Hello Albert and Pierre, I'm very sorry for my delayed answer! I still don't understand how to use the ./configure command since I have my hdf5 directory that is :
13:07:elisabettastrazzeri@MacBook-Pro-di-Elisabetta:hdf5-1.8.14:$> ls ACKNOWLEDGMENTS MANIFEST UserMacros.cmake *configure* *release_docs* CMakeFilters.cmake Makefile aclocal.m4 configure.ac *src* CMakeInstallation.cmake Makefile.am acsite.m4 *examples* *test* CMakeLists.txt Makefile.dist *bin* *fortran* *testpar* COPYING Makefile.in *c++* *hl* *tools* CTestConfig.cmake README.txt *config* *perform* *vms* /////////////////////////////////////////////////////////////////////////////////////////////////// so when I type the command : ./configure —prefix=<where_to_install> —enable-fortran —enable-cxx —with-szlib=<where szip library and header files are> what is the directory <szip library and header files are>? the directory <where to install> in my case is /Users/elisabettastrazzeri/hdf5-1.8.14 ? Thank you very much My Kindest Regards Elisabetta On Wed, Jul 8, 2015 at 7:25 PM, Pierre de Buyl < [email protected]> wrote: > Hi, > > Please read the email by Albert Cheng. As I don't use a mac currently and > never > use C++, I was not aware of the issues. > > What compiler and parallel do you have installed on your computer? > > Anyway, you should at least remove the "--enable-cxx" option. > > Regards, > > Pierre > > On Wed, Jul 08, 2015 at 05:09:57PM +0300, Elisabetta Strazzeri wrote: > > Hi Pierre, > > > > I tried different times to configure but it seems there is a problem with > > the configure file: > > > > 16:57:elisabettastrazzeri@MacBook-Pro-di-Elisabetta:hdf5-1.8.14:$> > > ./configure --prefix=/usr/local/hdf5 --enable-fortran > --enable-fortran2003 > > -- enable-shared --enable-parallel --enable-cxx > > --with-szlib=/Users/elisabettastrazzeri/hdf5-1.8.14 > > > > : command not found7: > > > > ./configure: line 47: syntax error near unexpected token `&&' > > > > '/configure: line 47: ` && (test "X`print -r -- $as_echo`" = > > "X$as_echo") 2>/dev/null; then > > Thank you > > My Kindest Regards > > Elisabetta > > > > On Wed, Jul 8, 2015 at 3:29 PM, Pierre de Buyl < > > [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 $(MAKE)... yes > > > > > > > > checking whether make supports nested variables... yes > > > > > > > > checking whether make supports nested variables... (cached) yes > > > > > > > > checking whether to enable maintainer-specific portions of > Makefiles... > > > no > > > > > > > > checking build system type... configure: error: /bin/sh > bin/config.sub > > > > --enable-cxx failed > > > > > > > > configure: WARNING: cache variable ac_cv_build contains a newline > > > > > > > > ------------------------------------------------------ > > > > > > > > Thank you > > > > > > > > My Kindest Regards > > > > > > > > Elisabetta > > > > > > > > On Wed, Jul 8, 2015 at 12:22 PM, Elisabetta Strazzeri < > > > > [email protected]> wrote: > > > > > > > > > Hi Pierre, > > > > > this is the situation of hdf5 in my computer: > > > > > > > > > > 11:34:elisabettastrazzeri@MacBook-Pro-di-Elisabetta:FortranCode:$> > 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] > > > > > 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] > > 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] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
