Installation Error - either use HDF5HOME env. var. or --with

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husanhao
Posts: 41
Joined: Thu Jul 10, 2014 9:17 am

Installation Error - either use HDF5HOME env. var. or --with

Post by husanhao » Sun Feb 15, 2015 9:47 am

Dear all,

I would like to install Code-Saturne 3.0.6 by using installer which provided on this website.
However, I have a error during configure stage of MED:

configure: error: either use HDF5HOME env. var. or --with-hdf5=<path>

If there anyone can help me to solve this problem?
The attach is my install_saturne.log file, thanks.

Best Regards
Eric
Attachments
install_saturne.log
(46.38 KiB) Downloaded 324 times

Yvan Fournier
Posts: 2825
Joined: Mon Feb 20, 2012 3:25 pm

Re: Installation Error - either use HDF5HOME env. var. or --

Post by Yvan Fournier » Sun Feb 15, 2015 9:34 pm

Hello,

I did not check the installer code in a while, but from memory, there may be issues with MED detecting HDF5's tools, which are installed in a subdirectory of the HDF5 install tree's "bin" directory (tools if I remember correctly) If this is the case, you have 2 options:

[*] type: export PATH=/home/hp/opt/hdf5-1.8.10/bin/tools:$PATH
before running the installer
[*] adapt the installer code search for (1.8.10 and 3.0.6) to replace HDF5 and MED versions with newer versions (1.8.14 for HDF5, 3.0.8 for MED

I have not has this issue recently, so either MED worked around the HDF5 installation subdirectory, or HDF5 reverted to a more classical structure. Looking at my home HDF5 install (1.8.12), I would guess at least the second proposition is true (so upgrading to HDF5 1.8.12 or better should be enough.

If you have a recent enough HDF5 build using packages on your system, you mays also tell the installer to use the system HDF5.

I'll thing of updating MED and HDF5 packages when we version release 3.0.7 (in a few weeks at most).

Regards,

Yvan

MartianDuan
Posts: 74
Joined: Fri Aug 02, 2013 4:26 pm

Re: Installation Error - either use HDF5HOME env. var. or --

Post by MartianDuan » Fri Aug 28, 2015 11:37 am

Hello Yvan,

I have the same problem with MED-3.0.8.

Suprisingly, I do not find the 'tools' directory in the 'bin' of HDF5-1.8.14. Is there any special requirement of it for the HDF5 library?

Thanks in advance,

Yu.
Yvan Fournier wrote:Hello,

I did not check the installer code in a while, but from memory, there may be issues with MED detecting HDF5's tools, which are installed in a subdirectory of the HDF5 install tree's "bin" directory (tools if I remember correctly) If this is the case, you have 2 options:

[*] type: export PATH=/home/hp/opt/hdf5-1.8.10/bin/tools:$PATH
before running the installer
[*] adapt the installer code search for (1.8.10 and 3.0.6) to replace HDF5 and MED versions with newer versions (1.8.14 for HDF5, 3.0.8 for MED

I have not has this issue recently, so either MED worked around the HDF5 installation subdirectory, or HDF5 reverted to a more classical structure. Looking at my home HDF5 install (1.8.12), I would guess at least the second proposition is true (so upgrading to HDF5 1.8.12 or better should be enough.

If you have a recent enough HDF5 build using packages on your system, you mays also tell the installer to use the system HDF5.

I'll thing of updating MED and HDF5 packages when we version release 3.0.7 (in a few weeks at most).

Regards,

Yvan

Yvan Fournier
Posts: 2825
Joined: Mon Feb 20, 2012 3:25 pm

Re: Installation Error - either use HDF5HOME env. var. or --

Post by Yvan Fournier » Sun Aug 30, 2015 8:38 pm

Hello,

The existence of the "tools" directory may depend on the HDF5 version, or the way it is installed.

Insread of:
export PATH=/home/hp/opt/hdf5-1.8.10/bin/tools:$PATH
Could you try
export PATH=/home/hp/opt/hdf5-1.8.10/bin:$PATH
before running the installer ?

You might also have issues with multiple HDF5 versions ?

Could you remind me what system you are running on ? Do you already have and HDF5 library installed ? If yes, does it have development headers installed ?

Regards,

Yvan

MartianDuan
Posts: 74
Joined: Fri Aug 02, 2013 4:26 pm

Re: Installation Error - either use HDF5HOME env. var. or --

Post by MartianDuan » Mon Aug 31, 2015 10:52 pm

Hello Yvan,

As the failure of the installer on the installation of MED-3.0.8. I created a bash file to configure the source. It is attached.

And I tried the you suggestion. Unfortunately, it does not work. I just installed one hdf5-1.8.14. I had tried 1.8.15 as well, the outcome is still negative. I am using the ubuntu-14.0.3. I am not sure whether the development headers were installed or not. It was done by the installer of code_saturne.

I had attached the configuration log for both HDF5 and MED. I think it probably will help to diagnose the problem.

Thank you very much.

Kindest regards,

Yu.

Yvan Fournier wrote:Hello,

The existence of the "tools" directory may depend on the HDF5 version, or the way it is installed.

Insread of:
export PATH=/home/hp/opt/hdf5-1.8.10/bin/tools:$PATH
Could you try
export PATH=/home/hp/opt/hdf5-1.8.10/bin:$PATH
before running the installer ?

You might also have issues with multiple HDF5 versions ?

Could you remind me what system you are running on ? Do you already have and HDF5 library installed ? If yes, does it have development headers installed ?

Regards,

Yvan
Attachments
HDF5_config.log
(1.56 MiB) Downloaded 321 times
MED-config.log
(24.89 KiB) Downloaded 316 times

Yvan Fournier
Posts: 2825
Joined: Mon Feb 20, 2012 3:25 pm

Re: Installation Error - either use HDF5HOME env. var. or --

Post by Yvan Fournier » Tue Sep 01, 2015 1:14 am

Hello,

In the log for MED, it seems it cannot link with "-lz".

I just checked on an Ubuntu 14 vm, and the "zlib1g" package only includes
/usr/lib/x86_64-linux-gnu/libz.so.1, so you need to install the "zlib1g-dev" package first...

If this is not enough you may also try:
export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
before running the installer, but this should probably not be necessary.

Regards,

Yvan

MartianDuan
Posts: 74
Joined: Fri Aug 02, 2013 4:26 pm

Re: Installation Error - either use HDF5HOME env. var. or --

Post by MartianDuan » Wed Sep 02, 2015 2:09 pm

Hi Yvan,

Thanks for the suggestion. The original problem had been solved.

But the new problem came out:

configure: error:
Could not link test program to Python. Maybe the main Python library has been
installed in some non-standard library path. If so, pass it to configure,
via the LDFLAGS environment variable.
Example: ./configure LDFLAGS="-L/usr/non-standard-path/python/lib"
============================================================================
ERROR!
You probably have to install the development version of the Python package
for your distribution. The exact name of this package varies among them.
============================================================================

It seems the problem is related to the Python. However, I had check the file of python they are in the right directory. Please see the configure.log and eviroment file of my system in the attachment.

Best regards,

Yu.
Yvan Fournier wrote:Hello,

In the log for MED, it seems it cannot link with "-lz".

I just checked on an Ubuntu 14 vm, and the "zlib1g" package only includes
/usr/lib/x86_64-linux-gnu/libz.so.1, so you need to install the "zlib1g-dev" package first...

If this is not enough you may also try:
export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH
before running the installer, but this should probably not be necessary.

Regards,

Yvan
Attachments
config.log
(68.97 KiB) Downloaded 249 times
enviroment.log
(3.22 KiB) Downloaded 276 times

Yvan Fournier
Posts: 2825
Joined: Mon Feb 20, 2012 3:25 pm

Re: Installation Error - either use HDF5HOME env. var. or --

Post by Yvan Fournier » Wed Sep 02, 2015 5:07 pm

Hello,

Here again, you probably need the python-dev package (installing "-dev" packages in general for needed packages is recommended in the install doc, as it is a frequent issue).

Another option is to add the --disable-python to the MED configure options (re-running the configure of MED, using the options listied at the beginning of the config.log, the rerunning make && make install), as the MED Python bindings are not needed for Code_Saturne.

Regards,

Yvan

artus_ns
Posts: 4
Joined: Fri Jun 24, 2016 1:45 pm

Re: Installation Error - either use HDF5HOME env. var. or --

Post by artus_ns » Fri Aug 19, 2016 12:43 pm

Hi,

I saw the main issue on this thread was with MED so decided to post here. I am installing the prerequisites for code_saturne on Ubuntu 14.04. I have installed HDF5-1.8.14 without any issues but when I ask for 'make check' and 'make installcheck' I get the following errors...

Code: Select all

make[4]: Entering directory `/home/meggitt/prerequisites/MED/med_build/tests/python'
autom4te --language=autotest -I ../../../med-3.0.7/config -I ../../config -I ../../../med-3.0.7/tests/python ../../../med-3.0.7/tests/python/python_installcheck_testsuite.at -o python_installcheck_testsuite.tmp
/bin/bash: autom4te: command not found
make[4]: *** [python_installcheck_testsuite] Error 127
make[4]: Leaving directory `/home/meggitt/prerequisites/MED/med_build/tests/python'
make[3]: *** [installcheck-local] Error 2
make[3]: Leaving directory `/home/meggitt/prerequisites/MED/med_build/tests/python'
make[2]: *** [installcheck-recursive] Error 1
make[2]: Leaving directory `/home/meggitt/prerequisites/MED/med_build/tests/python'
make[1]: *** [installcheck-recursive] Error 1
make[1]: Leaving directory `/home/meggitt/prerequisites/MED/med_build/tests'
make: *** [installcheck-recursive] Error 1
Is this problematic? How do I resolve them?

Many thanks,
Nico

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