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