Hello:
I am trying to compile and build hdf5 1.6 with parallel I/O on my laptop
running Ubuntu 9.10 on a virtual machine.
I have configured id with the following command:
$CC=gcc F9X=/usr/bin/gfortran CPPFLAGS=-I/usr/include/mpi/
FFLAGS=-I/usr/include/mpich2/ ./configure
--prefix=/home/kunalgrao/Desktop/hdf5_parallel --enable-parallel
--enable-fortran |tee configure_parallel.log
But when I do $ make
I get the following error after some time :
make[3]: Entering directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'
/usr/bin/gfortran -I. -I/usr/include/mpich2/ -I. -I../src -c
thyperslab_wr.f90 -o thyperslab_wr.o
thyperslab_wr.f90:54.26:
comm = MPI_COMM_WORLD
1
Error: Symbol 'mpi_comm_world' at (1) has no IMPLICIT type
thyperslab_wr.f90:55.25:
info = MPI_INFO_NULL
1
Error: Symbol 'mpi_info_null' at (1) has no IMPLICIT type
make[3]: *** [thyperslab_wr.lo] Error 1
make[3]: Leaving directory
`/home/kunalgrao/Desktop/hdf5-1.6.10/fortran/testpar'
Can you please tell me how to rectify this?
I am attaching the log file for configure for your reference.
Thanks & Regards,
Kunal
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config i686-pc-linux-gnu... no
checking for config i686-pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config i686-linux-gnu... no
checking for config i686-linux-gnu... no
checking for config i686-pc... no
checking for config linux-gnu... found
compiler 'gcc' is GNU gcc-4.4.1
checking for config ./config/site-specific/host-kunalgrao-laptop... no
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking if fortran interface enabled... yes
checking if c++ interface enabled... no
checking if should build only statically linked executables... no
checking for perl... perl
checking for ar... ar
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... /usr/bin/install -c
shared libraries disabled in parallel
checking for ld used by GCC... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependant libraries... pass_all
checking command to parse /usr/bin/nm -B output... ok
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for ranlib... ranlib
checking for strip... strip
checking for objdir... .libs
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.lo... yes
checking if gcc supports -fno-rtti -fno-exceptions... no
checking whether the linker (/usr/bin/ld) supports shared libraries... yes
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
creating libtool
checking make... GNU make
checking how make searches directories... VPATH=DIR1 DIR2 ...
checking for production mode... production
checking for ceil in -lm... yes
checking for ANSI C header files... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking for difftime... yes
checking for gettimeofday... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking for sys/stat.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/types.h... (cached) yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking setjmp.h usability... yes
checking setjmp.h presence... yes
checking for setjmp.h... yes
checking features.h usability... yes
checking features.h presence... yes
checking for features.h... yes
checking for stdint.h... (cached) yes
checking io.h usability... no
checking io.h presence... no
checking for io.h... no
checking winsock.h usability... no
checking winsock.h presence... no
checking for winsock.h... no
checking sys/timeb.h usability... yes
checking sys/timeb.h presence... yes
checking for sys/timeb.h... yes
checking for large file support mode on Linux... enabled
checking for lseek64... yes
checking for fseek64... no
checking for fseeko... yes
checking for ftello... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking whether byte ordering is bigendian... no
checking for char... yes
checking size of char... 1
checking for short... yes
checking size of short... 2
checking for int... yes
checking size of int... 4
checking for long... yes
checking size of long... 4
checking for long long... yes
checking size of long long... 8
checking for __int64... no
checking size of __int64... 0
checking for float... yes
checking size of float... 4
checking for double... yes
checking size of double... 8
checking for long double... yes
checking size of long double... 12
checking for int8_t... yes
checking size of int8_t... 1
checking for uint8_t... yes
checking size of uint8_t... 1
checking for int_least8_t... yes
checking size of int_least8_t... 1
checking for uint_least8_t... yes
checking size of uint_least8_t... 1
checking for int_fast8_t... yes
checking size of int_fast8_t... 1
checking for uint_fast8_t... yes
checking size of uint_fast8_t... 1
checking for int16_t... yes
checking size of int16_t... 2
checking for uint16_t... yes
checking size of uint16_t... 2
checking for int_least16_t... yes
checking size of int_least16_t... 2
checking for uint_least16_t... yes
checking size of uint_least16_t... 2
checking for int_fast16_t... yes
checking size of int_fast16_t... 4
checking for uint_fast16_t... yes
checking size of uint_fast16_t... 4
checking for int32_t... yes
checking size of int32_t... 4
checking for uint32_t... yes
checking size of uint32_t... 4
checking for int_least32_t... yes
checking size of int_least32_t... 4
checking for uint_least32_t... yes
checking size of uint_least32_t... 4
checking for int_fast32_t... yes
checking size of int_fast32_t... 4
checking for uint_fast32_t... yes
checking size of uint_fast32_t... 4
checking for int64_t... yes
checking size of int64_t... 8
checking for uint64_t... yes
checking size of uint64_t... 8
checking for int_least64_t... yes
checking size of int_least64_t... 8
checking for uint_least64_t... yes
checking size of uint_least64_t... 8
checking for int_fast64_t... yes
checking size of int_fast64_t... 8
checking for uint_fast64_t... yes
checking size of uint_fast64_t... 8
checking for size_t... (cached) yes
checking size of size_t... 4
checking for ssize_t... (cached) yes
checking size of ssize_t... 4
checking for off_t... (cached) yes
checking size of off_t... 8
checking if dev_t is scalar... yes
checking for dmalloc library... suppressed
checking zlib.h usability... no
checking zlib.h presence... no
checking for zlib.h... no
checking for compress2 in -lz... no
checking for compress2... no
checking for szlib... suppressed
checking for pthread... suppressed
checking for thread safe support... no
checking whether HDF5 v1.4 compatibility functions enabled... no
checking for tm_gmtoff in struct tm... yes
checking for __tm_gmtoff in struct tm... no
checking for global timezone variable... no
checking whether struct tm is in sys/time.h or time.h... time.h
checking for struct tm.tm_zone... yes
checking for struct timezone... yes
checking whether gettimeofday() gives timezone... yes
checking for st_blocks in struct stat... yes
checking for _getvideoconfig... no
checking for gettextinfo... no
checking for GetConsoleScreenBufferInfo... no
checking for _scrsize... no
checking for ioctl... yes
checking for struct videoconfig... no
checking for struct text_info... no
checking for TIOCGWINSZ... yes
checking for TIOCGETD... yes
checking for alarm... yes
checking for fork... yes
checking for frexpf... yes
checking for frexpl... yes
checking for gethostname... yes
checking for getpwuid... yes
checking for getrusage... yes
checking for BSDgettimeofday... no
checking for longjmp... yes
checking for setsysinfo... no
checking for sigaction... yes
checking for signal... yes
checking for snprintf... yes
checking for vsnprintf... yes
checking for strdup... yes
checking for system... yes
checking for waitpid... yes
checking for an ANSI C-conforming const... yes
checking for inline... __inline__
checking for __attribute__ extension... yes
checking for __FUNCTION__ extension... yes
checking how to print long long... %lld and %llu
checking Threads support system scope... yes
checking for gpfs... suppressed
checking for debug flags... none
checking whether function stack tracking is enabled... no
checking for API tracing... no
checking for instrumented library... no
checking whether to clear file buffers... yes
checking for parallel support files... provided by compiler
checking for MPI_Init in -lmpi... yes
checking prefix for running on one processor...
checking prefix for running in parallel... mpirun -np $${NPROCS:=3}
checking whether a simple MPI-IO program can be linked... yes
checking for MPE... suppressed
checking if MPI_File_set_size works for files over 2GB... yes
checking if MPI_File_get_size is enabled... yes
checking if irregular hyperslab optimization code works inside MPI-IO... (cached) no
checking for I/O filters... all (shuffle,fletcher32)
checking if converting denormalized floating-point values is possible... yes
checking if high level library is enabled... yes
checking Whether to perform strict file format checks... no
checking Whether to have library information embedded in the executables... yes
configure: creating ./config.status
=== configuring in fortran (/home/kunalgrao/Desktop/hdf5-1.6.10/fortran)
configure: running /bin/bash ./configure '--prefix=/home/kunalgrao/Desktop/hdf5_parallel' '--enable-parallel' '--enable-fortran' 'CC=gcc' 'CPPFLAGS=-I/usr/include/mpi/' --cache-file=/dev/null --srcdir=.
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking shell variables initial values... done
checking for cached host... none
checking for config i686-pc-linux-gnu... no
checking for config i686-pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config i686-linux-gnu... no
checking for config i686-linux-gnu... no
checking for config i686-pc... no
checking for config linux-gnu... found
compiler 'gcc' is GNU gcc-4.4.1
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking whether make sets $(MAKE)... yes
checking for a BSD-compatible install... /usr/bin/install -c
shared libraries disabled in parallel
checking for ld used by GCC... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependant libraries... pass_all
checking command to parse /usr/bin/nm -B output... ok
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for ranlib... ranlib
checking for strip... strip
checking for objdir... .libs
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.lo... yes
checking if gcc supports -fno-rtti -fno-exceptions... no
checking whether the linker (/usr/bin/ld) supports shared libraries... yes
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
creating libtool
checking for perl... perl
checking for production mode... "production"
checking for ceil in -lm... yes
checking if should build only statically linked executables... no
checking for large file support mode on Linux... enabled
checking for f90... /usr/bin/gfortran
checking whether the Fortran 9X compiler (/usr/bin/gfortran -I/usr/include/mpich2/ ) works... yes
checking whether the Fortran 9X compiler (/usr/bin/gfortran -I/usr/include/mpich2/ ) is a cross-compiler... no
checking whether we are using GNU Fortran 95... yes
checking whether /usr/bin/gfortran accepts -g... yes
checking what /usr/bin/gfortran does with modules... module.mod
checking how /usr/bin/gfortran finds modules... -I
checking zlib.h usability... no
checking zlib.h presence... no
checking for zlib.h... no
checking for compress2 in -lz... no
checking for compress2... no
checking szlib.h usability... no
checking szlib.h presence... no
checking for szlib.h... no
checking for SZ_BufftoBuffCompress in -lsz... no
checking if compiler supports -I. option... yes
checking for I/O filters... all (shuffle,fletcher32)
checking for parallel support files... provided by compiler
checking prefix for running on one processor...
checking prefix for running in parallel... mpirun -np $${NPROCS:=2}
checking whether a simple MPI-IO program can be linked... yes
checking for MPI_Comm_c2f and MPI_Comm_f2c functions... yes
checking for MPI_Info_c2f and MPI_Info_f2c functions... yes
checking for MPE... suppressed
checking make... GNU make
checking for gpfs... suppressed
configure: creating ./config.status
config.status: creating config/depend1
config.status: creating config/depend2
config.status: creating config/depend3
config.status: creating config/depend4
config.status: creating config/dependN
config.status: creating config/commence
config.status: creating config/conclude
config.status: creating Makefile
config.status: creating src/h5fc
config.status: creating src/H5fortran_types.f90
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating testpar/Makefile
config.status: creating examples/testh5fc.sh
config.status: creating examples/Makefile
config.status: creating src/H5config_fortran.h
config.status: src/H5config_fortran.h is unchanged
config.status: executing default-1 commands
creating src/H5pubconf_fortran.h
src/H5pubconf_fortran.h is unchanged
config.status: creating src/libhdf5.settings
config.status: creating config/depend1
config.status: creating config/depend2
config.status: creating config/depend3
config.status: creating config/depend4
config.status: creating config/dependN
config.status: creating config/commence
config.status: creating config/conclude
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating test/testcheck_version.sh
config.status: creating test/testlibinfo.sh
config.status: creating testpar/Makefile
config.status: creating testpar/testph5.sh
config.status: creating perform/Makefile
config.status: creating tools/Makefile
config.status: creating tools/h5dump/Makefile
config.status: creating tools/h5dump/testh5dump.sh
config.status: creating tools/h5ls/testh5ls.sh
config.status: creating tools/h5import/Makefile
config.status: creating tools/h5diff/Makefile
config.status: creating tools/h5jam/Makefile
config.status: creating tools/h5jam/testh5jam.sh
config.status: creating tools/h5repack/Makefile
config.status: creating tools/h5repack/h5repack.sh
config.status: creating tools/h5ls/Makefile
config.status: creating tools/lib/Makefile
config.status: creating tools/misc/Makefile
config.status: creating tools/misc/h5cc
config.status: creating examples/Makefile
config.status: creating examples/testh5cc.sh
config.status: creating doc/Makefile
config.status: creating doc/html/Makefile
config.status: creating doc/html/ed_libs/Makefile
config.status: creating doc/html/ed_styles/Makefile
config.status: creating doc/html/ADGuide/Makefile
config.status: creating doc/html/Graphics/Makefile
config.status: creating doc/html/Intro/Makefile
config.status: creating doc/html/PSandPDF/Makefile
config.status: creating doc/html/TechNotes/Makefile
config.status: creating doc/html/cpplus/Makefile
config.status: creating doc/html/cpplus_RM/Makefile
config.status: creating doc/html/cpplus_RM/header_files/Makefile
config.status: creating doc/html/fortran/Makefile
config.status: creating hl/Makefile
config.status: creating hl/examples/Makefile
config.status: creating hl/src/Makefile
config.status: creating hl/test/Makefile
config.status: creating hl/tools/Makefile
config.status: creating hl/tools/gif2h5/Makefile
config.status: creating src/H5config.h
config.status: executing default-1 commands
creating src/H5pubconf.h
src/H5pubconf.h is unchanged
Configure Summary
Compiling Options:
Compilation Mode: Production
C Compiler: gcc
CFLAGS: -ansi -O0 -fomit-frame-pointer -finline-functions
CPPFLAGS: -UH5_DEBUG_API -DNDEBUG -I/usr/include/mpi/ -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE
LDFLAGS:
Debug Mode: None
Shared Libraries: No
Static Libraries: Yes
Statically Linked Executables: No
Tracing: No
Optimization Instrumentation: No
Languages:
----------
C++: No
Fortran: Yes
Fortran Compiler: /usr/bin/gfortran
FFLAGS: -I. -I/usr/include/mpich2/ -I.
C Compiler: gcc
CFLAGS: -march=i686 -ansi -O3 -fomit-frame-pointer -finline-functions
CPPFLAGS: -D_BSD_SOURCE -D_POSIX_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/mpi/
LDFLAGS:
Features:
---------
dmalloc: No
Function Stack Tracing: Disabled
GPFS: No
Strict File Format Checks: Disabled
HDF5 v1.4 Compatibility: No
I/O filters (external):
I/O filters (internal): shuffle,fletcher32
Linux Large File Support (LFS): Enabled
MPE: No
Parallel HDF5: Yes
Threadsafety: Disabled
High Level library: Enabled
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