92 lines
2.9 KiB
Markdown
92 lines
2.9 KiB
Markdown
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Notes on installing and running qpms on Triton
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==============================================
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Running anything in a cluster environment can cause some unexpected problems.
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With these notes, one should be able to run qpms successfully on Aalto's Triton.
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The main problem is that it is often not completely trivial to ensure
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mutual compatibility of various libraries and tools on which qpms depends.
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## Triton+anaconda
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### Installing qpms with anaconda
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This section shows how to use qpms in an anaconda virtual environment.
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First, we purge the modules to ensure that no other other conflicting python instances are loaded.
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Then we load an anaconda3 module.
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```
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module purge
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module load anaconda3
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```
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Next, conda needs to infect our shell with some code in order to work properly.
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(If you use a different shell than bash, modify the following command accordingly.)
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```
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conda init bash
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```
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This adds several lines to `~/.bashrc` (or elsewhere, depending on the shell).
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Then we might be required to restart the shell.
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Next, we create and activate a virtual environment to be used with qpms.
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It will be called `trqpms` throughout this document.
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We will also need to have `cython` installed before even trying to install qpms.
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```
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conda create trqpms
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conda activate trqpms
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conda install cython
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```
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Moreover, we need to load the GCC and gsl modules. GCC has to be loaded *after*
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loading anaconda3 and activating the conda virtual environment, otherwise
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anaconda will try to use its own (likely broken) compiler when installing qpms.
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And we also need cmake for building amos.
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Lastly, we save the list of loaded modules for later use as `qpms_conda`.
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```
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module load gsl
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module load GCC
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module load cmake
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module save qpms_conda
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```
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From now on, we need to be in the qpms source root directory.
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```
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cd /path/to/qpms
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```
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Now it's time to build `amos`. First, we clean all the files previously
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created by `cmake` (if needed). This is to ensure that `cmake` uses the same
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`gfortran` that is in the current `PATH`; otherwise, `cmake` might use some
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Fortran compiler detected earlier (`cmake` apparently does not update
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that information) and that might later cause mismatch between
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libgfortran versions.
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```
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rm -r CMakeFiles CMakeCache.txt
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cmake .
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make clean
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make amos
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```
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Cmake builds in other directories are not supported right now, as qpms setup scripts now expects
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certain amos files at fixed relative paths. Therefore the `.` in `cmake .`.
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And finaly, build qpms.
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```
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python3 setup.py install
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```
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At this point, qpms should be installed successfully. If not, this document
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needs updates.
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### Running qpms with anaconda
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After installing the qpms python module, one should be able to import it and to use
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the scripts in the misc directory in the same shell session used for installing
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qpms.
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To use qpms also later, one has to restore the environment, i.e. load the same modules and
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activate the anaconda virtual environment.
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```
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module restore qpms_conda
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conda activate trqpms
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```
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