1 Mar
2022
1 Mar
'22
12:47 p.m.
Dear NESTML Users,
when I try the NESTML Izhikevich tutorial, I have a problem in the generate_nest_target
function. The output in the terminal is the following:
***
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: UNKNOWN
Built: Jan 18 2022 13:53:41
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 GNU 9.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestml_izhikevich_module 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/opt/nest/include/nest -I/usr/include -I/usr/include
-I/usr/include -I/opt/music-install/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/include
NEST libraries flags : -L/opt/nest/lib/nest -lnestutil -lnest -lsli -lnestkernel -fopenmp
/usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libreadline.so
/usr/lib/x86_64-linux-gnu/libncurses.so /usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so /opt/music-install/lib/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 'nestml_izhikevich_module' using
make
make install
The library file libnestml_izhikevich_module.so will be installed to
/opt/nest/lib/nest
The module can be loaded into NEST using
(nestml_izhikevich_module) Install (in SLI)
nest.Install(nestml_izhikevich_module) (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 3.22)
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: /tmp/nestml-component
[ 16%] Building CXX object
CMakeFiles/nestml_izhikevich_module_module.dir/nestml_izhikevich_module.o
In file included from /opt/nest/include/nest/connector_base.h:35,
from /opt/nest/include/nest/connection_manager.h:36,
from /opt/nest/include/nest/connection_manager_impl.h:26,
from /tmp/nestml-component/nestml_izhikevich_module.cpp:26:
/opt/nest/include/nest/sort.h:36:10: fatal error: boost/sort/spreadsort/spreadsort.hpp: No
such file or directory
36 | #include <boost/sort/spreadsort/spreadsort.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [CMakeFiles/nestml_izhikevich_module_module.dir/build.make:76:
CMakeFiles/nestml_izhikevich_module_module.dir/nestml_izhikevich_module.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:112:
CMakeFiles/nestml_izhikevich_module_module.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
***
While the Jupyter notebook output is the following:
***
Warning: PyGSL is not available. The stiffness test will be skipped.
Warning: No module named 'pygsl'
Option "nest_path" does not exist in builder
---------------------------------------------------------------------------
CalledProcessError Traceback (most recent call last)
/opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self)
149 try:
--> 150 subprocess.check_call(make_all_cmd, stderr=subprocess.STDOUT,
shell=shell,
151 cwd=str(os.path.join(target_path)))
/usr/lib/python3.8/subprocess.py in check_call(*popenargs, **kwargs)
363 cmd = popenargs[0]
--> 364 raise CalledProcessError(retcode, cmd)
365 return 0
CalledProcessError: Command '['make', 'all']' returned non-zero
exit status 2.
During handling of the above exception, another exception occurred:
GeneratedCodeBuildException Traceback (most recent call last)
<ipython-input-2-f7696df63255> in <module>
----> 1 generate_nest_target(input_path="izhikevich_solution.nestml",
2 target_path="/tmp/nestml-component",
3 module_name="nestml_izhikevich_module",
4 suffix="_nestml",
5 logging_level="ERROR",
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in
generate_nest_target(input_path, target_path, install_path, logging_level, module_name,
store_log, suffix, dev, codegen_opts)
181 A dictionary containing additional options for the target code generator.
182 """
--> 183 generate_target(input_path, target_platform="NEST",
target_path=target_path, logging_level=logging_level,
184 module_name=module_name, store_log=store_log, suffix=suffix,
install_path=install_path,
185 dev=dev, codegen_opts=codegen_opts)
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in generate_target(input_path,
target_platform, target_path, install_path, logging_level, module_name, store_log, suffix,
dev, codegen_opts)
150 FrontendConfiguration.set_codegen_opts(codegen_opts)
151
--> 152 if not process() == 0:
153 raise Exception("Error(s) occurred while processing the model")
154
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in process()
278
options=FrontendConfiguration.get_codegen_opts())
279 if _builder is not None:
--> 280 _builder.build()
281
282 if FrontendConfiguration.store_log:
/opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self)
151 cwd=str(os.path.join(target_path)))
152 except subprocess.CalledProcessError as e:
--> 153 raise GeneratedCodeBuildException('Error occurred during
\'make all\'! More detailed error messages can be found in stdout.')
154
155 # finally execute make install
GeneratedCodeBuildException: Error occurred during 'make all'! More detailed error
messages can be found in stdout.
***
I installed Boost with 'sudo apt-get install libboost-all-dev' from the terminal.
Can you help me?
Best,
Salvo
2 Mar
2 Mar
7:35 p.m.
It seems that Boost might have been installed to a non-default location (/opt?)
For example, for me, it is installed in /usr/include:
$ find / -name spreadsort.hpp
/usr/include/boost/sort/spreadsort/spreadsort.hpp
And this is on the default search path for g++:
$ g++ -E -v -
include <...> search starts here:
/usr/lib/gcc/x86_64-linux-gnu/10/include
/usr/local/include
/usr/include/x86_64-linux-gnu
/usr/include
End of search list.
If it is not on the default search path, then we should check if it's the case that
NEST finds it, but NESTML does not. Could you check if, during the build of NEST
Simulator, at the first step when you run "cmake", there is a line in the output
that says "Use Boost : Yes"?
I just want to mention the possibility of running NESTML via the Docker image
<https://nestml.readthedocs.io/en/latest/installation.html#docker-installation>.
There is a convenient Jupyterhub interface via your browser, and practically zero
installation effort (other than Docker itself). But I'll happily debug this issue
further, perhaps we have the opportunity here to improve something in NESTML.
On Tue, Mar 1, 2022, at 12:47, Salvo T wrote:
Dear NESTML Users,
when I try the NESTML Izhikevich tutorial, I have a problem in the
generate_nest_target function. The output in the terminal is the
following:
***
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: UNKNOWN
Built: Jan 18 2022 13:53:41
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 GNU 9.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestml_izhikevich_module 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/opt/nest/include/nest -I/usr/include
-I/usr/include -I/usr/include -I/opt/music-install/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/include
NEST libraries flags : -L/opt/nest/lib/nest -lnestutil -lnest -lsli
-lnestkernel -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libreadline.so
/usr/lib/x86_64-linux-gnu/libncurses.so
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so
/opt/music-install/lib/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 'nestml_izhikevich_module' using
make
make install
The library file libnestml_izhikevich_module.so will be installed to
/opt/nest/lib/nest
The module can be loaded into NEST using
(nestml_izhikevich_module) Install (in SLI)
nest.Install(nestml_izhikevich_module) (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 3.22)
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: /tmp/nestml-component
[ 16%] Building CXX object
CMakeFiles/nestml_izhikevich_module_module.dir/nestml_izhikevich_module.o
In file included from /opt/nest/include/nest/connector_base.h:35,
from /opt/nest/include/nest/connection_manager.h:36,
from
/opt/nest/include/nest/connection_manager_impl.h:26,
from
/tmp/nestml-component/nestml_izhikevich_module.cpp:26:
/opt/nest/include/nest/sort.h:36:10: fatal error:
boost/sort/spreadsort/spreadsort.hpp: No such file or directory
36 | #include <boost/sort/spreadsort/spreadsort.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: ***
[CMakeFiles/nestml_izhikevich_module_module.dir/build.make:76:
CMakeFiles/nestml_izhikevich_module_module.dir/nestml_izhikevich_module.o]
Error 1
make[1]: *** [CMakeFiles/Makefile2:112:
CMakeFiles/nestml_izhikevich_module_module.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
***
While the Jupyter notebook output is the following:
***
Warning: PyGSL is not available. The stiffness test will be skipped.
Warning: No module named 'pygsl'
Option "nest_path" does not exist in builder
---------------------------------------------------------------------------
CalledProcessError Traceback (most recent call
last)
/opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self)
149 try:
--> 150 subprocess.check_call(make_all_cmd,
stderr=subprocess.STDOUT, shell=shell,
151
cwd=str(os.path.join(target_path)))
/usr/lib/python3.8/subprocess.py in check_call(*popenargs, **kwargs)
363 cmd = popenargs[0]
--> 364 raise CalledProcessError(retcode, cmd)
365 return 0
CalledProcessError: Command '['make', 'all']' returned non-zero
exit status 2.
During handling of the above exception, another exception occurred:
GeneratedCodeBuildException Traceback (most recent call last)
<ipython-input-2-f7696df63255> in <module>
----> 1 generate_nest_target(input_path="izhikevich_solution.nestml",
2 target_path="/tmp/nestml-component",
3 module_name="nestml_izhikevich_module",
4 suffix="_nestml",
5 logging_level="ERROR",
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in
generate_nest_target(input_path, target_path, install_path,
logging_level, module_name, store_log, suffix, dev, codegen_opts)
181 A dictionary containing additional options for the
target code generator.
182 """
--> 183 generate_target(input_path, target_platform="NEST",
target_path=target_path, logging_level=logging_level,
184 module_name=module_name,
store_log=store_log, suffix=suffix, install_path=install_path,
185 dev=dev, codegen_opts=codegen_opts)
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in
generate_target(input_path, target_platform, target_path, install_path,
logging_level, module_name, store_log, suffix, dev, codegen_opts)
150 FrontendConfiguration.set_codegen_opts(codegen_opts)
151
--> 152 if not process() == 0:
153 raise Exception("Error(s) occurred while processing the
model")
154
/opt/data/nestml/pynestml/frontend/pynestml_frontend.py in process()
278
options=FrontendConfiguration.get_codegen_opts())
279 if _builder is not None:
--> 280 _builder.build()
281
282 if FrontendConfiguration.store_log:
/opt/data/nestml/pynestml/codegeneration/nest_builder.py in build(self)
151
cwd=str(os.path.join(target_path)))
152 except subprocess.CalledProcessError as e:
--> 153 raise GeneratedCodeBuildException('Error occurred
during \'make all\'! More detailed error messages can be found in
stdout.')
154
155 # finally execute make install
GeneratedCodeBuildException: Error occurred during 'make all'! More
detailed error messages can be found in stdout.
***
I installed Boost with 'sudo apt-get install libboost-all-dev' from the
terminal.
Can you help me?
Best,
Salvo
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3 Mar
3 Mar
9:28 a.m.
I use the docker method. What NEST and NESTML versions do you suggest? At this moment I am
using NEST 3.2 and NESTML 5.0.
Thanks.
Salvo.
778
days inactive
780
days old
2 comments
2 participants
participants (2)
-
Charl Linssen -
Salvo T