Hi Seb,
The problem points to the old version of open-mpi. Shall I try to
install open-mpi-1.4.3 into a different path? Thanks!
CJ
---------------
grep VERSION /usr/local/include/mpi.h | head
#define MPI_VERSION 1
#define MPI_SUBVERSION 2
mpirun --version
mpirun (Open MPI) 1.2.8
mpicxx --version
i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
mpicxx -show-me
g++ -D_REENTRANT -Wl,-u,_munmap -Wl,-multiply_defined,suppress
-lmpi_cxx -lmpi -lopen-rte -lopen-pal
ompi_info | 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
Prefix: /usr
Configured architecture: x86_64-apple-darwin10.0
Configured by: root
Configured on: Mon May 18 22:57:36 PDT 2009
g++ --version
i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3)
uname -a
Darwin 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT
2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
2011/9/7 Sébastien Boisvert <[email protected]>:
> You are probably mixing versions of glibc and/or gcc/g++ and/or open-mpi.
>
> Can you post the output of these commands:
>
>
> grep VERSION /usr/local/include/mpi.h | head
>
>
> mpirun --version
>
>
> mpicxx --version
>
>
> mpicxx -show-me
>
>
> ompi_info | head
>
>
> g++ --version
>
>
> uname -a
>
>
>
>
> Thank you.
>
>
> Sébastien
>
> http://github.com/sebhtml/ray
>
>> ________________________________________
>> De : CJ [[email protected]]
>> Date d'envoi : 7 septembre 2011 08:51
>> À : [email protected]
>> Objet : Re: [Denovoassembler-users] RE : Problem to compile on a Mac
>>
>> Hi,
>>
>> I'm using openmpi-1.4.3. It should be universal. What may be the problem?
>>
>> Thanks!
>>
>> CJ
>>
>> 2011/9/6 Sébastien Boisvert <[email protected]>:
>>> Hello,
>>>
>>> The compilation warning in VirtualCommunicator.cpp are already fixed in the
>>> git repository.
>>>
>>>
>>> The compilation errors are within your mpi.h.
>>>
>>>
>>>> /usr/local/include/mpi.h:439: error: expected initializer before ‘__ARGS’
>>>
>>>
>>> Which implementation of the message-passing interface are you using ?
>>>
>>>
>>>
>>>
>>> Sébastien
>>>
>>> http://github.com/sebhtml/ray
>>>
>>>> ________________________________________
>>>> De : CJ [[email protected]]
>>>> Date d'envoi : 6 septembre 2011 12:29
>>>> À : [email protected]
>>>> Objet : [Denovoassembler-users] Problem to compile on a Mac
>>>>
>>>> Hi,
>>>>
>>>> I tried to compile Ray1.6.1 on a Mac 10.6 and had the following error
>>>> message. How can I solve the problem? Many thanks!
>>>>
>>>> ----------
>>>>
>>>> Compilation and linking flags (generated automatically)
>>>>
>>>> CXXFLAGS = -Icode -D MAXKMERLENGTH=32 -O3
>>>> LDFLAGS =
>>>>
>>>> MPICXX code/memory/OnDiskAllocator.cpp
>>>> MPICXX code/memory/ReusableMemoryStore.cpp
>>>> MPICXX code/memory/MyAllocator.cpp
>>>> MPICXX code/memory/RingAllocator.cpp
>>>> MPICXX code/memory/malloc_types.cpp
>>>> MPICXX code/memory/allocator.cpp
>>>> MPICXX code/memory/DefragmentationGroup.cpp
>>>> MPICXX code/memory/ChunkAllocatorWithDefragmentation.cpp
>>>> MPICXX code/memory/DefragmentationLane.cpp
>>>> MPICXX code/communication/mpi_tags.cpp
>>>> MPICXX code/communication/VirtualCommunicator.cpp
>>>> code/communication/VirtualCommunicator.cpp: In member function ‘void
>>>> VirtualCommunicator::printStatistics()’:
>>>> code/communication/VirtualCommunicator.cpp:342: warning: format ‘%lu’
>>>> expects type ‘long unsigned int’, but argument 3 has type ‘uint64_t’
>>>> code/communication/VirtualCommunicator.cpp:342: warning: format ‘%lu’
>>>> expects type ‘long unsigned int’, but argument 4 has type ‘uint64_t’
>>>> MPICXX code/communication/BufferedData.cpp
>>>> MPICXX code/communication/Message.cpp
>>>> MPICXX code/communication/MessageProcessor.cpp
>>>> MPICXX code/communication/MessagesHandler.cpp
>>>> In file included from code/communication/MessagesHandler.h:25,
>>>> from code/communication/MessagesHandler.cpp:23:
>>>> /usr/local/include/mpi.h:439: error: expected initializer before ‘__ARGS’
>>>> /usr/local/include/mpi.h:441: error: expected initializer before ‘__ARGS’
>>>> ............
>>>> /usr/local/include/mpi.h:1095: error: expected initializer before ‘__ARGS’
>>>> /usr/local/include/mpi.h:1096: error: expected initializer before ‘__ARGS’
>>>> code/communication/MessagesHandler.cpp: In member function ‘void
>>>> MessagesHandler::sendMessages(StaticVector*, int)’:
>>>> code/communication/MessagesHandler.cpp:58: error: ‘MPI_Isend’ was not
>>>> declared in this scope
>>>> code/communication/MessagesHandler.cpp:59: error: ‘MPI_Request_free’
>>>> was not declared in this scope
>>>> code/communication/MessagesHandler.cpp: In member function ‘void
>>>> MessagesHandler::receiveMessages(StaticVector*, RingAllocator*, int)’:
>>>> code/communication/MessagesHandler.cpp:102: error: ‘MPI_Test’ was not
>>>> declared in this scope
>>>> code/communication/MessagesHandler.cpp:111: error: ‘MPI_Get_count’ was
>>>> not declared in this scope
>>>> code/communication/MessagesHandler.cpp:120: error: ‘MPI_Start’ was not
>>>> declared in this scope
>>>> code/communication/MessagesHandler.cpp: In member function ‘void
>>>> MessagesHandler::initialiseMembers()’:
>>>> code/communication/MessagesHandler.cpp:158: error: ‘MPI_Recv_init’ was
>>>> not declared in this scope
>>>> code/communication/MessagesHandler.cpp:159: error: ‘MPI_Start’ was not
>>>> declared in this scope
>>>> code/communication/MessagesHandler.cpp: In member function ‘void
>>>> MessagesHandler::freeLeftovers()’:
>>>> code/communication/MessagesHandler.cpp:165: error: ‘MPI_Cancel’ was
>>>> not declared in this scope
>>>> code/communication/MessagesHandler.cpp:166: error: ‘MPI_Request_free’
>>>> was not declared in this scope
>>>> code/communication/MessagesHandler.cpp: In member function ‘void
>>>> MessagesHandler::constructor(int*, char***)’:
>>>> code/communication/MessagesHandler.cpp:180: error: ‘MPI_Init’ was not
>>>> declared in this scope
>>>> code/communication/MessagesHandler.cpp:184: error:
>>>> ‘MPI_Get_processor_name’ was not declared in this scope
>>>> code/communication/MessagesHandler.cpp:185: error: ‘MPI_Comm_rank’ was
>>>> not declared in this scope
>>>> code/communication/MessagesHandler.cpp:186: error: ‘MPI_Comm_size’ was
>>>> not declared in this scope
>>>> code/communication/MessagesHandler.cpp: In member function ‘void
>>>> MessagesHandler::destructor()’:
>>>> code/communication/MessagesHandler.cpp:200: error: ‘MPI_Finalize’ was
>>>> not declared in this scope
>>>> code/communication/MessagesHandler.cpp: In member function ‘void
>>>> MessagesHandler::barrier()’:
>>>> code/communication/MessagesHandler.cpp:216: error: ‘MPI_Barrier’ was
>>>> not declared in this scope
>>>> code/communication/MessagesHandler.cpp: In member function ‘void
>>>> MessagesHandler::version(int*, int*)’:
>>>> code/communication/MessagesHandler.cpp:220: error: ‘MPI_Get_version’
>>>> was not declared in this scope
>>>> make: *** [code/communication/MessagesHandler.o] Error 1
>>>>
>>>>
>>>> ----------
>>>> CJ
>>>>
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>>
>> ------------------------------------------------------------------------------
>> Using storage to extend the benefits of virtualization and iSCSI
>> Virtualization increases hardware utilization and delivers a new level of
>> agility. Learn what those decisions are and how to modernize your storage
>> and backup environments for virtualization.
>> http://www.accelacomm.com/jaw/sfnl/114/51434361/
>> _______________________________________________
>> Denovoassembler-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
>>
------------------------------------------------------------------------------
Using storage to extend the benefits of virtualization and iSCSI
Virtualization increases hardware utilization and delivers a new level of
agility. Learn what those decisions are and how to modernize your storage
and backup environments for virtualization.
http://www.accelacomm.com/jaw/sfnl/114/51434361/
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