compiling hdf5 gcc 4.8.1 fortran error

Jason_Temple · February 25, 2014, 10:14am

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

brtnfld · February 25, 2014, 6:09pm

I could reproduce the problem you reported and we are looking into it.

It works if you disable shared, --disable-shared, and build the static libraries. It also works for --enable-shared if you remove --enable-cxx, but I'm assuming you need C++ support.

Scot

···

________________________________________
From: Hdf-forum <hdf-forum-bounces@lists.hdfgroup.org> on behalf of Jason Temple <jtemple@cscs.ch>
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

_______________________________________________
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Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

brtnfld · February 26, 2014, 3:20pm

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:

github.com/libMesh/libmesh

Bug in libmesh libtool script affecting Fortran and shared libs

opened 08:40PM - 18 Jun 13 UTC

closed 08:25PM - 27 Jun 13 UTC

jwpeterson

We have some folks trying to use the libmesh-generated libtool script to link Fo…rtran libraries and executables on Linux. It may be the first time someone has tried this (?) and therefore we've never noticed the issue before, but I think I've tracked it down to the "postdeps" line in the "FC" section of $LIBMESH_DIR/contrib/bin/libtool, which I've pasted below. ``` postdeps="-L/opt/packages/mpich/mpich-3.0.2/gcc-opt/lib -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread -l -l -L/opt/packages/mpich/mpich-3.0.2/gcc-opt/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/opt/packages/tbb/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread -lgfortran -lm -lgcc_s -lquadmath -lm -lgcc_s -lc -lgcc_s" ``` As you can see, there are two naked "-l" flags in this variable, and whenever libtool tries to use it to link a Fortran shared library, it obviously fails. Unfortunately I don't know where to go from here in debugging the problem... note that it doesn't seem to affect Macs: the postdeps line is just blank for that OS. Also, if I hand edit the libtool script file and remove those -l's things seem to work fine.