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

System Calls

Path Manipulation

chdir()

Syntax:: h.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()

Syntax:: h.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()

Name:

neuronhome – installation path

Syntax:

h.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()

Syntax:

h("strdef name")

h.machine_name(h.name)

Description:

returns the hostname of the machine.

unix_mac_pc()

Syntax:

h.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 h
type = h.unix_mac_pc()

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

nrnversion()

Syntax:

h.nrnversion()

h.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 h
>>> h.nrnversion(9)
'2'

Example:

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

for i in range(10):
    print(f'{i} : {h.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_MODULE_INSTALL=OFF' '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

Execute a Command

WinExec()

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

system()

Name:

system — issue a shell command

Syntax:

exitcode = h.system(cmdstr)

exitcode = h.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:

h.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.

Timing

startsw()

Syntax:

h.startsw()

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

stopsw()

Syntax:

h.stopsw()

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

Description:

Really the idiom

x = h.startsw()
h.startsw() - x

should be used since it allows nested timing intervals.

Example:

from neuron import h
from math import sin
h.startsw()
for i in range(100000):
    x = sin(0.2)
print(h.stopsw())

Note

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

Miscellaneous

nrn_load_dll()

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

show_winio()

Syntax:: h.show_winio(0or1)
Description:: MSWin and Mac version only. Hides or shows the console window.