Installation Issues with NetCDF, GRIB2, HDF

Added by Justin Balbierer over 8 years ago

Good Afternoon,

I am attempting to install CDO with the available libraries for netcdf, grib and hdf on CentOS 6.6.

Per the instructions on http://www.studytrails.com/blog/install-climate-data-operator-cdo-with-netcdf-grib2-and-hdf5-support/
I created a folder /opt/cdo-install then added the libraries and CDO software.

Broken down, the following folders are in the /opt/cdo-install directory:
zlib-1.2.8
hdf5-1.8.13
netcdf-4.4.0
grib_api-1.15-0-Source
jasper-1.900.1

From within /opt/cdo-install/zlib-1.2.8, I ran the command "./configure --prefix=/opt/cdo-install"
It completed without issue.

I then invoked, "make && make check && make install. Again, no issues/errors.

My issue comes when I try to install HDF5.

From within /opt/cdo-install/hdf5-1.8.13, I ran the command "./configure --with-zlib=/opt/cdo-install --prefix=/opt/cdo-install CFLAGS=-fPIC.
Again, no errors reported.

When I ran, "make && make check && make install", then I ran into an endless warning log saying, "will never be executed." It doesn't appear to be able to find the needed files.

Here is a starting sample of the log below. Has anything changed with the installation directions?

[awips@justin hdf5-1.8.13]$ make && make check && make install
You have mail in /var/spool/mail/awips
Making all in src
make¹: Entering directory `/opt/cdo-install/hdf5-1.8.13/src'
make all-am
make²: Entering directory `/opt/cdo-install/hdf5-1.8.13/src'
CC H5Olink.lo
cc1: warning: /opt/cdo-install/zlib-1.2.8/include: No such file or directory <<< where is this supposed to actually point to?
H5Olink.c: In function 'H5O_link_encode':
H5Olink.c:344: warning: will never be executed
H5Olink.c:323: warning: will never be executed
H5Olink.c:323: warning: will never be executed
H5Olink.c: In function 'H5O_link_decode':
H5Olink.c:153: warning: will never be executed
CC H5Omessage.lo
cc1: warning: /opt/cdo-install/zlib-1.2.8/include: No such file or directory
CC H5Omtime.lo
cc1: warning: /opt/cdo-install/zlib-1.2.8/include: No such file or directory
CC H5Oname.lo
cc1: warning: /opt/cdo-install/zlib-1.2.8/include: No such file or directory
CC H5Onull.lo
cc1: warning: /opt/cdo-install/zlib-1.2.8/include: No such file or directory
CC H5Opline.lo
cc1: warning: /opt/cdo-install/zlib-1.2.8/include: No such file or directory
In file included from H5Opline.c:67:
H5Oshared.h: In function 'H5O_pline_shared_post_copy_file':
H5Oshared.h:386: warning: unused parameter 'oloc_src'
H5Oshared.h: In function 'H5O_pline_shared_debug':
H5Oshared.h:484: warning: will never be executed

Any suggestions?

Replies (6)

RE: Installation Issues with NetCDF, GRIB2, HDF - Added by Ralf Mueller over 8 years ago

Hi Justin!

you don't need to install zlib manually. Every UNIX-like OS should have it under /usr
you could use conda to get a precompiled binary: Anaconda
to be honest: hdf5 causes headache

RE: Installation Issues with NetCDF, GRIB2, HDF - Added by Justin Balbierer over 8 years ago

Hi Ralph.

It looks like I have successfully moved past that step.

Now my issue is when I "make && make check && make install" cdo.

I am attaching both the terminal and config log if you or anyone else may be able to help.

Download all files

terminal_log.txt (16 KB) terminal_log.txt
config.log (78.4 KB) config.log

RE: Installation Issues with NetCDF, GRIB2, HDF - Added by Ralf Mueller over 8 years ago

every thing looks fine - only

make check

fails, which indecates missing netcdf4 support, but

this is very likely due to non-thread-safe hdf5 installation

run

make check CDO=/opt/cdo-install/cdo-1.7.x/src/cdo -L

for serialization of IO.

I get the same error on my arch linux system

You could also re-build hdf5 with

--enable-threadsafe

which should prevent this

RE: Installation Issues with NetCDF, GRIB2, HDF - Added by Justin Balbierer over 8 years ago

Would I include "--enable-threadsafe " in the "./configure" invocation?

I ran the following invocation, "./configure --with-zlib=/opt/cdo-install --prefix=/opt/cdo-install CFLAGS=-fPIC --enable-threadsafe" and received this error, "checking for thread safe support... configure: error: The thread-safe library is incompatible with the high-level library. --disable-hl can be used to prevent building the high-level library (recommended). Alternatively, --enable-unsupported will allow building the high-level library, though this configuration is not supported by The HDF Group."

Once everything is ready to go, where do I actually run the command to run CDO? I had tried to run the command, "cdo -v" but received a command not found. I looked in "/opt/cdo-install/bin" but did not see a binary for it.

RE: Installation Issues with NetCDF, GRIB2, HDF - Added by Justin Balbierer over 8 years ago

Also, was "make check CDO=/opt/cdo-install/cdo-1.7.x/src/cdo -L" added when installing the HDF5 library or when installing CDO? I assumed it was added for when installing CDO, but I wanted to double-check...

RE: Installation Issues with NetCDF, GRIB2, HDF - Added by Justin Balbierer over 8 years ago

Justin Balbierer wrote:

Also, was "make check CDO=/opt/cdo-install/cdo-1.7.x/src/cdo -L" added when installing the HDF5 library or when installing CDO? I assumed it was added for when installing CDO, but I wanted to double-check...

I added "make check CDO=/opt/cdo-install/cdo-1.7.x/src/cdo -L" for CDO and now all the tests fail.

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