[Bioclusters] mpiBlast OS X
Aaron Darling
bioclusters@bioinformatics.org
Fri, 01 Oct 2004 09:13:47 -0500
I haven't tried it (I don't have an OS X machine handy at the moment),
but based on a perusal of NCBI's darwin.ncbi.mk file, it looks like they
add "-framework CoreServices" and "-lc" to the link command. You may
also need "-framework Carbon", but I'm guessing not since that looks
like it's just for gui apps on OS X.
Good luck, hope it works this time around!
-Aaron
Nick Brockner wrote:
> I now have it almost linking, except for this:
>
> ld: Undefined symbols:
> _DisposeHandle
> _HLock
> _HUnlock
> _MemError
> _NewHandle
> _SetHandleSize
> _FSPathMakeRef
> mpiCC: No such file or directory
>
> Using this command to link:
>
> mpiCC -O2 -DINSTALL_PREFIX="\"/usr/local\"" -g -O2 -o mpiblast
> mpiblast-blastjob.o mpiblast-db_spec.o mpiblast-blast_hooks.o
> mpiblast-embed_rank.o mpiblast-file_util.o mpiblast-fragment_list.o
> mpiblast-mpiblast_util.o mpiblast-mpiblast.o
> mpiblast-mpiblast_config.o mpiblast-ncbi_sizeof.o
> mpiblast-distributed_bioseq.o /usr/local/ncbi/build/ncbithr.o
> -lncbitool -lncbiobj -lncbi -L/usr/local/ncbi/lib/ -lm -lpthread
> -lstdc++
>
> I searched all over and cannot find what to link with for these. I
> appreciate all the help you have given so far with this.
>
> Thanks,
>
> -Nick
> On Sep 30, 2004, at 5:49 PM, Aaron Darling wrote:
>
>> Yes, looks like something wrong with the build environment. Looks
>> like it's not linking to the c++ library. Usually the GNU standard
>> c++ library can be linked with -lstdc++. You could either add that
>> to the CXXFLAGS environment variable and reconfigure or just copy the
>> link command, add -lstdc++, and run it from within the src dir. In
>> the past we've only tested releases on Linux and Windows, sounds like
>> that needs to change :)
>>
>> -Aaron
>>
>> Nick Brockner wrote:
>>
>>> Ok, now that getopt() is out of the way it compiles, but then when
>>> it goes to link I get this garbage:
>>>
>>> ld: Undefined symbols:
>>> std::basic_ostream<char, std::char_traits<char>
>>> >::operator<<(std::basic_ostream<char, std::char_traits<char> >&
>>> (*)(std::basic_ostream<char, std::char_traits<char> >&))
>>> std::basic_ostream<char, std::char_traits<char> >::operator<<(double)
>>> std::basic_ostream<char, std::char_traits<char> >::operator<<(long)
>>> std::basic_ostream<char, std::char_traits<char>
>>> >::operator<<(unsigned long)
>>> std::basic_string<char, std::char_traits<char>, std::allocator<char>
>>> >::_Rep::_M_destroy(std::allocator<char> const&)
>>> .
>>> .
>>> .
>>>
>>> I think this has nothing to do with the mpiBlast code, and has
>>> something to do with Apple's build environment. Difficult build,
>>> this is.
>>>
>>> Thanks,
>>>
>>> -Nick Brockner
>>> On Sep 30, 2004, at 3:35 PM, Aaron Darling wrote:
>>>
>>>> This happens on OS X, Solaris, and AIX because our getopt()
>>>> detection was broken in 1.2.1. A quick fix is to comment out line
>>>> 147 of mpiBLAST-1.2.1/src/getopt.h
>>>> e.g. change:
>>>> extern int getopt ();
>>>> to:
>>>> /* extern int getopt (); */
>>>>
>>>> -Aaron
>>>>
>>>> Nick Brockner wrote:
>>>>
>>>>> Hi Aaron,
>>>>>
>>>>> Thanks for the pointer. Using the Oct. 2003 ncbi toolkit worked
>>>>> for the previous error, but now I have a more sinister looking error:
>>>>>
>>>>> In file included from /usr/include/pthread.h:61,
>>>>> from
>>>>> /usr/include/gcc/darwin/3.3/c++/ppc-darwin/bits/gthr-default.h:37,
>>>>> from
>>>>> /usr/include/gcc/darwin/3.3/c++/ppc-darwin/bits/gthr.h:98,
>>>>> from
>>>>> /usr/include/gcc/darwin/3.3/c++/ppc-darwin/bits/c++io.h:37,
>>>>> from /usr/include/gcc/darwin/3.3/c++/bits/fpos.h:44,
>>>>> from /usr/include/gcc/darwin/3.3/c++/iosfwd:49,
>>>>> from
>>>>> /usr/include/gcc/darwin/3.3/c++/bits/stl_algobase.h:70,
>>>>> from /usr/include/gcc/darwin/3.3/c++/algorithm:66,
>>>>> from mpiblast.cpp:86:
>>>>> /usr/include/unistd.h:183: error: declaration of C function `int
>>>>> getopt(int,
>>>>> char* const*, const char*)' conflicts with
>>>>> getopt.h:147: error: previous declaration `int getopt()' here
>>>>> In file included from file_util.hpp:58,
>>>>> from mpiblast.hpp:71,
>>>>> from mpiblast.cpp:88:
>>>>>
>>>>>
>>>>> Has anyone seen this before? Looks OS X specific.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> -Nick Brockner
>>>>>
>>>>> On Sep 30, 2004, at 2:51 PM, Aaron Darling wrote:
>>>>>
>>>>>> Assuming you are using mpiBLAST 1.2.1, you need to use the
>>>>>> October 2003 release of the NCBI Toolbox from here:
>>>>>> ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/old/
>>>>>>
>>>>>> Each version of mpiBLAST is designed to compile against a
>>>>>> specific version of the NCBI Toolbox, as mentioned on our
>>>>>> download page here:
>>>>>>
>>>>>> http://mpiblast.lanl.gov/download.html
>>>>>>
>>>>>> Later toolbox releases changed the API to BlastMakeMultQueries
>>>>>> and BXMLPrintOutput, which is why you are seeing those build errors.
>>>>>>
>>>>>> Regards,
>>>>>> -Aaron
>>>>>>
>>>>>> Nick Brockner wrote:
>>>>>>
>>>>>>> Hi All,
>>>>>>>
>>>>>>> I think I am missing something here, but attempting to compile
>>>>>>> mpiBlast gets me the following:
>>>>>>>
>>>>>>> blast_hooks.c: In function `getFakeBioseq':
>>>>>>> blast_hooks.c:785: error: too few arguments to function
>>>>>>> `BlastMakeMultQueries'
>>>>>>> blast_hooks.c: In function `outputResults':
>>>>>>> blast_hooks.c:1334: error: too few arguments to function
>>>>>>> `BXMLPrintOutput'
>>>>>>> blast_hooks.c:1345: error: too few arguments to function
>>>>>>> `BXMLPrintOutput'
>>>>>>> blast_hooks.c:1493: error: too few arguments to function
>>>>>>> `BXMLPrintOutput'
>>>>>>> blast_hooks.c:1498: error: too few arguments to function
>>>>>>> `BXMLPrintOutput'
>>>>>>> mpicc: No such file or directory
>>>>>>> make[1]: *** [mpiblast-blast_hooks.o] Error 1
>>>>>>> make: *** [all-recursive] Error 1
>>>>>>>
>>>>>>>
>>>>>>> My setup:
>>>>>>> OS X Server 10.3.5
>>>>>>> gcc version 3.3 20030304 (Apple Computer, Inc. build 1495)
>>>>>>> NCBI toolkit installed
>>>>>>> LAM-MPI version 7.0.6
>>>>>>>
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> -Nick Brockner
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioclusters maillist - Bioclusters@bioinformatics.org
>>>>>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioclusters maillist - Bioclusters@bioinformatics.org
>>>>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioclusters maillist - Bioclusters@bioinformatics.org
>>>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioclusters maillist - Bioclusters@bioinformatics.org
>>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioclusters maillist - Bioclusters@bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>
>>
>> _______________________________________________
>> Bioclusters maillist - Bioclusters@bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>
>
> _______________________________________________
> Bioclusters maillist - Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters