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sebhtml / ray

Ray -- Parallel genome assemblies for parallel DNA sequencing
http://denovoassembler.sf.net
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Ray does not run if only 2 cores are assigned #221

Closed bastian-wur closed 10 years ago

bastian-wur commented 10 years ago

As the title says, if I try to run Ray on only 2 cores, then it just doesn't work. Problem does not appear with 1, 3, or a higher amount of cores.

Tested command: mpiexec -n 2 ./Ray -p /home/bastian/data/Raw_data/NG-XXX_1_1.fastq /home/bastian/data/Raw_data/NG-XXX_1_2.fastq

output:

This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions; see "LICENSE.txt" for details.

Ray Copyright (C) 2010, 2011, 2012, 2013 Sébastien Boisvert Centre de recherche en infectiologie de l'Université Laval Project funded by the Canadian Institutes of Health Research (Doctoral award 200902CGM-204212-172830 to S.B.) http://denovoassembler.sf.net/

References to cite:

Sébastien Boisvert, Frédéric Raymond, Élénie Godzaridis, François Laviolette and Jacques Corbeil. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biology (BioMed Central Ltd). 13:R122, Published: 22 December 2012 http://dx.doi.org/doi:10.1186/gb-2012-13-12-r122

Sébastien Boisvert, François Laviolette & Jacques Corbeil. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. Journal of Computational Biology (Mary Ann Liebert, Inc. publishers, New York, U.S.A.). November 2010, Volume 17, Issue 11, Pages 1519-1533. http://dx.doi.org/doi:10.1089/cmb.2009.0238

Ray version 2.3.0 License for Ray: GNU General Public License version 3 RayPlatform version: 2.0.0 License for RayPlatform: GNU Lesser General Public License version 3

MAXKMERLENGTH: 201 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 2.1 MPI library: Open-MPI 1.4.3 Compiler: GNU gcc/g++ 4.6.3 MPI I/O: n

And then nothing happens.

sebhtml commented 10 years ago

THis is a regression caused by: d50a972c81b1ca0c9160648ad3053be8319f85f5

(gdb) bt

0 0x0000003fa50135a1 in __ieee754_pow () from /lib64/libm.so.6

1 0x0000003fa50143ab in __ieee754_pow () from /lib64/libm.so.6

2 0x0000003fa50254e5 in pow () from /lib64/libm.so.6

3 0x00000000004e2c17 in Parameters::setDefaultRoutingOptions (this=0x2b7d64a6f9a8) at code/Mock/Parameters.cpp:1123

4 0x00000000004f2bd4 in Parameters::constructor (this=0x2b7d64a6f9a8, argc=4, argv=0x7fff7639eb28, rank=Unhandled dwarf expression opcode 0xf3

) at code/Mock/Parameters.cpp:1083

5 0x00000000004895e8 in Machine::start (this=0x2b7d64a32040) at code/application_core/Machine.cpp:312

6 0x0000000000487ee7 in startMiniRank (this=0x7fff7639e3b0) at RayPlatform/RayPlatform/core/RankProcess.h:318

7 RankProcess::run (this=0x7fff7639e3b0) at RayPlatform/RayPlatform/core/RankProcess.h:235

8 0x0000000000488162 in main (argc=4, argv=0x7fff7639eb28) at code/application_core/ray_main.cpp:32

(gdb) f 3

3 0x00000000004e2c17 in Parameters::setDefaultRoutingOptions (this=0x2b7d64a6f9a8) at code/Mock/Parameters.cpp:1123

1123 int computedVertices = (int)pow(radix, dimension); (gdb) info locals computedVertices = dimension = foundSolution = false actualVertices = 2 radix = -2571390

sebhtml commented 10 years ago

https://github.com/sebhtml/ray/commit/9729dbce542fca2cbe45ea9cd5a436d573461b87

bastian-wur commented 10 years ago

Merci :).

From: Sébastien Boisvert [notifications@github.com] Sent: Thursday, November 21, 2013 4:24 PM To: sebhtml/ray Cc: Hornung, Bastian Subject: Re: [ray] Ray does not run if only 2 cores are assigned (#221)

Closed #221https://github.com/sebhtml/ray/issues/221.

— Reply to this email directly or view it on GitHubhttps://github.com/sebhtml/ray/issues/221.