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 >