We are preparing update of Jupyter Notebook functionality in Collaboratory.
Details can be found here
https://collab.humanbrainproject.eu/#/collab/509/nav/11838
The update should be deployed by the end of August to give people enough time to test their notebooks before HBP Summit in October.
Please, report here any objections, issues or questions.
Yury
Dear Yury,
are there plans to make a NEST installation per default available in the notebooks?
Best,
Johanna
Hi Johanna,
We are planning to add NEST to the notebooks container.
Should it be configured in some special way?
That is current configuration summary:
C compiler : gcc
C compiler flags : -W -Wall -pedantic -Wno-long-long -O2 -g -O2 -fopenmp
C++ compiler : g++
C++ compiler flags : -W -Wall -pedantic -Wno-long-long -O2 -fopenmp
Built-in modules : models precise topology
User modules : None
Python bindings : Yes (Python 2.7: /usr/bin/python)
Use threading : Yes (OpenMP)
Use GSL : No
Use MPI : No
Use MUSIC : No
Use libneurosim : No
Yury
I think GSL support is essential, as many NEST models depend on it. libneurosim would be nice to have, especially for PyNN users.
Hi Andrew,
I added GSL support.
About libnuerosim I have no idea what it is and where I can find installation instructions.
Yury
Here is some background information: http://journal.frontiersin.org/article/10.3389/fninf.2014.00043/full
At the moment, I think the primary repository is http://software.incf.org/software/libneurosim
Hi Andrew,
I didn’t find any documentation on how to compile libneurosim inside svn repo.
Do you have experience with it? Could you provide instructions?
Thanks,
Yury
Hi Yury,
thanks for adding GSL, this is indeed essential.
Besides, it would be great to enable MPI and MUSIC so that Collab users will be able to combine, e.g., NEST and Neuron or NEST and ROS.
NEST 2.10.0 is the right version for now.
PyNN should also be installed. I guess, version 0.8.1.
Best,
Johanna
As Andrew said, you have to compile libneurosim like this:
svn co --username Anonymous --password Anonymous http://svn.incf.org/svn/libneurosim/trunk libneurosim
cd libneurosim
./autogen.sh
./configure --prefix=$HOME/opt/libneurosim --with-mpi
make && make install
Then you compile NEST like this (latest GitHub master):
cmake -DCMAKE_INSTALL_PREFIX:PATH=$HOME/opt/nest -Dwith-mpi=ON -Dwith-libneurosim=$HOME/opt/libneurosim .Jochen: I think that the default NEST installation in Collab Notebooks should be the latest released version, not the development version from master.
With older versions you need to replace the cmake line with
./configure --prefix=$HOME/opt/nest --with-mpi --with-libneurosim=$HOME/opt/libneurosim
In both cases, you have to compile and install using
make && make install
Thank you to everybody for the help.
Nest compiled and installed with libneurosim but for now without mpi.
Also added PyNN 0.8.1.
These changes should be available in prod during this week.
Yury
P.S
C compiler : gcc
C compiler flags : -W -Wall -pedantic -Wno-long-long -O2 -g -O2 -fopenmp
C++ compiler : g++
C++ compiler flags : -W -Wall -pedantic -Wno-long-long -O2 -fopenmp
Built-in modules : models precise topology conngen
User modules : None
Python bindings : Yes (Python 2.7: /usr/bin/python)
Use threading : Yes (OpenMP)
Use GSL : Yes
Use MPI : No
Use MUSIC : No
Use libneurosim : Yes
libneurosim inlude: -I/home/jupyter/.local/include
libneurosim libs : -L/home/jupyter/.local/lib -lneurosim -lpyneurosim
The NEST executable will be installed to:
/home/jupyter/.local/bin/
Documentation and examples will be installed to:
/home/jupyter/.local/share/doc/nest/
PyNEST will be installed to:
/home/jupyter/.local/lib/python2.7/site-packages