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Re: [Apbs-users] mpi with apbs 4
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From: Todd D. <to...@cc...> - 2005-12-22 14:27:52
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Hi Bill - As Chris mentioned, we came across this error the other day - apparently when fixing one configure-related MPI bug, another was introduced for certain compilers. The issue is that when checking for MPI libraries a pat= h is passed in without the -L flag, and while some compilers just ignore this as an extra argument, others fail, causing the check to fail and therefore miss the MPI library. I've placed a patched configure script at http://agave.wustl.edu/apbs/download/apbs-0.4.0/configure which should resolve this issue, or you can use Chris' solution below. Todd On 12/21/05, Chang, Christopher <Chr...@nr...> wrote: > > I ran into a similar error, related to formatting of a line in > "configure". Should be in the archive, but I've pasted in my workaround > below. Hope it helps. > > Chris > > Christopher H. Chang, Ph.D. > Research Associate > National Renewable Energy Laboratory > 1617 Cole Blvd., Mail Stop 1608 > Golden, CO 80401 > Phone (303) 275-3751 > Fax (303) 275-4007 > > > > (1) After configure/make/make install of MALOC with MPI enabled and > > BLAS disabled (I linked against the ATLAS libraries), the APBS > > configure with command > > > > --------------- > > ./configure --prefix=3D${FETK_PREFIX} --with-blas=3D"-L${BLAS_DIR} -lbl= as" > > > >& configure1.log & > > --------------- > > > > failed with message > > > > --------------- > > checking for /copt/mpich.pgi/1.2.6-fPIC/lib/libmpich.a... > > yes > > checking for /copt/mpich.pgi/1.2.6-fPIC/lib/libmpich.so... > > no > > checking for main in -lmpich... no > > checking for main in -lmpi... no > > MALOC was compiled with MPI enabled > > MALOC needs to link against the MPI library Try defining > > FETK_MPI_INCLUDE and FETK_MPI_LIBRARY > > configure: error: MPI library or header is missing!! > > ---------------- > > > > which was associated with lines in config.log: > > > > ---------------- > > configure:10372: checking for > > /copt/mpich.pgi/1.2.6-fPIC/lib/libmpich.a > > configure:10387: result: yes > > configure:10394: checking for > > /copt/mpich.pgi/1.2.6-fPIC/lib/libmpich.so > > configure:10409: result: no > > configure:10417: checking for main in -lmpich > > configure:10443: pgcc -o conftest -O2 -fPIC -tp amd64 -fastsse > > -I/copt/mpich.pgi/1.2.6-fPIC/include > > -L/copt/mpich.pgi/1.2.6-fPIC/lib > > -L/copt/mpich.pgi/1.2.6-fPIC/lib conftest.c -lmpich > > /copt/mpich.pgi/1.2.6-fPIC/lib >&5 > > > > conftest.c: > > File with unknown suffix passed to linker: > > /copt/mpich.pgi/1.2.6-fPIC/lib > > /copt/mpich.pgi/1.2.6-fPIC/lib: file not recognized: Is a directory > > ----------------- > > > > which I traced back to line 10426 (I believe) in file configure: > > > > ----------------- > > LIBS=3D"-lmpich ${mpi_lib_path} $LIBS" > > ----------------- > > > > Commenting out and changing to > > > > ----------------- > > # LIBS=3D"-lmpich $LIBS" > > ----------------- > > > > seemed to clear this up. > > > > > > -----Original Message----- > > From: apb...@li... > > [mailto:apb...@li...] On Behalf Of > > William Scott > > Sent: Wednesday, December 21, 2005 3:30 PM > > To: apb...@li... > > Subject: [Apbs-users] mpi with apbs 4 > > > > Hi: > > > > I'm having trouble configuring apbs 4 with mpi. Previously, > > I used lammpi with success, with the previous version of > > apbs. This time configure fails (see below) > > > > I then recompiled maloc with mpich, and tried that. It also > > fails (somewhat differently). > > > > Any hints? > > > > Thanks. > > > > Bill Scott > > > > > > > > with lammpi (worked with previous version of apbs): > > > > ---------- begin configuring for MALOC linkage ------------ > > checking for FETK_INCLUDE... yes checking for FETK_LIBRARY... > > yes checking maloc/maloc.h usability... yes checking > > maloc/maloc.h presence... yes checking for maloc/maloc.h... > > yes checking for maloc_link in -lmaloc... yes checking for > > maloc_needs_mpi in -lmaloc... yes checking for > > FETK_MPI_INCLUDE environmental variable... yes checking for > > FETK_MPI_LIBRARY environmental variable... yes checking for > > --with-mpiinc option... yes checking for --with-mpilib > > option... yes Looking for MPI header with -I/sw/include ... > > checking mpi.h usability... yes > > checking mpi.h presence... yes > > checking for mpi.h... yes > > Looking for MPI library with /sw/lib... > > checking for /sw/lib/libmpi.a... yes > > checking for /sw/lib/libmpi.so... no > > checking for main in -lmpi... no > > checking for main in -lmpi... (cached) no MALOC was compiled > > with MPI enabled MALOC needs to link against the MPI library > > Try defining FETK_MPI_INCLUDE and FETK_MPI_LIBRARY > > configure: error: MPI library or header is missing!! > > > > > > > > with mpich: > > > > looks for libmpi.a instead of libmpich.a, then fails. > > > > > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you grep > > through log files for problems? Stop! Download the new AJAX > > search engine that makes searching your log files as easy as > > surfing the web. DOWNLOAD SPLUNK! > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > > _______________________________________________ > > apbs-users mailing list > > apb...@li... > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! 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