Request to install Geopsy

Presentation

Dear HPC Team,
There is a software for seismology analyses called “Geopsy” that I have used for my work and installed myself on the cluster that multiple students in my research group (M. Lupi’s) and colleagues now want to use as well. While I put the C executables in a shared folder ( /home/share/cdff/Geopsy ), the library dependencies are installed via an anaconda environment with a dirty fix that was needed to compile, where I manually link one shared library into the anaconda environment directory tree (LibGL.so). I would like to find a solution for others to also run Geopsy executables.

To provide more details, the instructions to install Geopsy are here:
https://www.geopsy.org/wiki/index.php/Installation:Linux

  1. I downloaded the “geopsypack-core” version, since we don’t need the GUI for now (but it wouldn’t hurt to have the full version with the GUI).
  2. I create an anaconda environment with the listed dependencies. You can find my exported environment “geopsy” in /home/share/cdff/conda_environment_exports/environment_geopsy.yml
  3. I apply this fix mentioned here to link /usr/lib64/libGL.so.1.7.0 to /home/users/s/savardg/anaconda3/envs/geopsy/x86_64-conda-linux-gnu/sysroot/usr/lib64/libGL.so which was necessary to not have make fail.

Would it be possible to install Geopsy for our research group as a module?

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Dear @Adrien.Albert, @Gael.Rossignol, @Yann.Sagon, could you please comment on whether it would be possible to install geospy on baobab? An installation would be very helpful for us.

Thanks,
Imahn

@imahn.shekhzadeh I realize maybe it’s overkill to ask HPC staff to have it as a module… I’ve thought about it again and if you can be be added to the cdff group users, then you can access the executables (or maybe you can already access them? They are in /home/share/cdff/Geopsy/bin) and then simply create an anaconda environment like mine and run the ln linking command. I’ll send you the conda file.

Hi @Genevieve.Savard and @imahn.shekhzadeh I am right now checking if I’m able to build it with EasyBuild to provide it as module for the users.

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I just installed geopsy on baobab in my home, so I’m adding a bit of precision regarding the install: for the configure step, before make, the lib and include folder in the conda environment have to be linked explicitely and one must put the flag to ignore Qt check:

So the steps are:

  1. I downloaded the “geopsypack-core” version, since we don’t need the GUI for now (but it wouldn’t hurt to have the full version with the GUI).
  2. I create an anaconda environment with the listed dependencies. You can find my exported environment “geopsy” in /home/share/cdff/conda_environment_exports/environment_geopsy.yml
  3. I apply this fix mentioned here to link /usr/lib64/libGL.so.1.7.0 to /home/users/s/savardg/.conda/envs/geopsy/x86_64-conda-linux-gnu/sysroot/usr/lib64/libGL.so which was necessary to not have make fail.
  4. Unpack geopsypack-core and go into parent directory.
  5. Configure
    ./configure -builddir /home/users/s/savardg/build -prefix /home/users/s/savardg/Geopsy -march native -skip-qt-check -L /home/users/s/savardg/.conda/envs/geopsy/lib -I /home/users/s/savardg/.conda/envs/geopsy/include
  6. Make and install
    make -j 8 -C /home/users/s/savardg/build
    make install -C /home/users/s/savardg/build
  7. Add Geopsy and conda environment to paths when running it:
    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/users/s/savardg/.conda/envs/geopsy/lib:/home/users/s/savardg/Geopsy/lib
    export PATH=$PATH:/home/users/s/savardg/Geopsy/bin

Dear @Yann.Sagon , any update about EasyBuild + Geopsy?

Kind regards,
Genevieve

Hello,

I know the HPC staff is busy with many things right now, but if someone could, please, just tell me if “yes” or “no” this software will/can be installed so that multiple users can use it, It would be great. Not to be pushy, but this thread has been open for 4 months now with no follow-up.

If not, then I’ll forward the directives to the 6+ people affiliated in our group who are all going to need this software installed manually in their $HOME.

Regards,
Genevieve

Dear @Genevieve.Savard you are right and this is a pity.

I’ll give a last try this Friday and keep you posted.

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Hi, in fact the installation was almost working, I was stuck with a technical detail, but after three months of “deep thinking” it was a piece of cake :sweat_smile:. I could contribute this software to EasyBuild as no one did it before.

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Thank you so much @Yann.Sagon :pray: our whole team will benefit and we are super grateful for this :slightly_smiling_face:

Best regards
Geneviève