open TELEMAC-MASCARET The mathematically superior suite of solvers

Hello

I'm installing v7p2r0 in Ubuntu 18.04.
All dependencies were correctly installed until the last one: MED.
IAfter runinng ./configure inside ~/Downloads/med-3.2.0, it complains that it did not find some files (it finds the majority of the files). I have already used --with-hdf5=/usr, exported HDF5HOME, spent some hours stuck in this, no clue from forum discussions (I always wonder why these linux installations are so painfull...)

Here is the end of the listing, showing the missing files:
(...)
checking for stdint.h... yes
checking for unistd.h... yes
checking absolute name of <H5public.h>... checking H5public.h usability... no
checking H5public.h presence... no
checking for H5public.h... no
checking absolute name of <H5Ipublic.h>... checking H5Ipublic.h usability... no
checking H5Ipublic.h presence... no
checking for H5Ipublic.h... no
checking for H5open in -lhdf5... no
configure: error: either use HDF5HOME env. var. or --with-hdf5=<path>

Any insight will be appreciated.
Thanks!

Have a look at the the log of the configure.
You might be missing another library (for me most of the time it was zlib).
In the log (configure.log if i remember correctly) you should should see the exact error.

Hi Yugi
Thank you for helping.

From a Code-aster forum I also read something about zlib. The I did:

> apt-cache search zlib | grep -i zlib

and I got a plethora of options. Anyway I think I would need these ones:

> sudo apt-get install zlib1g zlib1g-dbg zlib1g-dev

Only zlib1g-dbg was not installed. Yet no luck.


I inspectioned config.log file (there is no configure.log). Did not find some clue about a missing package, but a list of errors. Some have to do with how some gcc compiler options were set, but that goes far beyond my knowlegde.

> grep error config.log

Configured with: ../src/configure -v --with-pkgversion='Ubuntu 7.3.0-27ubuntu1~18.04' --with-bugurl=file:///usr/share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++ --prefix=/usr --with-gcc-major-version-only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
gcc: error: unrecognized command line option '-qversion'; did you mean '--version'?
gcc: fatal error: no input files
conftest.c:12:10: fatal error: ac_nonexistent.h: No such file or directory
conftest.c:12:10: fatal error: ac_nonexistent.h: No such file or directory
conftest.c:55:10: fatal error: H5public.h: No such file or directory
conftest.c:22:10: fatal error: H5public.h: No such file or directory
conftest.c:56:10: fatal error: H5Ipublic.h: No such file or directory
conftest.c:23:10: fatal error: H5Ipublic.h: No such file or directory
collect2: error: ld returned 1 exit status
| /* Override any GCC internal prototype to avoid an error.
configure:6930: error: either use HDF5HOME env. var. or --with-hdf5=<path>

Thanks!

Hi,

Can you repost your config.log but change the extension.
I can not open it the forum is blocking it.

The H5public error is worrisome.

I should be able to tell you after i've read the config.log.

As for zlib the one needed was zlib1g-dev so that is not the issue.

Hi Yugi
Here it goes, I changed the log extension to fool the forum firewall.
Thank you.

The file is missing.

yet again

I think i see the issue.
How exactly did you install hdf5 ?
I think it might work without the option --with-hdf5.
the -with-hdf5 assume that it contains lib, bin, include...

He lol Yugi

Sorry for the late answer, I had some deadlines to honour at the end of the week.

I first installed HDF5 according to instructions in Telemac page, saving it to
/home/luke/Documentos/Telemac3D/HDF5, as I did with Metis (.. /Telemac/Metis)
Then I tryied MED instalation pointing to it using the option --with-hdf5.

Secondly I installed HDF5 withou specifying a folder and tried MED instalation without the option --with-hdf5.

Then I tried HDF5 installation from Ubuntu 18.04 repositories and tried again MED instalation with and without --with-hdf5 option.

Today I repeated the installation downloading HDF and MEE from Telemac site links, without specifiying instalation folders.
I see a lot of errors after executing HDF5 "make". I tried to save then in a txt file using "tee" linux command and using ">" linux command, but somehow only a few of lines that I see in screen are passed to the output txt file. So I copied them manually from the terminal screen. It is too big so the begining is missing. Anyway you'll find many errors.

Please find attached files.
Thank you.

PS.: I eventually compiled Telema3D without HDF5 and MED just to be able to finish my work, but I would definetely like to know what is happening and compile again with all the add-ons.

The listing in the make file is normal.
It's only warning messages.
It looks ok.

Did you run make install ?
did you add this path: /home/luke/Downloads/hdf5-1.8.14/hdf5
to --with-hdf5=