16 Jun
2020
16 Jun
'20
3:12 a.m.
Hans and Nest User Community,
I was wondering if you had any advice for my errors when I
compile/register the custom Synapse Model, stdp_izh_connection.h/.cpp as I
can compile/install without issue using the example custom models
like pif_psc_alpha and drop_odd_synapse alone.
Two quick questions.
#1 Which synapse model registration statement should I use in
"my2module.cpp":
-
nest::kernel().model_manager.register_connection_model<STDPIzhConnection<targetidentifierT
>( "stdp_izh_connection" );
-
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< nest::TargetIdentifierPtrRport >
>("stdp_izh_connection"
);
- nest::kernel().model_manager.register_prototype_connection<
STDPIzhConnection< nest::TargetIdentifierPtrRport >
>("stdp_izh_connection"
);
- nest::kernel().model_manager.register_prototype_connection<
STDPIzhConnection>(net_, "stdp_izh_connection" );
#2 Which argument, "targetidentifierT" or "TargetIdentifierPtrRport",
should I use:
- in "my2module.cpp" model registration?
- and in my synapse model, "stdp_izh_connection.h", templates?
I've included one of my error messages below for reference. I received
similar error messages for each of the registration statements used above.
Thank you for any advice you may offer.
Best Regards,
--Allen
********* Background on the Custom Synapse Model********
- stdp_izh_connection.h/.cpp has been updated for nest 5g kernel per
https://nest.github.io/nest-simulator/model_conversion_5g
- stdp_izh_connection.h/.cpp has reformatted using
https://github.com/nest/nest-simulator/blob/master/models/stdp_connection_h…
as an example.
*********************************************************************
*********** Nest Compile Errors when including:
stdp_izh_connection.h/.cpp***********
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h: In member function
‘void nest::STDPIzhConnection<targetidentifierT>::send(nest::Event&,
nest::thread, const nest::STDPIzhCommonProperties&)’:
/home/nest/examples/My2Module/stdp_izh_connection.h:305:5: error: ‘class
nest::Event’ has no member named ‘set_multiplicity’
e.set_multiplicity( -1 );
^~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/stdp_izh_connection.h:306:5: error: ‘class
nest::Event’ has no member named ‘set_delay’; did you mean ‘set_sender’?
e.set_delay( ConnectionBase::get_delay_steps() ); // ConnectionBase not
used in sample
^~~~~~~~~
set_sender
/home/nest/examples/My2Module/stdp_izh_connection.h:309:18: error:
‘t_spike’ was not declared in this scope
t_lastspike_ = t_spike; // added per ref:
https://nest.github.io/nest-simulator/model_conversion_5g
^~~~~~~
/home/nest/examples/My2Module/stdp_izh_connection.h:309:18: note: suggested
alternative:
In file included from /home/nest/work/nest-install/include/nest/node.h:37:0,
from
/home/nest/work/nest-install/include/nest/common_synapse_properties.h:29,
from
/home/nest/work/nest-install/include/nest/connection.h:27,
from
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27,
from /home/nest/examples/My2Module/my2module.cpp:29:
/home/nest/work/nest-install/include/nest/nest_names.h:424:19: note:
‘nest::names::t_spike’
extern const Name t_spike;
^~~~~~~
/home/nest/examples/My2Module/my2module.cpp: In member function ‘virtual
void mynest::My2Module::init(SLIInterpreter*)’:
/home/nest/examples/My2Module/my2module.cpp:142:59: error:
‘STDPIzhConnection’ was not declared in this scope
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:142:59: note: suggested
alternative:
In file included from /home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h:114:7: note:
‘nest::STDPIzhConnection’
class STDPIzhConnection: public nest::Connection< targetidentifierT >
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:142:78: error:
‘targetidentifierT’ was not declared in this scope
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:143:27: warning: comparison
with string literal results in unspecified behavior [-Waddress]
"stdp_izh_connection" );
^
/home/nest/examples/My2Module/my2module.cpp:142:98: error: invalid operands
of types ‘<unresolved overloaded function type>’ and ‘const char [20]’ to
binary ‘operator>’
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
"stdp_izh_connection" );
~~~~~~~~~~~~~~~~~~~~~~~
CMakeFiles/my2module_module.dir/build.make:62: recipe for target
'CMakeFiles/my2module_module.dir/my2module.cpp.o' failed
make[2]: *** [CMakeFiles/my2module_module.dir/my2module.cpp.o] Error 1
CMakeFiles/Makefile2:67: recipe for target
'CMakeFiles/my2module_module.dir/all' failed
make[1]: *** [CMakeFiles/my2module_module.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2
On Fri, May 22, 2020 at 8:24 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
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(a)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
<https://secure-web.cisco.com/1pvWX8gcr0ktPCO_pJ-XSV7OsLHFiWmE4gqVEtVzPY62QxY1eQ-8GQWP65ZAm2UnzB305znKhGBeGwk3pBCBzl8VOR2DbwaEVtwB6IqqgcUZ00aQ3KCz0pZCavFLjDbhwHT4dDzuJDzmZfXfPOh43poIG8N04bRnb8yWGChAfBw_d6FveE9QCARl1P7RLbZx2JO3Jutn_6NeHuvQ0US81N-LR2KHLRq2OP2zVHL989CZBuJHc2L7rHt8e95I7GsWuJ3nWlu8gts8AL8Q0aGjxo0Kzn1ZZbaQDJeBZkM7a8aQGjOjHfq24TEYMImyCtMnNUrAJciz44-6tObOUK8QDbtLQq6fszadM72YPHar9u1kjbVNXqRfAN6N6YNs3faASL0TwqOGptnApRBX2ImM9ySgQBFW48w8-871pKl3Dw83zEcxHGZ9dvmzsLptIVDNL/https%3A%2F%2Fgithub.com%2Fnest%2Fnest-simulator%2Fissues%2F1331>.
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(a)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(a)nmbu.no> wrote:
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
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--
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
<http://secure-web.cisco.com/1nd3Dn41NSvMCZuqSxusD7gKebEdh81Q4sSm7WqGfmTpD98eMdRbko3iFKsYYyH0v-Rq3hKbZ-NmkF8WEGl_CwIq5sX4c19CZ9477L19Gtrel3_Ptmn-cvOuuMV3ig2KkmysLVdb4e6MjQMXdwY4eaflxKe_ymORYjasNRPHBMh5utr9uwUtP_sySj9K7QoF0j55RbN8yXne0tbD6U1y8uRymd7rY28hB1YkkNDcHm2tiCcmMWl_WXxNx-v5Otfqv5iAWhKYHvmkHkB9dP1d1qtkl6DMrLsy8wrmt_pBC-zjZWkFFMlzrp-lroQIlPIiZj7kGu_NAP09PynPIhz25hVzaNDtfZ4e6L9KS7ACVjaH32KFrogiLravhZV6QQDTB_hf-P1qjaWPZmR-KaWPjKBdVsa5g8WnFUdtAc8CAnFgz5ysCDDiIrCVP0WipCdt2e-B1QZi4YHNpcucciAE9HQ/http%3A%2F%2Farken.nmbu.no%2F%7Eplesser>
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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-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APmBFD6LJj5zzZE42doCxkKRobTud5P4AT-oAs4WO_e4LtGvMBLDNRl2akKXbAPU8F8r9Rm4A-tpRybnnEUh062b56HNleUWk7QJ6N1WbDPtfI2tSIZfBrNSy7ZS4MsvzYfYHFlpG8GQQde5gApJecM5CFQEEP9CGymqYZ18LQ3zj1pcYeYG_L4XhXZhfL9be5WtSMrDZVy_ZeB0g3Qorb-lhDrLguvPgqUhCze8vfsqesaXfTpE3HtpsEMUcfd3Xc5vUP1KU6rRWzSAw8az7wM5CxmAlax7wYyP8eT_0bQAweIakbsUW3bXaCT9znQv15l-qoBLExOyTKQvbcyNiwLEBNflla-_MsLueEemTJ1NRiHSI7kGavYtpaKaeXtlSy7q0YU9lIMHnnS0AWr5keolzddt0U0uCpJmO2uL9FUA/https%3A%2F%2Fnest.github.io%2Fnest-simulator%2Fextension_modules>
.
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(a)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>
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--
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
<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>
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_______________________________________________
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--
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
<http://secure-web.cisco.com/1iP5XxSIgK1wF5QUFextVYBJcuhTvD7uZziUM9b_0s3CJyt4coQ-JaojYPcWkHY6GfIgOzSAlr4NFfZhr8Z172zC5SaCAWrN7Zz9ApSd4f6eA5bPremYXBOqAH_0MM6CCSJR7eDvRFU9Qd1y6vawZ91iPX2y5qaoU-0SyZyHI2UD7rp6FmPOi7PWHBHk9gXb6fp6qP1wbpMV8lwrvMGDglP_bw3HnLWIpw2DZKS0sDuzdrn7ECQmCzGHhIivmcUOsZgWNtnuP6A2WrPlnyAaeLuxwfQ4BYv7288-Qq4k9w4w5jGWOpMHFPs837kFW4zLht7l_9Dz4nsqCl8dSn1RmhHmeHEd412A_NctYEoizC86CDJutdeZ0jhh6K2HEDCT5snwo68iJAPnc20uucORO3mJinauyJ5801Fqj5-1zqMAIXt2rvrHJBTIrMSgG_dzU0jtP9ZS2AYhy13V_mxMYvA/http%3A%2F%2Fnmbu.no%2F>
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