Installation and debugging

The command-line tools listed in this section can be used to install, debug an installation, or test an installation of Myokit.

compiler

Myokit simulations make use of a locally installed compiler. The myokit compiler command tests this functionality, by compiling a small test module that queries the system for the installed compiler.

Example:

$ myokit compiler

Example output:

Compilation successful. Found: GCC 11.2.1

If compilation is unsuccessful, more information may be obtained by using:

$ myokit compiler --debug

icons

Installs shortcut icons on Linux or Windows. On Linux, it also creates the .mmt mime-type and registers Myokit as a tool to handle .mmt and various other file types.

Example:

$ myokit icons

opencl

Displays information about the current OpenCL configuration.

See opencl-select for information about setting a preferred device.

Example:

$ myokit opencl

Example output:

Platform 0
 Current id : 22734896
 Name       : Intel(R) OpenCL
 Vendor     : Intel(R) Corporation
 Version    : OpenCL 1.2 LINUX
 Profile    : FULL_PROFILE
 Extensions : cl_khr_fp64 cl_khr_icd
 Devices    :
  Device 0
   Current id      : 21277656
   Name            : Intel(R) Core(TM) i5-2520M CPU @ 2.50GHz
   Vendor          : Intel(R) Corporation
   Version         : OpenCL 1.2 (Build 67279)
   Driver          : 1.2
   Clock speed     : 2500 MHz
   Global memory   : 7870 MB
   Local memory    : 32 KB
   Constant memory : 128 KB
   Max work groups : 1024
   Max work items  : [1024, 1024, 1024]
   Max param size  : 3840 bytes

For the full syntax, see:

$ myokit opencl --help

opencl-select

Allows the Myokit-wide OpenCL device selection to be inspected and set.

See opencl for more about obtaining detailed information about platforms and devices.

Example:

$ myokit opencl-select

Example output:

Loading Myokit...
======================================================================
Myokit OpenCL device selection
======================================================================
Selected platform: No preference
Selected device  : No preference
======================================================================
Available devices:
----------------------------------------------------------------------
(1) Select automatically.
----------------------------------------------------------------------
(2) Platform: NVIDIA CUDA
    Device: GeForce GT 640
    901 MHz, 3.9 GB global, 48.0 KB local, 64.0 KB const
----------------------------------------------------------------------
Please select an OpenCL device by typing 1 or 2
Leave blank to keep current selection.
Select device:

If you have multiple OpenCL devices, this will allow a preference to be set. If no preferred device of platform is set, Myokit is will pick the first platform and device, but with a preference for GPUs over CPUs.

reset

Resets all user settings by removing all Myokit configuration files. This will cause Myokit to recreate the files with default settings the next time Myokit is run.

Typical use:

$ myokit reset

This will prompt you to confirm (by typing “yes” or “y”) the reset. To bypass the reset, use:

$ myokit reset --force

sundials

Compiles a small test module that queries the system for the installed SUNDIALS version (if any).

Example:

$ myokit sundials

Example output:

Found Sundials version 5.6.1

system

Retrieves and prints system information which can be used to debug a Myokit installation.

Example:

$ myokit system

Example output:

== System information ==
Myokit: 1.33.1
Python: 3.9.7 (default, Aug 30 2021, 00:00:00)
        [GCC 11.2.1 20210728 (Red Hat 11.2.1-1)]
OS: Linux (linux, posix)

== Python requirements ==
NumPy: 1.20.1
SciPy: 1.6.2
Matplotlib: 3.4.3
ConfigParser: OK
Setuptools: 53.0.0

== Python extras ==
SymPy: 1.8
MoviePy: 1.0.3

== GUI ==
PyQt5: 5.15.2
  Sip: OK
PyQt4: 4.8.7
  Sip: OK
PySide: Not found
PySide2: 5.15.2

== Development tools ==
Sphinx: 3.4.3
Flake8: 3.8.4

== Simulation tools ==
Compiler: GCC 11.2.1
Sundials: 5.6.1
OpenCL: 2 device(s) found
  Intel(R) Core(TM) i9-10885H CPU @ 2.40GHz on Intel(R) CPU Runtime for OpenCL(TM) Applications
  Intel(R) UHD Graphics [0x9bc4] on Intel(R) OpenCL HD Graphics
  Use `python -m myokit opencl` for more information.

= /home/michael/.config/myokit/myokit.ini =
[myokit]
# This file can be used to set global configuration options for Myokit.

[time]
# Date format used throughout Myokit
# Format should be acceptable for time.strftime
date_format = %Y-%m-%d %H:%M:%S
# Time format used throughout Myokit
time_format = %H:%M:%S

[debug]
# Add line numbers to debug output of simulations
line_numbers = True

[gui]
# Backend to use for graphical user interface.
# Valid options are "pyqt5", "pyqt4" or "pyside".
# Leave unset for automatic selection.
#backend = pyqt5
#backend = pyqt4
#backend = pyside

[sundials]
# Location of sundials shared libary files (.so or .dll).
# Multiple paths can be set using ; as separator.
#lib = /usr/local/lib;/opt/local/lib
# Location of sundials header files (.h).
#inc = /usr/local/include;/opt/local/include
version = 50300

[opencl]
# Location of opencl shared libary files (.so or .dll).
# Multiple paths can be set using ; as separator.
lib = /usr/lib64;/usr/lib64/nvidia;/usr/local/cuda/lib64
# Location of opencl header files (.h).
inc = /usr/include/CL;/usr/local/cuda/include

test

Runs Myokit’s unit tests. On a successful installation, these should complete without failures

Example:

$ myokit test

When run form a development source tree (i.e. from within a cloned myokit repository) this command provides additional options, e.g. for style and documentation checking.

version

Displays the current Myokit version.

$ myokit version

Example output:

 Myokit version 1.21.0         |/\
_______________________________|  |______

To leave out the decorations, use:

$ myokit version --raw

which returns:

1.21.0