Jupyter Notebook update (August, 2016)

brukau 2016-08-17 08:03:29 UTC #1

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

senk 2016-08-23 10:22:46 UTC #2

Dear Yury,

are there plans to make a NEST installation per default available in the notebooks?

Best,
Johanna

brukau 2016-08-25 12:14:33 UTC #3

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:

NEST 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

andrew_davison 2016-08-26 08:51:22 UTC #4

I think GSL support is essential, as many NEST models depend on it. libneurosim would be nice to have, especially for PyNN users.

brukau 2016-08-26 09:43:47 UTC #5

Hi Andrew,

I added GSL support.
About libnuerosim I have no idea what it is and where I can find installation instructions.

Yury

andrew_davison 2016-08-26 11:01:29 UTC #6

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

brukau 2016-08-29 12:06:53 UTC #7

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

senk 2016-08-29 12:25:33 UTC #8

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

andrew_davison 2016-08-29 12:30:48 UTC #9

If I remember correctly, it is the classic "./configure; make; make install"

brukau 2016-08-29 12:31:47 UTC #10

There is no configure file in svn repo. Only configure.ac

andrew_davison 2016-08-29 12:33:48 UTC #11

Try running "./autogen.sh" first

eppler 2016-08-29 14:01:00 UTC #12

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 .

andrew_davison 2016-08-29 14:28:04 UTC #13

Jochen: I think that the default NEST installation in Collab Notebooks should be the latest released version, not the development version from master.

eppler 2016-08-29 14:50:08 UTC #14

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

brukau 2016-08-30 07:23:41 UTC #15

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

NEST 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 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