Hi, HDF5 does not provide parallel (MPI) for C++ API. Specify —enable-parallel and —enable-cxx together will cause configure to issue an error. You can add "--enable-unsupported” to override it but there is not much point in specifying both “—enable-parallel —enable-cxx” together since it still does not provide parallel C++ support.
Also, configure defaults to use clang as the C compiler in a Mac OSX platform. Clang is not an MPI parallel compiler. You need to set $CC to a MPI compiler (e.g., mpicc if that is the name of the MPI compiler in your system) when you want to configure with —enable-parallel. If you are not using the MPI parallel feature in HDF5, you may try this configure command to build a simple serial HDF5. $ ./configure —prefix=<where_to_install> —enable-fortran —enable-cxx —with-szlib=<where szip library and header files are> Hope this helps. -Albert Cheng THG staff On Jul 8, 2015, at 7:29 AM, Pierre de Buyl <[email protected]<mailto:[email protected]>> wrote: Hi, There are several confusing parts. 1. You have copied the hdf5 software in /usr/local/hdf5-1.8.14 2. There is a backslash '\' in your configure line I suggest the following: 1. remove all hdf5 related files from your computer. 2. download again the hdf5-1.8.14 source code. do not put it in /usr or /usr/local 3. go to the hdf5-1.8.14 directory 4. configure with ./configure --prefix=/usr/local/hdf5 --enable-fortran --enable-fortran2003 --enable-shared --enable-parallel --enable-cxx --with-szlib=PATH_TO_SZIP (if you don't need C++ remove enable-cxx) the command should be in a single line. else you need to put a backslash but /only/ at the interruption at the end of the line. then, make and make install afterwards, ls /usr/local/hdf5/bin should contain h5pfc On Wed, Jul 08, 2015 at 02:55:21PM +0300, Elisabetta Strazzeri wrote: Hi Pierre, I've installed again HDF5 with the Fortran and C++ interfaces and with SZIP compression and there is an error: ---------------------------------------------------- 14:51:elisabettastrazzeri@MacBook-Pro-di-Elisabetta:hdf5-1.8.14:$> ./configure --prefix=/usr/local/hdf5 --enable-fortran \ --enable-cxx --with-szlib=PATH_TO_SZIP configure: WARNING: you should use --build, --host, --target configure: WARNING: invalid host type: --enable-cxx checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /sw/bin/gmkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... configure: error: /bin/sh bin/config.sub --enable-cxx failed configure: WARNING: cache variable ac_cv_build contains a newline ------------------------------------------------------ Thank you My Kindest Regards Elisabetta On Wed, Jul 8, 2015 at 12:22 PM, Elisabetta Strazzeri < [email protected]<mailto:[email protected]>> wrote: Hi Pierre, this is the situation of hdf5 in my computer: 11:34:elisabettastrazzeri@MacBook-Pro-di-Elisabetta:FortranCode:$> ls /usr/local/hdf5-1.8.14/bin *COPYING* *compile* *dependencies* *install-sh* *make_err* *missing* output_filter.sh *trace* *buildhdf5* *config.guess* *deploy* *iostats* *make_overflow* *mkdirs* *release* *yodconfigure* *chkmanifest* *config.sub* distdep *locate_sw* *make_vers* *mkinstalldirs* *snapshot* *cmakehdf5* *depcomp* *h5vers* ltmain.sh *makehelp* *newer* test-driver 12:10:elisabettastrazzeri@MacBook-Pro-di-Elisabetta:FortranCode:$> ls /usr/local/hdf5-1.8.14/lib ls: /usr/local/hdf5-1.8.14/lib: No such file or directory 12:10:elisabettastrazzeri@MacBook-Pro-di-Elisabetta:FortranCode:$> It's missing the libraries folder. 1. I've installed hdf5 following the instructions in the page : https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL . 2. The code in fortran is not parallel and I've tried to use h5fc instead of h5pfc. 3. The informations on my gfortran version are: 12:21:elisabettastrazzeri@MacBook-Pro-di-Elisabetta:hdf5-1.8.14:$> gfortran -v Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin14/4.9.2/lto-wrapper Target: x86_64-apple-darwin14 Configured with: ../gcc-4.9.2/configure --prefix=/usr/local/gfortran --with-gmp=/opt/gcc-4.8 --enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin14 Thread model: posix gcc version 4.9.2 (GCC) Thank you My Kindest Regards Elisabetta On Mon, Jul 6, 2015 at 2:17 PM, Pierre de Buyl < [email protected]> wrote: Hi, On Sun, Jul 05, 2015 at 02:00:30PM +0300, Elisabetta Strazzeri wrote: my set in bashrc is this : export HDF5=/usr/local/hdf5-1.8.14 export PATH=$PATH:${HDF5}/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HDF5}/lib but when I have to use it with hdf5, it doesn't work. can you post the result of ls /usr/local/hdf5-1.8.14/bin ls /usr/local/hdf5-1.8.14/lib This would help to diagnose the problem. A few more questions: 1. How did you install hdf5? If you compiled it yourself you should make sure that you have enabled the parallel feature. 2. Is your code parallel? If not, you can use h5fc instead of h5pfc 3. It also matters to match the fortran compiler used to compile HDF5 and the one you use to build your code. Pierre On Sun, Jul 5, 2015 at 1:20 PM, Elisabetta Strazzeri < [email protected]> wrote: Hi Pierre, the command : which h5pfc doesn't give me any location of the directory so I need to setup the shell variable Path and others. is there a tutorial of how to set the variables in the bash_profile? thank you my kindest regards Elisabetta On Wed, Jul 1, 2015 at 8:55 PM, Pierre de Buyl < [email protected]> wrote: Hi Elisabetta, The information you give is a bit light. If h5pfc is indeed installed, its location will be returned by the command which h5pfc Note that depending on where you installed HDF5 on your computer, you may need to setup your environment (the shell variables PATH and others). Pierre On Wed, Jul 01, 2015 at 07:35:20PM +0300, Elisabetta Strazzeri wrote: Hello everyone! I’m working with a MacBook Pro OS X Yosemite Version 10.10.4 I’ve installed h5pfc and I’m running a Fortran based software, but I read this error: 19:18:elisabettastrazzeri@MacBook-Pro-di-Elisabetta:FortranCode:$> make h5pfc -O3 -cpp -fno-range-check -ffree-line-length-none -ffast-math -c parameters.F90 make: h5pfc: No such file or directory make: *** [parameters.o] Error 1 Where is the problem? Thank you very much My Kindest Regards Elisabetta _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 -- ----------------------------------------------------------- Pierre de Buyl KU Leuven - Institute for Theoretical Physics T +32 16 3 27355 W http://pdebuyl.be/ ----------------------------------------------------------- _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected]<mailto:[email protected]> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 -- ----------------------------------------------------------- Pierre de Buyl KU Leuven - Institute for Theoretical Physics T +32 16 3 27355 W http://pdebuyl.be/ ----------------------------------------------------------- _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected]<mailto:[email protected]> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
_______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
