2 Aug
2023
2 Aug
'23
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
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--
Stefan Dvoretskii