On 2. Aug 2023, at 12:34, Hans Ekkehard Plesser <hans.ekkehard.plesser@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@nmbu.no

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From: Stefan Dvoretskii <stefan.dvorezky@gmail.com>
Date: Wednesday, 2 August 2023 at 12:14
To: NEST User Mailing List <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@gmail.com. Learn why this is important

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@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/003d17a6425c3f8d88ed3aedd8d8e1d76245966e/tests/nest_tests/stdp_window_test.py#L58 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)). 

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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