>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

Reply via email to