Hi Sébastien, I recently upgraded to Ubuntu 12.04 and have had trouble
compiling Ray since. Today I grabbed the latest v2rc7 and tried again,
here is the error I get:
shunter@envy:/bio/software/HT_sequence/Ray-assembler/Ray-v2.0.0-rc7/RayPlatform$
make
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
memory/ReusableMemoryStore.o memory/ReusableMemoryStore.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
memory/MyAllocator.o memory/MyAllocator.cpp
In file included from /usr/lib/mpich/include/mpi2c++/mpi++.h:162:0,
from /usr/lib/mpich/include/mpi.h:688,
from ./communication/MessagesHandler.h:25,
from ./core/OperatingSystem.h:45,
from memory/MyAllocator.cpp:25:
/usr/lib/mpich/include/mpi2c++/comm_inln.h: In static member function
‘static int PMPI::Comm::NULL_COPY_FN(const PMPI::Comm&, int, void*,
void*, void*, MPI2CPP_BOOL_T&)’:
/usr/lib/mpich/include/mpi2c++/comm_inln.h:477:27: warning: the
address of ‘int MPIR_null_copy_fn(MPI_Comm, int, void*, void*, void*,
int*)’ will never be NULL [-Waddress]
/usr/lib/mpich/include/mpi2c++/comm_inln.h: In static member function
‘static int PMPI::Comm::NULL_DELETE_FN(PMPI::Comm&, int, void*,
void*)’:
/usr/lib/mpich/include/mpi2c++/comm_inln.h:527:29: warning: the
address of ‘int MPIR_null_delete_fn(MPI_Comm, int, void*, void*)’ will
never be NULL [-Waddress]
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
memory/RingAllocator.o memory/RingAllocator.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
memory/allocator.o memory/allocator.cpp
In file included from /usr/lib/mpich/include/mpi2c++/mpi++.h:162:0,
from /usr/lib/mpich/include/mpi.h:688,
from ./communication/MessagesHandler.h:25,
from ./core/OperatingSystem.h:45,
from memory/allocator.cpp:27:
/usr/lib/mpich/include/mpi2c++/comm_inln.h: In static member function
‘static int PMPI::Comm::NULL_COPY_FN(const PMPI::Comm&, int, void*,
void*, void*, MPI2CPP_BOOL_T&)’:
/usr/lib/mpich/include/mpi2c++/comm_inln.h:477:27: warning: the
address of ‘int MPIR_null_copy_fn(MPI_Comm, int, void*, void*, void*,
int*)’ will never be NULL [-Waddress]
/usr/lib/mpich/include/mpi2c++/comm_inln.h: In static member function
‘static int PMPI::Comm::NULL_DELETE_FN(PMPI::Comm&, int, void*,
void*)’:
/usr/lib/mpich/include/mpi2c++/comm_inln.h:527:29: warning: the
address of ‘int MPIR_null_delete_fn(MPI_Comm, int, void*, void*)’ will
never be NULL [-Waddress]
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
memory/DefragmentationGroup.o memory/DefragmentationGroup.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
memory/ChunkAllocatorWithDefragmentation.o
memory/ChunkAllocatorWithDefragmentation.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
memory/DefragmentationLane.o memory/DefragmentationLane.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
routing/GraphImplementation.o routing/GraphImplementation.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
routing/GraphImplementationRandom.o
routing/GraphImplementationRandom.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
routing/GraphImplementationComplete.o
routing/GraphImplementationComplete.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
routing/GraphImplementationDeBruijn.o
routing/GraphImplementationDeBruijn.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
routing/GraphImplementationKautz.o
routing/GraphImplementationKautz.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
routing/GraphImplementationExperimental.o
routing/GraphImplementationExperimental.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
routing/GraphImplementationGroup.o
routing/GraphImplementationGroup.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
routing/ConnectionGraph.o routing/ConnectionGraph.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
communication/mpi_tags.o communication/mpi_tags.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
communication/VirtualCommunicator.o
communication/VirtualCommunicator.cpp
In file included from /usr/lib/mpich/include/mpi2c++/mpi++.h:162:0,
from /usr/lib/mpich/include/mpi.h:688,
from ./communication/MessagesHandler.h:25,
from ./core/OperatingSystem.h:45,
from communication/VirtualCommunicator.cpp:24:
/usr/lib/mpich/include/mpi2c++/comm_inln.h: In static member function
‘static int PMPI::Comm::NULL_COPY_FN(const PMPI::Comm&, int, void*,
void*, void*, MPI2CPP_BOOL_T&)’:
/usr/lib/mpich/include/mpi2c++/comm_inln.h:477:27: warning: the
address of ‘int MPIR_null_copy_fn(MPI_Comm, int, void*, void*, void*,
int*)’ will never be NULL [-Waddress]
/usr/lib/mpich/include/mpi2c++/comm_inln.h: In static member function
‘static int PMPI::Comm::NULL_DELETE_FN(PMPI::Comm&, int, void*,
void*)’:
/usr/lib/mpich/include/mpi2c++/comm_inln.h:527:29: warning: the
address of ‘int MPIR_null_delete_fn(MPI_Comm, int, void*, void*)’ will
never be NULL [-Waddress]
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
communication/BufferedData.o communication/BufferedData.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
communication/Message.o communication/Message.cpp
mpicxx -O3 -Wall -ansi -D RAYPLATFORM_VERSION=\"1.0.2\" -I. -c -o
communication/MessagesHandler.o communication/MessagesHandler.cpp
In file included from /usr/lib/mpich/include/mpi2c++/mpi++.h:162:0,
from /usr/lib/mpich/include/mpi.h:688,
from ./communication/MessagesHandler.h:25,
from communication/MessagesHandler.cpp:22:
/usr/lib/mpich/include/mpi2c++/comm_inln.h: In static member function
‘static int PMPI::Comm::NULL_COPY_FN(const PMPI::Comm&, int, void*,
void*, void*, MPI2CPP_BOOL_T&)’:
/usr/lib/mpich/include/mpi2c++/comm_inln.h:477:27: warning: the
address of ‘int MPIR_null_copy_fn(MPI_Comm, int, void*, void*, void*,
int*)’ will never be NULL [-Waddress]
/usr/lib/mpich/include/mpi2c++/comm_inln.h: In static member function
‘static int PMPI::Comm::NULL_DELETE_FN(PMPI::Comm&, int, void*,
void*)’:
/usr/lib/mpich/include/mpi2c++/comm_inln.h:527:29: warning: the
address of ‘int MPIR_null_delete_fn(MPI_Comm, int, void*, void*)’ will
never be NULL [-Waddress]
communication/MessagesHandler.cpp: In member function ‘void
MessagesHandler::probeAndRead(int, int, StaticVector*,
RingAllocator*)’:
communication/MessagesHandler.cpp:328:25: error:
‘MPI_UNSIGNED_LONG_LONG’ was not declared in this scope
communication/MessagesHandler.cpp: In member function ‘void
MessagesHandler::constructor(int*, char***)’:
communication/MessagesHandler.cpp:409:13: error:
‘MPI_UNSIGNED_LONG_LONG’ was not declared in this scope
make: *** [communication/MessagesHandler.o] Error 1
Do you have any suggestions on getting this to work?
Thanks,
Sam
On Thu, May 17, 2012 at 8:02 AM, Sébastien Boisvert
<sebastien.boisver...@ulaval.ca> wrote:
> Hello !
>
> I am proud to announce the immediate availability of the Ray assembler
> version 2.0.0 release candidate 7, code name "Dark Astrocyte of Knowledge".
>
> This version ships with RayPlatform v1.0.2, code name "Timely Gate of
> Yields".
>
>
> Link for download: http://denovoassembler.sourceforge.net/
>
>
> Changes in Ray
>
> * The CMakeList file was updated.
> * GC content for contigs are dumped in XML files.
> * New option -one-color-per-file for graph coloring.
> * Optimized file system input/output operations.
> * Network testing is more verbose.
> * Fixed an integer overflow bug in the scaffolder.
> * New guide in Documentation/ for software message routing.
> * Fixed an integer overflow bug in the profiler.
> * Fixed a synchronization bug in the coloring algorithm.
> * Increased the sensitivity of the biological profiling algorithms.
> * Disabled the plugin for neighbourhoods.
> * New plugin to compute gene ontology profiles.
> * Added various missing code headers.
> * Simplified the plugin creation process.
> * Fixed some divisions per 0.
> * Fixed a synchronization bug for gene ontology.
> * Added simple profile files for sequence abundance, taxonomy profiles
> and gene ontology profiles.
> * A bug that caused k-mers with >= 65536 coverage to have less coverage
> was fixed.
> ---> This was a long-standing bug that caused some issues.
> * Added some datatypes.
>
>
> Changes in RayPlatform
>
> * Command line arguments can be obtained.
> * Simplified the plugin creation process.
> * Fixed two divisions per 0.
> * Added some datatypes.
>
>
>
> seb
>
>
> ------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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