e) [0x4781ce] >>> [floccinaucinihilipilification:11454] [ 2] >>> Ray(_ZN7Machine10runVanillaEv+0x76) [0x4430e6] >>> [floccinaucinihilipilification:11454] [ 3] Ray(_ZN7Machine5startEv+0xd27) >>> [0x448f27] >>> [floccinaucinihilipilification:11454] [ 4] Ray(main+0x3a) [0x496a8a] >>> [floccinaucinihilipilification:11454] [ 5] >>> /lib/libc.so.6(__libc_start_main+0xf4) [0x7fd8776da4f4] >>> [floccinaucinihilipilification:11454] [ 6] Ray(__gxx_personality_v0+0x1f9) >>> [0x422ee9] >>> [floccinaucinihilipilification:11454] *** End of error message *** >>> Rank 0 is selecting optimal read markers [1180001/8725982] >>> Rank 0 is selecting optimal read markers [1190001/8725982] >>> Rank 0 is selecting optimal read markers [1200001/8725982] >>> Rank 0 is selecting optimal read markers [1210001/8725982] >>> Rank 0 is selecting optimal read markers [1220001/8725982] >>> Rank 0 is purging edges [41700001/51238092] >>> Rank 0 is purging edges [39650001/51238092] >>> Rank 0 is selecting optimal read markers [1230001/8725982] >>> Rank 0 is selecting optimal read markers [1240001/8725982] >>> Rank 0 is selecting optimal read markers [1250001/8725982] >>> Rank 0 is selecting optimal read markers [1260001/8725982] >>> Rank 0 is selecting optimal read markers [1270001/8725982] >>> Rank 0 is purging edges [41750001/51238092] >>> Rank 0 is selecting optimal read markers [1280001/8725982] >>> Rank 0 is purging edges [39700001/51238092] >>> Rank 0 is selecting optimal read markers [1290001/8725982] >>> Rank 0 is selecting optimal read markers [1300001/8725982] >>> Rank 0 is selecting optimal read markers [1310001/8725982] >>> Rank 0 is selecting optimal read markers [1320001/8725982] >>> Rank 0 is selecting optimal read markers [1330001/8725982] >>> Rank 0 is purging edges [41800001/51238092] >>> Rank 0 is purging edges [39750001/51238092] >>> Rank 0 is selecting optimal read markers [1340001/8725982] >>> Rank 0 is selecting optimal read markers [1350001/8725982] >>> Rank 0 is selecting optimal read markers [1360001/8725982] >>> Rank 0 is selecting optimal read markers [1370001/8725982] >>> Rank 0 is selecting optimal read markers [1380001/8725982] >>> Rank 0 is purging edges [41850001/51238092] >>> Rank 0 is selecting optimal read markers [1390001/8725982] >>> Rank 0 is purging edges [39800001/51238092] >>> Rank 0 is selecting optimal read markers [1400001/8725982] >>> Rank 0 is selecting optimal read markers [1410001/8725982] >>> Rank 0 is selecting optimal read markers [1420001/8725982] >>> Rank 0 is selecting optimal read markers [1430001/8725982] >>> Rank 0 is selecting optimal read markers [1440001/8725982] >>> Rank 0 is purging edges [41900001/51238092] >>> Rank 0 is purging edges [39850001/51238092] >>> Rank 0 is selecting optimal read markers [1450001/8725982] >>> Rank 0 is selecting optimal read markers [1460001/8725982] >>> ----------------------------------------------------------------------------- >>> It seems that [at least] one of the processes that was started with >>> mpirun did not invoke MPI_INIT before quitting (it is possible that >>> more than one process did not invoke MPI_INIT -- mpirun was only >>> notified of the first one, which was on node n0). >>> >>> mpirun can *only* be used with MPI programs (i.e., programs that >>> invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program >>> to run non-MPI programs over the lambooted nodes. >>> ----------------------------------------------------------------------------- >>> balcazar@floccinaucinihilipilification:/project/nicolas/run_RAY> >>> >>> >>> THANKS for your help! >>> Nicolas >>> >>> >>> >>> >>> 2011/8/17 Sébastien Boisvert >>> <sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>>>> >>> Your problem is with LAM/MPI, not with Ray. >>> >>> I never used LAM/MPI. >>> >>> >>> Can you verify that lamboot, mpic++ and mpirun are from the LAM/MPI. >>> >>> >>> Try searching the LAM/MPI mailing list for similar issues. >>> >>> >>> >>> Sébastien >>> ________________________________________ >>> De : >>> nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>>> >>> >>> [nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>>>] >>> de la part de Nicolas Balcazar >>> [balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>>>] >>> Date d'envoi : 16 août 2011 20:20 >>> À : Sébastien Boisvert >>> Objet : Re: RE : RAY just on LAM/MPI? >>> >>> Thank you for your quick replay. >>> In deed i had to start lamboot first. Luckily this was installed already on >>> the server, open-mpi is not installed :( and i cannot install anything >>> there. mpic++ is in my path, so i didnt change the MPICXX option. >>> >>> But now still i get this error message: >>> >>> cannot execute binary file >>> ----------------------------------------------------------------------------- >>> It seems that [at least] one of the processes that was started with >>> mpirun did not invoke MPI_INIT before quitting (it is possible that >>> more than one process did not invoke MPI_INIT -- mpirun was only >>> notified of the first one, which was on node n0). >>> >>> mpirun can *only* be used with MPI programs (i.e., programs that >>> invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program >>> to run non-MPI programs over the lambooted nodes. >>> ----------------------------------------------------------------------------- >>> >>> Is there something i can do without having to install something complicated >>> on the server? >>> I'm really looking forward to use RAY! >>> >>> Thanks again, >>> Nicolas >>> >>> >>> >>> >>> 2011/8/16 Sébastien Boisvert >>> <sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>>><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca><mailto:sebastien.boisver...@ulaval.ca<mailto:sebastien.boisver...@ulaval.ca>>>>> >>> MPI is a requirement for Ray. >>> >>> The messages will just transit in shared memory if all processes are on the >>> same host. >>> >>> You can run Ray on 1 single core too. The single MPI rank will then send >>> messages to itself. >>> >>> >>> >>> Sébastien >>> ________________________________________ >>> De : >>> nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>>><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>>>> >>> >>> [nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>>><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com><mailto:nicolasber...@gmail.com<mailto:nicolasber...@gmail.com>>>>] >>> de la part de Nicolas Balcazar >>> [balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>>>>] >>> Date d'envoi : 15 août 2011 23:57 >>> À : >>> s...@boisvert.info<mailto:s...@boisvert.info><mailto:s...@boisvert.info<mailto:s...@boisvert.info>><mailto:s...@boisvert.info<mailto:s...@boisvert.info><mailto:s...@boisvert.info<mailto:s...@boisvert.info>>><mailto:s...@boisvert.info<mailto:s...@boisvert.info><mailto:s...@boisvert.info<mailto:s...@boisvert.info>><mailto:s...@boisvert.info<mailto:s...@boisvert.info><mailto:s...@boisvert.info<mailto:s...@boisvert.info>>>> >>> Objet : Re: RAY just on LAM/MPI? >>> >>> Hi Sebastien, >>> >>> sorry, its me again, >>> i just wanted to specify my question. I work on a machine with some other >>> people that has 32 cores and 132GB RAM. >>> I dont think i really need a Lamboot/LAM/MPI. >>> So: can i make RAY work, without that? >>> >>> THANKS!! :) >>> >>> Nicolas >>> >>> >>> >>> >>> On Tue, Aug 16, 2011 at 5:47 AM, Nicolas Balcazar >>> <balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>>>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de><mailto:balca...@molgen.mpg.de<mailto:balca...@molgen.mpg.de>>>>>> >>> wrote: >>> Hi Sébastien, >>> >>> i tryed to use RAY and after having all my data nicely lined up, i get this >>> error message just after starting the program from the commandline: >>> >>> mpirun -np 25 ../../RAY/Ray-1.6.1/Ray-Large-kmers-gz/Ray -k 101 -p >>> ../data_solexa/C_GCCAAT_L001_R1_001.fastq >>> ../data_solexa/C_GCCAAT_L001_R2_001.fastq >>> ----------------------------------------------------------------------------- >>> It seems that there is no lamd running on the host >>> tiaotiao.molgen.mpg.de<http://tiaotiao.molgen.mpg.de><http://tiaotiao.molgen.mpg.de><http://tiaotiao.molgen.mpg.de><http://tiaotiao.molgen.mpg.de><http://tiaotiao.molgen.mpg.de>. >>> >>> This indicates that the LAM/MPI runtime environment is not operating. >>> The LAM/MPI runtime environment is necessary for the "mpirun" command. >>> >>> Please run the "lamboot" command the start the LAM/MPI runtime >>> environment. See the LAM/MPI documentation for how to invoke >>> "lamboot" across multiple machines. >>> ----------------------------------------------------------------------------- >>> >>> If u could tell me if i can make it work somehow, >>> i would be very thankful!! >>> >>> Thanks, >>> Nicolas >>> >>> >>> >>> >>> >> >> > > > > > > ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users