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NEURON Simulator
http://nrn.readthedocs.io
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How to build NEURON on windows? #319

Closed pramodk closed 1 year ago

pramodk commented 4 years ago

This issues is to document process to build Windows instructions.

Here are brief steps (WIP):

msys2.org
download x86_64 installer and follow instructions. i.e.
  run the installer
    tick the "run MSYS now" at end
  in the terminal ---
  pacman -Syu
  close msysw terminal and open any msys2 terminal again from start menu.
  pacman -Su #until no further installations
  pacman -S git
  pacman -S zip unzip

after installing from above
pacman -S --needed base-devel mingw-w64-x86_64-toolchain
(I chose default=all for the first group and '3' for the toolchain)

for complete mpi see mingw_notes
for more or less complete python
pacman -S mingw-w64-x86_64-cython
#note above failed at end. Succeeded with
#pacman -R mingw-w64-x86_64-cython
#pacman -S mingw-w64-x86_64-cython2
#and add to configure, CYTHON=cython2

#pacman -S mingw64/mingw-w64-x86_64-python3-scipy  #python 3.6.4
Note: the pacman installed version of python has a library naming
convention that is similar to linux versions and so is not compatible
with windows versions. i.e. python3.6m.dll instead of python36.dll .
For this reason it is best to download and install windows versions of
python from python.org. In my case I installed (into drive E:)
python27, python35, and python36 respectively from
python-2.7.14.amd64.msi
python-3.5.4-amd64.exe
python-3.6.4-amd64.exe
and the "howto" file assumes this. These do not have scipy, so for
testing rxd, I also have a version of anaconda installed.

Installed msmpisdk.msi and MsMpiSetup.exe in c:\ms-mpi (version 10.0)

version 10 Lib is already lib

Change Bin, Lib, Include to bin, lib, include

cp c:/Windows/System32/msmpi.dll c:/ms-mpi/lib/x64 cp c:/Windows/SysWoW64/msmpi.dll c:/ms-mpi/lib/x86 #optional

stdint.h now in version 10 so next not needed.

add #include in /c/ms-mpi/include/mpi.h

important. Wasted a day because I did not do this. the symptom is a

crash in libnrnmpi.dll

I don't know if this is needed anymore or not for version 10 as

libmsmpi.a does exist.

gendef msmpi.dll # creates msmpi.def

x86_64-w64-mingw32-dlltool -d msmpi.def -l libmsmpi.a -D msmpi.dll

dlltool -d msmpi.def -l libmsmpi.a -D msmpi.dll # creates libmsmpi.a

gendef can be built from mingw source via

git clone https://github.com/msys2-contrib/mingw-w64

cd mingw-w64/mingw-w64-tools/gendef

./configure --prefix=pwd

make # may have to get rid of the -Werror

cp gendef.exe /mingw64/bin



- https://github.com/neuronsimulator/nrn/blob/master/mingw_files/nrnmingwenv.sh
nrnhines commented 4 years ago

There are two installer messagebox commands that can be commented out to see if that helps

    MessageBox MB_OKCANCEL "${NEURON} already installed at $R1. Press OK to install again." IDOK ok

and

        MessageBox MB_OK "The installation path is not allowed to have spaces."

but for the latter you may also need to reduce the line skip from 3 to 2 in

        StrCmp $R0 "" +3 ; if no spaces then go on
pramodk commented 4 years ago

I started Windose Server 2019 on AWS to test the installer:

image

And I am able to run it in silent mode without any issue:

image

Also I went to AppVeyor for quickly testing installer on their windows CI and using following configuration:

install:
  - cmd: dir .
  - cmd: echo "Starting ==========>"
  - cmd: .\nrn8.0setup-AMD64.exe
  - cmd: echo "Finished ==========>"
  - cmd: dir C:\nrn

We see this log where installation finishes without any issue:

echo "Starting ==========>"
61"Starting ==========>"
62.\nrn8.0setup-AMD64.exe
63echo "Finished ==========>"
64"Finished ==========>"
65dir C:\nrn
66 Volume in drive C is Windows
67 Volume Serial Number is D4AB-4044
68
69 Directory of C:\nrn
70
7105/24/2020  12:24 PM    <DIR>          .
7205/24/2020  12:24 PM    <DIR>          ..
7305/24/2020  12:24 PM    <DIR>          bin
7405/24/2020  12:24 PM    <DIR>          demo
7505/24/2020  12:24 PM    <DIR>          include
7605/24/2020  12:24 PM    <DIR>          lib
7705/24/2020  12:24 PM    <DIR>          mingw
7805/23/2020  10:34 PM             6,010 notes.txt
7905/24/2020  12:24 PM    <DIR>          share
8005/23/2020  10:34 PM               124 test0.hoc
8105/23/2020  10:34 PM               594 test0.py
8205/24/2020  12:24 PM            44,174 uninstall.exe
83               4 File(s)         50,902 bytes
84               8 Dir(s)  43,851,468,800 bytes free
85echo "End ==========>"
86"End ==========>"
87Discovering tests...OK
88

So this issue is something very specific to Azure CI. Sometime later I will post the issue to Azure CI support. I will go ahead with finalising other parts of CI before revisiting this issue.

nrnhines commented 4 years ago

Nice that you got so far with the diagnosis. I wasted the morning looking into nsis logging but in my hands I could not get the nsislog plugin to work at all on my machine. I installed nsis-3.05-log.zip , a special build that enables logging support, also on my machine, but the first line in the log file is

CreateDirectory: "c:\nrn" created

which looks to be too late for any useful diagnosis.

pramodk commented 4 years ago

Also I went to AppVeyor for quickly testing installer on their windows CI and using following configuration. We see this log where installation finishes without any issue.

I was wrong in above analysis! I was using an installer without any MessageBox in .nsi file and that's why it was successful on AppVeyor CI. I used the same installer on Azure and it also worked. On the other hand, if I use original installer with MessageBox usage, it doesn't work on Azure as well as AppVeyor.

So, it seems like our installer is not truly Silent. I came across an example on nsis documentation : https://nsis.sourceforge.io/Examples/silent.nsi.

I believe we need to use those extra documented flags to make our installer Silent compatible.

I don’t know nsi script well. @nrnhines : Could you help with updating nsi script?

pramodk commented 4 years ago

Above issue is fixed in #562. Installer is now working fine in Silent mode! 🎉

Bringing back unanswered question from #562 :

In this test log I see that only Python3.8 test is failing with below error:

Traceback (most recent call last):
  File "C:\nrn\lib\python\neuron\__init__.py", line 124, in <module>
    import hoc
ModuleNotFoundError: No module named 'hoc'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\nrn\lib\python\neuron\__init__.py", line 128, in <module>
    import neuron.hoc
ImportError: DLL load failed while importing hoc: The specified module could not be found.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\nrn\lib\python\neuron\__init__.py", line 130, in <module>
    exec("import neuron.hoc%d%d as hoc" % (sys.version_info[0], sys.version_info[1]))
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'neuron.hoc38'
##[error]Cmd.exe exited with code '1'.

Python 2 and 3.5/6/7 working fine. You can see in the build log, all pythons are correctly initialised.

Any hint / suggestions? Here is the installer created from Azure CI that one can install locally to reproduce the issue : https://github.com/pramodk/nrn/releases/download/nightly/nrn8.0setup-AMD64.exe

nrnhines commented 4 years ago

This is a puzzle and occurs also when I install from a setup.exe built on my virtualbox guest. There are many possible user environments. On mine the default python when I start the bash terminal from the NEURON program group is

bash-4.4$ which python
/cygdrive/c/Users/hines/Anaconda3/python
bash-4.4$ echo $PYTHONHOME
C:/Users/hines/Anaconda3
bash-4.4$ echo $NRN_PYLIB
C:/Users/hines/Anaconda3/python36.dll
bash-4.4$

So my first step is

bash-4.4$ export PATH=/cygdrive/e/python38:$PATH
bash-4.4$ nrnpyenv.sh
# Ignoring existing PYTHONHOME=C:/Users/hines/Anaconda3.
...
# if launch nrniv, then likely need:
export PYTHONHOME="E:/python38"
export NRN_PYLIB="E:/python38/python38.dll"

so with copy/paste I have good success when launching nrniv

bash-4.4$ export PYTHONHOME="E:/python38"
bash-4.4$ export NRN_PYLIB="E:/python38/python38.dll"
bash-4.4$ nrniv -python
NEURON -- VERSION 8.0.dev-103-g9426d754 nrnmech_fix (9426d754) 2020-05-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2019
See http://neuron.yale.edu/neuron/credits

>>> import neuron
>>> quit()

Unfortunately, I get the same problem as you when I launch python

bash-4.4$ python
Python 3.8.0 (tags/v3.8.0:fa919fd, Oct 14 2019, 19:37:50) [MSC v.1916 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import neuron
Traceback (most recent call last):
  File "C:\nrn\lib\python\neuron\__init__.py", line 124, in <module>
    import hoc
ModuleNotFoundError: No module named 'hoc'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\nrn\lib\python\neuron\__init__.py", line 128, in <module>
    import neuron.hoc
ImportError: DLL load failed while importing hoc: The specified module could not be found.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\nrn\lib\python\neuron\__init__.py", line 130, in <module>
    exec("import neuron.hoc%d%d as hoc" % (sys.version_info[0], sys.version_info[1]))
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'neuron.hoc38'
>>>

Despite the existence of

bash-4.4$ ls c:/nrn/lib/python/neuron/hoc*
c:/nrn/lib/python/neuron/hoc.cp35-win_amd64.pyd  c:/nrn/lib/python/neuron/hoc.cp38-win_amd64.pyd
c:/nrn/lib/python/neuron/hoc.cp36-win_amd64.pyd  c:/nrn/lib/python/neuron/hoc.pyd
c:/nrn/lib/python/neuron/hoc.cp37-win_amd64.pyd

I will continue to look into this.

pramodk commented 4 years ago

@nrnhines : Instead of using exe that I provided, could you check if you see same issue if you build installer with Python 3.8.2 locally and install it?

It would be helpful to identify if this is an issue with my azure CI setup or appears with local setup as well.

nrnhines commented 4 years ago

That is what I did. And when I install on another vbox guest that has only 3.8.3 the problem remains. I noticed the following but have not thought about it sufficiently to know if it is relevant. https://docs.python.org/3/whatsnew/3.8.html

DLL dependencies for extension modules and DLLs loaded with ctypes on Windows are now resolved more securely. Only the system paths, the directory containing the DLL or PYD file, and directories added with add_dll_directory() are searched for load-time dependencies. Specifically, PATH and the current working directory are no longer used, and modifications to these will no longer have any effect on normal DLL resolution. If your application relies on these mechanisms, you should check for add_dll_directory() and if it exists, use it to add your DLLs directory while loading your library. Note that Windows 7 users will need to ensure that Windows Update KB2533623 has been installed (this is also verified by the installer). (Contributed by Steve Dower in bpo-36085.)

nrnhines commented 4 years ago

Here is a big hint relevant to the 'dll dependency' quote above. When I copy all c:/nrn/bin/*.dll into the neuron module, 'import neuron' works.

pramodk commented 4 years ago

Specifically, PATH and the current working directory are no longer used, and modifications to these will no longer have any effect on normal DLL resolution. If your application relies on these mechanisms, you should check for add_dll_directory() and if it exists,

Ah ok! that seems very relevant!

nrnhines commented 4 years ago

os.add_dll_directory fixes the issue. A pull request will be forthcoming shortly.

pramodk commented 4 years ago

great that fixes the issue!

@nrnhines : could you guide me how to test nrnivmodl and nrniv on Windows?

nrnhines commented 4 years ago

In a command prompt, you should be able to

C:\Users\hines>mpiexec -n 2 nrniv -mpi c:/nrn/test0.hoc
NEURON -- VERSION 8.0.dev-102-gc2265c65 dll-resolution (c2265c65) 2020-05-27
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2019
See http://neuron.yale.edu/neuron/credits

numprocs=2
I am 1 of 2
I am 0 of 2

The problem with running neuron.test() is that windows generates the error (@adamjhn ?)

C:\Users\hines>set PATH=e:\python38;%PATH%

C:\Users\hines>nrniv -python -c "import neuron ; neuron.test() ; quit()"
NEURON -- VERSION 8.0.dev-102-gc2265c65 dll-resolution (c2265c65) 2020-05-27
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2019
See http://neuron.yale.edu/neuron/credits

testBytesize (neuron.tests.test_vector.VectorTestCase)
Test that Vector.__array_interface__ returns the proper bytesize (of a double) ... ok
...
testExtendedSection (neuron.tests.test_neuron.NeuronTestCase) ... NEURON -- VERSION 8.0.dev-102-gc2265c65 dll-resolution (c2265c65) 2020-05-27
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2019
See http://neuron.yale.edu/neuron/credits

c:\nrn\bin\nrniv.exe: syntax error
 near line 1
 from multiprocessing.spawn import spawn_main; spawn_main(parent_pid=7460, pipe_handle=500)
                    ^
c:\nrn\bin\nrniv.exe: arg not valid statement: from multiprocessing.spawn import spawn_main; spawn_main(parent_pid=7460, pipe_handle=500)
 near line 0
 ^
0 c:\nrn\bin\nrniv.exe: can't open --multiprocessing-fork
nrnhines commented 4 years ago

A test of association with hoc files is possible in a command prompt with the following temp.bat file

del temp.txt
echo wopen("temp.txt") > .\temp.hoc
echo fprint("hello\n") >> .\temp.hoc
echo wopen() >> .\temp.hoc
echo quit() >> .\temp.hoc
start .\temp.hoc
timeout /T 10
cat temp.txt

I was worried about using start /wait instead of the timout since if there is a hoc failure the temp.hoc will hang.

pramodk commented 4 years ago

c:\nrn\bin\nrniv.exe: arg not valid statement: from multiprocessing.spawn import spawn_main; spawn_main(parent_pid=7460, pipe_handle=500) near line 0 ^ 0 c:\nrn\bin\nrniv.exe: can't open --multiprocessing-fork

No knowledge of windows but this looks related : https://blender.stackexchange.com/questions/8530/how-to-get-python-multiprocessing-module-working-on-windows

A test of association with hoc files is possible in a command prompt with the following temp.bat file

I have to understand what this test is doing :)

What about nrnivmodl? how we can test that compiling environment is correct and nrnivmodl is working fine?

nrnhines commented 4 years ago

The hoc association test needs a hoc file and that is created by the echo lines. The file is launched with start which runs neuron.exe (hoc extension is associated with that) which opens a bash terminal in a new window and runs nrniv. The quit() at the end of the hoc file is needed or nrniv would just wait for user input. The temp.hoc writes to a file temp.txt in order to produce something that persists after nrniv exits and the bash terminal window closes.

A test of mknrndll just needs a folder with a mod file and a py file that creates a section and inserts the mechanism to verify that the dll is working. e.g foo.mod

NEURON {
  SUFFIX foo
  RANGE a
}
PARAMETER { a }

foo.py

from neuron import h
s = h.Section()
s.insert('foo')
quit()

and test with

cd  folder/containing/mod/and/py/files
mknrndll
python foo.py
#check $?
nrnhines commented 4 years ago

Let's work around the multiprocessing bug on windows by avoiding running neuron.test() with nrniv and instead only check the python launch. eg. in a command prompt

C:\Users\hines>set PATH=e:\python38;%PATH%

C:\Users\hines>python -c "import neuron;neuron.test()"
testBytesize (neuron.tests.test_vector.VectorTestCase)
Test that Vector.__array_interface__ returns the proper bytesize (of a double) ... ok
testEndian (neuron.tests.test_vector.VectorTestCase)
...
Test section, segment, mechanism, rangevar iterators. ... ok
testRxDexistence (neuron.tests.test_neuron.NeuronTestCase) ... scipy not available
ok
testpsection (neuron.tests.test_neuron.NeuronTestCase) ... ok

----------------------------------------------------------------------
Ran 11 tests in 6.251s

OK

C:\Users\hines>
nrnhines commented 4 years ago

No knowledge of windows but this looks related : https://blender.stackexchange.com/questions/8530/how-to-get-python-multiprocessing-module-working-on-windows

I was not successful with

nrniv -python
import sys
sys.executable = 'e:\\python38\\python.exe'
import neuron
neuron.hoc.__file__=  'c:\\nrn\\lib\\python\\neuron\\hoc.cp38-win_amd64.pyd'
neuron.test()

But I was unclear about what they meant by __file__.

pramodk commented 4 years ago

A test of mknrndll just needs a folder with a mod file and a py file that creates a section and inserts the mechanism to verify that the dll is working. e.g foo.mod

To test mknrndll, am I supposed to launch mknrndll from bash and not from cmd itself?

Currently I am doing:

C:\Users\kumbhar> C:\nrn\mingw\usr\bin\bash -c "export N=/cygdrive/c/nrn && mknrndll"

I see that mknrndll rely on N env var and I needed to define that if I am starting bash from cmd. It works fine if launch bash shortcut by double click. (something trivial about env variables sourcing I guess).

I see that it generates dll

-rw-r--r-- 1 kumbhar None       53 May 30 01:44  test.mod
-rw-r--r-- 1 kumbhar None      389 May 30 01:48  mod_func.c
-rw-r--r-- 1 kumbhar None     1264 May 30 01:48  mod_func.o
-rw-r--r-- 1 kumbhar None     6399 May 30 01:48  test.c
-rw-r--r-- 1 kumbhar None     4815 May 30 01:48  test.o
-rwxr-xr-x 1 kumbhar None    55320 May 30 01:48  nrnmech.dll

and now I can do:

C:\Users\kumbhar>C:\Python37\python.exe
Python 3.7.4 (tags/v3.7.4:e09359112e, Jul  8 2019, 20:34:20) [MSC v.1916 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import neuron
>>> from neuron import h
>>> s = h.Section()
>>> s.insert('foo')
__nrnsec_0000021495dfd550

So, there is no special created like linux/osx?

nrnhines commented 4 years ago

To test mknrndll, am I supposed to launch mknrndll from bash and not from cmd itself?

I realize I've never done this except from the mknrndll shortcut or from the bash terminal popped up from the bash shortcut. You are correct that bash with a bit of extra environment is needed. Also when I start a command prompt, I see that the %PATH% is incomplete and I needed

 set PATH=%PATH%;c:\nrn\mingw\mingw64\bin

although I hate to add more things to the PATH it does not work to copy the few files from mingw/mingw64/bin into mingw/usr/bin as then gcc cannot find cc1

So, there is no special created like linux/osx?

That is correct.

pramodk commented 4 years ago

Just as a note : sourceforge download of NSIS doesn't seem robust and fails sometime (3-5% builds):

nsis.install v3.05 [Approved]
nsis.install package files install completed. Performing other installation steps.
Attempt to get headers for https://svwh.dl.sourceforge.net/project/nsis/NSIS%203/3.05/nsis-3.05-setup.exe failed.
  The remote file either doesn't exist, is unauthorized, or is forbidden for url 'https://svwh.dl.sourceforge.net/project/nsis/NSIS%203/3.05/nsis-3.05-setup.exe'. Exception calling "GetResponse" with "0" argument(s): "Unable to connect to the remote server"
Downloading nsis.install 
  from 'https://svwh.dl.sourceforge.net/project/nsis/NSIS%203/3.05/nsis-3.05-setup.exe'
ERROR: The remote file either doesn't exist, is unauthorized, or is forbidden for url 'https://svwh.dl.sourceforge.net/project/nsis/NSIS%203/3.05/nsis-3.05-setup.exe'. Exception calling "GetResponse" with "0" argument(s): "Unable to connect to the remote server" 
This package is likely not broken for licensed users - see https://chocolatey.org/docs/features-private-cdn.
The install of nsis.install was NOT successful.
Error while running 'C:\ProgramData\chocolatey\lib\nsis.install\tools\chocolateyInstall.ps1'.
 See log for details.

~I will upload installer to some GitHub repo from it can be fetched without failure.~ I will download from https://fossies.org/windows/misc/nsis-3.05-setup.exe/

pramodk commented 4 years ago

Additional notes:

C:\Users\kumbhar\nrn>C:\nrn_test\mingw\usr\bin\bash -c "mknrndll"   || goto :error
/usr/bin/bash: /cygdrive/c/nrn_test/bin/mknrndll: sh^M: bad interpreter: No such file or directory

Fixing the end line terminator.

C:\Users\kumbhar\nrn>C:\nrn_test\mingw\usr\bin\bash -c "mknrndll"   || goto :error
set: bad interpreter: No such file or directoryl: sh

Needed to do set PATH=C:\nrn_test\mingw\usr\bin;%PATH%

nrnhines commented 4 years ago

Needed to do set PATH=C:\nrn_test\mingw\usr\bin;%PATH%

I don't doubt this but it is strange as that path item was set during installation (by default) as was c:\nrn\bin. What was really missing is c:\nrn\mingw\mingw64\bin to get gcc. All this was done in the startup script for the bash terminal icon. ie in c:/nrn/lib/bshstart.sh

Fixing the end line terminator.

I don't understand this. Isn't the problem just with the sh being in c:/nrn/mingw/usr/bin

nrnhines commented 4 years ago

On my virtual box windows 10 guest with full msys2 development and an installation of neuron. From a command prompt, I see

C:\Users\hines>echo %PATH%
...;c:\nrn\bin;c:\nrn\mingw\usr\bin

Then, executing bash. I get

C:\Users\hines>bash
bash-4.4$ echo $PATH
...:/cygdrive/c/nrn/bin:/usr/bin

and this really is my neuron installed bash since ls /usr/bin only shows the items in c:\nrn\mingw\usr\bin

It turns out you can use the bshstart.sh start script but you must start in the install folder. e.g.

C:\Users\hines>cd c:\nrn

c:\nrn>bash --rcfile c:/nrn/lib/bshstart.sh
bash-4.4$ echo $PATH
/cygdrive/C/Users/hines/Anaconda3/Library/bin:/cygdrive/c/nrn/bin:/cygdrive/c/nrn/mingw/usr/bin:/cygdrive/c/nrn/mingw/mingw64/bin:/cygdrive/c/ms-mpi/Bin:/cygdrive/c/WINDOWS/system32:/cygdrive/c/WINDOWS:/cygdrive/c/WINDOWS/System32/Wbem:/cygdrive/c/WINDOWS/System32/WindowsPowerShell/v1.0:/cygdrive/c/WINDOWS/System32/OpenSSH:/cygdrive/c/Users/hines/AppData/Local/Programs/Python/Launcher:/cygdrive/c/Users/hines/Anaconda3:/cygdrive/c/Users/hines/Anaconda3/Scripts:/cygdrive/c/Users/hines/Anaconda3/Library/bin:/cygdrive/c/Users/hines/AppData/Local/Microsoft/WindowsApps:/cygdrive/c/Users/hines/AppData/Local/Programs/Microsoft VS Code/bin:/cygdrive/c/nrn/bin:/usr/bin

Notice the addition of the three paths again near the beginning of the PATH. From here you can go to a folder containing mod files and run mknrndll. e.g.

bash-4.4$ rm *.dll
bash-4.4$ mknrndll
x86_64-w64-mingw32-gcc.exe -DDLL_EXPORT -DPIC -I/cygdrive/c/nrn/include -I/cygdrive/c/nrn/src/scopmath -I/cygdrive/c/nrn/src/nrnoc -I/cygdrive/c/nrn/src/oc  -c mod_func.c
nocmodl cabpump
Translating cabpump.mod into cabpump.c
Notice: Assignment to the GLOBAL variable, "vol", is not thread safe
x86_64-w64-mingw32-gcc.exe -DDLL_EXPORT -DPIC -I/cygdrive/c/nrn/include -I/cygdrive/c/nrn/src/scopmath -I/cygdrive/c/nrn/src/nrnoc -I/cygdrive/c/nrn/src/oc  -c cabpump.c
...
x86_64-w64-mingw32-gcc.exe  -shared mod_func.o cabpump.o cachan1.o camchan.o capump.o invlfire.o khhchan.o mcna.o nacaex.o nachan.o release.o \
  -L/cygdrive/c/nrn/bin -lnrniv -lpthread -o 1464.nrnmech.dll
#rebase -b 0x64000000 -v nrnmech.dll
bash-4.4$
ramcdougal commented 4 years ago

On Windows, starting with NEURON 7.7, you can type nrnivmodl from the cmd prompt and that should do the right thing with telling bash to tell mknrndll to do the right thing.

pramodk commented 4 years ago

At least that doesn't seem to be the case with CMake installation on windows : I see nrnivmodl in bin directory but that is still shell script :

image

ramcdougal commented 4 years ago

The file itself is in src/mswin/bin/nrnivmodl.bat

My guess is that maybe the windows-specific stuff isn't being put into the right place by the cmake version?

Here's the commit that added the bat version: https://github.com/neuronsimulator/nrn/commit/88b2fa546ef98ba00c1cc8e0f4857743362ff71b

I notice that src/mswin/batch/instalmingw.sh had to explicitly include a copy command for the nrnivmodl.bat file.

pramodk commented 4 years ago

Ah Ok! I haven't worked on this part. I will let @nrnhines to make necessary changes if this is something we should fix.

nrnhines commented 4 years ago

I completely forgot about pull request #142. I will add that autotools addition to cmake. I.e nrnivmodl as a copy of mknrndll and the new (then), nrnivmodl.bat. I guess for reduced confusion, mknrndll.bat should be also added as a copy of nrnivmodl.bat .

pramodk commented 4 years ago 
A test of association with hoc files is possible in a command prompt with the following temp.bat file

del temp.txt
echo wopen("temp.txt") > .\temp.hoc
echo fprint("hello\n") >> .\temp.hoc
echo wopen() >> .\temp.hoc
echo quit() >> .\temp.hoc
start .\temp.hoc
timeout /T 10
cat temp.txt

I was worried about using start /wait instead of the timout since if there is a hoc failure the temp.hoc will hang.

@nrnhines : I noticed that even if I use start /wait or start /wait /b (as suggested here) doesn't work i.e. we resume to next command (timeout in this case) right away. This works but not 100% robust.

nrnhines commented 4 years ago

Since it is not robust, but perhaps usually correct, perhaps it can become a warning to us just to check it ourselves if it fails? But is never a failure from the perspective of the azure CI.

pramodk commented 4 years ago

For now I have enabled that as failure. If we see this result into multiple build failures, we can change this default behaviour as non-fatal.