conda - hdf5 version issue about gprmax

[craig-warren]

I have fixed the indentation error, but that shouldn't have effected being able to run gprMax. What error did you get when trying to run?

[mzunguman]

@craig-warren,

Thanks for the quick reply. Thought as much. The error I get is below. Probably not related to gprMax but to the Miniconda environment and that it can't get the right version of the HDF5 libary, even though the new version is installed. I think it's an issue with the path.

[craig-warren]

Yeh, I think you probably need to update the gprMax environment. Just run conda update --all with the environment activated.

[mzunguman]

@craig-warren,

I did the update and the version in Miniconda is 1.8.16, while the version on our server is 1.8.17. The latter is the one he finds and complains about, even though he should be looking in the Miniconda environment.

[craig-warren]

Yeh, that does sound like a path issue. Is the conda environment listed first when you do echo $PATH?

[mzunguman]

Yes it is. I want to show you a new error I get. I tried installing it again without the Miniconda environment, as I've always done in the past, but I get this strange error now which I don't understand.

EDIT: I forgot to mention, that this is the installation process and not running an input file. Also I tried to install a 1 week old commit that worked for me ~ 10 days ago.

[craig-warren]

@obtitus Do you think the SyntaxError in input_cmd_funcs.py is related to Python 3.4?

@mzunguman This is not a problem that should effect you unless you are using Python in your input files and using functions from input_cmd_funcs.py.

[obtitus]

Sorry about that, the pull request should fix it.

[craig-warren]

@obtitus Awesome thanks.

[mzunguman]

@craig-warren

Just wanted to make a last remark, in the hopes that it might help others as well. I solved my problem by manually setting the PATH and LD_LIBRARY_PATH variables in my .bashrc file. I don't know enough about administrating linux servers and how these path variables are handled on a multi-user system, but the following step was necessary for me. I would be thankful for suggestions, improvements or explanations for this. By entering the conda environment, a library path to the /miniconda/envs/gprMax/lib has to be set, otherwise he was using the hdf5 version installed on the system. I previously thought the path which is set by miniconda when entering the gprMax environment was sufficient. Below are the two lines I added:

- export PATH="/home/stadler/miniconda3/bin:/home/stadler/miniconda3/envs/gprMax/bin:$PATH"
- export LD_LIBRARY_PATH="/home/stadler/miniconda3/lib:/home/stadler/miniconda3/envs/gprMax/lib:$LD_LIBRARY_PATH"

[craig-warren]

I think when you first install Miniconda it gives you the option for it to add the Miniconda bin directory to your path, usually via your .bash_profile

[mzunguman]

yeah it does. That's the first portion of the path, and I thought that was enough too. But, for me at least, only after I add the second set of paths does it seem to work.

[craig-warren]

Are you sure the environment is being activated correctly? When I activate an environment the following happens:

w5067:~ cwarren$ source activate gprMax
discarding /Users/cwarren/miniconda3/bin from PATH
prepending /Users/cwarren/miniconda3/envs/gprMax/bin to PATH
(gprMax)w5067:~ cwarren$

[mzunguman]

In the past as well as now, I got the same message. It must be the new LD_LIBRARY_PATH path I entered that did the trick for me. Don't know why...