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| -rw-r--r-- | topics/profiling_python_code.gmi | 22 | ||||
| -rw-r--r-- | topics/running_pudb_from_external_environment.gmi | 22 |
2 files changed, 44 insertions, 0 deletions
diff --git a/topics/profiling_python_code.gmi b/topics/profiling_python_code.gmi new file mode 100644 index 0000000..d7f9ea0 --- /dev/null +++ b/topics/profiling_python_code.gmi @@ -0,0 +1,22 @@ +# Profiling Python code + +As part of improving the system, there is need to identify and fix/improve the performance bottlenecks in the code. This document details examples of how one would run various profilers, for both GeneNetwork2 and GeneNetwork3 + +## GeneNetwork3 + +### cProfile + +Syntax: + +* env [various-env-vars] python3 -m cProfile the-script.py + +where + +* `[various-env-vars]` is a number of environment variables that might be needed for the running of the script, e.g. `SQL_URI` which is used to define how to connect to the database. +* `the-script.py` is the name of the python script to be run under the profiler + +The output can be redirected, e.g. + +* env [various-env-vars] python3 -m cProfile the-script.py 2>error.log 1>performance.log + +which should help will separating errors from the performance data, for easier analysis diff --git a/topics/running_pudb_from_external_environment.gmi b/topics/running_pudb_from_external_environment.gmi new file mode 100644 index 0000000..be9bf14 --- /dev/null +++ b/topics/running_pudb_from_external_environment.gmi @@ -0,0 +1,22 @@ +# Running pudb From an External Environment + +Currently (22nd December 2021), it is a tad difficult to get pudb running under the various guix environments without having to update a lot of stuff. This documents a workaround that seems to work for me (@fredm). + +## GeneNetwork3 + +1) Install pudb in a virtual environment: + +* $ python -m venv pudb_env + +2) Activate the environment and install pudb: + +* $ source pudb_env/bin/activate +* $ pip install pudb + +3) Run the GN3 container, exposing the new virtual environment with something like: + +* env GUIX_PACKAGE_PATH=~/genenetwork/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --expose="$HOME/genotype_files/"="${HOME}/genotype_files" --expose="${HOME}/genenetwork/pudb_env/"="${HOME}/pudb_env" --load=guix.scm + +4) Inside the container, run the debugger with something like: + +* env PYTHONPATH="${PYTHONPATH}:${HOME}/pudb_env/lib/python3.8/site-packages" ... python3 -m pudb script.py |