chdir · getcwd · machine_name · neuronhome · nrn_load_dll · nrnversion · show_winio · startsw · stopsw · system · unix_mac_pc · WinExec

System Calls

If you’re using Python, many of these system calls have equivalents in Python’s os module <https://docs.python.org/3/library/os.html>`_

Path Manipulation

chdir()

Python

Syntax:: n.chdir("path")
Description:: Change working directory to the indicated path. Returns 0 if successful otherwise -1, ie the usual unix os shell return style.

HOC

Syntax:: chdir("path")
Description:: Change working directory to the indicated path. Returns 0 if successful otherwise -1, ie the usual unix os shell return style.

getcwd()

Python

Syntax:: n.getcwd()
Description:: Returns absolute path of current working directory in unix format. The last character of the path name is ‘/’. Must be less than 1000 characters long.

HOC

Syntax:: string = getcwd()
Description:: Returns absolute path of current working directory in unix format. The last character of the path name is ‘/’. Must be less than 1000 characters long.

neuronhome()

Python

Syntax:

n.neuronhome()

Description:

Returns the full installation path in unix format or, if it exists, the NEURONHOME environment variable in unix format.

Note that for unix, it isn’t exactly the installation path but the –prefix/share/nrn directory where –prefix is the location specified during installation. For the Windows version, it is the location selected during installation and the value is derived from the location of neuron.exe in neuronhome()/bin/neuron.exe. For macOS, it is the folder that contains the neuron executable program.

HOC

Name:

neuronhome – installation path

Syntax:

string = neuronhome()

Description:

Returns the full installation path in unix format or, if it exists, the NEUROHOME environment variable in unix format.

Note that for unix, it isn’t exactly the installation path but the –prefix/share/nrn directory where –prefix is the location specified during installation. For the mswin version it is the location selected during installation and the value is derived from the location of neuron.exe in neuronhome()/bin/neuron.exe. For mac it is the folder that contains the neuron executable program.

Machine Identification

machine_name()

Python

Syntax:

n.machine_name(strdef)

Description:

Sets the NEURON string (not a Python string) strdef to the hostname of the machine. Create a NEURON string via, e.g., n.ref('').

Example:

from neuron import n
my_machine_name = n.ref('')
n.machine_name(my_machine_name)
print(f"My hostname is {my_machine_name[0]}")

HOC

Syntax:

strdef name

machine_name(name)

Description:

returns the hostname of the machine.

unix_mac_pc()

Python

Syntax:

n.unix_mac_pc()

Description:

Return 1 if unix, 2 if (an older) mac, 3 if mswin, or 4 if mac osx darwin is the operating system. This is useful when deciding if a machine specific function can be called or a dll can be loaded.

Example:

from neuron import n
type = n.unix_mac_pc()

if type == 1:
    print("This os is unix based")
elif type == 2:
    print("This os is classic mac based")
elif type == 3:
    print("This os is mswin based")
elif type == 4:
    print("This os is mac osx darwin based")

HOC

Syntax:: type = unix_mac_pc()
Description:: Return 1 if unix, 2 if mac, 3 if mswin, or 4 if mac osx darwin is the operating system. This is useful when deciding if a machine specific function can be called or a dll can be loaded.

nrnversion()

Python

Syntax:

n.nrnversion()

n.nrnversion(i)

Description:

Returns a string consisting of version information. When this function was introduced the majorstring was “5.6” and the branch string was “2004/01/22 Main (36)”. Now the arg can range from 0 to 6. The value of 6 returns the args passed to configure. When this function was last changed the return values were.

An arg of 7 now returns a space separated string of the arguments used during launch. e.g.

$ nrniv -nobanner -c 'nrnversion()' -c 'nrnversion(7)'
NEURON -- VERSION 7.2 twophase_multisend (534:2160ccb31406) 2010-12-09
nrniv -nobanner -c nrnversion() -c nrnversion(7)
$

An arg of 8 now returns the host-triplet. E.g.

$ nrniv -nobanner -c 'nrnversion(8)'
x86_64-unknown-linux-gnu

An arg of 9 now returns “1” if the neuron main program was launched, “2” if the library was loaded by Python, and “0” if the launch progam is unknown

$ nrniv -nobanner -c 'nrnversion(9)'
1

$ python 2</dev/null
>>> from neuron import n
>>> n.nrnversion(9)
'2'

Example:

from neuron import n, gui
n.nrnversion()
'NEURON -- VERSION 8.2.2 HEAD (93d41fafd) 2022-12-15'

for i in range(10):
    print(f'{i} : {n.nrnversion(i)}')

0 : 8.2.2
1 : NEURON -- VERSION 8.2.2 HEAD (93d41fafd) 2022-12-15
2 : VERSION 8.2.2 HEAD (93d41fafd)
3 : 93d41fafd
4 : 2022-12-15
5 : 8.2.2
6 : cmake option default differences: 'NRN_ENABLE_RX3D=OFF' 'NRN_ENABLE_CORENEURON=ON' 'NRN_ENABLE_PYTHON_DYNAMIC=ON' 'NRN_MPI_DYNAMIC=/usr/local/opt/openmpi/include;/usr/local/opt/mpich/include' 'CMAKE_BUILD_TYPE=Release' 'CMAKE_INSTALL_PREFIX=/Users/runner/work/1/s/build/cmake_install' 'CMAKE_C_COMPILER=/Applications/Xcode_13.2.1.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc' 'CMAKE_CXX_COMPILER=/Applications/Xcode_13.2.1.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++' 'PYTHON_EXECUTABLE=/Users/runner/work/1/s/nrn_build_venv38_-4745831/bin/python'
7 : NEURON
8 : x86_64-Darwin
9 : 2

HOC

Syntax:

versionstring = nrnversion()

string = nrnversion(i)

Description:

oc>nrnversion()
NEURON -- VERSION 7.1 (296:ff4976021aae) 2009-02-27
oc>for i=0,6 print i,": ", nrnversion(i)
0 : 7.1
1 : NEURON -- VERSION 7.1 (296:ff4976021aae) 2009-02-27
2 : VERSION 7.1 (296:ff4976021aae)
3 : ff4976021aae
4 : 2009-02-27
5 : 296
6 : '--prefix=/home/hines/neuron/nrnmpi' '--srcdir=../nrn' '--with-paranrn' '--with-nrnpython'
oc>

Warning

An arg of 7 now returns a space separated string of the arguments used during launch. e.g.

$ nrniv -nobanner -c 'nrnversion()' -c 'nrnversion(7)'
NEURON -- VERSION 7.2 twophase_multisend (534:2160ccb31406) 2010-12-09
nrniv -nobanner -c nrnversion() -c nrnversion(7)
$

An arg of 8 now returns the host-triplet. E.g.

$ nrniv -nobanner -c 'nrnversion(8)'
x86_64-unknown-linux-gnu

An arg of 9 now returns “1” if the neuron main program was launched, “2” if the library was loaded by Python, and “0” if the launch progam is unknown

$ nrniv -nobanner -c 'nrnversion(9)'
1

$ python 2</dev/null
>>> from neuron import n
>>> n.nrnversion(9)
'2'

Execute a Command

WinExec()

Python

Syntax:: n.WinExec("mswin command")
Description:: MSWin version only. Use system() for a more generic solution, or use os.system or subprocess.run in Python.

HOC

Syntax:: WinExec("mswin command")
Description:: MSWin version only.

system()

Python

Name:

system — issue a shell command

Syntax:

exitcode = n.system(cmdstr)

exitcode = n.system(cmdstr, stdout_str)

Description:

Executes cmdstr as though it had been typed as command to a unix shell from the terminal. NEURON waits until the command is completed. If the second strdef arg is present, it receives the stdout stream from the command. Only available memory limits the line length and number of lines.

Example:

n.system("ls")
Prints a directory listing in the console terminal window. will take up where it left off when the user types the exit command

Warning

Fully functional on unix, mswin under cygwin, and mac osx.

Does not work on the mac os 9 version.

Following is obsolete: Under mswin, executes the string under the cygwin sh.exe in $NEURONHOME/bin via the wrapper, $NEURONHOME/lib/nrnsys.sh. Normally, stdout is directed to the file tmpdos2.tmp in the working directory and this is copied to the terminal. The neuron.exe busy waits until the nrnsys.sh script creates a tmpdos1.tmp file signaling that the system command has completed. Redirection of stdout to a file can only be done with the idiom “command > filename”. No other redirection is possible except by modifying nrnsys.sh.

Note

A pure Python alternative would be to use os.system or subprocess.run.

HOC

Name:

system — issue a shell command

Syntax:

exitcode = system(cmdstr)

exitcode = system(cmdstr, stdout_str)

Description:

Executes cmdstr as though it had been typed as command to a unix shell from the terminal. HOC waits until the command is completed. If the second strdef arg is present, it receives the stdout stream from the command. Only available memory limits the line length and number of lines.

Example:

system("ls")
Prints a directory listing in the console terminal window. will take up where it left off when the user types the exit command

Warning

Fully functional on unix, mswin under cygwin, and mac osx.

Does not work on the mac os 9 version.

Timing

startsw()

Python

Syntax:

n.startsw()

Initializes a stopwatch with a resolution of 0.01 second. See stopsw().

HOC

Initializes a stopwatch with a resolution of 0.01 second. See stopsw().

stopsw()

Python

Syntax:

n.stopsw()

Returns the time in seconds since the stopwatch was last initialized with a startsw() .

Description:

Really the idiom

x = n.startsw()
n.startsw() - x

should be used since it allows nested timing intervals.

Example:

from neuron import n
from math import sin
n.startsw()
for i in range(100_000):
    x = sin(0.2)
print(n.stopsw())

Note

A pure Python alternative would be to use the time module’s perf_counter function.

from neuron import n
from math import sin
import time

start = time.perf_counter()
for i in range(100_000):
    x = sin(0.2)

print(time.perf_counter() - start)

HOC

Returns the time in seconds since the stopwatch was last initialized with a startsw() .

startsw()
for i=1,1000000 { x = sin(.2) ]
stopsw()

Miscellaneous

nrn_load_dll()

Python

Syntax:: n.nrn_load_dll(dll_file_name)
Description:: Loads a dll containing membrane mechanisms (i.e., compiled MOD files). This works for mswin, mac, and linux.

HOC

Syntax:: nrn_load_dll(dll_file_name)
Description:: Loads a dll containing membrane mechanisms. This works for mswin, mac, and linux.

show_winio()

Python

Syntax:: n.show_winio(0or1)

Description:

Does nothing in recent NEURON versions.

In some older versions, could hide or show the console window in MSWin and Mac.

HOC

Syntax:: show_winio(0or1)

Description:

Does nothing in recent NEURON versions.

In some older versions, could hide or show the console window in MSWin and Mac.