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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. It concerns you when you get the message about the kernel was restarted when running code involving numpy usage.
Some people in MLP have been affected by a recent update to the `numpy` and `numerical`
libraries on DICE on 3 October. The problem affects you if you get a message stating that the kernel was restarted when you run code involving `numpy`.
In case you experience those issues you either 1) ended up with
default atlas libraries (which have been updated in the meantime) or 2) re-compiled
numpy with the new DICE OpenBLAS already available, but LD_LIBRARY_PATH you set last week put
priority to load OpenBLAS libraries compiled last time - which could introduce some unexepcted behaviour at runtime.
If you have experienced these issues you have either:
1. ended up using the default `atlas` libraries with `numpy` (which have been updated in the meantime)
2. or re-compiled `numpy` with the new DICE `OpenBLAS` that is available, but the `LD_LIBRARY_PATH` that you set during the first lab last week gave priority to load the `OpenBLAS` libraries compiled last time - which could introduce some unexepcted behaviour at runtime.
## The Fix
Follow the below stdps **before** you activate the old virtual environment (or deactivate it once activated). 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.
Follow the below steps **before** you activate the old virtual environment (or deactivate it if it is activated). The fix basically involves rebuilding the virtual environments. But the whole process is now much simpler due to the fact `OpenBLAS` is now a default numerical library on DICE.
1) Comment out (or remove) `export=$LD_LIBRARY_PATH...` line in your ~/.bashrc script. Then type
`unset LD_LIBRARY_PATH` in the terminal. To make sure this variable is not
1. Comment out (or remove) the `export=$LD_LIBRARY_PATH...` line in your ~/.bashrc file. 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:
2. Go to `~/mlpractical/repos-3rd/virtualenv` and install the new virtual
environment (`venv2`) 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:
3. Activate your new virtual environment by typing:
* pip install pip --upgrade
* pip install numpy
* pip install ipython
* pip install notebook
* pip install matplotlib
```
source $MLP_WDIR/venv2/bin/activate
```
and install the usual packages required by MLP using pip:
```
pip install pip --upgrade
pip install numpy
pip install ipython
pip install notebook
pip install matplotlib
```
4. Change directory to `~/mlpractical/repo-mlp` and check that `numpy` is linked to the DICE-standard `OpenBLAS` (and works) by starting ipython notebook:
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 the old `venv` and other not needed anymore
directories with numpy and OpenBLAS sources in `~/mlpractical/repos-3rd` directory.
then run the first two interactive examples from `00_Introduction.py.` If they run, then you can simply modify the `activate_mlp` alias in `./bashrc` to point to `venv2` instead of `venv`
5. You can also remove both the old `venv` and the other unrequired directories that contain `numpy` and `OpenBLAS` sources in the `~/mlpractical/repos-3rd` directory.