error while installing MED

sofiane73 · October 13, 2016, 9:26am

Hi
I am having trouble installing MED

this is what I am getting :

please help

note that HDF5 and cgnlib have been successfully installed

checking for a BSD-compatible install… /usr/bin/install -c
checking whether build environment is sane… yes
checking for a thread-safe mkdir -p… /bin/mkdir -p
checking for gawk… no
checking for mawk… mawk
checking whether make sets $(MAKE)… yes
checking whether make supports nested variables… yes
checking how to create a ustar tar archive… gnutar
checking whether to compile using MPI… no
checking for style of include used by make… GNU
checking for gcc… /usr/bin/cc
checking whether the C compiler works… yes
checking for C compiler default output file name… a.out
checking for suffix of executables…
checking whether we are cross compiling… no
checking for suffix of object files… o
checking whether we are using the GNU C compiler… yes
checking whether /usr/bin/cc accepts -g… yes
checking for /usr/bin/cc option to accept ISO C89… none needed
checking dependency style of /usr/bin/cc… gcc3
checking for /usr/bin/cc option to accept ISO C99… none needed
checking whether to compile using MPI… no
checking build system type… x86_64-unknown-linux-gnu
checking host system type… x86_64-unknown-linux-gnu
configure: Can’t find a parallel version of HDF.
checking how to run the C preprocessor… /usr/bin/cc -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 absolute name of <H5public.h>… checking H5public.h usability… yes
checking H5public.h presence… yes
checking for H5public.h… yes
///home/sofiane/Code_Saturne/4.0.6/hdf5-1.8.14/arch/Linux_x86_64/include/H5public.h
checking absolute name of <H5Ipublic.h>… checking H5Ipublic.h usability… yes
checking H5Ipublic.h presence… yes
checking for H5Ipublic.h… yes
///home/sofiane/Code_Saturne/4.0.6/hdf5-1.8.14/arch/Linux_x86_64/include/H5Ipublic.h
checking for H5open in -lhdf5… no
configure: error: either use HDF5HOME env. var. or --with-hdf5=

Yvan_Fournier · October 16, 2016, 5:58pm

Hello,

Could you provide the other recommended info (install method, logs, …as per the forum guidelines) ?

Regards,

Yvan

sofiane73 · October 29, 2016, 9:19am

Hi

Attached
Thanks
install_saturne.log (2.18 KB)

Yvan_Fournier · October 29, 2016, 2:45pm

Hello,

You still did not specify whether you used the automatic installer or the MED configure directly.

If you used the installer, could you specify your setup file ?

In any case, if you export HDF5HOME to the HDF5 path before running the install, the issue should disappear (though this should not be necessary).

Regards,

Yvan

sofiane73 · January 25, 2017, 8:20am

Hi

I did and I hope it is the right way

export HDF5HOME=/home/sofiane/Code_Saturne/4.0.6/hdf5-1.8.14/arch/Linux_x86_64
echo $HDF5HOME
/home/sofiane/Code_Saturne/4.0.6/hdf5-1.8.14/arch/Linux_x86_64/

but still have the same error when installing MED

Please help

Regards
Sofiane

Yvan_Fournier · January 26, 2017, 12:43am

Hello,

could you post the “config.log” from the MED build directory (a subdirectory in the Code_Saturne build if you used the automatic installer) ?.

Regards,

Yvan

sofiane73 · January 26, 2017, 4:40am

I have attached it
I am using the setup file and executing the install_saturne.py
config.log (21.1 KB)

Yvan_Fournier · January 26, 2017, 9:22am

Hello,

It seems the error is due to a missing “-lz” library. So you must install libz and its headers.

Which type of system are you running on ?

Regards,

Yvan

sofiane73 · January 28, 2017, 10:30am

Hi

I am using Ubuntu 16.04 LTS

Yvan_Fournier · January 28, 2017, 5:58pm

Hello,

Not sure of the package’s name on Ubuntu, but I think it is libz4g-dev.

Regards,

Yvan

sofiane73 · January 30, 2017, 11:07am

Hi

I have installed zlib1g-dev the i got another error while installing MED

I solved it with installing python-dev

no I have another problem with the installation of scotch

I have attached the log. I did install mpi but in vain

Regards
Sofiane
install_saturne.log (294 KB)

Yvan_Fournier · January 31, 2017, 12:17am

Hello,

Could you please provide the other details as per the forum’s recommendations ?

You seem to be missing MPI development headers.

Regards,

Yvan

sofiane73 · January 31, 2017, 10:30am

sorry
I attached the config.log
config.log (196 KB)

Yvan_Fournier · January 31, 2017, 4:12pm

Hello,

Scotch is optional, and sometimes a pain to install (especially when we try t automate that step), so if you have issues with it, you can opt not to use it in the setup configuration.

Regards,

Yvan

sofiane73 · February 1, 2017, 10:54am

Hi

I did. Hope it will not limit the capabilities of the code version i will use

I moved to parmetis and i have got an error during the installation

I attached the files

Regards
Sofiane
install_saturne.log (150 KB)
config.log (196 KB)

Yvan_Fournier · February 1, 2017, 11:33am

Hello,

As I said in a previous message, you are missing mpi.h. You need to install MPI developement headers (openmpi-dev or mpich-dev or something similar) if you want to compile with MPI.

Regards,

Yvan

sofiane73 · February 2, 2017, 4:45am

I did
/usr/include/mpich/mpi.h
the installation script fails to locate it
how can i get around this problem?

Regards
Sofiane

Yvan_Fournier · February 2, 2017, 2:21pm

Hello,

Again, what do you have in the installer’s “setup” file ?

Regards,

Yvan

sofiane73 · February 8, 2017, 4:17am

Hi

both mpiCompcxx and mpiCompc are set as auto

I have attached the setup

Regards
Sofiane

Yvan_Fournier · February 8, 2017, 12:35pm

Hello,

I believe you forgot the attachment.

Regards,

Yvan