Wow, good catch. I will try this tomorrow morning (I am in Zurich time zone) and report my results.
Thanks, Jason On 02/26/2014 04:20 PM, Scot Breitenfeld wrote: > We believe libtool is getting generated with several blank '-l''s in its > postdeps variable due to mvapich's mpif90 wrapper. If you compare the output > from mvapich's mpif90: > > mvapich2-2.0b/mvapich2/bin/mpif90 -shared -v > > it lists the gfortran library as "-l gfortran", with a space. > > However, if you do the same for mpich: > > mpif90 -shared -v > > it lists the gfortran library as "-lgfortran", no space, so libtool is > processing this extra space and generating the blank "-l". > > One solution is to edit "libtool" in the hdf5 library after you've run > configure and remove the blank "-l"s from postdeps= > > This maybe related to: > http://lists.gnu.org/archive/html/bug-libtool/2012-03/msg00004.html > and the comments thread here: > https://github.com/libMesh/libmesh/issues/107 > > > ________________________________________ > From: Hdf-forum <[email protected]> on behalf of Jason > Temple <[email protected]> > Sent: Tuesday, February 25, 2014 4:14 AM > To: HDF Users Discussion List > Subject: [Hdf-forum] compiling hdf5 gcc 4.8.1 fortran error > > Hello, > > I am unable to compile the fortran bindings for parallel hdf5 with gcc > 4.8.1 (works fine with gcc 4.7.3) and mvapich2. > > Here is my compile configuration: > > ./configure --prefix=/apps/monch/hdf5/1.8.12-parallel/gcc/4.8.1/mvapich2 > --enable-unsupported --enable-fortran --enable-cxx --enable-shared > --enable-production --enable-threadsafe --enable-clear-file-buffers > --enable-filters=all --enable-direct-vfd --enable-dconv-exception > --enable-dconv-accuracy --enable-hl --enable-deprecated-symbols > --enable-embedded-libinfo --with-pthread=/usr/include --enable-parallel > --with-szlib=/apps/monch/szip/intel CFLAGS=-fPIC CC=mpicc FC=mpif90 > F90=mpif90 F77=mpif77 CXX=mpicxx > > I am using mvapich2-1.9. > > SUMMARY OF THE HDF5 CONFIGURATION > ================================= > > General Information: > ------------------- > HDF5 Version: 1.8.12 > Configured on: Tue Feb 25 10:45:12 CET 2014 > Configured by: jtemple@monch03 > Configure mode: production > Host system: x86_64-unknown-linux-gnu > Uname information: Linux monch03 > 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed Jun 12 03:34:52 UTC 2013 x86_64 > x86_64 x86_64 GNU/Linux > Byte sex: little-endian > Libraries: static, shared > Installation point: > /apps/monch/hdf5/1.8.12-parallel/gcc/4.8.1/mvapich2 > > Compiling Options: > ------------------ > Compilation Mode: production > C Compiler: > /apps/monch/mvapich2/1.9/gcc/4.8.1/bin/mpicc > CFLAGS: -fPIC > H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra > -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual > -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return > -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations > -Wredundant-decls -Wnested-externs -Winline -Wfloat-equal > -Wmissing-format-attribute -Wmissing-noreturn -Wpacked > -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels > -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch > -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default > -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat > -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand > -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 > -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion > -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 > -Wvector-operation-performance -Wsuggest-attribute=pure > -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -O3 > -fomit-frame-pointer -finline-functions > AM_CFLAGS: > CPPFLAGS: > H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG > -UH5_DEBUG_API > AM_CPPFLAGS: -I/usr/include/include > -I/apps/monch/szip/intel/include -D_LARGEFILE_SOURCE > -D_LARGEFILE64_SOURCE -D_BSD_SOURCE > Shared C Library: yes > Static C Library: yes > Statically Linked Executables: no > LDFLAGS: > H5_LDFLAGS: > AM_LDFLAGS: -L/apps/monch/szip/intel/lib > -L/usr/include/lib > Extra libraries: -lpthread -lsz -lz -ldl -lm > Archiver: ar > Ranlib: ranlib > Debugged Packages: > API Tracing: no > > Languages: > ---------- > Fortran: yes > Fortran Compiler: > /apps/monch/mvapich2/1.9/gcc/4.8.1/bin/mpif90 > Fortran 2003 Compiler: no > Fortran Flags: > H5 Fortran Flags: > AM Fortran Flags: > Shared Fortran Library: yes > Static Fortran Library: yes > > C++: yes > C++ Compiler: > /apps/monch/mvapich2/1.9/gcc/4.8.1/bin/mpicxx > C++ Flags: > H5 C++ Flags: > AM C++ Flags: > Shared C++ Library: yes > Static C++ Library: yes > > Features: > --------- > Parallel HDF5: yes > High Level library: yes > Threadsafety: yes > Default API Mapping: v18 > With Deprecated Public Symbols: yes > I/O filters (external): deflate(zlib),szip(encoder) > I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset > MPE: > Direct VFD: no > dmalloc: no > Clear file buffers before write: yes > Using memory checker: no > Function Stack Tracing: no > GPFS: no > Strict File Format Checks: no > Optimization Instrumentation: no > Large File Support (LFS): yes > > After successfully compiling the c bindings, the build moves onto the > fortran side of things, and bombs out with this error: > > Making all in fortran > make[1]: Entering directory > `/apps/monch/src/hdf5/hdf5-1.8.12-parallel-gcc-4.8.1/fortran' > Making all in src > make[2]: Entering directory > `/apps/monch/src/hdf5/hdf5-1.8.12-parallel-gcc-4.8.1/fortran/src' > make all-am > make[3]: Entering directory > `/apps/monch/src/hdf5/hdf5-1.8.12-parallel-gcc-4.8.1/fortran/src' > FCLD libhdf5_fortran.la > /usr/bin/ld: cannot find > -l-L/apps/monch/gcc/4.8.1/lib/gcc/x86_64-unknown-linux-gnu/4.8.1 > collect2: error: ld returned 1 exit status > make[3]: *** [libhdf5_fortran.la] Error 1 > make[3]: Leaving directory > `/apps/monch/src/hdf5/hdf5-1.8.12-parallel-gcc-4.8.1/fortran/src' > make[2]: *** [all] Error 2 > make[2]: Leaving directory > `/apps/monch/src/hdf5/hdf5-1.8.12-parallel-gcc-4.8.1/fortran/src' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > `/apps/monch/src/hdf5/hdf5-1.8.12-parallel-gcc-4.8.1/fortran' > make: *** [all-recursive] Error 1 > > The key problem lying here: > > cannot find -l-L/apps/monch/gcc/4.8.1/lib/gcc/x86_64-unknown-linux-gnu/4.8.1 > > It looks like something in the configure is passing a variable to > reference a gnu library, and it is returning the library path instead. > > With the exact same configuration and flags, compiling with gcc-4.7.3 > poses no problem and compiles successfully. > > Thanks in advance for your help. > > -Jason > > > > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
