From 7a70c04a09f0eb12f68c2a3c6fa53d72058e6df5 Mon Sep 17 00:00:00 2001 From: pswietojanski Date: Fri, 9 Oct 2015 17:36:42 +0100 Subject: [PATCH] kernel issues description --- kernel_issue_fix.md | 48 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 kernel_issue_fix.md diff --git a/kernel_issue_fix.md b/kernel_issue_fix.md new file mode 100644 index 0000000..4fbf769 --- /dev/null +++ b/kernel_issue_fix.md @@ -0,0 +1,48 @@ + +# How to fix notebook's "kernel issues" on DICE + +Some of the people in mlpractical have been affected by a recent update to the numpy and numercial +library pushed to DICE last week. The symptom was restarting notebook kernel when someone +tried to run the exercise involving numpy usage. + +The reason of this most likely affected people who either 1) ended up with +default atlas libraries (which has been updated in the meantime) or 2) re-compiled +numpy with new DICE OpenBLAS already available, but LD_LIBRARY_PATH pointed to the +version compiled last time - which could introduce some unexepcted behaviours. + +## Fix + +Follow the below setps **before** you activate the old virtual environment. The fix +basically involves rebuilding the virtual environments. But the whole process is now +much simpler (due to the fact OpenBLAS is now a deafult numerical library on DICE). + +1. Comment out (or remove) `export=$LD_LIBRARY_PATH...` line in your ~/.bashrc script. Then type +`unset LD_LIBRARY_PATH` in the terminal. To make sure this variable is not +set, type `export` and check visually in the printed list of variables + +2. Go to `~/mlpractical/repos-3rd/virtualenv` and install the new virtual +environment by typing: + +``` +./virtualenv.py --python /usr/bin/python2.7 --no-site-packages $MLP_WDIR/venv2 +``` + +3. Activate it by typing: source $MLP_WDIR/venv2/bin/activate and install the usual for the course packages using pip: + + * pip install pip --upgrade + * pip install numpy + * pip install ipython + * pip install notebook + * pip install matplotlib + +4) Now enter `~/mlpractical/repo-mlp` and see whether numpy has been +linked to DICE-standard OpenBLAS (and works) by starting python notebook: +``` +ipython notebook +``` +and running two first interactive examples from 00_Introduction.py. +If they run, you can simply modify `activate_mlp` alias in `./bashrc`to point to +`venv2` instead of `venv` + +5) You can also remove both old `venv` amd other not needed anymore +directories with numpy and OpenBLAS sources in `~/mlpractical/repos-3rd` directory. \ No newline at end of file