Errors when using Brian2GeNN

[ajitlimaye]

Hi: I installed Brian2, GeNN and Brian2GeNN per the instructions (Windows10-Pro machine, CUDA 10.1, Visual Studio 19, 17, 15 installed), and tried to run the following:

import os
os.environ['GENN_PATH'] = 'c:\genn'
os.environ['PATH'] = os.environ['PATH'] + ';' + 'c:\genn\bin' + ';' + 'c:\genn\lib\bin'
os.environ['CUDA_PATH']
os.environ['GENN_PATH']
os.environ['PATH']
from brian2 import *
import brian2genn
set_device('genn')
start_scope()

tau = 10*ms
eqs = '''
dv/dt = (1-v)/tau : 1 (unless refractory)
'''

G = NeuronGroup(1, eqs, threshold='v>0.8', reset='v = 0', refractory=5*ms, method='exact')

statemon = StateMonitor(G, 'v', record=0)
spikemon = SpikeMonitor(G)

run(50*ms)

plot(statemon.t/ms, statemon.v[0])
for t in spikemon.t:
    axvline(t/ms, ls='--', c='C1', lw=3)
xlabel('Time (ms)')
ylabel('v');

This gives the following error messages - can you help me understand the root cause, and how to fix it?

INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
running brian code generation ...
building genn executable ...
Microsoft (R) Build Engine version 4.7.3190.0
[Microsoft .NET Framework, version 4.0.30319.42000]
Copyright (C) Microsoft Corporation. All rights reserved.

Build started 4/30/2019 1:17:21 PM.
Project "c:\genn\lib\generate.vcxproj" on node 1 (default targets).
c:\genn\lib\generate.vcxproj(26,3): error MSB4019: The imported project "C:\Microsoft.Cpp.default.props" was not found. Confirm that the path in the <Import> declaration is correct, and that the file exists on disk.
Done Building Project "c:\genn\lib\generate.vcxproj" (default targets) -- FAILED.

Build FAILED.

"c:\genn\lib\generate.vcxproj" (default target) (1) ->
  c:\genn\lib\generate.vcxproj(26,3): error MSB4019: The imported project "C:\Microsoft.Cpp.default.props" was not found. Confirm that the path in the <Import> declaration is correct, and that the file exists on disk.

    0 Warning(s)
    1 Error(s)

Time Elapsed 00:00:00.02
model build complete
    del main.exe *.obj *.ilk *.pdb 2>nul
    cd magicnetwork_model_CODE && nmake clean /nologo
'".\generateALL.exe"' is not recognized as an internal or external command,
operable program or batch file.

Microsoft (R) Program Maintenance Utility Version 14.00.24245.0
Copyright (C) Microsoft Corporation.  All rights reserved.

The system cannot find the path specified.
NMAKE : fatal error U1077: 'cd' : return code '0x1'
Stop.
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
~\Anaconda3\lib\site-packages\brian2genn\device.py in build(self, directory, compile, run, use_GPU, debug, with_output, direct_call)
    781             try:
--> 782                 self.compile_source(debug, directory, use_GPU)
    783             except CalledProcessError as ex:

~\Anaconda3\lib\site-packages\brian2genn\device.py in compile_source(self, debug, directory, use_GPU)
    993                 cmd += ' && nmake /f WINmakefile clean && nmake /f WINmakefile'
--> 994                 check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
    995             else:

~\Anaconda3\lib\subprocess.py in check_call(*popenargs, **kwargs)
    290             cmd = popenargs[0]
--> 291         raise CalledProcessError(retcode, cmd)
    292     return 0

CalledProcessError: Command '"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" x86_amd64 && c:\genn\lib\bin\genn-buildmodel.bat magicnetwork_model.cpp && nmake /f WINmakefile clean && nmake /f WINmakefile' returned non-zero exit status 2.

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
<ipython-input-1-2e2df092b86a> in <module>
     20 spikemon = SpikeMonitor(G)
     21 
---> 22 run(50*ms)
     23 
     24 plot(statemon.t/ms, statemon.v[0])

~\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py in new_f(*args, **kwds)
   2373                                                      get_dimensions(newkeyset[k]))
   2374 
-> 2375             result = f(*args, **kwds)
   2376             if 'result' in au:
   2377                 if au['result'] == bool:

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(duration, report, report_period, namespace, profile, level)
    369     '''
    370     return magic_network.run(duration, report=report, report_period=report_period,
--> 371                              namespace=namespace, profile=profile, level=2+level)
    372 run.__module__ = __name__
    373 

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(self, duration, report, report_period, namespace, profile, level)
    229         self._update_magic_objects(level=level+1)
    230         Network.run(self, duration, report=report, report_period=report_period,
--> 231                     namespace=namespace, profile=profile, level=level+1)
    232 
    233     def store(self, name='default', filename=None, level=0):

~\Anaconda3\lib\site-packages\brian2\core\base.py in device_override_decorated_function(*args, **kwds)
    272             curdev = get_device()
    273             if hasattr(curdev, name):
--> 274                 return getattr(curdev, name)(*args, **kwds)
    275             else:
    276                 return func(*args, **kwds)

~\Anaconda3\lib\site-packages\brian2genn\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1632                                             report_period=report_period,
   1633                                             namespace=namespace,
-> 1634                                             level=level + 1)
   1635         self.run_statement_used = True
   1636 

~\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1374                                    'device.build call to use multiple run '
   1375                                    'statements with this device.')
-> 1376             self.build(direct_call=False, **self.build_options)
   1377 
   1378     def network_store(self, net, *args, **kwds):

~\Anaconda3\lib\site-packages\brian2genn\device.py in build(self, directory, compile, run, use_GPU, debug, with_output, direct_call)
    786                                     'See the output above (if any) for more '
    787                                     'details.').format(cmd=ex.cmd,
--> 788                                                        returncode=ex.returncode)
    789                                    )
    790         if run:

RuntimeError: Project compilation failed (Command "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" x86_amd64 && c:\genn\lib\bin\genn-buildmodel.bat magicnetwork_model.cpp && nmake /f WINmakefile clean && nmake /f WINmakefile failed with error code 2).
See the output above (if any) for more details.

[ajitlimaye]

In c:\genn\lib there is indeed a project named generate.vcxproj, and some code in it is apparently trying to find the project "C:\Microsoft.Cpp.default.props". This seems to be a value for a key in the registry - is my guess even close? If so, what is the name of the registry key? On a wild hunch, I defined an environment variable as follows:

os.environ['VCTargetsPath'] = 'C:\\Program Files (x86)\\MSBuild\\Microsoft.Cpp\\v4.0\\V140' With this, I get a different error - as follows:

INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
running brian code generation ...
building genn executable ...
Microsoft (R) Build Engine version 4.7.3190.0
[Microsoft .NET Framework, version 4.0.30319.42000]
Copyright (C) Microsoft Corporation. All rights reserved.

Build started 4/30/2019 6:46:32 PM.
Project "c:\genn\lib\generate.vcxproj" on node 1 (default targets).
Project "c:\genn\lib\generate.vcxproj" (1) is building "c:\genn\lib\lib_genn.vcxproj" (2) on node 1 (default targets).
C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Microsoft.Cpp.Current.targets(64,5): error MSB4062: The "SetEnv" task could not be loaded from the assembly C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Microsoft.Build.CppTasks.Common.dll. Could not load file or assembly 'Microsoft.Build.Utilities.Core, Version=14.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a' or one of its dependencies. The system cannot find the file specified. Confirm that the <UsingTask> declaration is correct, that the assembly and all its dependencies are available, and that the task contains a public class that implements Microsoft.Build.Framework.ITask. [c:\genn\lib\lib_genn.vcxproj]
Done Building Project "c:\genn\lib\lib_genn.vcxproj" (default targets) -- FAILED.
Done Building Project "c:\genn\lib\generate.vcxproj" (default targets) -- FAILED.

Build FAILED.

"c:\genn\lib\generate.vcxproj" (default target) (1) ->
"c:\genn\lib\lib_genn.vcxproj" (default target) (2) ->
(SetBuildDefaultEnvironmentVariables target) -> 
  C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Microsoft.Cpp.Current.targets(64,5): error MSB4062: The "SetEnv" task could not be loaded from the assembly C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Microsoft.Build.CppTasks.Common.dll. Could not load file or assembly 'Microsoft.Build.Utilities.Core, Version=14.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a' or one of its dependencies. The system cannot find the file specified. Confirm that the <UsingTask> declaration is correct, that the assembly and all its dependencies are available, and that the task contains a public class that implements Microsoft.Build.Framework.ITask. [c:\genn\lib\lib_genn.vcxproj]

    0 Warning(s)
    1 Error(s)

Time Elapsed 00:00:00.17
model build complete
    del main.exe *.obj *.ilk *.pdb 2>nul
    cd magicnetwork_model_CODE && nmake clean /nologo
'".\generateALL.exe"' is not recognized as an internal or external command,
operable program or batch file.

Microsoft (R) Program Maintenance Utility Version 14.00.24245.0
Copyright (C) Microsoft Corporation.  All rights reserved.

The system cannot find the path specified.
NMAKE : fatal error U1077: 'cd' : return code '0x1'
Stop.
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
~\Anaconda3\lib\site-packages\brian2genn\device.py in build(self, directory, compile, run, use_GPU, debug, with_output, direct_call)
    781             try:
--> 782                 self.compile_source(debug, directory, use_GPU)
    783             except CalledProcessError as ex:

~\Anaconda3\lib\site-packages\brian2genn\device.py in compile_source(self, debug, directory, use_GPU)
    993                 cmd += ' && nmake /f WINmakefile clean && nmake /f WINmakefile'
--> 994                 check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
    995             else:

~\Anaconda3\lib\subprocess.py in check_call(*popenargs, **kwargs)
    290             cmd = popenargs[0]
--> 291         raise CalledProcessError(retcode, cmd)
    292     return 0

CalledProcessError: Command '"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" x86_amd64 && c:\genn\lib\bin\genn-buildmodel.bat magicnetwork_model.cpp && nmake /f WINmakefile clean && nmake /f WINmakefile' returned non-zero exit status 2.

During handling of the above exception, another exception occurred:

RuntimeError                              Traceback (most recent call last)
<ipython-input-3-14a141395004> in <module>
     14 spikemon = SpikeMonitor(G)
     15 
---> 16 run(50*ms)
     17 
     18 plot(statemon.t/ms, statemon.v[0])

~\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py in new_f(*args, **kwds)
   2373                                                      get_dimensions(newkeyset[k]))
   2374 
-> 2375             result = f(*args, **kwds)
   2376             if 'result' in au:
   2377                 if au['result'] == bool:

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(duration, report, report_period, namespace, profile, level)
    369     '''
    370     return magic_network.run(duration, report=report, report_period=report_period,
--> 371                              namespace=namespace, profile=profile, level=2+level)
    372 run.__module__ = __name__
    373 

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(self, duration, report, report_period, namespace, profile, level)
    229         self._update_magic_objects(level=level+1)
    230         Network.run(self, duration, report=report, report_period=report_period,
--> 231                     namespace=namespace, profile=profile, level=level+1)
    232 
    233     def store(self, name='default', filename=None, level=0):

~\Anaconda3\lib\site-packages\brian2\core\base.py in device_override_decorated_function(*args, **kwds)
    272             curdev = get_device()
    273             if hasattr(curdev, name):
--> 274                 return getattr(curdev, name)(*args, **kwds)
    275             else:
    276                 return func(*args, **kwds)

~\Anaconda3\lib\site-packages\brian2genn\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1632                                             report_period=report_period,
   1633                                             namespace=namespace,
-> 1634                                             level=level + 1)
   1635         self.run_statement_used = True
   1636 

~\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1374                                    'device.build call to use multiple run '
   1375                                    'statements with this device.')
-> 1376             self.build(direct_call=False, **self.build_options)
   1377 
   1378     def network_store(self, net, *args, **kwds):

~\Anaconda3\lib\site-packages\brian2genn\device.py in build(self, directory, compile, run, use_GPU, debug, with_output, direct_call)
    786                                     'See the output above (if any) for more '
    787                                     'details.').format(cmd=ex.cmd,
--> 788                                                        returncode=ex.returncode)
    789                                    )
    790         if run:

RuntimeError: Project compilation failed (Command "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" x86_amd64 && c:\genn\lib\bin\genn-buildmodel.bat magicnetwork_model.cpp && nmake /f WINmakefile clean && nmake /f WINmakefile failed with error code 2).
See the output above (if any) for more details.

Right then - enough flailing. I shall wait for an informed, considered response from people who know what they are doing (i.e. not me . . . yet!)

[tnowotny]

@neworderofjamie , I am afraid this might be a windows build problem in GeNN rather than a brian2genn specific issue but I could be wrong. What do you think?

[neworderofjamie]

c:\genn\lib\generate.vcxproj(26,3): error MSB4019: The imported project "C:\Microsoft.Cpp.default.props" was not found. Confirm that the path in the <Import> declaration is correct, and that the file exists on disk. suggests that this is last year's mystery https://github.com/genn-team/genn/issues/189 which seems to often happen if you have multiple visual studios installed. I think, counter-intuitively, trying to blank this environment variable out is the best fix so try: SET VCTargetsPath ""

[ajitlimaye]

Blanking VCTargetsPath did not help, so I did the following:

1. Uninstall all older versions of CUDA, keeping only 9.2 and 10.1
2. Uninstall all versions of Visual Studio (I had 2019, 2017 and 2015 installed)
3. Reboot
4. Install Visual Studio 2017 only

Following these steps, I re-ran my test script, and this time I get permission errors, but it is difficult to tell from the messages exactly which file cannot be accessed. The exact test script, and the error messages, are reproduced below:

Test script:

import os

# For now, we set up environment variables locally so I can control them - eventually, move these to
# Windows environment variables.
#
os.environ['GENN_PATH'] = 'c:\\genn'
os.environ['PATH'] = os.environ['PATH'] + ';' + 'c:\\genn\\lib\\bin'
os.environ['CUDA_PATH'] = 'C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v9.2'

from brian2 import *
import brian2genn
set_device('genn')

# Define the path to vcvarsall.bat
#
prefs.codegen.cpp.msvc_vars_location = 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2017\\Community\\VC\\Auxiliary\\Build'
start_scope()

tau = 10*ms
eqs = '''
dv/dt = (1-v)/tau : 1 (unless refractory)
'''

G = NeuronGroup(1, eqs, threshold='v>0.8', reset='v = 0', refractory=5*ms, method='exact')

statemon = StateMonitor(G, 'v', record=0)
spikemon = SpikeMonitor(G)

run(50*ms)

plot(statemon.t/ms, statemon.v[0])
for t in spikemon.t:
    axvline(t/ms, ls='--', c='C1', lw=3)
xlabel('Time (ms)')
ylabel('v');

Error Trace:

INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
running brian code generation ...
building genn executable ...
---------------------------------------------------------------------------
PermissionError                           Traceback (most recent call last)
<ipython-input-1-4cd8243ff4d2> in <module>
     27 spikemon = SpikeMonitor(G)
     28 
---> 29 run(50*ms)
     30 
     31 plot(statemon.t/ms, statemon.v[0])

~\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py in new_f(*args, **kwds)
   2373                                                      get_dimensions(newkeyset[k]))
   2374 
-> 2375             result = f(*args, **kwds)
   2376             if 'result' in au:
   2377                 if au['result'] == bool:

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(duration, report, report_period, namespace, profile, level)
    369     '''
    370     return magic_network.run(duration, report=report, report_period=report_period,
--> 371                              namespace=namespace, profile=profile, level=2+level)
    372 run.__module__ = __name__
    373 

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(self, duration, report, report_period, namespace, profile, level)
    229         self._update_magic_objects(level=level+1)
    230         Network.run(self, duration, report=report, report_period=report_period,
--> 231                     namespace=namespace, profile=profile, level=level+1)
    232 
    233     def store(self, name='default', filename=None, level=0):

~\Anaconda3\lib\site-packages\brian2\core\base.py in device_override_decorated_function(*args, **kwds)
    272             curdev = get_device()
    273             if hasattr(curdev, name):
--> 274                 return getattr(curdev, name)(*args, **kwds)
    275             else:
    276                 return func(*args, **kwds)

~\Anaconda3\lib\site-packages\brian2genn\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1632                                             report_period=report_period,
   1633                                             namespace=namespace,
-> 1634                                             level=level + 1)
   1635         self.run_statement_used = True
   1636 

~\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1374                                    'device.build call to use multiple run '
   1375                                    'statements with this device.')
-> 1376             self.build(direct_call=False, **self.build_options)
   1377 
   1378     def network_store(self, net, *args, **kwds):

~\Anaconda3\lib\site-packages\brian2genn\device.py in build(self, directory, compile, run, use_GPU, debug, with_output, direct_call)
    780         if compile:
    781             try:
--> 782                 self.compile_source(debug, directory, use_GPU)
    783             except CalledProcessError as ex:
    784                 raise RuntimeError(('Project compilation failed (Command {cmd} '

~\Anaconda3\lib\site-packages\brian2genn\device.py in compile_source(self, debug, directory, use_GPU)
    992                     cmd += ' -c'
    993                 cmd += ' && nmake /f WINmakefile clean && nmake /f WINmakefile'
--> 994                 check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
    995             else:
    996                 buildmodel_cmd = os.path.join(genn_path, 'lib', 'bin', 'genn-buildmodel.sh')

~\Anaconda3\lib\subprocess.py in check_call(*popenargs, **kwargs)
    284     check_call(["ls", "-l"])
    285     """
--> 286     retcode = call(*popenargs, **kwargs)
    287     if retcode:
    288         cmd = kwargs.get("args")

~\Anaconda3\lib\subprocess.py in call(timeout, *popenargs, **kwargs)
    265     retcode = call(["ls", "-l"])
    266     """
--> 267     with Popen(*popenargs, **kwargs) as p:
    268         try:
    269             return p.wait(timeout=timeout)

~\Anaconda3\lib\subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
    707                                 c2pread, c2pwrite,
    708                                 errread, errwrite,
--> 709                                 restore_signals, start_new_session)
    710         except:
    711             # Cleanup if the child failed starting.

~\Anaconda3\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
    995                                          env,
    996                                          os.fspath(cwd) if cwd is not None else None,
--> 997                                          startupinfo)
    998             finally:
    999                 # Child is launched. Close the parent's copy of those pipe

PermissionError: [WinError 5] Access is denied

Thanks.

Ajit

[ajitlimaye]

Hi Marcel & Thomas:

As an experiment, I tried running the following abbreviated script (to eliminate any issues with plotting):

import os

# For now, we set up environment variables locally so I can control them - eventually, move these to
# Windows environment variables.
#
os.environ['GENN_PATH'] = 'c:\\genn'
os.environ['PATH'] = os.environ['PATH'] + ';' + 'c:\\genn\\lib\\bin'
os.environ['CUDA_PATH'] = 'C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v9.2'

from brian2 import *
import brian2genn
set_device('genn')

# Define the path to vcvarsall.bat
#
prefs.codegen.cpp.msvc_vars_location = 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2017\\Community\\VC\\Auxiliary\\Build'
start_scope()

tau = 10*ms
eqs = '''
dv/dt = (1-v)/tau : 1 (unless refractory)
'''

G = NeuronGroup(1, eqs, threshold='v>0.8', reset='v = 0', refractory=5*ms, method='exact')

statemon = StateMonitor(G, 'v', record=0)
spikemon = SpikeMonitor(G)

run(50*ms)

This gives the same errors as shown earlier in this thread. Then I tried the same script directly in a shell (i.e. without using JupyterLab). This gives ADDITIONAL information as shown below. What is particularly interesting is the bit which says the "Brian 2 encountered an unexpected error . . ." - this does not appear when running in Jupyter.

The full error trace is shown below, and I have also attached the file brian_debug_4088owuf.log that the message asks the user to include in the report.

running brian code generation ...
building genn executable ...
ERROR      Brian 2 encountered an unexpected error. If you think this is bug in Brian 2, please report this issue either to the mailing list at <http://groups.google.com/group/brian-development/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: C:\Users\Ajit\AppData\Local\Temp\brian_debug_4088owuf.log  You can also include a copy of the redirected std stream outputs, available at C:\Users\Ajit\AppData\Local\Temp\brian_stdout_ur9jnzxp.log and C:\Users\Ajit\AppData\Local\Temp\brian_stderr_e571c15w.log Thanks! [brian2]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py", line 2375, in new_f
    result = f(*args, **kwds)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\core\magic.py", line 371, in run
    namespace=namespace, profile=profile, level=2+level)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\core\magic.py", line 231, in run
    namespace=namespace, profile=profile, level=level+1)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\core\base.py", line 274, in device_override_decorated_function
    return getattr(curdev, name)(*args, **kwds)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2genn\device.py", line 1634, in network_run
    level=level + 1)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py", line 1376, in network_run
    self.build(direct_call=False, **self.build_options)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2genn\device.py", line 782, in build
    self.compile_source(debug, directory, use_GPU)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2genn\device.py", line 994, in compile_source
    check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 286, in check_call
    retcode = call(*popenargs, **kwargs)
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 267, in call
    with Popen(*popenargs, **kwargs) as p:
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 997, in _execute_child
    startupinfo)
PermissionError: [WinError 5] Access is denied

brian_debug_4088owuf.log

I didn't attach the other file specified in the message (brian_stdout_ur9jnzxp.log) because it is empty. I have run out of things to try: any guidance or suggestions from the experts would be greatly appreciated.

Thanks!

[tnowotny]

Can you post C:\Users\Ajit\AppData\Local\Temp\brian_stderr_e571c15w.log or is it empty as well? (also, please bear with us - Marcel is still on vacation).

[ajitlimaye]

I know that supporting Brian2 is a volunteer effort, and I thank you, Marcel and the brian-team for helping the user community!

While experimenting with various versions of Visual Studio, I appear to have broken Cython (I think I corrupted my PATH variable). Even after "repairing" the Visual Studio 2017 installation, and re-installing Anaconda & Brian2, manually clearing the cache ("brian2.clear_cache('cython'), when I run brian2.test(), I get the following error. Any suggestions on how I can fix this (after I fix this, I'll look for the file you asked for to see if it is empty)?

So far, I've re-installed Visual Studio 2017 and Anaconda (after first uninstalling them), but that has not resolved this error. I also ran "repair" on Visual Studio 2017, but that didn't help either.

>>> brian2.test()
Running tests in C:\Users\Ajit\Anaconda3\lib\site-packages\brian2 for targets numpy, cython (excluding long tests)
Testing codegen-independent code
Resetting to default preferences

Running tests that do not use code generation
.................S.................S........WARNING    Integrating equations with GSL is still considered experimental [brian2.stateupdaters.GSL]
.........WARNING    C:\Users\Ajit\Anaconda3\lib\site-packages\Cython\Compiler\Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: C:\Users\Ajit\.cython\brian_extensions\_cython_magic_758f051e3ba79ebc10a9676b2e2ebdd7.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
 [py.warnings]--- Logging error ---
b'"\x00R\x00u\x00n\x00n\x00i\x00n\x00g\x00 \x00m\x00y\x00 \x00.\x00b\x00a\x00s\x00h\x00r\x00c\x00 \x00f\x00o\x00r\x00 \x00W\x00i\x00n\x00d\x00o\x00w\x00s\x00 \x00(\x00e\x00:\x00\\\x00R\x00e\x00s\x00e\x00a\x00r\x00c\x00h\x00\\\x00b\x00a\x00s\x00h\x00r\x00c\x00_\x00w\x00i\x00n\x00.\x00b\x00a\x00t\x00)\x00,\x00 \x00c\x00u\x00r\x00r\x00e\x00n\x00t\x00l\x00y\x00 \x00e\x00m\x00p\x00t\x00y\x00 \x00e\x00x\x00c\x00e\x00p\x00t\x00 \x00f\x00o\x00r\x00 \x00t\x00h\x00i\x00s\x00 \x00m\x00e\x00s\x00s\x00a\x00g\x00e\x00"\x00\r\x00\n\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00\r\x00\n\x00*\x00*\x00 \x00V\x00i\x00s\x00u\x00a\x00l\x00 \x00S\x00t\x00u\x00d\x00i\x00o\x00 \x002\x000\x001\x007\x00 \x00D\x00e\x00v\x00e\x00l\x00o\x00p\x00e\x00r\x00 \x00C\x00o\x00m\x00m\x00a\x00n\x00d\x00 \x00P\x00r\x00o\x00m\x00p\x00t\x00 \x00v\x001\x005\x00.\x009\x00.\x001\x001\x00\r\x00\n\x00*\x00*\x00 \x00C\x00o\x00p\x00y\x00r\x00i\x00g\x00h\x00t\x00 \x00(\x00c\x00)\x00 \x002\x000\x001\x007\x00 \x00M\x00i\x00c\x00r\x00o\x00s\x00o\x00f\x00t\x00 \x00C\x00o\x00r\x00p\x00o\x00r\x00a\x00t\x00i\x00o\x00n\x00\r\x00\n\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00*\x00\r\x00\n\x00T\x00h\x00e\x00 \x00s\x00y\x00n\x00t\x00a\x00x\x00 \x00o\x00f\x00 \x00t\x00h\x00e\x00 \x00c\x00o\x00m\x00m\x00a\x00n\x00d\x00 \x00i\x00s\x00 \x00i\x00n\x00c\x00o\x00r\x00r\x00e\x00c\x00t\x00.\x00\r\x00\n\x00'
WARNING    Cannot use Cython, a test compilation failed: [WinError 6] The handle is invalid (OSError) [brian2.codegen.runtime.cython_rt.cython_rt.failed_compile_test]

[ajitlimaye]

I finally got my machine back to where it is passing the Brian2 self-test. So I went to the brian2genn page here (https://brian2genn.readthedocs.io/en/latest/introduction/) for the instructions. But the link to "GeNN Installation Instructions" is gone - did you move it? I need to re-install genn so I can send you the other file that you requested.

[ajitlimaye]

I closed the issue in error (clicked on "Close and comment" rather than "Comment".

[tnowotny]

Installation instructions are in the README: https://github.com/genn-team/genn/blob/master/README.md

[ajitlimaye]

OK. I installed genn (4.0.0-RC1), and then tried the following test (in a JupyterLab window):

from brian2 import *
import brian2genn
set_device('genn')
prefs.devices.genn.path = 'C:\genn-4.0.0-RC1'
prefs.codegen.cpp.msvc_vars_location = 'C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build'
start_scope()

tau = 10*ms
eqs = '''
dv/dt = (1-v)/tau : 1 (unless refractory)
'''

G = NeuronGroup(1, eqs, threshold='v>0.8', reset='v = 0', refractory=5*ms, method='exact')

statemon = StateMonitor(G, 'v', record=0)
spikemon = SpikeMonitor(G)

run(50*ms)

plot(statemon.t/ms, statemon.v[0])
for t in spikemon.t:
    axvline(t/ms, ls='--', c='C1', lw=3)
xlabel('Time (ms)')
ylabel('v');

This yields the following messages:

INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
running brian code generation ...
building genn executable ...
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-1-aabf2b5d13d8> in <module>
     16 spikemon = SpikeMonitor(G)
     17 
---> 18 run(50*ms)
     19 
     20 plot(statemon.t/ms, statemon.v[0])

~\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py in new_f(*args, **kwds)
   2373                                                      get_dimensions(newkeyset[k]))
   2374 
-> 2375             result = f(*args, **kwds)
   2376             if 'result' in au:
   2377                 if au['result'] == bool:

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(duration, report, report_period, namespace, profile, level)
    369     '''
    370     return magic_network.run(duration, report=report, report_period=report_period,
--> 371                              namespace=namespace, profile=profile, level=2+level)
    372 run.__module__ = __name__
    373 

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(self, duration, report, report_period, namespace, profile, level)
    229         self._update_magic_objects(level=level+1)
    230         Network.run(self, duration, report=report, report_period=report_period,
--> 231                     namespace=namespace, profile=profile, level=level+1)
    232 
    233     def store(self, name='default', filename=None, level=0):

~\Anaconda3\lib\site-packages\brian2\core\base.py in device_override_decorated_function(*args, **kwds)
    272             curdev = get_device()
    273             if hasattr(curdev, name):
--> 274                 return getattr(curdev, name)(*args, **kwds)
    275             else:
    276                 return func(*args, **kwds)

~\Anaconda3\lib\site-packages\brian2genn\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1632                                             report_period=report_period,
   1633                                             namespace=namespace,
-> 1634                                             level=level + 1)
   1635         self.run_statement_used = True
   1636 

~\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1374                                    'device.build call to use multiple run '
   1375                                    'statements with this device.')
-> 1376             self.build(direct_call=False, **self.build_options)
   1377 
   1378     def network_store(self, net, *args, **kwds):

~\Anaconda3\lib\site-packages\brian2genn\device.py in build(self, directory, compile, run, use_GPU, debug, with_output, direct_call)
    780         if compile:
    781             try:
--> 782                 self.compile_source(debug, directory, use_GPU)
    783             except CalledProcessError as ex:
    784                 raise RuntimeError(('Project compilation failed (Command {cmd} '

~\Anaconda3\lib\site-packages\brian2genn\device.py in compile_source(self, debug, directory, use_GPU)
    992                     cmd += ' -c'
    993                 cmd += ' && nmake /f WINmakefile clean && nmake /f WINmakefile'
--> 994                 check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
    995             else:
    996                 buildmodel_cmd = os.path.join(genn_path, 'lib', 'bin', 'genn-buildmodel.sh')

~\Anaconda3\lib\subprocess.py in check_call(*popenargs, **kwargs)
    284     check_call(["ls", "-l"])
    285     """
--> 286     retcode = call(*popenargs, **kwargs)
    287     if retcode:
    288         cmd = kwargs.get("args")

~\Anaconda3\lib\subprocess.py in call(timeout, *popenargs, **kwargs)
    265     retcode = call(["ls", "-l"])
    266     """
--> 267     with Popen(*popenargs, **kwargs) as p:
    268         try:
    269             return p.wait(timeout=timeout)

~\Anaconda3\lib\subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
    707                                 c2pread, c2pwrite,
    708                                 errread, errwrite,
--> 709                                 restore_signals, start_new_session)
    710         except:
    711             # Cleanup if the child failed starting.

~\Anaconda3\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
    995                                          env,
    996                                          os.fspath(cwd) if cwd is not None else None,
--> 997                                          startupinfo)
    998             finally:
    999                 # Child is launched. Close the parent's copy of those pipe

FileNotFoundError: [WinError 2] The system cannot find the file specified

[tnowotny]

Ouch ... I probably should have warned earlier, but GeNN 4 is not yet supported by brian2genn (it's only a release candidate as of yet). Please use the last stable release from GeNN (3.3.0).

Then, the errors you copied only tell me that something went wrong during the "buildmodel", the "make" or the "execution" stage of brian2genn. In order to say something sensible I would have to see stderr output produced during those stages.

But in the meantime, can you run your test script outside JupyterLab (e.g. from a powershell) and see whether you can locate a newly created sub-directory "GeNNworkspace"? It should contain the relevant C++ files for GeNN. If you find this, we can try to debug your problem on the GeNN level.

[ajitlimaye]

Sorry about that . . . I downloaded GeNN 3.3.0, and ran my test script in a shell window. This yielded the following:

(base) E:\Research>python
Python 3.6.7 (default, Feb 28 2019, 07:28:18) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> os.environ['CUDA_PATH'] = 'C:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v10.1'
>>> from brian2 import *
>>> import brian2genn
>>> set_device('genn')
INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
>>> prefs.devices.genn.path = 'C:\\genn\\genn-3.3.0'
>>> prefs.codegen.cpp.msvc_vars_location = 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2017\\Community\\VC\\Auxiliary\\Build'
>>> start_scope()
>>>
>>> tau = 10*ms
>>> eqs = '''
... dv/dt = (1-v)/tau : 1 (unless refractory)
... '''
>>>
>>> G = NeuronGroup(1, eqs, threshold='v>0.8', reset='v = 0', refractory=5*ms, method='exact')
>>>
>>> statemon = StateMonitor(G, 'v', record=0)
>>> spikemon = SpikeMonitor(G)
>>>
>>> run(50*ms)
running brian code generation ...
building genn executable ...
ERROR      Brian 2 encountered an unexpected error. If you think this is bug in Brian 2, please report this issue either to the mailing list at <http://groups.google.com/group/brian-development/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: C:\Users\Ajit\AppData\Local\Temp\brian_debug_jut9f7p9.log  You can also include a copy of the redirected std stream outputs, available at C:\Users\Ajit\AppData\Local\Temp\brian_stdout_9wshfu39.log and C:\Users\Ajit\AppData\Local\Temp\brian_stderr__to655kx.log Thanks! [brian2]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py", line 2375, in new_f
    result = f(*args, **kwds)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\core\magic.py", line 371, in run
    namespace=namespace, profile=profile, level=2+level)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\core\magic.py", line 231, in run
    namespace=namespace, profile=profile, level=level+1)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\core\base.py", line 274, in device_override_decorated_function
    return getattr(curdev, name)(*args, **kwds)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2genn\device.py", line 1634, in network_run
    level=level + 1)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py", line 1376, in network_run
    self.build(direct_call=False, **self.build_options)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2genn\device.py", line 782, in build
    self.compile_source(debug, directory, use_GPU)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2genn\device.py", line 994, in compile_source
    check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 286, in check_call
    retcode = call(*popenargs, **kwargs)
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 267, in call
    with Popen(*popenargs, **kwargs) as p:
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 997, in _execute_child
    startupinfo)
PermissionError: [WinError 5] Access is denied
>>>

The directory GeNNworkspace does get created, and a tarball (or rather zipball) of it is attached. GeNNworkspace_ZIP.zip

[tnowotny]

Ok - so it seems "buildmodel" already fails. Can you please use a shell & go to the GeNNworkspace directory and run "c:\genn\lib\bin\genn-buildmodel.bat magicnetwork_model.cpp" and please post the error messages received.

[ajitlimaye]

The messages were as follows:

(base) E:\Research\GeNNworkspace>set GENN_PATH='c:\genn\genn-3.3.0'

(base) E:\Research\GeNNworkspace>c:\genn\genn-3.3.0\lib\bin\genn-buildmodel.bat magicnetwork_model.cpp
'msbuild' is not recognized as an internal or external command,
operable program or batch file.
'".\generateALL.exe"' is not recognized as an internal or external command,
operable program or batch file.
model build complete

(base) E:\Research\GeNNworkspace>

[tnowotny]

hum ... I think we are now running into separate problems with the debugging approach. Can you execute the appropriate vcvarsall.bat before trying c:\genn\lib\bin\genn-buildmodel.bat magicnetwork_model.cpp? Or have you done that already?

[ajitlimaye]

I cleaned up my Visual Studio installation so only Visual Studio 2017 is installed. I do have both CUDA 10.1 and 9.2 installed: CUDA_PATH points to C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1. With that, here is the trace:

(base) E:\Research>set GENN_PATH='c:\genn\genn-3.3.0'

(base) E:\Research>"C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat" x86_amd64
**********************************************************************
** Visual Studio 2017 Developer Command Prompt v15.9.11
** Copyright (c) 2017 Microsoft Corporation
**********************************************************************
[vcvarsall.bat] Environment initialized for: 'x86_x64'

(base) E:\Research>cd GeNNworkspace

(base) E:\Research\GeNNworkspace>dir
 Volume in drive E has no label.
 Volume Serial Number is 440E-415C

 Directory of E:\Research\GeNNworkspace

05/08/2019  02:21 PM    <DIR>          .
05/08/2019  02:21 PM    <DIR>          ..
05/08/2019  02:21 PM    <DIR>          b2glib
05/08/2019  02:21 PM    <DIR>          brianlib
05/08/2019  02:21 PM    <DIR>          code_objects
05/08/2019  02:21 PM             3,792 engine.cpp
05/08/2019  02:21 PM             1,033 engine.h
05/08/2019  02:21 PM             5,399 magicnetwork_model.cpp
05/08/2019  02:21 PM             4,166 main.cpp
05/08/2019  02:21 PM               904 main.h
05/08/2019  02:21 PM                 0 network.cpp
05/08/2019  02:21 PM               193 network.h
05/08/2019  02:21 PM            14,099 objects.cpp
05/08/2019  02:21 PM             2,399 objects.h
05/08/2019  02:21 PM    <DIR>          results
05/08/2019  02:21 PM    <DIR>          static_arrays
05/08/2019  02:21 PM                 0 synapses_classes.cpp
05/08/2019  02:21 PM             2,084 synapses_classes.h
05/08/2019  02:21 PM               428 WINmakefile
              12 File(s)         34,497 bytes
               7 Dir(s)  8,910,438,449,152 bytes free

(base) E:\Research\GeNNworkspace>c:\genn\genn-3.3.0\lib\bin\genn-buildmodel.bat magicnetwork_model.cpp
Microsoft (R) Build Engine version 15.9.21+g9802d43bc3 for .NET Framework
Copyright (C) Microsoft Corporation. All rights reserved.

MSBUILD : error MSB1009: Project file does not exist.
Switch: 'c:\genn\genn-3.3.0'\lib\generate.vcxproj
'".\generateALL.exe"' is not recognized as an internal or external command,
operable program or batch file.
model build complete

(base) E:\Research\GeNNworkspace>

[tnowotny]

it seems to suggest that generate.vcxproj cannot be found in c:\genn\genn-3.3.0\lib\. Is it not there? Are the quotation marks around c:\genn\genn-3.3.0 causing trouble?

[ajitlimaye]

It is there. However, the quotation marks around c:\genn\genn-3.3.0 were causing trouble: when I removed them, I got the far more satisfactory trace below:

(base) E:\Research>"C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat" x86_amd64
**********************************************************************
** Visual Studio 2017 Developer Command Prompt v15.9.11
** Copyright (c) 2017 Microsoft Corporation
**********************************************************************
[vcvarsall.bat] Environment initialized for: 'x86_x64'

(base) E:\Research>set GENN_PATH=c:\genn\genn-3.3.0

(base) E:\Research>echo %GENN_PATH%
c:\genn\genn-3.3.0

(base) E:\Research>cd GeNNworkspace

(base) E:\Research\GeNNworkspace>c:\genn\genn-3.3.0\lib\bin\genn-buildmodel.bat magicnetwork_model.cpp
Microsoft (R) Build Engine version 15.9.21+g9802d43bc3 for .NET Framework
Copyright (C) Microsoft Corporation. All rights reserved.

Build started 5/9/2019 9:00:03 AM.
Project "c:\genn\genn-3.3.0\lib\generate.vcxproj" on node 1 (default targets).
Project "c:\genn\genn-3.3.0\lib\generate.vcxproj" (1) is building "c:\genn\genn-3.3.0\lib\lib_genn.vcxproj" (2) on node
 1 (default targets).
PrepareForBuild:
  Creating directory "obj\x64\Release\".
  Creating directory "lib\".
  Creating directory "obj\x64\Release\lib_genn.tlog\".
InitializeBuildStatus:
  Creating "obj\x64\Release\lib_genn.tlog\unsuccessfulbuild" because "AlwaysCreate" was specified.
ClCompile:
  C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\CL.exe /c /Ii
  nclude /I"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\include" /Zi /nologo /W1 /WX- /diagnostics:classic
   /O2 /Gm- /EHsc /MT /GS /fp:precise /Zc:wchar_t /Zc:forScope /Zc:inline /Fo"obj\x64\Release\\" /Fd"obj\x64\Release\li
  b_genn.pdb" /Gd /TP /FC /errorReport:queue src\binomial.cc src\global.cc src\modelSpec.cc src\neuronModels.cc src\syn
  apseModels.cc src\postSynapseModels.cc src\utils.cc src\codeStream.cc src\codeGenUtils.cc src\sparseUtils.cc src\hr_t
  ime.cc src\currentSourceModels.cc src\newNeuronModels.cc src\newWeightUpdateModels.cc src\newPostsynapticModels.cc sr
  c\initSparseConnectivitySnippet.cc src\initVarSnippet.cc src\currentSource.cc src\neuronGroup.cc src\synapseGroup.cc
  src\standardSubstitutions.cc src\standardGeneratedSections.cc
  binomial.cc
  global.cc
  modelSpec.cc
  neuronModels.cc
  synapseModels.cc
  postSynapseModels.cc
  utils.cc
  codeStream.cc
  codeGenUtils.cc
  sparseUtils.cc
  hr_time.cc
  currentSourceModels.cc
  newNeuronModels.cc
  newWeightUpdateModels.cc
  newPostsynapticModels.cc
  initSparseConnectivitySnippet.cc
  initVarSnippet.cc
  currentSource.cc
  neuronGroup.cc
  synapseGroup.cc
  Generating Code...
  Compiling...
  standardSubstitutions.cc
  standardGeneratedSections.cc
  Generating Code...
Lib:
  C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\Lib.exe /OUT:
  "lib\genn.lib" /NOLOGO /MACHINE:X64 obj\x64\Release\binomial.obj
  obj\x64\Release\global.obj
  obj\x64\Release\modelSpec.obj
  obj\x64\Release\neuronModels.obj
  obj\x64\Release\synapseModels.obj
  obj\x64\Release\postSynapseModels.obj
  obj\x64\Release\utils.obj
  obj\x64\Release\codeStream.obj
  obj\x64\Release\codeGenUtils.obj
  obj\x64\Release\sparseUtils.obj
  obj\x64\Release\hr_time.obj
  obj\x64\Release\currentSourceModels.obj
  obj\x64\Release\newNeuronModels.obj
  obj\x64\Release\newWeightUpdateModels.obj
  obj\x64\Release\newPostsynapticModels.obj
  obj\x64\Release\initSparseConnectivitySnippet.obj
  obj\x64\Release\initVarSnippet.obj
  obj\x64\Release\currentSource.obj
  obj\x64\Release\neuronGroup.obj
  obj\x64\Release\synapseGroup.obj
  obj\x64\Release\standardSubstitutions.obj
  obj\x64\Release\standardGeneratedSections.obj
  lib_genn.vcxproj -> c:\genn\genn-3.3.0\lib\lib\genn.lib
FinalizeBuildStatus:
  Deleting file "obj\x64\Release\lib_genn.tlog\unsuccessfulbuild".
  Touching "obj\x64\Release\lib_genn.tlog\lib_genn.lastbuildstate".
Done Building Project "c:\genn\genn-3.3.0\lib\lib_genn.vcxproj" (default targets).

PrepareForBuild:
  Creating directory "E:\Research\GeNNworkspace\obj_generate\x64\Release\".
  Creating directory "E:\Research\GeNNworkspace\obj_generate\x64\Release\generate.tlog\".
InitializeBuildStatus:
  Creating "E:\Research\GeNNworkspace\obj_generate\x64\Release\generate.tlog\unsuccessfulbuild" because "AlwaysCreate"
  was specified.
ClCompile:
  C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\CL.exe /c /Ii
  nclude /I"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\include" /Zi /nologo /W1 /WX- /diagnostics:classic
   /O2 /D "MODEL=\"E:\Research\GeNNworkspace\magicnetwork_model.cpp\"" /D "NVCC=\"C:/Program Files/NVIDIA GPU Computing
   Toolkit/CUDA/v10.1/bin/nvcc.exe\"" /Gm- /EHsc /MT /GS /fp:precise /Zc:wchar_t /Zc:forScope /Zc:inline /Fo"E:\Researc
  h\GeNNworkspace\obj_generate\x64\Release\\" /Fd"E:\Research\GeNNworkspace\obj_generate\x64\Release\vc141.pdb" /Gd /TP
   /FC /errorReport:queue src\generateALL.cc src\generateCPU.cc src\generateInit.cc src\generateKernels.cc src\generate
  Runner.cc
  generateALL.cc
  generateCPU.cc
  generateInit.cc
  generateKernels.cc
  generateRunner.cc
  Generating Code...
Link:
  C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Tools\MSVC\14.16.27023\bin\HostX86\x64\link.exe /ERR
  ORREPORT:QUEUE /OUT:"E:\Research\GeNNworkspace\generateALL.exe" /NOLOGO kernel32.lib user32.lib gdi32.lib winspool.li
  b comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib odbc32.lib odbccp32.lib lib\genn.lib "C:\Prog
  ram Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\lib\x64\cudart.lib" "C:\Program Files\NVIDIA GPU Computing Toolkit\
  CUDA\v10.1\lib\x64\cuda.lib" /MANIFEST /MANIFESTUAC:"level='asInvoker' uiAccess='false'" /manifest:embed /DEBUG:FULL
  /PDB:"E:\Research\GeNNworkspace\generateALL.pdb" /TLBID:1 /DYNAMICBASE /NXCOMPAT /IMPLIB:"E:\Research\GeNNworkspace\g
  enerateALL.lib" /MACHINE:X64 E:\Research\GeNNworkspace\obj_generate\x64\Release\generateALL.obj
  E:\Research\GeNNworkspace\obj_generate\x64\Release\generateCPU.obj
  E:\Research\GeNNworkspace\obj_generate\x64\Release\generateInit.obj
  E:\Research\GeNNworkspace\obj_generate\x64\Release\generateKernels.obj
  E:\Research\GeNNworkspace\obj_generate\x64\Release\generateRunner.obj
  generate.vcxproj -> E:\Research\GeNNworkspace\generateALL.exe
FinalizeBuildStatus:
  Deleting file "E:\Research\GeNNworkspace\obj_generate\x64\Release\generate.tlog\unsuccessfulbuild".
  Touching "E:\Research\GeNNworkspace\obj_generate\x64\Release\generate.tlog\generate.lastbuildstate".
Done Building Project "c:\genn\genn-3.3.0\lib\generate.vcxproj" (default targets).

Build succeeded.
    0 Warning(s)
    0 Error(s)

Time Elapsed 00:00:47.46
call was .\generateALL.exe E:\Research\GeNNworkspace
optimizing block size...
Global memory required for core model: 0 MB.
17179869184 for device 0
dry-run compile for device 0
""C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1/bin/nvcc.exe" -cubin -x cu -arch sm_61 -O3 -I"%GENN_PATH%\lib\include" -o "E:\Research\GeNNworkspace\runner.cubin" "E:\Research\GeNNworkspace\magicnetwork_model_CODE\runner.cc""
runner.cc
Global memory required for core model: 0 MB.
17179869184 for device 0
dry-run compile for device 0
""C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1/bin/nvcc.exe" -cubin -x cu -arch sm_61 -O3 -I"%GENN_PATH%\lib\include" -o "E:\Research\GeNNworkspace\runner.cubin" "E:\Research\GeNNworkspace\magicnetwork_model_CODE\runner.cc""
runner.cc
Global memory required for core model: 0 MB.
17179869184 for device 1
dry-run compile for device 1
""C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1/bin/nvcc.exe" -cubin -x cu -arch sm_61 -O3 -I"%GENN_PATH%\lib\include" -o "E:\Research\GeNNworkspace\runner.cubin" "E:\Research\GeNNworkspace\magicnetwork_model_CODE\runner.cc""
runner.cc
Global memory required for core model: 0 MB.
17179869184 for device 1
dry-run compile for device 1
""C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1/bin/nvcc.exe" -cubin -x cu -arch sm_61 -O3 -I"%GENN_PATH%\lib\include" -o "E:\Research\GeNNworkspace\runner.cubin" "E:\Research\GeNNworkspace\magicnetwork_model_CODE\runner.cc""
runner.cc
Using device 0 (Quadro P5000), with up to 640 warps of summed kernel occupancy.
pre synapse reset block size: 0
synapse block size: 0
learn block size
```: 0
synapseDynamics block size: 0
neuron block size: 32
init block size:0
sparse init block size:0
Global memory required for core model: 0 MB.
17179869184 for device 0
model build complete

(base) E:\Research\GeNNworkspace>

Then I tried again in a JupyterLab window after setting the environment variable GENN_PATH to c:\genn\genn-3.3.0 and adding c:\genn\genn-3.3.0\lib\bin to the PATH. But something is still missing in that environment because I still get the FileNotFoundError.

What to do?

[tnowotny]

Ok ... this looks much more promising. But it's only half the way; let's still continue on the GeNN level and let's now try nmake /f WINmakefile clean && nmake /f WINmakefile in the GeNNworspace directory. What does that yield?

[tnowotny]

if successful, follow up with .\main.exe test 0.01 1

[ajitlimaye]

Curiouser and curiouser: that all seemed to work as expected. Trace below:

(base) E:\Research\GeNNworkspace>nmake /f WINmakefile clean && nmake /f WINmakefile

Microsoft (R) Program Maintenance Utility Version 14.16.27030.1
Copyright (C) Microsoft Corporation.  All rights reserved.

        del main.exe *.obj *.ilk *.pdb 2>nul
        cd magicnetwork_model_CODE && nmake clean /nologo
        del runner.obj 2>nul

Microsoft (R) Program Maintenance Utility Version 14.16.27030.1
Copyright (C) Microsoft Corporation.  All rights reserved.

        cl  /nologo /EHsc /Ox /w /arch:AVX2 /MP /c /Fomain.obj main.cpp /I %CD% /I brianlib/randomkit /I"C:\genn\genn-3.3.0\lib\include" /I"C:\genn\genn-3.3.0\userproject\include" /I"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\include"
main.cpp
        cl  /nologo /EHsc /Ox /w /arch:AVX2 /MP /c /Foobjects.obj objects.cpp /I %CD% /I brianlib/randomkit /I"C:\genn\genn-3.3.0\lib\include" /I"C:\genn\genn-3.3.0\userproject\include" /I"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\include"
objects.cpp
        cl  /nologo /EHsc /Ox /w /arch:AVX2 /MP /c /Focode_objects/statemonitor_codeobject.obj code_objects/statemonitor_codeobject.cpp /I %CD% /I brianlib/randomkit /I"C:\genn\genn-3.3.0\lib\include" /I"C:\genn\genn-3.3.0\userproject\include" /I"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\include"
statemonitor_codeobject.cpp
        cl  /nologo /EHsc /Ox /w /arch:AVX2 /MP /c /Focode_objects/spikemonitor_codeobject.obj code_objects/spikemonitor_codeobject.cpp /I %CD% /I brianlib/randomkit /I"C:\genn\genn-3.3.0\lib\include" /I"C:\genn\genn-3.3.0\userproject\include" /I"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\include"
spikemonitor_codeobject.cpp
        cl  /nologo /EHsc /Ox /w /arch:AVX2 /MP /c /Fobrianlib/randomkit/randomkit.obj brianlib/randomkit/randomkit.cc /I %CD% /I brianlib/randomkit /I"C:\genn\genn-3.3.0\lib\include" /I"C:\genn\genn-3.3.0\userproject\include" /I"C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\include"
randomkit.cc
        cd magicnetwork_model_CODE && nmake /nologo
        "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v10.1/bin/nvcc.exe" -c -x cu -arch sm_61 -O3 -I"C:\genn\genn-3.3.0\lib\include" runner.cc
runner.cc
        cl  /nologo /EHsc /Ox /w /arch:AVX2 /MP /Femain.exe main.obj  objects.obj  code_objects/statemonitor_codeobject.obj  code_objects/spikemonitor_codeobject.obj  brianlib/randomkit/randomkit.obj magicnetwork_model_CODE\runner.obj advapi32.lib "C:\genn\genn-3.3.0\lib\lib\genn.lib" "C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\lib\x64\cudart.lib" "C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.1\lib\x64\cuda.lib"

(base) E:\Research\GeNNworkspace>.\main.exe test 0.01 1
# DT 0.000100
# totalTime 0.010000
# We are running with fixed time step 0.000100
0.01 done ...
everything finished.

(base) E:\Research\GeNNworkspace>

So now the issue is with running in JupyterLab!

[tnowotny]

It appears so. Maybe you can try an intermediate test where you run your Python script from a powershell (rather than from JupyterLab). Have you tried that?

[ajitlimaye]

I just did co, up to and including "run(50ms)" but leaving out the plotting bits. That yielded the following error trace (I've also attached [brian_debug_ibwoh3ej.log](https://github.com/brian-team/brian2genn/files/3163416/brian_debug_ibwoh3ej.log: the redirected std stream output files are empty):

(base) PS>python
Python 3.6.7 (default, Feb 28 2019, 07:28:18) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from brian2 import *
>>> import brian2genn
>>> set_device('genn')
INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
>>> prefs.codegen.cpp.msvc_vars_location = 'C:\\Program Files (x86)\\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build'
>>> start_scope()
>>>
>>> tau = 10*ms
>>> eqs = '''
... dv/dt = (1-v)/tau : 1 (unless refractory)
... '''
>>>
>>> G = NeuronGroup(1, eqs, threshold='v>0.8', reset='v = 0', refractory=5*ms, method='exact')
>>>
>>> statemon = StateMonitor(G, 'v', record=0)
>>> spikemon = SpikeMonitor(G)
>>>
>>> run(50*ms)
running brian code generation ...
building genn executable ...
ERROR      Brian 2 encountered an unexpected error. If you think this is bug in Brian 2, please report this issue either to the mailing list at <http://groups.google.com/group/brian-development/>, or to the issue tracker at <https://github.com/brian-team/brian2/issues>. Please include this file with debug information in your report: C:\Users\Ajit\AppData\Local\Temp\brian_debug_ibwoh3ej.log  You can also include a copy of the redirected std stream outputs, available at C:\Users\Ajit\AppData\Local\Temp\brian_stdout_iy3ubgrb.log and C:\Users\Ajit\AppData\Local\Temp\brian_stderr_07f1gj4d.log Thanks! [brian2]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py", line 2375, in new_f
    result = f(*args, **kwds)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\core\magic.py", line 371, in run
    namespace=namespace, profile=profile, level=2+level)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\core\magic.py", line 231, in run
    namespace=namespace, profile=profile, level=level+1)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\core\base.py", line 274, in device_override_decorated_function
    return getattr(curdev, name)(*args, **kwds)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2genn\device.py", line 1634, in network_run
    level=level + 1)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py", line 1376, in network_run
    self.build(direct_call=False, **self.build_options)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2genn\device.py", line 782, in build
    self.compile_source(debug, directory, use_GPU)
  File "C:\Users\Ajit\Anaconda3\lib\site-packages\brian2genn\device.py", line 994, in compile_source
    check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 286, in check_call
    retcode = call(*popenargs, **kwargs)
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 267, in call
    with Popen(*popenargs, **kwargs) as p:
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 709, in __init__
    restore_signals, start_new_session)
  File "C:\Users\Ajit\Anaconda3\lib\subprocess.py", line 997, in _execute_child
    startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
>>>

[ajitlimaye]

I performed a controlled experiment, in which I gave the following Python commands:

from brian2 import *
import brian2genn
set_device('genn')
prefs.codegen.cpp.msvc_vars_location = 'C:\\Program Files (x86)\\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat'
start_scope()

tau = 10*ms
eqs = '''
dv/dt = (1-v)/tau : 1 (unless refractory)
'''

G = NeuronGroup(1, eqs, threshold='v>0.8', reset='v = 0', refractory=5*ms, method='exact')

statemon = StateMonitor(G, 'v', record=0)
spikemon = SpikeMonitor(G)

run(50*ms)

. . . in each of the following environments:

• An Anaconda shell
• An Anaconda powershell
• In a JupyterLab window

In every case, I got the "FileNotFoundError" indicated earlier in this thread. However, in every case, a GeNNworkspace directory was created - the JupyterLab run just put that directory in a different place.

But if I "cd" into this resulting GeNNworkspacedirectory for any of the three alternatives described above, and give the following commands:

"C:\\Program Files (x86)\\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat" x86_amd64
genn-buildmodel magicnetwork_model.cpp
nmake /f WINmakefile clean && nmake /f WINmakefile
.\main.exe test 0.01 1

. . . everything runs properly with the following final output:

# DT 0.000100
# totalTime 0.010000
# We are running with fixed time step 0.000100
0.01 done ...
everything finished.

So it looks like the GeNNworkspace directory is being created properly, but something chokes after that step.

[tnowotny]

I am sorry, but it's impossible to tell what's going on from this ... can it be that the path settings that work in your manual tests are lost when the calls are issued from Python? ... @mstimberg , are you back? Any ideas? BTW: have you set the GENN_PATH and modifications to PATH permanently or only within the particular shell (SET or SETX?)

[ajitlimaye]

I think we got thrown off by my unforced errors with the Windows PATH. Once I rebuilt my machine and set up GENN_PATH, CUDA_PATH, adding %GENN_PATH%\lib\bin and the path to vcvarsall.bat in the system (rather than user) environment variables, we reached the crux of the problem.

It seems GeNN works in two steps: first it builds GeNNworkspace (and contents). Second, it uses that workspace to build the final solution.

I think the first step is solid - it works in all three environments to properly build GeNNworkspace, since I can manually finish the job successfully. So the issue seems to be the automation of the following:

"C:\\Program Files (x86)\\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat" x86_amd64
genn-buildmodel magicnetwork_model.cpp
nmake /f WINmakefile clean && nmake /f WINmakefile
.\main.exe test 0.01 1

[mstimberg]

Hi, I'm back :) I had a quick look at the discussion, and I don't see anything obvious for now. However, Brian2GeNN is hiding all output from GeNN by default which makes things much harder to debug. @swami74: could you replace set_device('genn') by set_device('genn', debug=True) in your minimal example? This should make it clearer where the error occurs.

[ajitlimaye]

Hi Marcel: I turned on debug as you suggested, and gave the following input:

from brian2 import *
import brian2genn
set_device('genn', debug=True)
prefs.codegen.cpp.msvc_vars_location = 'C:\\Program Files (x86)\\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat'
start_scope()

tau = 10*ms
eqs = '''
dv/dt = (1-v)/tau : 1 (unless refractory)
'''

G = NeuronGroup(1, eqs, threshold='v>0.8', reset='v = 0', refractory=5*ms, method='exact')

statemon = StateMonitor(G, 'v', record=0)
spikemon = SpikeMonitor(G)

run(50*ms)

This yielded the following trace:

INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
running brian code generation ...
building genn executable ...
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-1-fe1476121a2d> in <module>
     15 spikemon = SpikeMonitor(G)
     16 
---> 17 run(50*ms)

~\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py in new_f(*args, **kwds)
   2373                                                      get_dimensions(newkeyset[k]))
   2374 
-> 2375             result = f(*args, **kwds)
   2376             if 'result' in au:
   2377                 if au['result'] == bool:

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(duration, report, report_period, namespace, profile, level)
    369     '''
    370     return magic_network.run(duration, report=report, report_period=report_period,
--> 371                              namespace=namespace, profile=profile, level=2+level)
    372 run.__module__ = __name__
    373 

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(self, duration, report, report_period, namespace, profile, level)
    229         self._update_magic_objects(level=level+1)
    230         Network.run(self, duration, report=report, report_period=report_period,
--> 231                     namespace=namespace, profile=profile, level=level+1)
    232 
    233     def store(self, name='default', filename=None, level=0):

~\Anaconda3\lib\site-packages\brian2\core\base.py in device_override_decorated_function(*args, **kwds)
    272             curdev = get_device()
    273             if hasattr(curdev, name):
--> 274                 return getattr(curdev, name)(*args, **kwds)
    275             else:
    276                 return func(*args, **kwds)

~\Anaconda3\lib\site-packages\brian2genn\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1632                                             report_period=report_period,
   1633                                             namespace=namespace,
-> 1634                                             level=level + 1)
   1635         self.run_statement_used = True
   1636 

~\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1374                                    'device.build call to use multiple run '
   1375                                    'statements with this device.')
-> 1376             self.build(direct_call=False, **self.build_options)
   1377 
   1378     def network_store(self, net, *args, **kwds):

~\Anaconda3\lib\site-packages\brian2genn\device.py in build(self, directory, compile, run, use_GPU, debug, with_output, direct_call)
    780         if compile:
    781             try:
--> 782                 self.compile_source(debug, directory, use_GPU)
    783             except CalledProcessError as ex:
    784                 raise RuntimeError(('Project compilation failed (Command {cmd} '

~\Anaconda3\lib\site-packages\brian2genn\device.py in compile_source(self, debug, directory, use_GPU)
    992                     cmd += ' -c'
    993                 cmd += ' && nmake /f WINmakefile clean && nmake /f WINmakefile'
--> 994                 check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
    995             else:
    996                 buildmodel_cmd = os.path.join(genn_path, 'lib', 'bin', 'genn-buildmodel.sh')

~\Anaconda3\lib\subprocess.py in check_call(*popenargs, **kwargs)
    284     check_call(["ls", "-l"])
    285     """
--> 286     retcode = call(*popenargs, **kwargs)
    287     if retcode:
    288         cmd = kwargs.get("args")

~\Anaconda3\lib\subprocess.py in call(timeout, *popenargs, **kwargs)
    265     retcode = call(["ls", "-l"])
    266     """
--> 267     with Popen(*popenargs, **kwargs) as p:
    268         try:
    269             return p.wait(timeout=timeout)

~\Anaconda3\lib\subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
    707                                 c2pread, c2pwrite,
    708                                 errread, errwrite,
--> 709                                 restore_signals, start_new_session)
    710         except:
    711             # Cleanup if the child failed starting.

~\Anaconda3\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
    995                                          env,
    996                                          os.fspath(cwd) if cwd is not None else None,
--> 997                                          startupinfo)
    998             finally:
    999                 # Child is launched. Close the parent's copy of those pipe

FileNotFoundError: [WinError 2] The system cannot find the file specified

[tnowotny]

... and what can you find in the stderr and stdout dumps?

[ajitlimaye]

Sorry about that . . . debug file attached. brian_debug_situc4rw.log

[ajitlimaye]

PS: I re-ran the test and attached the debug file for that new run. The corresponding screen trace is as follows:

INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
running brian code generation ...
building genn executable ...
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-1-fe1476121a2d> in <module>
     15 spikemon = SpikeMonitor(G)
     16 
---> 17 run(50*ms)

~\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py in new_f(*args, **kwds)
   2373                                                      get_dimensions(newkeyset[k]))
   2374 
-> 2375             result = f(*args, **kwds)
   2376             if 'result' in au:
   2377                 if au['result'] == bool:

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(duration, report, report_period, namespace, profile, level)
    369     '''
    370     return magic_network.run(duration, report=report, report_period=report_period,
--> 371                              namespace=namespace, profile=profile, level=2+level)
    372 run.__module__ = __name__
    373 

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(self, duration, report, report_period, namespace, profile, level)
    229         self._update_magic_objects(level=level+1)
    230         Network.run(self, duration, report=report, report_period=report_period,
--> 231                     namespace=namespace, profile=profile, level=level+1)
    232 
    233     def store(self, name='default', filename=None, level=0):

~\Anaconda3\lib\site-packages\brian2\core\base.py in device_override_decorated_function(*args, **kwds)
    272             curdev = get_device()
    273             if hasattr(curdev, name):
--> 274                 return getattr(curdev, name)(*args, **kwds)
    275             else:
    276                 return func(*args, **kwds)

~\Anaconda3\lib\site-packages\brian2genn\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1632                                             report_period=report_period,
   1633                                             namespace=namespace,
-> 1634                                             level=level + 1)
   1635         self.run_statement_used = True
   1636 

~\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1374                                    'device.build call to use multiple run '
   1375                                    'statements with this device.')
-> 1376             self.build(direct_call=False, **self.build_options)
   1377 
   1378     def network_store(self, net, *args, **kwds):

~\Anaconda3\lib\site-packages\brian2genn\device.py in build(self, directory, compile, run, use_GPU, debug, with_output, direct_call)
    780         if compile:
    781             try:
--> 782                 self.compile_source(debug, directory, use_GPU)
    783             except CalledProcessError as ex:
    784                 raise RuntimeError(('Project compilation failed (Command {cmd} '

~\Anaconda3\lib\site-packages\brian2genn\device.py in compile_source(self, debug, directory, use_GPU)
    992                     cmd += ' -c'
    993                 cmd += ' && nmake /f WINmakefile clean && nmake /f WINmakefile'
--> 994                 check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
    995             else:
    996                 buildmodel_cmd = os.path.join(genn_path, 'lib', 'bin', 'genn-buildmodel.sh')

~\Anaconda3\lib\subprocess.py in check_call(*popenargs, **kwargs)
    284     check_call(["ls", "-l"])
    285     """
--> 286     retcode = call(*popenargs, **kwargs)
    287     if retcode:
    288         cmd = kwargs.get("args")

~\Anaconda3\lib\subprocess.py in call(timeout, *popenargs, **kwargs)
    265     retcode = call(["ls", "-l"])
    266     """
--> 267     with Popen(*popenargs, **kwargs) as p:
    268         try:
    269             return p.wait(timeout=timeout)

~\Anaconda3\lib\subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
    707                                 c2pread, c2pwrite,
    708                                 errread, errwrite,
--> 709                                 restore_signals, start_new_session)
    710         except:
    711             # Cleanup if the child failed starting.

~\Anaconda3\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
    995                                          env,
    996                                          os.fspath(cwd) if cwd is not None else None,
--> 997                                          startupinfo)
    998             finally:
    999                 # Child is launched. Close the parent's copy of those pipe

FileNotFoundError: [WinError 2] The system cannot find the file specified
​

[mstimberg]

Hmm, this is still quite mysterious to me... Given that the last output is "building genn executable ...", I think the process is failing within genn-buildmodel.bat. Could you change the @echo off at the top of that file (should be C:\genn\genn-3.3.0\lib\bin\genn-buildmodel.bat) to @echo on? This might give us more information on where it fails exactly.

[ajitlimaye]

Hi Marcel: I did that. The resulting brian_debug. . . file is attached, and the screen trace is as follows:

INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
running brian code generation ...
building genn executable ...
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-1-fe1476121a2d> in <module>
     15 spikemon = SpikeMonitor(G)
     16 
---> 17 run(50*ms)

~\Anaconda3\lib\site-packages\brian2\units\fundamentalunits.py in new_f(*args, **kwds)
   2373                                                      get_dimensions(newkeyset[k]))
   2374 
-> 2375             result = f(*args, **kwds)
   2376             if 'result' in au:
   2377                 if au['result'] == bool:

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(duration, report, report_period, namespace, profile, level)
    369     '''
    370     return magic_network.run(duration, report=report, report_period=report_period,
--> 371                              namespace=namespace, profile=profile, level=2+level)
    372 run.__module__ = __name__
    373 

~\Anaconda3\lib\site-packages\brian2\core\magic.py in run(self, duration, report, report_period, namespace, profile, level)
    229         self._update_magic_objects(level=level+1)
    230         Network.run(self, duration, report=report, report_period=report_period,
--> 231                     namespace=namespace, profile=profile, level=level+1)
    232 
    233     def store(self, name='default', filename=None, level=0):

~\Anaconda3\lib\site-packages\brian2\core\base.py in device_override_decorated_function(*args, **kwds)
    272             curdev = get_device()
    273             if hasattr(curdev, name):
--> 274                 return getattr(curdev, name)(*args, **kwds)
    275             else:
    276                 return func(*args, **kwds)

~\Anaconda3\lib\site-packages\brian2genn\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1632                                             report_period=report_period,
   1633                                             namespace=namespace,
-> 1634                                             level=level + 1)
   1635         self.run_statement_used = True
   1636 

~\Anaconda3\lib\site-packages\brian2\devices\cpp_standalone\device.py in network_run(self, net, duration, report, report_period, namespace, profile, level, **kwds)
   1374                                    'device.build call to use multiple run '
   1375                                    'statements with this device.')
-> 1376             self.build(direct_call=False, **self.build_options)
   1377 
   1378     def network_store(self, net, *args, **kwds):

~\Anaconda3\lib\site-packages\brian2genn\device.py in build(self, directory, compile, run, use_GPU, debug, with_output, direct_call)
    780         if compile:
    781             try:
--> 782                 self.compile_source(debug, directory, use_GPU)
    783             except CalledProcessError as ex:
    784                 raise RuntimeError(('Project compilation failed (Command {cmd} '

~\Anaconda3\lib\site-packages\brian2genn\device.py in compile_source(self, debug, directory, use_GPU)
    992                     cmd += ' -c'
    993                 cmd += ' && nmake /f WINmakefile clean && nmake /f WINmakefile'
--> 994                 check_call(cmd.format(genn_path=genn_path), cwd=directory, env=env)
    995             else:
    996                 buildmodel_cmd = os.path.join(genn_path, 'lib', 'bin', 'genn-buildmodel.sh')

~\Anaconda3\lib\subprocess.py in check_call(*popenargs, **kwargs)
    284     check_call(["ls", "-l"])
    285     """
--> 286     retcode = call(*popenargs, **kwargs)
    287     if retcode:
    288         cmd = kwargs.get("args")

~\Anaconda3\lib\subprocess.py in call(timeout, *popenargs, **kwargs)
    265     retcode = call(["ls", "-l"])
    266     """
--> 267     with Popen(*popenargs, **kwargs) as p:
    268         try:
    269             return p.wait(timeout=timeout)

~\Anaconda3\lib\subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, encoding, errors)
    707                                 c2pread, c2pwrite,
    708                                 errread, errwrite,
--> 709                                 restore_signals, start_new_session)
    710         except:
    711             # Cleanup if the child failed starting.

~\Anaconda3\lib\subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, unused_restore_signals, unused_start_new_session)
    995                                          env,
    996                                          os.fspath(cwd) if cwd is not None else None,
--> 997                                          startupinfo)
    998             finally:
    999                 # Child is launched. Close the parent's copy of those pipe

FileNotFoundError: [WinError 2] The system cannot find the file specified

brian_debug_eck9lwt0.log

[mstimberg]

Actually I just realized that the "building genn executable" is coming from Brian2GeNN and not from GeNN, you are therefore not getting any output at all, so it could be already the vcvarsall.bat call that fails.

[mstimberg]

Uh, is this your actual definition of the preference?

prefs.codegen.cpp.msvc_vars_location = 'C:\\Program Files (x86)\\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat'

The latter backslashes are not correctly escaped:

>>> print('C:\\Program Files (x86)\\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvarsall.bat')
C:\Program Files (x86)\Microsoft Visual Studio�7\Community\VC\Auxiliary\Buildcvarsall.bat

[ajitlimaye]

Occam's razor strikes again. In any case, I fixed the preference definition, after which I no longer get the error messages. So I added plotting code and ran the following experiment:

from brian2 import *
import brian2genn
set_device('genn', debug=True)
prefs.codegen.cpp.msvc_vars_location = 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2017\\Community\\VC\\Auxiliary\\Build\\vcvarsall.bat'
start_scope()

tau = 10*ms
eqs = '''
dv/dt = (1-v)/tau : 1 (unless refractory)
'''

G = NeuronGroup(1, eqs, threshold='v>0.8', reset='v = 0', refractory=5*ms, method='exact')

statemon = StateMonitor(G, 'v', record=0)
spikemon = SpikeMonitor(G)

run(50*ms)

plot(statemon.t/ms, statemon.v[0])
for t in spikemon.t:
    axvline(t/ms, ls='--', c='C1', lw=3)
xlabel('Time (ms)')
ylabel('v');

Now I see the following output, but (even after 15 minutes) no plot:

INFO       The following preferences have been changed for Brian2GeNN, reset them manually if you use a different device later in the same script: codegen.loop_invariant_optimisations, core.network.default_schedule [brian2.devices.genn]
running brian code generation ...
building genn executable ...
executing genn binary on GPU ...

[tnowotny]

Uhm ... include show() at the end of your script?

[ajitlimaye]

Right then - I am now able to run my trivial examples end-to-end both with (+GeNN) and without (Brian2 only) a GPU engaged. Thank you Thomas and Marcel for your patience with this Brian2 neophyte.

[mstimberg]

Glad everything works now, and happy that there is no fix for Windows builds needed from our side :smile: