22 May
2020
22 May
'20
2:24 p.m.
Hi Allen,
Thanks. It looks like a relative path has ended up in your nest-config file where it
should have been an absolute path. Could you open file
nest-install/bin/nest-config
and go to roughly line 55, where you should find something like
--includes)
echo " -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include -I/usr/local/include
-I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include"
;;
Please replace within
-I../nest-install/include/nest
the .. with the absolute path. Then run cmake and make again in the My2Module build
directory. You may want to delete anything in that build directory first to avoid old
Cmake cached data.
Best,
Hans Ekkehard
On 21 May 2020, at 22:13, Allen Rabayda
<arabayda@masonlive.gmu.edu<mailto:arabayda@masonlive.gmu.edu>> wrote:
Hans,
Below is the output from my 1) "cmake" and 2)
"{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags"
commands.
Thank you,
--Allen
Charl, I had not yet tried any of the processes on
https://github.com/nest/nest-simulator/issues/1331. Thank you,--Allen
*****************
1) CMAKE OUTPUT:
*****************
nest@nestvm:~/examples/My2Module$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config
../My2Module
-------------------------------------------------------
my2module Configuration Summary
-------------------------------------------------------
C++ compiler : /usr/bin/c++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
NEST include dirs : -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include -I/usr/local/include
-I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
NEST libraries flags : -L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest
-lrandom -lsli -lnestkernel -ltopology -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/local/lib/libneurosim.so /usr/local/lib/libpyneurosim.so
/usr/lib/x86_64-linux-gnu/libmusic.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-------------------------------------------------------
You can now build and install 'my2module' using
make
make install
The library file libmy2module.so will be installed to
/home/nest/work/nest-install/lib/nest
Help files will be installed to
/home/nest/work/nest-install/share/doc/nest
The module can be loaded into NEST using
(my2module) Install (in SLI)
nest.Install('my2module') (in PyNEST)
The module will be installed into a non-default location!
Make sure to set the environment variables:
export NEST_MODULE_PATH=/home/nest/work/nest-install/lib/nest:$NEST_MODULE_PATH
export SLI_PATH=/home/nest/work/nest-install/share/nest/sli:$SLI_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/nest/examples/My2Module
-----------------------------------------------------
*****************
2) "{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags OUTPUT
*****************
nest@nestvm:~$ export NEST_INSTALL_DIR=/home/nest/work/nest-install
nest@nestvm:~$ {NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
bash: {NEST_INSTALL_DIR}/bin/nest-config: No such file or directory
*****************
then added absolute path to produce output below
*****************
nest@nestvm:~$ /home/nest/work/nest-install/bin/nest-config --prefix --includes --libs
--cflags
/home/nest/work/nest-install
-I/home/nest/work/nest-simulator-2.18.0/conngen -I../nest-install/include/nest
-I/usr/include -I/usr/include -I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest -lrandom -lsli -lnestkernel
-ltopology -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/local/lib/libneurosim.so /usr/local/lib/libpyneurosim.so
/usr/lib/x86_64-linux-gnu/libmusic.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
*****************
END
*****************
On Wed, May 20, 2020 at 3:08 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
Hi Allen,
Below I show how I adapted/complied the example MyModule included on github and the
error message I get (bottom of email).
The steps look generally good.
two absolute paths inserted (correct missing file error):
#include "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
You should not need the absolute paths, just the filenames should suffice.
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
$ make
Could you post the output of the cmake command?
And also the output of the following command
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
Best,
Hans Ekkehard
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10: fatal error:
connection.h: No such file or directory #include "connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
Hi Allen,
Several steps are required to add a model to NEST. The recommended way of adding a model
is to create your own NEST module outside the NEST source code tree. You will find an
example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules<https://secure-w…es>.
Placing code for custom models in the models directory in the NEST source code tree also
works, but makes it more difficult to move to newer versions of NEST or to share your
custom models with colleagues.
Briefly, in addition to adding the source code files to the models directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the string the name it will
have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda
<arabayda@masonlive.gmu.edu<mailto:arabayda@masonlive.gmu.edu>> wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict
for a list of available models.', 'UnknownModelName', <SLILiteral:
CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model
name. Please check the modeldict for a list of available models.')
********************************************************
<issue_UnknownModelName_4_May_2020>_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email
hans.ekkehard.plesser@nmbu.no<http://secure-web.cisco.com/1oGxjTBn6G3zlyNTvv_hoyiXx9VwKKhVYGsnt8WkKZtjey0jolrbMkgNX8nwZ1_mVOfMZGiux9uomyEPFv1tB5lZkHqSDndkoq7WT3154Yx4mGDr8Arv_7jWQmncdw7br50zI6WljWy5IK7VdXa7cWJJMsib-PBr0HtFYGs5gbgToIMYR4w5rKqurTb-v0rgSNtJsrdJncRz5eqmnGWYbcKnShFCDiXti1pbbYmie86yWljTQbF0AtIphD_zoqJhi-TJYrXXjeVGyc2k_WQiq9cNQvbZlxfWAY8GM2CJWq_YnFnAj_wgKoFCuxVcs6gPmu6B-M8f9ZylTFcZTKA4SjnK6SJPiDig8sJf7qhGQW0aB1CMf88nIeQJFd5NE_nXYNkveMYHT2So_RNGY06D7hdDTA1VoxJgrV-JxlTvip1uelk7bGF8CPbWbPaNV-TAvtps_fwU_5vhhGiNNNPML6Q/http%3A%2F%2Fnmbu.no%2F>
Home
http://arken.nmbu.no/~plesser<http://secure-web.cisco.com/1NGU903Sz1mZbu…
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser@nmbu.no<http://nmbu.no/>
Home
http://arken.nmbu.no/~plesser<http://secure-web.cisco.com/1Yaz1kjc6VGnCj…
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser