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NeuralEnsemble / PyNN

A Python package for simulator-independent specification of neuronal network models.

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Build failure trying to build 0.11.0 for Fedora

penguinpee opened this issue · comments

commented

I had a first shot at updating PyNN to 0.11.0 in Fedora. The build failed with:

In file included from /builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/pynn_extensions.cpp:14:
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/simple_stochastic_synapse.h: In member function 'nest::port pynn::simple_stochastic_synapse<targetidentifierT>::ConnTestDummyNode::handles_test_event(nest::SpikeEvent&, nest::rport)':
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/simple_stochastic_synapse.h:100:20: error: 'invalid_port' is not a member of 'nest'; did you mean 'invalid_port_'?
  100 |       return nest::invalid_port;
      |                    ^~~~~~~~~~~~
      |                    invalid_port_
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/simple_stochastic_synapse.h: In member function 'nest::port pynn::simple_stochastic_synapse<targetidentifierT>::ConnTestDummyNode::handles_test_event(nest::DSSpikeEvent&, nest::rport)':
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/simple_stochastic_synapse.h:106:20: error: 'invalid_port' is not a member of 'nest'; did you mean 'invalid_port_'?
  106 |       return nest::invalid_port;
      |                    ^~~~~~~~~~~~
      |                    invalid_port_
In file included from /builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/pynn_extensions.cpp:15:
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/stochastic_stp_synapse.h: In member function 'nest::port pynn::stochastic_stp_synapse<targetidentifierT>::ConnTestDummyNode::handles_test_event(nest::SpikeEvent&, nest::rport)':
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/stochastic_stp_synapse.h:116:20: error: 'invalid_port' is not a member of 'nest'; did you mean 'invalid_port_'?
  116 |       return nest::invalid_port;
      |                    ^~~~~~~~~~~~
      |                    invalid_port_
In file included from /builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/pynn_extensions.cpp:14:
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/simple_stochastic_synapse.h: In member function 'nest::port pynn::simple_stochastic_synapse<targetidentifierT>::ConnTestDummyNode::handles_test_event(nest::SpikeEvent&, nest::rport)':
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/simple_stochastic_synapse.h:100:20: error: 'invalid_port' is not a member of 'nest'; did you mean 'invalid_port_'?
  100 |       return nest::invalid_port;
      |                    ^~~~~~~~~~~~
      |                    invalid_port_
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/simple_stochastic_synapse.h: In member function 'nest::port pynn::simple_stochastic_synapse<targetidentifierT>::ConnTestDummyNode::handles_test_event(nest::DSSpikeEvent&, nest::rport)':
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/simple_stochastic_synapse.h:106:20: error: 'invalid_port' is not a member of 'nest'; did you mean 'invalid_port_'?
  106 |       return nest::invalid_port;
      |                    ^~~~~~~~~~~~
      |                    invalid_port_
In file included from /builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/pynn_extensions.cpp:15:
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/stochastic_stp_synapse.h: In member function 'nest::port pynn::stochastic_stp_synapse<targetidentifierT>::ConnTestDummyNode::handles_test_event(nest::SpikeEvent&, nest::rport)':
/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/stochastic_stp_synapse.h:116:20: error: 'invalid_port' is not a member of 'nest'; did you mean 'invalid_port_'?
  116 |       return nest::invalid_port;
      |                    ^~~~~~~~~~~~
      |                    invalid_port_
gmake[2]: *** [CMakeFiles/pynn_extensions_lib.dir/build.make:79: CMakeFiles/pynn_extensions_lib.dir/pynn_extensions.cpp.o] Error 1
gmake[2]: Leaving directory '/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/redhat-linux-build'
gmake[1]: *** [CMakeFiles/Makefile2:141: CMakeFiles/pynn_extensions_lib.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs....
gmake[2]: Leaving directory '/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/redhat-linux-build'
gmake[2]: *** [CMakeFiles/pynn_extensions_module.dir/build.make:79: CMakeFiles/pynn_extensions_module.dir/pynn_extensions.cpp.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:115: CMakeFiles/pynn_extensions_module.dir/all] Error 2
gmake[1]: Leaving directory '/builddir/build/BUILD/PyNN-0.11.0/build/lib/pyNN/nest/extensions/redhat-linux-build'
gmake: *** [Makefile:159: all] Error 2

Any clues? Am I missing a step? This is in rawhide, where Python 3.12 and Cython 3.0.0 have recently landed.

-------------------------------------------------------
pynn_extensions Configuration Summary
-------------------------------------------------------

C++ compiler         : /usr/bin/g++
Build static libs    : OFF
-- Configuring done (0.5s)
C++ compiler flags   : -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer
NEST compiler flags  : -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++11 -Wall -fopenmp -fdiagnostics-color=auto
NEST include dirs    :  -I/usr/include/nest -I/usr/include -I/usr/include -I/usr/include -I/usr/include -I/usr/include
NEST libraries flags : -L/usr/lib64/ -lnestutil -lnest -lsli -lnestkernel -fopenmp /lib64/libltdl.so /lib64/libreadline.so /lib64/libncurses.so /usr/lib64/libgsl.so /usr/lib64/libgslcblas.so /usr/lib64/libneurosim.so /usr/lib64/libpy3neurosim.so

-------------------------------------------------------

Tagging @sanjayankur31 since he is the primary maintainer in Fedora. Not sure if he tried already. But this looks more like something in the code.

commented

Thanks @penguinpee . We need to update NEST first. I've had this open for NEST 3.4 for a while, but then 3.5 came out. I'll test it out again today and see if everything works:

https://src.fedoraproject.org/rpms/nest/pull-request/5

commented

Keep an eye on #779 then. 😉

commented

Yeh, we'll update to 3.4 and update pynn for now, and when it supports 3.5, we'll update nest and it together.

commented

By the way, I've tested PyNN 0.11.0 with NEST 3.5, and all the tests pass: https://github.com/NeuralEnsemble/PyNN/actions/runs/5387542842

commented

Yeh, we'll update to 3.4 and update pynn for now, and when it supports 3.5, we'll update nest and it together.

I was able to build PyNN 0.11.0 using NEST 3.4: https://copr.fedorainfracloud.org/coprs/gui1ty/neuro-sig/build/6203767/