De Novo Assembly using Ray

[Farhat]

Is there any information on how much RAM is required for Ray to run? I am using Ray-1.4.0 and everytime it crashes after swapping. I am trying to assemble about 30M 100 bp long paired Illumina reads. Is there any way in which RAM usage can be minimized?

[seb567]

Is there any information on how much RAM is required for Ray to run?

There is no simple formula for computing memory usage.

It depends mostly on the error rate and the number of reads and nucleotides.

The following paper talks about that topic in detail.

http://dx.doi.org/doi:10.1093/bioinformatics/btq697

Is there any way in which RAM usage can be minimized?

2 ways: (1) pack structures and (2) change the k-mer length.

If you use gcc/g++ (a C++ compiler), you can edit the Makefile and change the line

CFLAGS=-I. -O3 -Wall -Icode -fomit-frame-pointer -DASSERT -DHAVE_ZLIB -DHAVE_LIBBZ2 -DHAVE_CLOCK_GETTIME

for

CFLAGS=-I. -O3 -Wall -Icode -fomit-frame-pointer -DASSERT -DHAVE_ZLIB -DHAVE_LIBBZ2 -DHAVE_CLOCK_GETTIME -DFORCE_PACKING

(add -DFORCE_PACKING at the end of the line)


This will pack structures.
By default, compilers round to the higher 8-byte boundary.
If a structure has a size of 5 bytes, gcc rounds that to 8 bytes in order to have everything aligned. This way, you never get a 8-byte word sitting between two memory pages.


This works on x86 and x86_64.

It does not work on SPARC and on Itanium.

Velvet uses this approach by the way.


Also, the k-mer length impacts on the memory consumption.

In the upcoming Ray v1.6.0 (now at v1.6.0-rc2), Ray will use arbitrary long k-mers.

See https://github.com/sebhtml/ray

I am using Ray-1.4.0 and everytime it crashes after swapping. I am trying to assemble about 30M 100 bp long paired Illumina reads.

If you want to try it now:

git clone git://github.com/sebhtml/ray.git
cd ray
make PREFIX=build-kMAX=64-packed FORCE_PACKING=y MAXKMERLENGTH=64
# wait
make install
mpirun -np 66 ./build-kMAX=64-packed/Ray -k 49 \
-p lib1_1.fastq lib1_2.fastq \
-p lib2_1.fastq lib2_2.fastq \
-o DeadlyBug
# wait
ls DeadlyBug.Scaffolds.fasta

You may need to supply manually the insert sizes if they are large.

mpirun -np 66 ./build-kMAX=64-packed/Ray -k 49 \
-p lib1_1.fastq lib1_2.fastq \
-p lib2_1.fastq lib2_2.fastq 4000 400\
-o DeadlyBugManual



Where does it crash ?

How much memory do you have ?


Feel free to ask on the mailing list too: denovoassembler-users AT lists.sourceforge.net

p.s. I am the author of Ray.

Sébastien

http://denovoassembler.sf.net/

[Farhat]

Thanks, Sébastien. Trying with newer parameters now.

It crashes after it runs out of RAM and swap. I have about 280 GB of RAM.

ETA: It doesn't segfault so crash is a wrong word. It runs out of memory and stops.

[seb567]

Thanks, Sébastien. Trying with newer parameters now.

It crashes after it runs out of RAM and swap. I have about 280 GB of RAM.

ETA: It doesn't segfault so crash is a wrong word. It runs out of memory and stops.

You can also add the option --show-memory-usage.



This option only works on Linux.

[Saratoga]

Hi,

I'm very new in this arena.

I installed Ray 2.0 in MacOS (Snow Leopard) and I got a segmentation fault. Then I decided to update the compilers following http://sites.google.com/site/dwhipp/.../mac_compilers and then installed Open MPI http://sites.google.com/site/dwhipp/...pi-on-mac-os-x.

After that I tried to compile again but now I get a this error

ld: symbol(s) not found collect2:
ld returned 1 exit status make:
*** [Ray] Error 1

Please Advice

[seb567]

Hi,

You probably installed Ray v2.0.0-rc7 or v2.0.0-rc5 as v2.0.0 is not released yet !

Can you provide all the log of your compilation.

cd Ray-v2.0.0-rc7
make clean
make &> make.log

You can use http://pastebin.com

Hi,

I'm very new in this arena.

I installed Ray 2.0 in MacOS (Snow Leopard) and I got a segmentation fault. Then I decided to update the compilers following http://sites.google.com/site/dwhipp/.../mac_compilers and then installed Open MPI http://sites.google.com/site/dwhipp/...pi-on-mac-os-x.

After that I tried to compile again but now I get a this error

ld: symbol(s) not found collect2:
ld returned 1 exit status make:
*** [Ray] Error 1

Please Advice

[seb567]

I did test Ray on a Apple PowerBook G4 (PowerPC) running Linux and a Sun SunBlade 100 (Sparc).

What is the hardware of your Mac ?

Is it an Intel processor ?

I think Xcode on Mac OS is based of LLVM.

I remember that LLVM had problems linking sometimes of GNU/Linux for various applications.

Does that work at all on your Mac ?


mpiexec -n 3 date

Hi,

I'm very new in this arena.

I installed Ray 2.0 in MacOS (Snow Leopard) and I got a segmentation fault. Then I decided to update the compilers following http://sites.google.com/site/dwhipp/.../mac_compilers and then installed Open MPI http://sites.google.com/site/dwhipp/...pi-on-mac-os-x.

After that I tried to compile again but now I get a this error

ld: symbol(s) not found collect2:
ld returned 1 exit status make:
*** [Ray] Error 1

Please Advice

[Saratoga]

Hi,

This is the log



Compilation options (you can change them of course)

PREFIX = install-prefix
MAXKMERLENGTH = 32
FORCE_PACKING = n
ASSERT = n
HAVE_LIBZ = n
HAVE_LIBBZ2 = n
INTEL_COMPILER = n
MPICXX = mpicxx
GPROF = n
OPTIMIZE = y
DEBUG = n

Compilation and linking flags (generated automatically)

CXXFLAGS = -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\"
LDFLAGS =

mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/ReusableMemoryStore.o memory/ReusableMemoryStore.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/MyAllocator.o memory/MyAllocator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/RingAllocator.o memory/RingAllocator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/allocator.o memory/allocator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/DefragmentationGroup.o memory/DefragmentationGroup.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/ChunkAllocatorWithDefragmentation.o memory/ChunkAllocatorWithDefragmentation.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o memory/DefragmentationLane.o memory/DefragmentationLane.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementation.o routing/GraphImplementation.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationRandom.o routing/GraphImplementationRandom.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationComplete.o routing/GraphImplementationComplete.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationDeBruijn.o routing/GraphImplementationDeBruijn.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationKautz.o routing/GraphImplementationKautz.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationExperimental.o routing/GraphImplementationExperimental.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/GraphImplementationGroup.o routing/GraphImplementationGroup.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o routing/ConnectionGraph.o routing/ConnectionGraph.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/mpi_tags.o communication/mpi_tags.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/VirtualCommunicator.o communication/VirtualCommunicator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/BufferedData.o communication/BufferedData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/Message.o communication/Message.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/MessagesHandler.o communication/MessagesHandler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o communication/MessageRouter.o communication/MessageRouter.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o scheduling/VirtualProcessor.o scheduling/VirtualProcessor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o scheduling/TaskCreator.o scheduling/TaskCreator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o scheduling/SwitchMan.o scheduling/SwitchMan.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/slave_modes.o core/slave_modes.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/OperatingSystem.o core/OperatingSystem.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/master_modes.o core/master_modes.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/ComputeCore.o core/ComputeCore.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o core/statistics.o core/statistics.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o plugins/CorePlugin.o plugins/CorePlugin.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o plugins/RegisteredPlugin.o plugins/RegisteredPlugin.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o structures/StaticVector.o structures/StaticVector.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o profiling/Profiler.o profiling/Profiler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o profiling/Derivative.o profiling/Derivative.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o profiling/TickLogger.o profiling/TickLogger.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o profiling/TimePrinter.o profiling/TimePrinter.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/SlaveModeHandler.o handlers/SlaveModeHandler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/MasterModeHandler.o handlers/MasterModeHandler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/MessageTagHandler.o handlers/MessageTagHandler.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/MasterModeExecutor.o handlers/MasterModeExecutor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/SlaveModeExecutor.o handlers/SlaveModeExecutor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o handlers/MessageTagExecutor.o handlers/MessageTagExecutor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o cryptography/crypto.o cryptography/crypto.cpp
ar rcs libRayPlatform.a memory/ReusableMemoryStore.o memory/MyAllocator.o memory/RingAllocator.o memory/allocator.o memory/DefragmentationGroup.o memory/ChunkAllocatorWithDefragmentation.o memory/DefragmentationLane.o routing/GraphImplementation.o routing/GraphImplementationRandom.o routing/GraphImplementationComplete.o routing/GraphImplementationDeBruijn.o routing/GraphImplementationKautz.o routing/GraphImplementationExperimental.o routing/GraphImplementationGroup.o routing/ConnectionGraph.o communication/mpi_tags.o communication/VirtualCommunicator.o communication/BufferedData.o communication/Message.o communication/MessagesHandler.o communication/MessageRouter.o scheduling/VirtualProcessor.o scheduling/TaskCreator.o scheduling/SwitchMan.o core/slave_modes.o core/OperatingSystem.o core/master_modes.o core/ComputeCore.o core/statistics.o plugins/CorePlugin.o plugins/RegisteredPlugin.o structures/StaticVector.o profiling/Profiler.o profiling/Derivative.o profiling/TickLogger.o profiling/TimePrinter.o handlers/SlaveModeHandler.o handlers/MasterModeHandler.o handlers/MessageTagHandler.o handlers/MasterModeExecutor.o handlers/SlaveModeExecutor.o handlers/MessageTagExecutor.o cryptography/crypto.o
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o application_core/ray_main.o application_core/ray_main.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o application_core/Machine.o application_core/Machine.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o application_core/Parameters.o application_core/Parameters.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o application_core/common_functions.o application_core/common_functions.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Amos/Amos.o plugin_Amos/Amos.cpp
plugin_Amos/Amos.cpp: In member function ‘void Amos::call_RAY_SLAVE_MODE_AMOS()’:
plugin_Amos/Amos.cpp:136: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’
plugin_Amos/Amos.cpp:206: warning: format ‘%li’ expects type ‘long int’, but argument 3 has type ‘ReadHandle’
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_CoverageGatherer/CoverageGatherer.o plugin_CoverageGatherer/CoverageGatherer.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_CoverageGatherer/CoverageDistribution.o plugin_CoverageGatherer/CoverageDistribution.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_EdgePurger/EdgePurger.o plugin_EdgePurger/EdgePurger.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_EdgePurger/EdgePurgerWorker.o plugin_EdgePurger/EdgePurgerWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_FusionData/FusionData.o plugin_FusionData/FusionData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_FusionTaskCreator/FusionWorker.o plugin_FusionTaskCreator/FusionWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_FusionTaskCreator/FusionTaskCreator.o plugin_FusionTaskCreator/FusionTaskCreator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GeneOntology/KeyEncoder.o plugin_GeneOntology/KeyEncoder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GeneOntology/GeneOntology.o plugin_GeneOntology/GeneOntology.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GenomeNeighbourhood/GenomeNeighbourhood.o plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GenomeNeighbourhood/Neighbour.o plugin_GenomeNeighbourhood/Neighbour.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_GenomeNeighbourhood/NeighbourPair.o plugin_GenomeNeighbourhood/NeighbourPair.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_JoinerTaskCreator/JoinerWorker.o plugin_JoinerTaskCreator/JoinerWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_JoinerTaskCreator/JoinerTaskCreator.o plugin_JoinerTaskCreator/JoinerTaskCreator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/KmerAcademyBuilder.o plugin_KmerAcademyBuilder/KmerAcademyBuilder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/BloomFilter.o plugin_KmerAcademyBuilder/BloomFilter.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/Kmer.o plugin_KmerAcademyBuilder/Kmer.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/KmerAcademy.o plugin_KmerAcademyBuilder/KmerAcademy.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_KmerAcademyBuilder/KmerAcademyIterator.o plugin_KmerAcademyBuilder/KmerAcademyIterator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Library/LibraryPeakFinder.o plugin_Library/LibraryPeakFinder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Library/LibraryWorker.o plugin_Library/LibraryWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Library/Library.o plugin_Library/Library.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_MachineHelper/MachineHelper.o plugin_MachineHelper/MachineHelper.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_MessageProcessor/MessageProcessor.o plugin_MessageProcessor/MessageProcessor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_NetworkTest/NetworkTest.o plugin_NetworkTest/NetworkTest.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Partitioner/Partitioner.o plugin_Partitioner/Partitioner.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/PhylogenyViewer.o plugin_PhylogenyViewer/PhylogenyViewer.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/GenomeToTaxonLoader.o plugin_PhylogenyViewer/GenomeToTaxonLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/PhylogeneticTreeLoader.o plugin_PhylogenyViewer/PhylogeneticTreeLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_PhylogenyViewer/TaxonNameLoader.o plugin_PhylogenyViewer/TaxonNameLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/Scaffolder.o plugin_Scaffolder/Scaffolder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingLink.o plugin_Scaffolder/ScaffoldingLink.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/SummarizedLink.o plugin_Scaffolder/SummarizedLink.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingAlgorithm.o plugin_Scaffolder/ScaffoldingAlgorithm.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingVertex.o plugin_Scaffolder/ScaffoldingVertex.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Scaffolder/ScaffoldingEdge.o plugin_Scaffolder/ScaffoldingEdge.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/Searcher.o plugin_Searcher/Searcher.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/SearchDirectory.o plugin_Searcher/SearchDirectory.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/ContigSearchEntry.o plugin_Searcher/ContigSearchEntry.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/ContigHit.o plugin_Searcher/ContigHit.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/ColorSet.o plugin_Searcher/ColorSet.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/VirtualKmerColor.o plugin_Searcher/VirtualKmerColor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/QualityCaller.o plugin_Searcher/QualityCaller.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/DistributionWriter.o plugin_Searcher/DistributionWriter.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_Searcher/ColoredPeakFinder.o plugin_Searcher/ColoredPeakFinder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/SeedExtender.o plugin_SeedExtender/SeedExtender.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/Direction.o plugin_SeedExtender/Direction.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/VertexMessenger.o plugin_SeedExtender/VertexMessenger.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/ReadFetcher.o plugin_SeedExtender/ReadFetcher.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/BubbleTool.o plugin_SeedExtender/BubbleTool.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/Chooser.o plugin_SeedExtender/Chooser.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/OpenAssemblerChooser.o plugin_SeedExtender/OpenAssemblerChooser.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/TipWatchdog.o plugin_SeedExtender/TipWatchdog.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/NovaEngine.o plugin_SeedExtender/NovaEngine.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/ExtensionElement.o plugin_SeedExtender/ExtensionElement.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/DepthFirstSearchData.o plugin_SeedExtender/DepthFirstSearchData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedExtender/ExtensionData.o plugin_SeedExtender/ExtensionData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedingData/AssemblySeed.o plugin_SeedingData/AssemblySeed.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedingData/SeedWorker.o plugin_SeedingData/SeedWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SeedingData/SeedingData.o plugin_SeedingData/SeedingData.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/SequencesIndexer.o plugin_SequencesIndexer/SequencesIndexer.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/IndexerWorker.o plugin_SequencesIndexer/IndexerWorker.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/PairedRead.o plugin_SequencesIndexer/PairedRead.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesIndexer/ReadAnnotation.o plugin_SequencesIndexer/ReadAnnotation.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/SequencesLoader.o plugin_SequencesLoader/SequencesLoader.cpp
plugin_SequencesLoader/SequencesLoader.cpp: In member function ‘bool SequencesLoader::writeSequencesToAMOSFile(int, int, StaticVector*, RingAllocator*, bool*, BubbleData*, time_t*, Parameters*, int*, int*)’:
plugin_SequencesLoader/SequencesLoader.cpp:189: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘long long unsigned int’
plugin_SequencesLoader/SequencesLoader.cpp:189: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘long long unsigned int’
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/Read.o plugin_SequencesLoader/Read.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/ArrayOfReads.o plugin_SequencesLoader/ArrayOfReads.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/ColorSpaceDecoder.o plugin_SequencesLoader/ColorSpaceDecoder.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/ColorSpaceLoader.o plugin_SequencesLoader/ColorSpaceLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/FastaLoader.o plugin_SequencesLoader/FastaLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/FastqLoader.o plugin_SequencesLoader/FastqLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/SffLoader.o plugin_SequencesLoader/SffLoader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_SequencesLoader/Loader.o plugin_SequencesLoader/Loader.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/VerticesExtractor.o plugin_VerticesExtractor/VerticesExtractor.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/GridTable.o plugin_VerticesExtractor/GridTable.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/GridTableIterator.o plugin_VerticesExtractor/GridTableIterator.cpp
mpicxx -O3 -D MAXKMERLENGTH=32 -D RAY_VERSION=\"2.0.0-rc7\" -I ../RayPlatform -I. -c -o plugin_VerticesExtractor/Vertex.o plugin_VerticesExtractor/Vertex.cpp
ar rcs TheRayGenomeAssembler.a application_core/ray_main.o application_core/Machine.o application_core/Parameters.o application_core/common_functions.o plugin_Amos/Amos.o plugin_CoverageGatherer/CoverageGatherer.o plugin_CoverageGatherer/CoverageDistribution.o plugin_EdgePurger/EdgePurger.o plugin_EdgePurger/EdgePurgerWorker.o plugin_FusionData/FusionData.o plugin_FusionTaskCreator/FusionWorker.o plugin_FusionTaskCreator/FusionTaskCreator.o plugin_GeneOntology/KeyEncoder.o plugin_GeneOntology/GeneOntology.o plugin_GenomeNeighbourhood/GenomeNeighbourhood.o plugin_GenomeNeighbourhood/Neighbour.o plugin_GenomeNeighbourhood/NeighbourPair.o plugin_JoinerTaskCreator/JoinerWorker.o plugin_JoinerTaskCreator/JoinerTaskCreator.o plugin_KmerAcademyBuilder/KmerAcademyBuilder.o plugin_KmerAcademyBuilder/BloomFilter.o plugin_KmerAcademyBuilder/Kmer.o plugin_KmerAcademyBuilder/KmerAcademy.o plugin_KmerAcademyBuilder/KmerAcademyIterator.o plugin_Library/LibraryPeakFinder.o plugin_Library/LibraryWorker.o plugin_Library/Library.o plugin_MachineHelper/MachineHelper.o plugin_MessageProcessor/MessageProcessor.o plugin_NetworkTest/NetworkTest.o plugin_Partitioner/Partitioner.o plugin_PhylogenyViewer/PhylogenyViewer.o plugin_PhylogenyViewer/GenomeToTaxonLoader.o plugin_PhylogenyViewer/PhylogeneticTreeLoader.o plugin_PhylogenyViewer/TaxonNameLoader.o plugin_Scaffolder/Scaffolder.o plugin_Scaffolder/ScaffoldingLink.o plugin_Scaffolder/SummarizedLink.o plugin_Scaffolder/ScaffoldingAlgorithm.o plugin_Scaffolder/ScaffoldingVertex.o plugin_Scaffolder/ScaffoldingEdge.o plugin_Searcher/Searcher.o plugin_Searcher/SearchDirectory.o plugin_Searcher/ContigSearchEntry.o plugin_Searcher/ContigHit.o plugin_Searcher/ColorSet.o plugin_Searcher/VirtualKmerColor.o plugin_Searcher/QualityCaller.o plugin_Searcher/DistributionWriter.o plugin_Searcher/ColoredPeakFinder.o plugin_SeedExtender/SeedExtender.o plugin_SeedExtender/Direction.o plugin_SeedExtender/VertexMessenger.o plugin_SeedExtender/ReadFetcher.o plugin_SeedExtender/BubbleTool.o plugin_SeedExtender/Chooser.o plugin_SeedExtender/OpenAssemblerChooser.o plugin_SeedExtender/TipWatchdog.o plugin_SeedExtender/NovaEngine.o plugin_SeedExtender/ExtensionElement.o plugin_SeedExtender/DepthFirstSearchData.o plugin_SeedExtender/ExtensionData.o plugin_SeedingData/AssemblySeed.o plugin_SeedingData/SeedWorker.o plugin_SeedingData/SeedingData.o plugin_SequencesIndexer/SequencesIndexer.o plugin_SequencesIndexer/IndexerWorker.o plugin_SequencesIndexer/PairedRead.o plugin_SequencesIndexer/ReadAnnotation.o plugin_SequencesLoader/SequencesLoader.o plugin_SequencesLoader/Read.o plugin_SequencesLoader/ArrayOfReads.o plugin_SequencesLoader/ColorSpaceDecoder.o plugin_SequencesLoader/ColorSpaceLoader.o plugin_SequencesLoader/FastaLoader.o plugin_SequencesLoader/FastqLoader.o plugin_SequencesLoader/SffLoader.o plugin_SequencesLoader/Loader.o plugin_VerticesExtractor/VerticesExtractor.o plugin_VerticesExtractor/GridTable.o plugin_VerticesExtractor/GridTableIterator.o plugin_VerticesExtractor/Vertex.o
mpicxx code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
Undefined symbols:
"_MPI_Reduce_local", referenced from:
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(ray_main.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Machine.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(MachineHelper.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(MessageProcessor.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(EdgePurger.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Searcher.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(OperatingSystem.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(JoinerTaskCreator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Parameters.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(SeedExtender.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(ComputeCore.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(SwitchMan.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(MessagesHandler.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(SequencesLoader.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Amos.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(CoverageGatherer.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(GenomeNeighbourhood.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(PhylogenyViewer.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(TimePrinter.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(FusionTaskCreator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(GeneOntology.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(MessageRouter.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(FusionData.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Partitioner.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(SeedingData.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(VerticesExtractor.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(VirtualProcessor.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Scaffolder.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(TickLogger.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(KmerAcademyBuilder.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(Library.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(NetworkTest.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(GridTable.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(Derivative.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(SequencesIndexer.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(MyAllocator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(VirtualCommunicator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(Profiler.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(LibraryWorker.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(KmerAcademy.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(common_functions.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(VertexMessenger.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(ReadFetcher.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin libRayPlatform.a(allocator.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(DepthFirstSearchData.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(TipWatchdog.o)
"_MPI_Op_commutative", referenced from:
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(ray_main.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Machine.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(MachineHelper.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(MessageProcessor.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(EdgePurger.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Searcher.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(OperatingSystem.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(JoinerTaskCreator.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Parameters.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(SeedExtender.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(ComputeCore.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(SwitchMan.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(MessagesHandler.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(SequencesLoader.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Amos.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(CoverageGatherer.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GenomeNeighbourhood.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(PhylogenyViewer.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(TimePrinter.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(FusionTaskCreator.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GeneOntology.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(MessageRouter.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(FusionData.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Partitioner.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(SeedingData.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(VerticesExtractor.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(VirtualProcessor.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Scaffolder.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(TickLogger.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(KmerAcademyBuilder.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Library.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(NetworkTest.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GridTable.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(Derivative.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(SequencesIndexer.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(MyAllocator.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(VirtualCommunicator.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(Profiler.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(LibraryWorker.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(KmerAcademy.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(common_functions.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(VertexMessenger.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(ReadFetcher.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(allocator.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(DepthFirstSearchData.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(TipWatchdog.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [Ray] Error 1

[Saratoga]

My Mac is a MacPro 2x2.66 6-core Intel xeon
16 GB RAM

Ray was running but causing segmentation faults. So I decided to recompile after the compilers update and then the problem showed up.

Thanks!

[seb567]

Where did it seg fault exactly ?

My Mac is a MacPro 2x2.66 6-core Intel xeon
16 GB RAM

Ray was running but causing segmentation faults. So I decided to recompile after the compilers update and then the problem showed up.

Thanks!

[seb567]

What is the output of this:

mpicxx -showme:compile

mpicxx -showme:link

ompi_info -a|head

ompi_info -a|grep compiler

Maybe you installed 2 MPI libraries and it is linking against the wrong one.

Hi,

This is the log



Compilation options (you can change them of course)

PREFIX = install-prefix
MAXKMERLENGTH = 32
FORCE_PACKING = n
ASSERT = n
HAVE_LIBZ = n
HAVE_LIBBZ2 = n
INTEL_COMPILER = n
MPICXX = mpicxx
GPROF = n
OPTIMIZE = y
DEBUG = n


mpicxx code/TheRayGenomeAssembler.a RayPlatform/libRayPlatform.a -o Ray
Undefined symbols:
"_MPI_Reduce_local", referenced from:
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TheRayGenomeAssembler.a(ray_main.o)
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) TheRayGenomeAssembler.a(CoverageGatherer.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GenomeNeighbourhood.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(PhylogenyViewer.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(TimePrinter.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(FusionTaskCreator.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(GeneOntology.o)
MPI::Op::Is_commutative() constin libRayPlatform.a(MessageRouter.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(FusionData.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(Partitioner.o)
MPI::Op::Is_commutative() constin TheRayGenomeAssembler.a(TipWatchdog.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [Ray] Error 1

[Saratoga]

mpicxx -showme:compile
-D_REENTRANT

mpicxx -showme:link
-Wl,-u,_munmap -Wl,-multiply_defined,suppress -lmpi_cxx -lmpi -lopen-rte -lopen-pal

ompi_info -a|head
Open MPI: 1.2.8
Open MPI SVN revision: r19718
Open RTE: 1.2.8
Open RTE SVN revision: r19718
OPAL: 1.2.8
OPAL SVN revision: r19718
MCA backtrace: execinfo (MCA v1.0, API v1.0, Component v1.2.8)
MCA memory: darwin (MCA v1.0, API v1.0, Component v1.2.8)
MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2.8)
MCA timer: darwin (MCA v1.0, API v1.0, Component v1.2.8)

ompi_info -a|grep compiler
C compiler: gcc
C compiler absolute: /usr/bin/gcc
C++ compiler: g++
C++ compiler absolute: /usr/bin/g++
Fortran77 compiler: none
Fortran77 compiler abs: none
Fortran90 compiler: none
Fortran90 compiler abs: none

[seb567]

Hi,

You said you used this tutorial to install Open-MPI. In this tutorial, Open-MPI 1.4.3 is installed.

So I guess you installed Open-MPI 1.4.3.

But ompi_info indicates that you have (also) Open-MPI 1.2.8.

I think you are compiling the code with one version, but linking with the other version. That is why there are unresolved symbols.

Can you try what I describe in the next section.



Alternate way


If you have cmake installed, you can build Ray with it instead. CMake is cross-platform.



To build Ray with CMake:


tar xjf Ray-v2.0.0-rc7.tar.bz2

cd Ray-v2.0.0-rc7

remove the line " RayPlatform/scheduling/SwitchMan_adapters.cpp" from CMakeLists.txt

cd ..

mkdir Build-with-CMAKE

cd Build-with-CMAKE

cmake ../Ray-v2.0.0-rc7

make

ls Ray



Let me know if that works for you.

mpicxx -showme:compile
-D_REENTRANT

mpicxx -showme:link
-Wl,-u,_munmap -Wl,-multiply_defined,suppress -lmpi_cxx -lmpi -lopen-rte -lopen-pal

ompi_info -a|head
Open MPI: 1.2.8
Open MPI SVN revision: r19718
Open RTE: 1.2.8
Open RTE SVN revision: r19718
OPAL: 1.2.8
OPAL SVN revision: r19718
MCA backtrace: execinfo (MCA v1.0, API v1.0, Component v1.2.8)
MCA memory: darwin (MCA v1.0, API v1.0, Component v1.2.8)
MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2.8)
MCA timer: darwin (MCA v1.0, API v1.0, Component v1.2.8)

ompi_info -a|grep compiler
C compiler: gcc
C compiler absolute: /usr/bin/gcc
C++ compiler: g++
C++ compiler absolute: /usr/bin/g++
Fortran77 compiler: none
Fortran77 compiler abs: none
Fortran90 compiler: none
Fortran90 compiler abs: none

[Saratoga]

Hi,

Thank you so much for your effort helping me,

I did it but I got the following


-- The C compiler identification is GNU 4.2.1
-- The CXX compiler identification is GNU 4.2.1
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done
-- Build files have been written to: /Phylos/Build-with-CMAKE
cyanelle:Build-with-CMAKE cyanelle$ make
Scanning dependencies of target Ray
[ 0%] Building CXX object CMakeFiles/Ray.dir/code/plugin_MachineHelper/MachineHelper.cpp.o
[ 1%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Library/Library.cpp.o
[ 2%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Library/LibraryPeakFinder.cpp.o
[ 3%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Library/LibraryWorker.cpp.o
[ 3%] Building CXX object CMakeFiles/Ray.dir/code/plugin_FusionTaskCreator/FusionTaskCreator.cpp.o
[ 4%] Building CXX object CMakeFiles/Ray.dir/code/plugin_FusionTaskCreator/FusionWorker.cpp.o
[ 5%] Building CXX object CMakeFiles/Ray.dir/code/plugin_NetworkTest/NetworkTest.cpp.o
[ 6%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/SequencesLoader.cpp.o
/Phylos/Ray-v2.0.0-rc7/code/plugin_SequencesLoader/SequencesLoader.cpp: In member function ?bool SequencesLoader::writeSequencesToAMOSFile(int, int, StaticVector*, RingAllocator*, bool*, BubbleData*, time_t*, Parameters*, int*, int*)?:
/Phylos/Ray-v2.0.0-rc7/code/plugin_SequencesLoader/SequencesLoader.cpp:189: warning: format ?%lu? expects type ?long unsigned int?, but argument 3 has type ?long long unsigned int?
/Phylos/Ray-v2.0.0-rc7/code/plugin_SequencesLoader/SequencesLoader.cpp:189: warning: format ?%lu? expects type ?long unsigned int?, but argument 4 has type ?long long unsigned int?
[ 7%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/ArrayOfReads.cpp.o
[ 7%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/ColorSpaceDecoder.cpp.o
[ 8%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/FastqGzLoader.cpp.o
[ 9%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/SffLoader.cpp.o
[ 10%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/Read.cpp.o
[ 10%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/FastaLoader.cpp.o
[ 11%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/BzReader.cpp.o
[ 12%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/FastqBz2Loader.cpp.o
[ 13%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/Loader.cpp.o
[ 14%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/FastqLoader.cpp.o
[ 14%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesLoader/ColorSpaceLoader.cpp.o
[ 15%] Building CXX object CMakeFiles/Ray.dir/code/plugin_VerticesExtractor/Vertex.cpp.o
[ 16%] Building CXX object CMakeFiles/Ray.dir/code/plugin_VerticesExtractor/GridTable.cpp.o
[ 17%] Building CXX object CMakeFiles/Ray.dir/code/plugin_VerticesExtractor/GridTableIterator.cpp.o
[ 17%] Building CXX object CMakeFiles/Ray.dir/code/plugin_VerticesExtractor/VerticesExtractor.cpp.o
[ 18%] Building CXX object CMakeFiles/Ray.dir/code/plugin_JoinerTaskCreator/JoinerTaskCreator.cpp.o
[ 19%] Building CXX object CMakeFiles/Ray.dir/code/plugin_JoinerTaskCreator/JoinerWorker.cpp.o
[ 20%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedingData/SeedingData.cpp.o
[ 21%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedingData/SeedWorker.cpp.o
[ 21%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedingData/AssemblySeed.cpp.o
[ 22%] Building CXX object CMakeFiles/Ray.dir/code/plugin_FusionData/FusionData.cpp.o
[ 23%] Building CXX object CMakeFiles/Ray.dir/code/plugin_CoverageGatherer/CoverageGatherer.cpp.o
[ 24%] Building CXX object CMakeFiles/Ray.dir/code/plugin_CoverageGatherer/CoverageDistribution.cpp.o
[ 25%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/Direction.cpp.o
[ 25%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/TipWatchdog.cpp.o
[ 26%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/Chooser.cpp.o
[ 27%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/ExtensionElement.cpp.o
[ 28%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/SeedExtender.cpp.o
[ 28%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/ExtensionData.cpp.o
[ 29%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/VertexMessenger.cpp.o
[ 30%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/ReadFetcher.cpp.o
[ 31%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/BubbleTool.cpp.o
[ 32%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/NovaEngine.cpp.o
[ 32%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/DepthFirstSearchData.cpp.o
[ 33%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SeedExtender/OpenAssemblerChooser.cpp.o
[ 34%] Building CXX object CMakeFiles/Ray.dir/code/plugin_MessageProcessor/MessageProcessor.cpp.o
/Phylos/Ray-v2.0.0-rc7/code/plugin_MessageProcessor/MessageProcessor.cpp: In member function ?void MessageProcessor::call_RAY_MPI_TAG_VERTICES_DATA(Message*)?:
/Phylos/Ray-v2.0.0-rc7/code/plugin_MessageProcessor/MessageProcessor.cpp:727: warning: comparison between signed and unsigned integer expressions
[ 35%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Partitioner/Partitioner.cpp.o
[ 35%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesIndexer/SequencesIndexer.cpp.o
[ 36%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesIndexer/PairedRead.cpp.o
[ 37%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesIndexer/ReadAnnotation.cpp.o
[ 38%] Building CXX object CMakeFiles/Ray.dir/code/plugin_SequencesIndexer/IndexerWorker.cpp.o
[ 39%] Building CXX object CMakeFiles/Ray.dir/code/application_core/Parameters.cpp.o
[ 39%] Building CXX object CMakeFiles/Ray.dir/code/application_core/ray_main.cpp.o
[ 40%] Building CXX object CMakeFiles/Ray.dir/code/application_core/common_functions.cpp.o
[ 41%] Building CXX object CMakeFiles/Ray.dir/code/application_core/Machine.cpp.o
[ 42%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Amos/Amos.cpp.o
/Phylos/Ray-v2.0.0-rc7/code/plugin_Amos/Amos.cpp: In member function ?void Amos::call_RAY_SLAVE_MODE_AMOS()?:
/Phylos/Ray-v2.0.0-rc7/code/plugin_Amos/Amos.cpp:136: warning: format ?%lu? expects type ?long unsigned int?, but argument 4 has type ?long long unsigned int?
/Phylos/Ray-v2.0.0-rc7/code/plugin_Amos/Amos.cpp:206: warning: format ?%li? expects type ?long int?, but argument 3 has type ?ReadHandle?
[ 42%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/Kmer.cpp.o
[ 43%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/KmerAcademyBuilder.cpp.o
[ 44%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/KmerAcademy.cpp.o
[ 45%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/BloomFilter.cpp.o
[ 46%] Building CXX object CMakeFiles/Ray.dir/code/plugin_KmerAcademyBuilder/KmerAcademyIterator.cpp.o
[ 46%] Building CXX object CMakeFiles/Ray.dir/code/plugin_EdgePurger/EdgePurger.cpp.o
[ 47%] Building CXX object CMakeFiles/Ray.dir/code/plugin_EdgePurger/EdgePurgerWorker.cpp.o
[ 48%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/ColorSet.cpp.o
[ 49%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/ContigHit.cpp.o
[ 50%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/Searcher.cpp.o
[ 50%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/ContigSearchEntry.cpp.o
[ 51%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/VirtualKmerColor.cpp.o
[ 52%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/DistributionWriter.cpp.o
[ 53%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/ColoredPeakFinder.cpp.o
[ 53%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/QualityCaller.cpp.o
[ 54%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Searcher/SearchDirectory.cpp.o
[ 55%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/Scaffolder.cpp.o
[ 56%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/SummarizedLink.cpp.o
[ 57%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/ScaffoldingAlgorithm.cpp.o
[ 57%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/ScaffoldingVertex.cpp.o
[ 58%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/ScaffoldingEdge.cpp.o
[ 59%] Building CXX object CMakeFiles/Ray.dir/code/plugin_Scaffolder/ScaffoldingLink.cpp.o
[ 60%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GeneOntology/KeyEncoder.cpp.o
[ 60%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GeneOntology/GeneOntology.cpp.o
[ 61%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GenomeNeighbourhood/GenomeNeighbourhood.cpp.o
[ 62%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GenomeNeighbourhood/NeighbourPair.cpp.o
[ 63%] Building CXX object CMakeFiles/Ray.dir/code/plugin_GenomeNeighbourhood/Neighbour.cpp.o
[ 64%] Building CXX object CMakeFiles/Ray.dir/code/plugin_PhylogenyViewer/GenomeToTaxonLoader.cpp.o
[ 64%] Building CXX object CMakeFiles/Ray.dir/code/plugin_PhylogenyViewer/PhylogenyViewer.cpp.o
[ 65%] Building CXX object CMakeFiles/Ray.dir/code/plugin_PhylogenyViewer/PhylogeneticTreeLoader.cpp.o
[ 66%] Building CXX object CMakeFiles/Ray.dir/code/plugin_PhylogenyViewer/TaxonNameLoader.cpp.o
[ 67%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/MasterModeExecutor.cpp.o
[ 67%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/MessageTagHandler.cpp.o
[ 68%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/SlaveModeHandler.cpp.o
[ 69%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/MasterModeHandler.cpp.o
[ 70%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/SlaveModeExecutor.cpp.o
[ 71%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/handlers/MessageTagExecutor.cpp.o
[ 71%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/master_modes.cpp.o
[ 72%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/ComputeCore.cpp.o
[ 73%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/slave_modes.cpp.o
[ 74%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/OperatingSystem.cpp.o
[ 75%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/core/statistics.cpp.o
[ 75%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationExperimental.cpp.o
[ 76%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationKautz.cpp.o
[ 77%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/ConnectionGraph.cpp.o
[ 78%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementation.cpp.o
[ 78%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationGroup.cpp.o
[ 79%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationComplete.cpp.o
[ 80%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationDeBruijn.cpp.o
[ 81%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/routing/GraphImplementationRandom.cpp.o
[ 82%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/scheduling/TaskCreator.cpp.o
[ 82%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/scheduling/SwitchMan.cpp.o
[ 83%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/scheduling/VirtualProcessor.cpp.o
[ 84%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/profiling/Derivative.cpp.o
[ 85%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/profiling/TimePrinter.cpp.o
[ 85%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/profiling/Profiler.cpp.o
[ 86%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/profiling/TickLogger.cpp.o
[ 87%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/cryptography/crypto.cpp.o
[ 88%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/structures/StaticVector.cpp.o
[ 89%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/ReusableMemoryStore.cpp.o
[ 89%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/ChunkAllocatorWithDefragmentation.cpp.o
[ 90%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/DefragmentationGroup.cpp.o
[ 91%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/RingAllocator.cpp.o
[ 92%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/MyAllocator.cpp.o
[ 92%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/allocator.cpp.o
[ 93%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/memory/DefragmentationLane.cpp.o
[ 94%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/plugins/CorePlugin.cpp.o
[ 95%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/plugins/RegisteredPlugin.cpp.o
[ 96%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/VirtualCommunicator.cpp.o
[ 96%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/MessagesHandler.cpp.o
[ 97%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/MessageRouter.cpp.o
[ 98%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/Message.cpp.o
[ 99%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/mpi_tags.cpp.o
[100%] Building CXX object CMakeFiles/Ray.dir/RayPlatform/communication/BufferedData.cpp.o
Linking CXX executable Ray
Undefined symbols:
"_MPI_Reduce_local", referenced from:
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MachineHelper.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Library.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin LibraryWorker.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin FusionTaskCreator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin NetworkTest.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SequencesLoader.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin GridTable.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin VerticesExtractor.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin JoinerTaskCreator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SeedingData.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin FusionData.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin CoverageGatherer.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TipWatchdog.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SeedExtender.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin VertexMessenger.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin ReadFetcher.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin DepthFirstSearchData.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MessageProcessor.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Partitioner.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SequencesIndexer.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Parameters.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin ray_main.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin common_functions.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Machine.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Amos.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin KmerAcademyBuilder.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin KmerAcademy.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin EdgePurger.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Searcher.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Scaffolder.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin GeneOntology.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin GenomeNeighbourhood.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin PhylogenyViewer.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin ComputeCore.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin OperatingSystem.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin SwitchMan.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin VirtualProcessor.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Derivative.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TimePrinter.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin Profiler.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin TickLogger.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MyAllocator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin allocator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin VirtualCommunicator.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MessagesHandler.cpp.o
MPI::Op::Reduce_local(void const*, void*, int, MPI:atatype const&) constin MessageRouter.cpp.o
"_MPI_Op_commutative", referenced from:
MPI::Op::Is_commutative() constin MachineHelper.cpp.o
MPI::Op::Is_commutative() constin Library.cpp.o
MPI::Op::Is_commutative() constin LibraryWorker.cpp.o
MPI::Op::Is_commutative() constin FusionTaskCreator.cpp.o
MPI::Op::Is_commutative() constin NetworkTest.cpp.o
MPI::Op::Is_commutative() constin SequencesLoader.cpp.o
MPI::Op::Is_commutative() constin GridTable.cpp.o
MPI::Op::Is_commutative() constin VerticesExtractor.cpp.o
MPI::Op::Is_commutative() constin JoinerTaskCreator.cpp.o
MPI::Op::Is_commutative() constin SeedingData.cpp.o
MPI::Op::Is_commutative() constin FusionData.cpp.o
MPI::Op::Is_commutative() constin CoverageGatherer.cpp.o
MPI::Op::Is_commutative() constin TipWatchdog.cpp.o
MPI::Op::Is_commutative() constin SeedExtender.cpp.o
MPI::Op::Is_commutative() constin VertexMessenger.cpp.o
MPI::Op::Is_commutative() constin ReadFetcher.cpp.o
MPI::Op::Is_commutative() constin DepthFirstSearchData.cpp.o
MPI::Op::Is_commutative() constin MessageProcessor.cpp.o
MPI::Op::Is_commutative() constin Partitioner.cpp.o
MPI::Op::Is_commutative() constin SequencesIndexer.cpp.o
MPI::Op::Is_commutative() constin Parameters.cpp.o
MPI::Op::Is_commutative() constin ray_main.cpp.o
MPI::Op::Is_commutative() constin common_functions.cpp.o
MPI::Op::Is_commutative() constin Machine.cpp.o
MPI::Op::Is_commutative() constin Amos.cpp.o
MPI::Op::Is_commutative() constin KmerAcademyBuilder.cpp.o
MPI::Op::Is_commutative() constin KmerAcademy.cpp.o
MPI::Op::Is_commutative() constin EdgePurger.cpp.o
MPI::Op::Is_commutative() constin Searcher.cpp.o
MPI::Op::Is_commutative() constin Scaffolder.cpp.o
MPI::Op::Is_commutative() constin GeneOntology.cpp.o
MPI::Op::Is_commutative() constin GenomeNeighbourhood.cpp.o
MPI::Op::Is_commutative() constin PhylogenyViewer.cpp.o
MPI::Op::Is_commutative() constin ComputeCore.cpp.o
MPI::Op::Is_commutative() constin OperatingSystem.cpp.o
MPI::Op::Is_commutative() constin SwitchMan.cpp.o
MPI::Op::Is_commutative() constin VirtualProcessor.cpp.o
MPI::Op::Is_commutative() constin Derivative.cpp.o
MPI::Op::Is_commutative() constin TimePrinter.cpp.o
MPI::Op::Is_commutative() constin Profiler.cpp.o
MPI::Op::Is_commutative() constin TickLogger.cpp.o
MPI::Op::Is_commutative() constin MyAllocator.cpp.o
MPI::Op::Is_commutative() constin allocator.cpp.o
MPI::Op::Is_commutative() constin VirtualCommunicator.cpp.o
MPI::Op::Is_commutative() constin MessagesHandler.cpp.o
MPI::Op::Is_commutative() constin MessageRouter.cpp.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [Ray] Error 1
make[1]: *** [CMakeFiles/Ray.dir/all] Error 2
make: *** [all] Error 2

[seb567]

I am pretty sure you have two versions of Open-MPI installed (v1.4.3 and v1.2.8)


Run these:

echo $PATH

echo $LD_LIBRARY_PATH

type mpiexec

type mpicxx

type ompi_info

find /usr/local|grep mpi

Hi,

Thank you so much for your effort helping me,

I did it but I got the following


-- The C compiler identification is GNU 4.2.1
-- The CXX compiler identification is GNU 4.2.1
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Configuring done
-- Generating done

collect2: ld returned 1 exit status
make[2]: *** [Ray] Error 1
make[1]: *** [CMakeFiles/Ray.dir/all] Error 2
make: *** [all] Error 2