kernel issues description

kernel_issue_fix.md

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+
+# 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.