Yes sure.
Sébastien
http://github.com/sebhtml/ray
> ________________________________________
> De : CJ [cjfu1...@gmail.com]
> Date d'envoi : 7 septembre 2011 14:06
> À : denovoassembler-users@lists.sourceforge.net
> Objet : Re: [Denovoassembler-users] RE : RE : Problem to compile on a Mac
>
> 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 <sebastien.boisver...@ulaval.ca>:
>> 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 [cjfu1...@gmail.com]
>>> Date d'envoi : 7 septembre 2011 08:51
>>> À : denovoassembler-users@lists.sourceforge.net
>>> 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 <sebastien.boisver...@ulaval.ca>:
>>>> 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 [cjfu1...@gmail.com]
>>>>> Date d'envoi : 6 septembre 2011 12:29
>>>>> À : denovoassembler-users@lists.sourceforge.net
>>>>> 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
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Special Offer -- Download ArcSight Logger for FREE!
>>>>> Finally, a world-class log management solution at an even better
>>>>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>>>>> download Logger. Secure your free ArcSight Logger TODAY!
>>>>> http://p.sf.net/sfu/arcsisghtdev2dev
>>>>> _______________________________________________
>>>>> Denovoassembler-users mailing list
>>>>> Denovoassembler-users@lists.sourceforge.net
>>>>> 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/
>>> _______________________________________________
>>> Denovoassembler-users mailing list
>>> Denovoassembler-users@lists.sourceforge.net
>>> 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/
> _______________________________________________
> Denovoassembler-users mailing list
> Denovoassembler-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
> ________________________________________
> De : CJ [cjfu1...@gmail.com]
> Date d'envoi : 7 septembre 2011 14:06
> À : denovoassembler-users@lists.sourceforge.net
> Objet : Re: [Denovoassembler-users] RE : RE : Problem to compile on a Mac
>
> 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 <sebastien.boisver...@ulaval.ca>:
>> 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 [cjfu1...@gmail.com]
>>> Date d'envoi : 7 septembre 2011 08:51
>>> À : denovoassembler-users@lists.sourceforge.net
>>> 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 <sebastien.boisver...@ulaval.ca>:
>>>> 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 [cjfu1...@gmail.com]
>>>>> Date d'envoi : 6 septembre 2011 12:29
>>>>> À : denovoassembler-users@lists.sourceforge.net
>>>>> 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
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Special Offer -- Download ArcSight Logger for FREE!
>>>>> Finally, a world-class log management solution at an even better
>>>>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>>>>> download Logger. Secure your free ArcSight Logger TODAY!
>>>>> http://p.sf.net/sfu/arcsisghtdev2dev
>>>>> _______________________________________________
>>>>> Denovoassembler-users mailing list
>>>>> Denovoassembler-users@lists.sourceforge.net
>>>>> 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/
>>> _______________________________________________
>>> Denovoassembler-users mailing list
>>> Denovoassembler-users@lists.sourceforge.net
>>> 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/
> _______________________________________________
> Denovoassembler-users mailing list
> Denovoassembler-users@lists.sourceforge.net
> 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/
_______________________________________________
Denovoassembler-users mailing list
Denovoassembler-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
