Dear Nina,
The first error is
In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:30:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:92:1: error: expected class-name before ‘{’ token
{
^
and it looks a lot like everything following are consequences of this error. So if looks as if something may be off in the pif_psc_alpha.h file around lines 90-92. Are you trying to compile the example module exactly as cloned from Github
or have you made any changes to the code?
There could also be a small chance of problems "spilling" from the config.h file, which is in the build (not source) directory. That could explain why you experience problems using the docker container, while all works for your colleagues
using Linux.
BTW, do you know the adaptive multi-timescale models from the Shinomoto group (amat2_exp_psc), which can reproduce the same 20 response patterns as the Izhikevich model, but are mathematically simpler as they are linear? See
.. [3] Kobayashi R, Tsubo Y and Shinomoto S (2009). Made-to-order
spiking neuron model equipped with a multi-timescale adaptive
threshold. Frontiers in Computational Neuroscience, 3:9.
DOI: https://dx.doi.org/10.3389%2Fneuro.10.009.2009
.. [4] Yamauchi S, Kim H, Shinomoto S (2011). Elemental spiking neuron model
for reproducing diverse firing patterns and predicting precise
firing times. Frontiers in Computational Neuroscience, 5:42.
DOI: https://doi.org/10.3389/fncom.2011.00042
We also have the glif model families from the Allen institute available in NEST (glif_cond, glif_psc), see
.. [1] Teeter C, Iyer R, Menon V, Gouwens N, Feng D, Berg J, Szafer A,
Cain N, Zeng H, Hawrylycz M, Koch C, & Mihalas S (2018)
Generalized leaky integrate-and-fire models classify multiple neuron
types. Nature Communications 9:709.
These may be more up-to-date alternatives to the Izhikevich model. For some experiences with that model, see
Pauli R, Weidel P, Kunkel S and Morrison A (2018) Reproducing Polychronization: A Guide to Maximizing the Reproducibility of Spiking Network Models. Front. Neuroinform. 12:46. doi: 10.3389/fninf.2018.00046
Best regards,
Hans Ekkehard
Dear experts,
I've succesfully "made" the module with:
docker@84fabd16af99:~/mmb$ cmake -Dwith-nest=/home/docker/env/neurosci/nest_build/bin/nest-config ../nest-extension-module-master
It gives me the message:
You can now build and install 'mymodule' using
make
make install
The library file libmymodule.so will be installed to
/home/docker/env/neurosci/nest_build/lib/nest/
Help files will be installed to
/home/docker/env/neurosci/nest_build/share/doc/nest
The module can be loaded into NEST using
nest.Install('mymodule') (in PyNEST)
(mymodule) Install (in SLI
-- Configuring done
-- Generating done
-- Build files have been written to: /home/docker/mmb
However, when I try to "make". I get a bunch of errors that I have added at the end of this email. My colleague tried to install exactly the same module in exactly the same way on his linux machine and it worked perfectly. But somehow for me, I get these weird
errors that I haven't been able to resolve so far. Does anyone have an idea what the problem might be? It would be greatly appreciated. If you need any additional information please let me know.
Thank you in advance and have a nice day!
Kind regards,
Nina Doorn
Error message:
docker@84fabd16af99:~/mmb$ make
Scanning dependencies of target mymodule_module
[ 10%] Building CXX object src/CMakeFiles/mymodule_module.dir/mymodule.cpp.o
In file included from /home/docker/nest-extension-module-master/src/mymodule.cpp:30:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:92:1: error: expected class-name before ‘{’ token
{
^
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:115:21: error: type ‘nest::Node’ is not a base type for type
