Thread: [Apbs-users] Re: ...files as requested!
Biomolecular electrostatics software
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From: Nathan A. B. <ba...@ch...> - 2003-01-23 15:34:33
Attachments:
configure
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Hi Ben -- [Cc'ed to the APBS users list; for background: under Solaris 2.8, MALOC compiled with MPI but APBS could not ascertain that MALOC needed the MPI library] The source of the problem is in config_apbs.log: configure:9829: checking for maloc_needs_mpi in -lmaloc configure:9860: cc -o conftest -g conftest.c -lmaloc -L/home/bjc32/APBS/BEN_MPI_TESTDIR/dist/lib/sparc-sun-solaris2.8 -lmaloc -lsocket -lnsl -lm >&5 ld: fatal: library -lmaloc: not found ld: fatal: File processing errors. No output written to conftest There seems to be something funky with how the Solaris compilers are handling the linker commands as the earlier test: configure:9756: checking for maloc_link in -lmaloc configure:9787: cc -o conftest -g -I/home/bjc32/APBS/BEN_MPI_TESTDIR/dist/include -L/home/bjc32/APBS/BEN_MPI_TESTDIR/dist/lib/sparc-sun-solaris2.8 conftest.c -lmaloc -L/home/bjc32/APBS/BEN_MPI_TESTDIR/dist/lib/sparc-sun-solaris2.8 -lmaloc -lsocket -lnsl -lm >&5 configure:9790: $? = 0 configure:9793: test -s conftest configure:9796: $? = 0 configure:9808: result: yes In other words, it looks like the compilers/linkers are being exceedingly pedantic. I've patched up the configure script (attached). Can you substitute it for the one you currently have in the APBS directly and let me know how that works? Thanks, Nathan Ben Carrington <bj...@he...> (01-23-2003 10:22:42+0000): > >Thanks for looking at these Nathan, I do appreciate it. > >I had to use a 'A' instead of 'a' flag on... > >nm -A[a] ${FETK_LIBRARY}/sparc-sun-solaris2.8/libmaloc.a > >..doubt it makes much difference. > > >All the best, > >Ben > > > > End of message from Ben Carrington. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker |
From: Ben C. <bj...@he...> - 2003-01-24 14:58:55
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thanks for the new configure... so, i've tried it and now it's even more picky than before...it seems to me that the configure script looks for 'lmpich'...could I hazard a guess that this is the same as 'libmpich' for me?? this is the relevant configure output: ************************* checking for mpi.h... yes checking for main in -lmpi... no checking for main in -lmpich...configure: error: MPI library or header is missing!! no MALOC was compiled with MPI enabled MALOC needs to link against the MPI library Try defining FETK_MPI_INCLUDE and FETK_MPI_LIBRARY ************************* my FETK_MPI_LIBRARY points to a directory that contains the following files: ************************ libampe.a liblmpe.a libmpe_nompi.a libmpichf90.a libmpichfsup.a libpmpich.a mpe_prof.o libfmpich.a libmpe.a libmpich.a libmpichf90nc.a libpmpich++.a libtmpe.a shared ************************ ...can we just change what the configure script looks for? or is it more involved than that? (and if you think this is relevant to the list i'll leave you to post it) all yours again... Ben |
From: Nathan A. B. <ba...@ch...> - 2003-01-24 14:59:01
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Can you sent me the config.log? Thanks, Nathan Ben Carrington <bj...@he...> (01-23-2003 14:27:59+0000): > >thanks for the new configure... > >so, i've tried it and now it's even more picky than before...it seems to >me that the configure script looks for 'lmpich'...could I hazard a guess >that this is the same as 'libmpich' for me?? > >this is the relevant configure output: > >************************* >checking for mpi.h... yes >checking for main in -lmpi... no >checking for main in -lmpich...configure: error: MPI library or header is >missing!! no >MALOC was compiled with MPI enabled >MALOC needs to link against the MPI library >Try defining FETK_MPI_INCLUDE and FETK_MPI_LIBRARY >************************* > >my FETK_MPI_LIBRARY points to a directory that contains the following >files: > >************************ >libampe.a liblmpe.a libmpe_nompi.a libmpichf90.a libmpichfsup.a >libpmpich.a mpe_prof.o libfmpich.a libmpe.a libmpich.a libmpichf90nc.a >libpmpich++.a libtmpe.a shared >************************ > >...can we just change what the configure script looks for? or is it >more involved than that? (and if you think this is relevant to the list >i'll leave you to post it) > >all yours again... > >Ben > End of message from Ben Carrington. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker |
From: Ben C. <bj...@he...> - 2003-01-24 14:59:06
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here you go... |
From: Nathan A. B. <ba...@ch...> - 2003-01-24 14:59:11
Attachments:
configure
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OK -- let's try this again... I've attached a new configure script. I'm sorry about this iterative procedure; I just don't have easy access to a Sun machine to test the build on. Thanks, Nathan Ben Carrington <bj...@he...> (01-23-2003 14:34:03+0000): > >here you go... > > > <-- SNIP --> > End of message from Ben Carrington. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker |