Hi, I found a error when running the new version which didn't show in v2.1.0. Below is the log file with beginning and tail.
---- 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: 127 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 1.5.4 Compiler: GNU gcc/g++ 4.4.3 MPI I/O: n -k (to set the k-mer size) Value: 85 Paired library # 0 -p (paired-end sequences) Left sequences: trim/QC.1.trimmed.fastq Right sequences: trim/QC.2.trimmed.fastq Average length: automatic detection Standard deviation: automatic detection -s (single sequences) Sequences: trim/QC.unpaired.trimmed.fastq . . . Rank 24: assembler memory usage: 532224 KiB Rank 24 has 7500000 sequence reads Rank 24: assembler memory usage: 548612 KiB Rank 24 has 7600000 sequence reads Rank 24: assembler memory usage: 548612 KiB Rank 24 has 7608397 sequence reads (completed) Critical exception: The system is out of memory, returned NULL. Requested -213514032 bytes of type RAY_MALLOC_TYPE_BLOOM_FILTER Critical exception: The system is out of memory, returned NULL. Requested -213514032 bytes of type RAY_MALLOC_TYPE_BLOOM_FILTER On 4/17/13 8:56 AM, "Sébastien Boisvert" <sebastien.boisver...@ulaval.ca> wrote: >Hello, > >Ray v2.2.0 is now available worldwide. > >The delay between v2.1.0 and v2.2.0 was quite huge. > >Ray v2.2.0 brings a lot of bug fixes and some new features. > >The tarball is available at: > >http://sourceforge.net/projects/denovoassembler/files/Ray-v2.2.0.tar.bz2 > > > > > >The most significant changes include: > >* SequencesLoader: the Illumina export format is now supported >* add build option for MPI I/O >* void infinite loops during read recycling >* messages must not be passed by value >* Fixed a linking error caused by ordering >* FusionTaskCreator: don't lose genomic regions during merging >* new file GraphPartition.txt shows the distribution of objects >* readahead operations are used for reading gz files >* core: fixed a race condition occurring with -route-messages >* SeedingData: fix regression for seed checkpointing >* all the code of Ray was ported to this new GraphPath framework > >The GraphPath framework reduces the memory usage and avoid some >misassembly >errors by enforcing the Bruijn graph property. > >* Scaffolder: don't fetch reads from repeated objects > >This fixes running time issues on large genomes with repeats. > >* SeedingData: implemented a staggered mean algorithm > >* Mock: removed the limit on the number of input files >* Library: implemented checkpointing for paired reads >* removed all calls to fflush(stdout) and cout.flush() >* SeedExtender: reduce the verbosity of graph traversal >* reduced the amount of information in the standard output >* JoinerTaskCreator: reduced the default verbosity >* KmerAcademyBuilder: reduced the verbosity for graph construction >* implemented an adaptive Bloom filter >* store a path as a sequence instead of a vector of vertices for >efficiency >* SequencesLoader: add support for short file names > > > > > >All changes in Ray between v2.1.0 and v2.2.0 > >Charles Joly Beauparlant (1): > Added an example plugin. > >Sébastien Boisvert (160): > Some work around the minirank model. > Ported Ray plugins to the mini-ranks RayPlatform. > Ray plugins were ported to the mini-ranks. > Moved the destruction of allocators in RayPlatform. > I ported Ray to some changes in some classes in RayPlatform. > application_core: the application code was simplified > Social networks were added to the release procedure > Code names of old releases were added > Fixed a linking error caused by ordering > Fixed the scope of options in build system > The build system was simplified > AR and LD are not needed here > Ray must abort if the output directory exists > The RayCommand.txt file was fixed for mini-ranks > Added the name of each rank (or mini-rank) in network test > The subgraph must be built regardless if it will be used > Merge branch 'minirank-model' of git://github.com/sebhtml/ray.git > core: CONFIG_* variables are private > core: The option -mini-rank-per-rank was added > ship: removed 6 files in shipped products > core: don't return parameters by value > Mock: new plugin called that does nothing > SequencesLoader: a regression for .bz2 file support was fixed > messages must not be passed by value > Ordered all headers > Updated copyrights > Documentation: there is only one repository for research tools > reverted a wrong hunk from commit 7c361f1530d084c6f99 > FusionTaskCreator: don't lose genomic regions during merging > SeedExtender: properly format extension file name > Scaffolder: only put one new line after scaffold sequence > KmerAcademyBuilder: use vertexRank() to find who owns an object > new file GraphPartition.txt shows the distribution of objects > the line that shows the process identifier was moved > CoverageGatherer: kmers.txt should have 1 header only > recursive make was improved > readahead operations are used for reading gz files > SequencesLoader: added the rank number when loading files > core: the partitioner needs the correct rank number > core: fixed a race condition occurring with -route-messages > SeedExtender: display the number of traversed nucleotide symbols > Seeds: new runtime metrics for seeding algorithms > new header for SeedLengthDistribution.txt > new header for any paired read file LibraryN.txt > SequencesLoader: added a few assertions for read partitions > new header for CoverageDistribution.txt > Merge branch 'master' of github.com:sebhtml/ray > Documentation: added the polytope with 4225 vertices > SeedingData: fix regression for seed checkpointing > added documentation for using the torus > Documentation: added arguments for a 5D torus with 1024 vertices > Documentation: fixed permissions > removed the output file called MessagePassingInterface.txt > renamed the AssemblySeed to GraphPath so it can be reused > all the code of Ray was ported to this new GraphPath framework > Documentation: fixed the degree of the polytope > Scaffolder: don't fetch reads from repeated objects > SeedExtender: added documentation in the code for repeated vertices > fixed a couple of compilation warnings > SeedingData: implemented a staggered mean algorithm > Scaffolder: replaced getMode() by the new GraphPath framework > Mock: removed the limit on the number of input files > remove the limitation regarding the maximum number of files > moved message handlers from MessageProcessor to SequencesLoader > Scaffolder: fixed 2 compilation warnings > Library: implemented checkpointing for paired reads > SeedingData: reduced amount of printed information > removed all calls to fflush(stdout) and cout.flush() > SeedExtender: reduce the verbosity of graph traversal > reduced the amount of information in the standard output > JoinerTaskCreator: reduced the default verbosity > KmerAcademyBuilder: reduced the verbosity for graph construction > SequencesLoader: reduced verbosity > VerticesExtractor: reduced verbosity > reduced verbosity > reduced verbosity > SequencesLoader: the Illumina export format is now supported > added a loader interface for file formats > SequencesLoader: all supported formats use the interface > SequencesLoader: implemented a product factory > Mock: updated documentation for new export format > Mock: output a single file for library data > implemented an adaptive Bloom filter > improved the interface of path objects > add debug symbols by default > store a path as a sequence instead of a vector of vertices for >efficiency > Mock: the path storage using blocks is not ready > SeedingData: enforce de Bruijn graph property for path storage > SeedingData: use the GraphPath storage code to compute seeds > SeedingData: refactor code so that m_content is abstracted > SeedingData: use 2-bit encoding for paths > SeedingData: plugin options are parsed by plugins > use constants for symbols > SeedingData: correctly detect dead ends > add more information for coding style > MachineHelper: registerPlugin and resolveSymbols must be last > SeedingData: tips can not be seeds > SequencesLoader: add support for short file names > SeedingData: tips are not valid seeds > move some handlers in the Scaffolder plugin > Scaffolder: implement the handler for packed chunks > fix a race condition during directory probing > reduce verbosity of components > add documentation for building on IBM Blue Gene/Q > add code name for upcoming release > SequencesLoader: fix regression (added in ca979832) for line widths > add plugin PathEvaluator to evaluate paths > PathEvaluator: write ContigPaths checkpoints in parallel > reserve storage capacity for sequence file > perform parallel I/O operations > fix a bug when disabling scaffolding > use MPI I/O to write Contigs.fasta > use a file view for each MPI rank > add build option for MPI I/O > avoid parallel I/O without MPI I/O > avoid infinite loops during read recycling > update polytope documentation > add comments for old class > add a new plugin to process spurious seeds > port some plugins to the simplified RayPlatform API > iterate on seeds to filter them > register seed paths in the distributed graph > hide hash values for Bloom filter > push the workflow in a helper class > fetch ancestors of seed heads > seed lengths must be collected after analysis > write seed statistics after analysis > write seed checkpoints after the quality control analysis > write seed files after analysis (-write-seeds) > skip seed quality analysis if checkpoints exist > add steps for better dead end detection > hide mini-ranks in help if they are disabled > correct a bunch of bugs for adapters in Ray > reuse code paths to obtain sequence information > eliminate seeds that have a dead-end on the left > discard seeds with dead-ends on the right > increase the maximum depth for searches > add a class to fetch the attributes of a DNA sequence > create a class to fetch annotations in a portable way > fetch nearby paths to detect bubbles > fix a bug during the registration of seeds > remove any seed that is a weak part of a bubble > add 4 methods that will be implemented later > fix a regression that prevented the closing of a file > add new reference in the output > disable the seed filter when using short kmers > add a maximum coverage depth for dead end search > adapt the allowed depth in function of the data > add design blueprints for the new plugin > SpuriousSeedAnnihilator: disable debug messages by default > TaxonomyViewer: rename the plugin to TaxonomyViewer > remove plugin_ from all plugin directory names > add new line for publications > application_core: fix buggy message routing > SeedExtender: don't traverse path if it's consumed already > SeedingData: fix a bug for the phix system test > update the CMakeList.txt > use git to store version names > Disable the filtering code during the computation of seeds > This is Ray v2.2.0 > > > > >All changes in RayPlatform between v1.1.0 and v1.1.1 > > >Sébastien Boisvert (56): > initial work on miniranks with VirtualMachine and Minirank > I added some design documentation for mini-ranks. > spinlocks are more suitable for this job > added design documentation for mini-ranks. > First implementation of mini-ranks in RayPlatform > The core must provide the mini-rank number. > Documentation: added description of macros. > Fixed some bugs in the mini-ranks model. > Moved the destruction of allocators in the core. > Mini-rank source and mini-rank destination are required. > The desctructor of the middleware must be called. > A mini-rank must tell the rank that it has messages to send. > The class MessageQueue does the job of receiving messages. > Non-blocking queues will be used for the communication. > The non-blocking message queue for mini-ranks is ready. > MPI_Recv must be called to get the mini-rank numbers. > This is the branch for RayPlatform v7.0.0. > core: The old behavior (no mini-ranks) now works as expected > core: RayPlatform is responsible for creating mini-ranks > The old adapter API documentation was removed > Message reception is now interleaved with send operations. > More buffers are needed for mini-ranks > communication: don't register already registered buffers > The build system is less verbose > New API call to get the number of mini-ranks per rank > Added a method to get the MessagesHandler object > Merge branch 'minirank-model' of github.com:sebhtml/RayPlatform >into minirank-model > Merge branch 'minirank-model' of >git://github.com/sebhtml/RayPlatform.git > handlers: new option to cache operation codes > communication: messages must be passed with a pointer > Ordered headers in all files > Updated copyrights > The short name was updated in headers > The website was updated in every file > a retry is necessary when a message is pushed into a full ring > Documentation: updated RayPlatform mini-ranks blueprints > communication: moved writeFiles() in a second method > communication: removed a few debugging instructions > Documentation: added gate blueprints > Documentation: improved design for non-linear scheduling > routing: renamed the hypercube to polytope > Documentation: added Torus description > a radix of 2 produces a hypercube > use the Q and ASSERT build arguments in RayPlatform > routing: implemented a new communication graph: the torus > Merge branch 'master' of github.com:sebhtml/RayPlatform > core: use specific code to get memory usage on Blue Gene/Q > the next release will likely be 1.2.0 and not 7.0.0 > add option to provide public access to a master mode > add the core in each plugin > add two macros to configure handlers > fixed directives to compile mini-ranks > core: fix buggy message routing > improve the patch for message routing with a configuration > core: fix a regression for registered handle names > This is RayPlatform v1.1.0. > >-------------------------------------------------------------------------- >---- >Precog is a next-generation analytics platform capable of advanced >analytics on 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