27 Jul
2023
27 Jul
'23
12:25 p.m.
Hello,
I am using an example synapse model which utilizes both post and pre spikes
(nestml/models/synapses/stdp_nn_symm.nestml at master · nest/nestml
(github.com)
<https://github.com/nest/nestml/blob/master/models/synapses/stdp_nn_symm.nestml>
).
I get an error:
...
File
"/dss/dsshome1/00/ge72puf2/.conda/envs/nest/lib/python3.8/site-packages/pynestml/codegeneration/nest_code_generator.py",
line 469, in _get_synapse_model_namespace
assert len(namespace["pre_ports"]) <= 1, "Synapses only support one
spiking input port"
AssertionError: Synapses only support one spiking input port
It is confusing: can I or can I not use a model with 2 synaptic inputs
(post and pre)? Is that a version thing?
Best regards,
--
Stefan
28 Jul
28 Jul
8:20 p.m.
Hi,
My apologies for the confusing error message. It occurs because you have to explicitly
tell NESTML which postsynaptic neuron type it is connected to in the simulation. You can
see an example of that here:
https://github.com/nest/nestml/blob/003d17a6425c3f8d88ed3aedd8d8e1d76245966…
The port is then assigned as "postsynaptic" and it is not considered for the
error that you are seeing.
Please let me know if you run into any further trouble.
With kind regards,
Charl
On Thu, Jul 27, 2023, at 12:25, Stefan Dvoretskii wrote:
Hello,
I am using an example synapse model which utilizes both post and pre spikes
(nestml/models/synapses/stdp_nn_symm.nestml at master · nest/nestml (github.com)
<https://github.com/nest/nestml/blob/master/models/synapses/stdp_nn_symm.nestml>).
I get an error:
...
File
"/dss/dsshome1/00/ge72puf2/.conda/envs/nest/lib/python3.8/site-packages/pynestml/codegeneration/nest_code_generator.py",
line 469, in _get_synapse_model_namespace
assert len(namespace["pre_ports"]) <= 1, "Synapses only support one
spiking input port"
AssertionError: Synapses only support one spiking input port
It is confusing: can I or can I not use a model with 2 synaptic inputs (post and pre)? Is
that a version thing?
Best regards,
--
Stefan
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
2 Aug
2 Aug
12:13 p.m.
Dear Charl,
many thanks for your help - it does indeed make sense and starts to compile
now! After several days with struggle with NEST on cluster, I am also
finally able to run the HPC version we have at LRZ.
However, there is another error occurring - which seems to do either with
C++ NEST core or the compiler?
1 2023 13:22:15
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
-- The CXX compiler identification is Clang 13.0.0
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestmlmodule Configuration Summary
-------------------------------------------------------
C++ compiler :
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -Wall -fopenmp -O2
-fdiagnostics-color=auto -O2 -g -DNDEBUG
NEST include dirs :
-I/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/include/nest
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/include
NEST libraries flags :
-L/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
-lnest -lsli -fopenmp
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/lib/libltdl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/lib/libreadline.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/ncurses/6.2-gcc-47oirry/lib/libncurses.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgsl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgslcblas.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/libmpicxx.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/release/libmpi.so
/usr/lib64/librt.so /usr/lib64/libpthread.so /usr/lib64/libdl.so
-------------------------------------------------------
You can now build and install 'nestmlmodule' using
make
make install
The library file libnestmlmodule.so will be installed to
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
The module can be loaded into NEST using
(nestmlmodule) Install (in SLI)
nest.Install(nestmlmodule) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.10)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run "cmake --help-policy CMP0000".
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done
-- Generating done
-- Build files have been written to:
/dss/dsshome1/00/ge72puf2/structfun/targetScanning dependencies of
target nestmlmodule_module
[ 25%] Building CXX object CMakeFiles/nestmlmodule_module.dir/nestmlmodule.o
In file included from
/dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:47:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:9: error:
no type named 'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:56: error:
no type named 'rport' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:9: error:
no type named 'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:58: error:
no type named 'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:9: error:
no type named 'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:60: error:
no type named 'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:9: error:
no type named 'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:66: error:
no type named 'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:260:22: error:
no type named 'port' in namespace 'nest'
static const nest::port MIN_SPIKE_RECEPTOR = 0;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:261:22: error:
no type named 'port' in namespace 'nest'
static const nest::port PORT_NOT_AVAILABLE = -1;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:14: error:
no type named 'port' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target,
nest::rport receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:73: error:
no type named 'rport' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target,
nest::rport receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:14: error:
no type named 'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&,
nest::port receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:75: error:
no type named 'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&,
nest::port receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:14: error:
no type named 'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&,
nest::port receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:77: error:
no type named 'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&,
nest::port receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:14: error:
no type named 'port' in namespace 'nest'
inline nest::port
izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:87: error:
no type named 'port' in namespace 'nest'
inline nest::port
izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
In file included from
/dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:49:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich__with_stdp_synapse.h:164:9:
error: no type named 'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool) override;
~~~~~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
Are there any ideas as to what can be done to solve this issue?
Best regards,
Stefan
On Fri, 28 Jul 2023 at 20:21, Charl Linssen <nest-users(a)turingbirds.com>
wrote:
Hi,
My apologies for the confusing error message. It occurs because you have
to explicitly tell NESTML which postsynaptic neuron type it is connected to
in the simulation. You can see an example of that here:
https://github.com/nest/nestml/blob/003d17a6425c3f8d88ed3aedd8d8e1d76245966…
The port is then assigned as "postsynaptic" and it is not considered for
the error that you are seeing.
Please let me know if you run into any further trouble.
With kind regards,
Charl
On Thu, Jul 27, 2023, at 12:25, Stefan Dvoretskii wrote:
Hello,
I am using an example synapse model which utilizes both post and pre
spikes (nestml/models/synapses/stdp_nn_symm.nestml at master ·
nest/nestml (github.com)
<https://github.com/nest/nestml/blob/master/models/synapses/stdp_nn_symm.nestml>
).
I get an error:
...
File
"/dss/dsshome1/00/ge72puf2/.conda/envs/nest/lib/python3.8/site-packages/pynestml/codegeneration/nest_code_generator.py",
line 469, in _get_synapse_model_namespace
assert len(namespace["pre_ports"]) <= 1, "Synapses only support
one
spiking input port"
AssertionError: Synapses only support one spiking input port
It is confusing: can I or can I not use a model with 2 synaptic inputs
(post and pre)? Is that a version thing?
Best regards,
--
Stefan
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Stefan Dvoretskii
12:34 p.m.
Dear Stefan,
This looks like a version conflict between NEST and NESTML. In NEST 3.5 we have removed a
number of aliases for built-in data types. It looks like your version of NESTML generates
code that still relies on the old aliases.
There are two ways forward: Either install NEST 3.4, or get a newer version of NESTML. I
don't know which version of NESTML you would need, hope Charl or Pooja can help.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Department of Data Science
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<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
From: Stefan Dvoretskii <stefan.dvorezky(a)gmail.com>
Date: Wednesday, 2 August 2023 at 12:14
To: NEST User Mailing List <users(a)nest-simulator.org>
Subject: [NEST Users] Re: Synapses support only one spiking input port
Some people who received this message don't often get email from
stefan.dvorezky(a)gmail.com. Learn why this is
important<https://aka.ms/LearnAboutSenderIdentification>
Dear Charl,
many thanks for your help - it does indeed make sense and starts to compile now! After
several days with struggle with NEST on cluster, I am also finally able to run the HPC
version we have at LRZ.
However, there is another error occurring - which seems to do either with C++ NEST core or
the compiler?
1 2023 13:22:15
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org<https://www.nest-simulator.org/>
Type 'nest.help()' to find out more about NEST.
-- The CXX compiler identification is Clang 13.0.0
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestmlmodule Configuration Summary
-------------------------------------------------------
C++ compiler :
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -Wall -fopenmp -O2 -fdiagnostics-color=auto -O2 -g
-DNDEBUG
NEST include dirs :
-I/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/include/nest
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/include
NEST libraries flags :
-L/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
-lnest -lsli -fopenmp
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/lib/libltdl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/lib/libreadline.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/ncurses/6.2-gcc-47oirry/lib/libncurses.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgsl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgslcblas.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/libmpicxx.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/release/libmpi.so
/usr/lib64/librt.so /usr/lib64/libpthread.so /usr/lib64/libdl.so
-------------------------------------------------------
You can now build and install 'nestmlmodule' using
make
make install
The library file libnestmlmodule.so will be installed to
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
The module can be loaded into NEST using
(nestmlmodule) Install (in SLI)
nest.Install(nestmlmodule) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.10)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run "cmake --help-policy CMP0000".
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done
-- Generating done
-- Build files have been written to: /dss/dsshome1/00/ge72puf2/structfun/target
Scanning dependencies of target nestmlmodule_module
[ 25%] Building CXX object CMakeFiles/nestmlmodule_module.dir/nestmlmodule.o
In file included from /dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:47:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:9: error: no type named
'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:56: error: no type named
'rport' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:58: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:60: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:66: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:260:22: error: no type named
'port' in namespace 'nest'
static const nest::port MIN_SPIKE_RECEPTOR = 0;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:261:22: error: no type named
'port' in namespace 'nest'
static const nest::port PORT_NOT_AVAILABLE = -1;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:73: error: no type named
'rport' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:75: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:77: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:87: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
In file included from /dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:49:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich__with_stdp_synapse.h:164:9: error:
no type named 'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
Are there any ideas as to what can be done to solve this issue?
Best regards,
Stefan
On Fri, 28 Jul 2023 at 20:21, Charl Linssen
<nest-users@turingbirds.com<mailto:nest-users@turingbirds.com>> wrote:
Hi,
My apologies for the confusing error message. It occurs because you have to explicitly
tell NESTML which postsynaptic neuron type it is connected to in the simulation. You can
see an example of that here:
https://github.com/nest/nestml/blob/003d17a6425c3f8d88ed3aedd8d8e1d76245966…
The port is then assigned as "postsynaptic" and it is not considered for the
error that you are seeing.
Please let me know if you run into any further trouble.
With kind regards,
Charl
On Thu, Jul 27, 2023, at 12:25, Stefan Dvoretskii wrote:
Hello,
I am using an example synapse model which utilizes both post and pre spikes
(nestml/models/synapses/stdp_nn_symm.nestml at master · nest/nestml
(github.com)<https://github.com/nest/nestml/blob/master/models/synapses/s…l>).
I get an error:
...
File
"/dss/dsshome1/00/ge72puf2/.conda/envs/nest/lib/python3.8/site-packages/pynestml/codegeneration/nest_code_generator.py",
line 469, in _get_synapse_model_namespace
assert len(namespace["pre_ports"]) <= 1, "Synapses only support one
spiking input port"
AssertionError: Synapses only support one spiking input port
It is confusing: can I or can I not use a model with 2 synaptic inputs (post and pre)? Is
that a version thing?
Best regards,
--
Stefan
_______________________________________________
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>
_______________________________________________
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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>
--
Stefan Dvoretskii
4:27 p.m.
NESTML 5.3.0 (the current PIP version) and NEST 3.4.0 give me the following
new error:
[ 75%] Building CXX object
CMakeFiles/izh_stdp_test_module_module.dir/izhikevich__with_stdp_synapse.o
In file included from
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/izh_stdp_test_module/izhikevich__with_stdp_synapse.cpp:43:
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/izh_stdp_test_module/izhikevich__with_stdp_synapse.h:209:8:
warning: 'register_stdp_connection' overrides a member function but is
not marked 'override' [-Winconsistent-missing-override]
void register_stdp_connection( double t_first_read, double delay );
^
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.4-gcc-11.2.0-g3xsuwt/include/nest/archiving_node.h:126:8:
note: overridden virtual function is here
void register_stdp_connection( double t_first_read, double delay ) override;
^
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/izh_stdp_test_module/izhikevich__with_stdp_synapse.cpp:107:16:
warning: unused variable '__resolution' [-Wunused-variable]
const double __resolution = nest::Time::get_resolution().get_ms();
// do not remove, this is necessary for the resolution() function
^
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/izh_stdp_test_module/izhikevich__with_stdp_synapse.cpp:312:10:
warning: unused variable 'get_t' [-Wunused-variable]
auto get_t = [origin, lag](){ return nest::Time( nest::Time::step(
origin.get_steps() + lag + 1) ).get_ms(); };
^
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/izh_stdp_test_module/izhikevich__with_stdp_synapse.cpp:306:16:
warning: unused variable '__resolution' [-Wunused-variable]
const double __resolution = nest::Time::get_resolution().get_ms();
// do not remove, this is necessary for the resolution() function
^
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/izh_stdp_test_module/izhikevich__with_stdp_synapse.cpp:553:41:
error: expression is not assignable
S_.post_trace__for_stdp_synapse += 1;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
4 warnings and 1 error generated.
make[2]: *** [CMakeFiles/izh_stdp_test_module_module.dir/build.make:111:
CMakeFiles/izh_stdp_test_module_module.dir/izhikevich__with_stdp_synapse.o]
Error 1
make[1]: *** [CMakeFiles/Makefile2:68:
CMakeFiles/izh_stdp_test_module_module.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
Any help is highly appreciated.
Best regards
On Wed, 2 Aug 2023 at 12:35, Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Dear Stefan,
This looks like a version conflict between NEST and NESTML. In NEST 3.5 we
have removed a number of aliases for built-in data types. It looks like
your version of NESTML generates code that still relies on the old aliases.
There are two ways forward: Either install NEST 3.4, or get a newer
version of NESTML. I don't know which version of NESTML you would need,
hope Charl or Pooja can help.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Department of Data Science
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
*From: *Stefan Dvoretskii <stefan.dvorezky(a)gmail.com>
*Date: *Wednesday, 2 August 2023 at 12:14
*To: *NEST User Mailing List <users(a)nest-simulator.org>
*Subject: *[NEST Users] Re: Synapses support only one spiking input port
Some people who received this message don't often get email from
stefan.dvorezky(a)gmail.com. Learn why this is important
<https://aka.ms/LearnAboutSenderIdentification>
Dear Charl,
many thanks for your help - it does indeed make sense and starts to
compile now! After several days with struggle with NEST on cluster, I am
also finally able to run the HPC version we have at LRZ.
However, there is another error occurring - which seems to do either with
C++ NEST core or the compiler?
1 2023 13:22:15
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
-- The CXX compiler identification is Clang 13.0.0
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestmlmodule Configuration Summary
-------------------------------------------------------
C++ compiler :
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -Wall -fopenmp -O2 -fdiagnostics-color=auto -O2 -g
-DNDEBUG
NEST include dirs :
-I/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/include/nest
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/include
NEST libraries flags :
-L/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
-lnest -lsli -fopenmp
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/lib/libltdl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/lib/libreadline.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/ncurses/6.2-gcc-47oirry/lib/libncurses.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgsl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgslcblas.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/libmpicxx.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/release/libmpi.so
/usr/lib64/librt.so /usr/lib64/libpthread.so /usr/lib64/libdl.so
-------------------------------------------------------
You can now build and install 'nestmlmodule' using
make
make install
The library file libnestmlmodule.so will be installed to
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
The module can be loaded into NEST using
(nestmlmodule) Install (in SLI)
nest.Install(nestmlmodule) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.10)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run "cmake --help-policy CMP0000".
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done
-- Generating done
-- Build files have been written to: /dss/dsshome1/00/ge72puf2/structfun/target
*Scanning dependencies of target nestmlmodule_module*
[ 25%] Building CXX object CMakeFiles/nestmlmodule_module.dir/nestmlmodule.o
In file included from /dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:47:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:9: error: no type named
'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:56: error: no type named
'rport' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:58: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:60: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:66: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:260:22: error: no type named
'port' in namespace 'nest'
static const nest::port MIN_SPIKE_RECEPTOR = 0;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:261:22: error: no type named
'port' in namespace 'nest'
static const nest::port PORT_NOT_AVAILABLE = -1;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:73: error: no type named
'rport' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:75: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:77: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:87: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
In file included from /dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:49:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich__with_stdp_synapse.h:164:9: error:
no type named 'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
Are there any ideas as to what can be done to solve this issue?
Best regards,
Stefan
On Fri, 28 Jul 2023 at 20:21, Charl Linssen <nest-users(a)turingbirds.com>
wrote:
Hi,
My apologies for the confusing error message. It occurs because you have
to explicitly tell NESTML which postsynaptic neuron type it is connected to
in the simulation. You can see an example of that here:
https://github.com/nest/nestml/blob/003d17a6425c3f8d88ed3aedd8d8e1d76245966…
The port is then assigned as "postsynaptic" and it is not considered for
the error that you are seeing.
Please let me know if you run into any further trouble.
With kind regards,
Charl
On Thu, Jul 27, 2023, at 12:25, Stefan Dvoretskii wrote:
Hello,
I am using an example synapse model which utilizes both post and pre
spikes (nestml/models/synapses/stdp_nn_symm.nestml at master ·
nest/nestml (github.com)
<https://github.com/nest/nestml/blob/master/models/synapses/stdp_nn_symm.nestml>
).
I get an error:
...
File
"/dss/dsshome1/00/ge72puf2/.conda/envs/nest/lib/python3.8/site-packages/pynestml/codegeneration/nest_code_generator.py",
line 469, in _get_synapse_model_namespace
assert len(namespace["pre_ports"]) <= 1, "Synapses only support
one
spiking input port"
AssertionError: Synapses only support one spiking input port
It is confusing: can I or can I not use a model with 2 synaptic inputs
(post and pre)? Is that a version thing?
Best regards,
--
Stefan
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Stefan Dvoretskii
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Stefan Dvoretskii
5:09 p.m.
Hi Stefan,
The latest NESTML release (5.3.0) does not support the latest NEST release (3.5) yet.
Could I please ask you to install the latest NESTML master?
pip install git+https://github.com/nest/nestml.git
Apologies for the inconvenience. We will be doing a NESTML release soon which would fix
all of these issues without you having to install it from the source.
Thanks,
Pooja
On 2. Aug 2023, at 12:34, Hans Ekkehard Plesser
<hans.ekkehard.plesser(a)nmbu.no> wrote:
Dear Stefan,
This looks like a version conflict between NEST and NESTML. In NEST 3.5 we have removed a
number of aliases for built-in data types. It looks like your version of NESTML generates
code that still relies on the old aliases.
There are two ways forward: Either install NEST 3.4, or get a newer version of NESTML. I
don't know which version of NESTML you would need, hope Charl or Pooja can help.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Department of Data Science
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 <mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
From: Stefan Dvoretskii <stefan.dvorezky(a)gmail.com
<mailto:stefan.dvorezky@gmail.com>>
Date: Wednesday, 2 August 2023 at 12:14
To: NEST User Mailing List <users(a)nest-simulator.org
<mailto:users@nest-simulator.org>>
Subject: [NEST Users] Re: Synapses support only one spiking input port
Some people who received this message don't often get email from
stefan.dvorezky(a)gmail.com <mailto:stefan.dvorezky@gmail.com>. Learn why this is
important <https://aka.ms/LearnAboutSenderIdentification>
Dear Charl,
many thanks for your help - it does indeed make sense and starts to compile now! After
several days with struggle with NEST on cluster, I am also finally able to run the HPC
version we have at LRZ.
However, there is another error occurring - which seems to do either with C++ NEST core
or the compiler?
1 2023 13:22:15
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org <https://www.nest-simulator.org/>
Type 'nest.help()' to find out more about NEST.
-- The CXX compiler identification is Clang 13.0.0
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestmlmodule Configuration Summary
-------------------------------------------------------
C++ compiler :
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -Wall -fopenmp -O2 -fdiagnostics-color=auto -O2 -g
-DNDEBUG
NEST include dirs :
-I/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/include/nest
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/include
NEST libraries flags :
-L/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
-lnest -lsli -fopenmp
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/lib/libltdl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/lib/libreadline.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/ncurses/6.2-gcc-47oirry/lib/libncurses.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgsl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgslcblas.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/libmpicxx.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/release/libmpi.so
/usr/lib64/librt.so /usr/lib64/libpthread.so /usr/lib64/libdl.so
-------------------------------------------------------
You can now build and install 'nestmlmodule' using
make
make install
The library file libnestmlmodule.so will be installed to
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
The module can be loaded into NEST using
(nestmlmodule) Install (in SLI)
nest.Install(nestmlmodule) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.10)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run "cmake --help-policy CMP0000".
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done
-- Generating done
-- Build files have been written to: /dss/dsshome1/00/ge72puf2/structfun/target
Scanning dependencies of target nestmlmodule_module
[ 25%] Building CXX object CMakeFiles/nestmlmodule_module.dir/nestmlmodule.o
In file included from /dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:47:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:9: error: no type named
'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:56: error: no type named
'rport' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:58: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:60: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:66: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:260:22: error: no type named
'port' in namespace 'nest'
static const nest::port MIN_SPIKE_RECEPTOR = 0;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:261:22: error: no type named
'port' in namespace 'nest'
static const nest::port PORT_NOT_AVAILABLE = -1;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:73: error: no type named
'rport' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:75: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:77: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:87: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
In file included from /dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:49:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich__with_stdp_synapse.h:164:9: error:
no type named 'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
Are there any ideas as to what can be done to solve this issue?
Best regards,
Stefan
On Fri, 28 Jul 2023 at 20:21, Charl Linssen <nest-users(a)turingbirds.com
<mailto:nest-users@turingbirds.com>> wrote:
Hi,
My apologies for the confusing error message. It occurs because you have to explicitly
tell NESTML which postsynaptic neuron type it is connected to in the simulation. You can
see an example of that here:
https://github.com/nest/nestml/blob/003d17a6425c3f8d88ed3aedd8d8e1d76245966…
The port is then assigned as "postsynaptic" and it is not considered for the
error that you are seeing.
Please let me know if you run into any further trouble.
With kind regards,
Charl
On Thu, Jul 27, 2023, at 12:25, Stefan Dvoretskii wrote:
Hello,
I am using an example synapse model which utilizes both post and pre spikes
(nestml/models/synapses/stdp_nn_symm.nestml at master · nest/nestml (github.com)
<https://github.com/nest/nestml/blob/master/models/synapses/stdp_nn_symm.nestml>).
I get an error:
...
File
"/dss/dsshome1/00/ge72puf2/.conda/envs/nest/lib/python3.8/site-packages/pynestml/codegeneration/nest_code_generator.py",
line 469, in _get_synapse_model_namespace
assert len(namespace["pre_ports"]) <= 1, "Synapses only support one
spiking input port"
AssertionError: Synapses only support one spiking input port
It is confusing: can I or can I not use a model with 2 synaptic inputs (post and pre)? Is
that a version thing?
Best regards,
--
Stefan
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
<mailto:users@nest-simulator.org>
To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
<mailto:users@nest-simulator.org>
To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org>
--
Stefan Dvoretskii
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
5:25 p.m.
Thank you. That has finally worked with NEST 3.4 and the latest NESTML
master.
Note that the last error I get seems to be connected to Expression not
assignable in dopamine modulated STDP synapse · Issue #840 · nest/nestml
(github.com) <https://github.com/nest/nestml/issues/840>, although it
should have been solved before the NESTML 5.3.0 release that I was using
previously. This problem does not appear anymore on the NESTML master.
Thanks to everyone for prompt help and support!
Best regards,
Stefan
On Wed, 2 Aug 2023 at 17:09, Babu, Pooja <p.babu(a)fz-juelich.de> wrote:
Hi Stefan,
The latest NESTML release (5.3.0) does not support the latest NEST release
(3.5) yet. Could I please ask you to install the latest NESTML master?
pip install git+https://github.com/nest/nestml.git
Apologies for the inconvenience. We will be doing a NESTML release soon
which would fix all of these issues without you having to install it from
the source.
Thanks,
Pooja
On 2. Aug 2023, at 12:34, Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Dear Stefan,
This looks like a version conflict between NEST and NESTML. In NEST 3.5 we
have removed a number of aliases for built-in data types. It looks like
your version of NESTML generates code that still relies on the old aliases.
There are two ways forward: Either install NEST 3.4, or get a newer
version of NESTML. I don't know which version of NESTML you would need,
hope Charl or Pooja can help.
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Department of Data Science
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
*From: *Stefan Dvoretskii <stefan.dvorezky(a)gmail.com>
*Date: *Wednesday, 2 August 2023 at 12:14
*To: *NEST User Mailing List <users(a)nest-simulator.org>
*Subject: *[NEST Users] Re: Synapses support only one spiking input port
Some people who received this message don't often get email from
stefan.dvorezky(a)gmail.com. Learn why this is important
<https://aka.ms/LearnAboutSenderIdentification>
Dear Charl,
many thanks for your help - it does indeed make sense and starts to
compile now! After several days with struggle with NEST on cluster, I am
also finally able to run the HPC version we have at LRZ.
However, there is another error occurring - which seems to do either with
C++ NEST core or the compiler?
1 2023 13:22:15
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
-- The CXX compiler identification is Clang 13.0.0
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- Check for working CXX compiler:
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestmlmodule Configuration Summary
-------------------------------------------------------
C++ compiler :
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/x86_64/intel-oneapi-compilers/2021.4.0-gcc-xrzccgg/compiler/2021.4.0/linux/bin/icx
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -Wall -fopenmp -O2 -fdiagnostics-color=auto -O2 -g
-DNDEBUG
NEST include dirs :
-I/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/include/nest
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/include
-I/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/include
NEST libraries flags :
-L/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
-lnest -lsli -fopenmp
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/libtool/2.4.6-gcc-mggvdji/lib/libltdl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/readline/8.1-gcc-kl2epb2/lib/libreadline.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/ncurses/6.2-gcc-47oirry/lib/libncurses.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgsl.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/gsl/2.7-gcc-to2yxdj/lib/libgslcblas.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/libmpicxx.so
/dss/dsshome1/lrz/sys/spack/release/22.2.1/opt/haswell/intel-mpi/2019.12.320-gcc-5tsyll5/compilers_and_libraries_2020.4.320/linux/mpi/intel64/lib/release/libmpi.so
/usr/lib64/librt.so /usr/lib64/libpthread.so /usr/lib64/libdl.so
-------------------------------------------------------
You can now build and install 'nestmlmodule' using
make
make install
The library file libnestmlmodule.so will be installed to
/dss/dsshome1/00/ge72puf2/spack/opt/linux-sles15-haswell/nest/3.5-gcc-11.2.0-qmxto5u/lib64/nest
The module can be loaded into NEST using
(nestmlmodule) Install (in SLI)
nest.Install(nestmlmodule) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.10)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run "cmake --help-policy CMP0000".
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done
-- Generating done
-- Build files have been written to: /dss/dsshome1/00/ge72puf2/structfun/target
*Scanning dependencies of target nestmlmodule_module*
[ 25%] Building CXX object CMakeFiles/nestmlmodule_module.dir/nestmlmodule.o
In file included from /dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:47:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:9: error: no type named
'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:144:56: error: no type named
'rport' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:156:58: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:157:60: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:9: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:158:66: error: no type named
'port' in namespace 'nest'
nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:260:22: error: no type named
'port' in namespace 'nest'
static const nest::port MIN_SPIKE_RECEPTOR = 0;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:261:22: error: no type named
'port' in namespace 'nest'
static const nest::port PORT_NOT_AVAILABLE = -1;
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:512:73: error: no type named
'rport' in namespace 'nest'
inline nest::port izhikevich::send_test_event(nest::Node& target, nest::rport
receptor_type, nest::synindex, bool)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:522:75: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::SpikeEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:535:77: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::CurrentEvent&, nest::port
receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:14: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich.h:548:87: error: no type named
'port' in namespace 'nest'
inline nest::port izhikevich::handles_test_event(nest::DataLoggingRequest& dlr,
nest::port receptor_type)
~~~~~~^
In file included from /dss/dsshome1/00/ge72puf2/structfun/target/nestmlmodule.cpp:49:
/dss/dsshome1/00/ge72puf2/structfun/target/izhikevich__with_stdp_synapse.h:164:9: error:
no type named 'port' in namespace 'nest'
nest::port send_test_event(nest::Node& target, nest::rport receptor_type,
nest::synindex, bool) override;
~~~~~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
Are there any ideas as to what can be done to solve this issue?
Best regards,
Stefan
On Fri, 28 Jul 2023 at 20:21, Charl Linssen <nest-users(a)turingbirds.com>
wrote:
Hi,
My apologies for the confusing error message. It occurs because you have
to explicitly tell NESTML which postsynaptic neuron type it is connected to
in the simulation. You can see an example of that here:
https://github.com/nest/nestml/blob/003d17a6425c3f8d88ed3aedd8d8e1d76245966…
The port is then assigned as "postsynaptic" and it is not considered for
the error that you are seeing.
Please let me know if you run into any further trouble.
With kind regards,
Charl
On Thu, Jul 27, 2023, at 12:25, Stefan Dvoretskii wrote:
Hello,
I am using an example synapse model which utilizes both post and pre
spikes (nestml/models/synapses/stdp_nn_symm.nestml at master ·
nest/nestml (github.com)
<https://github.com/nest/nestml/blob/master/models/synapses/stdp_nn_symm.nestml>
).
I get an error:
...
File
"/dss/dsshome1/00/ge72puf2/.conda/envs/nest/lib/python3.8/site-packages/pynestml/codegeneration/nest_code_generator.py",
line 469, in _get_synapse_model_namespace
assert len(namespace["pre_ports"]) <= 1, "Synapses only support
one
spiking input port"
AssertionError: Synapses only support one spiking input port
It is confusing: can I or can I not use a model with 2 synaptic inputs
(post and pre)? Is that a version thing?
Best regards,
--
Stefan
_______________________________________________
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Stefan Dvoretskii
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Stefan Dvoretskii
429
days inactive
435
days old
6 comments
4 participants
participants (4)
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Babu, Pooja -
Charl Linssen -
Hans Ekkehard Plesser -
Stefan Dvoretskii