Jupyter kernels manipulation and in other environments (docker, Lmod, etc.)
Project description
Switch environments before running Jupyter kernels
Sometimes, one needs to execute Jupyter kernels in a different environment. Say you want to execute the kernel in a conda environment (that's easy, but actually misses setting certain environment variables). Or run it inside a Docker container. One could manually adjust the kernelspec files to set environment variables or run commands before starting the kernel, but envkernel automates this process.
envkernel is equally usable for end users (on their own systems or clusters) to easily access environments in Jupyter, or sysadmins deploying this access on systems they administer.
In general, there are two passes: First, install the kernel, e.g.:
envkernel virtualenv --name=my-venv /path/to/venv
. This parses some
options and writes a kernelspec file with the the --name
you
specify. When Jupyter tries to start this kernel, it will execute the
next phase. When Jupyter tries to run the kernel, the kernelspec file
will re-execute envkernel
in the run mode, which does whatever is
needed to set up the environment (in this case, sets PATH
to the
/path/to/venv/bin/
that is needed). Then it starts the normal
IPython kernel.
Available modes:
conda
: Activate a conda environment first.virtualenv
: Activate a virtualenv first.docker
: Run the kernel in a Docker container.singularity
: Run the kernel in a singularity container.Lmod
: Activate Lmod modules first.
Installation
Available on the PiPI: pip install envkernel
.
Or, you can install latest from Github in the usual way: pip install https://github.com/NordicHPC/envkernel/archive/master.zip
This is a single-file script and can be copied directly and added to
PATH
as well. By design, there are no dependencies except the basic
Jupyter client (not notebook or any UI), and that is only needed at
kernel-setup time, not at kernel-runtime. The script must be
available both when a kernel is set up, and
each time the kernel is started (and currently assumes they are in the
same location).
General usage and common arguments
General invocation:
envkernel [mode] [envkernel options] [mode-specific-options]
General arguments usable by all classes during the setup phase:
These options directly map to normal Jupyter kernel install options:
mode
:singularity
,docker
,lmod
, or whatever mode is desired.--name $name
: Name of kernel to install (required).--user
: Install kernel into user directory.--sys-prefix
: Install to the current Python'ssys.prefix
(the Python which is running envkernel).--prefix
: same as normal kernel install option.--display-name NAME
: Human-readable name.--replace
: Replace existing kernel (Jupyter option, unsure what this means).--language
: What language to tag this kernel (defaultpython
).
These are envkernel-specific options:
--verbose
,-v
: Print more debugging information when installing the kernel. It is always in verbose mode when actually running the kernel.--python
: Python interpreter to use when invoking inside the environment. (Defaultpython
. Unlike other kernels, this defaults to a relative path because the point of envkernel is to set up PATH properly.) If this is the special valueSELF
, this will be replaced with the value ofsys.executable
of the Python running envkernel.--kernel=NAME
: Auto-set--language
and--kernel-cmd
to that needed for these well-known kernels. Options includeipykernel
(the default),ir
, orimatlab
. But all of these hard-code a kernel command line and could possibly be wrong some day.--kernel-cmd
: a string which is the kernel to start - space separated, no shell quoting, it will be split when saving. The default ispython -m ipykernel_launcher -f {connection_file}
, which is suitable for IPython. For example, to start an R kernel in the environment useR --slave -e IRkernel::main() --args {connection_file}
as the value to this, being careful with quoting the spaces only once. To find what the strings should be, copy form some existing kernels.--kernel=NAME
includes shortcut for some popular kernels.--kernel-template
: An already-installed kernel name which is used as a template for the new envkernel. This is searched using the normal Jupyter search paths. This kernel json file is loaded and used as a template for all kernel options (--language
,--kernel-cmd
, etc). Also, any other file in this directory (such as logos) are copied to the new kernel (like kernel.js in irkernel).--kernel-make-path-relative
removes an absolute path from the kernel command (mainly useful with--kernel-template
). This would be useful, for example, where you are setting up an lmod install and the absolute path of the module might change, but you want it to always run Python relative to that module anyway.--env=NAME=VALUE
. Set these environment variables when running the kernel. These are actually just saved in thekernel.json
file under theenv
key, which is used by Jupyter itself. So, this is just a shorthand for adding variables there, it is not used at the envkernel stage at all.
Order of precedence of options (later in the list overrides earlier):
--kernel-template
, --kernel
, --kernel-cmd
, --language
,
--python
, --display-name
.
Conda
The Conda envkernel will activate Conda environments (set the PATH
,
CPATH
, LD_LIBRARY_PATH
, and LIBRARY_PATH
environment variables).
This is done manually, if anyone knows a better way to do this, please
inform us.
Conda example
This will load the anaconda
environment before invoking an IPython
kernel using the name python
, which will presumably be the one
inside the anaconda3
environment.
envkernel conda --name=conda-anaconda3 /path/to/anaconda3
Conda mode arguments
General invocation:
envkernel conda --name=NAME [envkernel options] conda-env-full-path
conda-env-full-path
: Full path to the conda environment to load.
Virtualenv
This operates identically to conda
mode, but with name virtualenv
on virtualenvs.
Virtualenv example
envkernel virtualenv --name=conda-anaconda3 /path/to/anaconda3
Docker
Docker is a containerization system that runs as a system service.
Note: docker has not been fully tested, but has been reported to work.
Docker example
envkernel docker --name=NAME --pwd --bind /m/jh/coursedata/:/coursedata /path/to/image.simg
Docker mode arguments
General invocation:
envkernel docker --name=NAME [envkernel options] [docker options] [image]
-
image
: Required positional argument: name of docker image to run. -
--pwd
: Bind-mount the current working directory and use it as the current working directory inside the notebook. This is usually useful. -
A few more yet-undocumented and untested arguments...
Any unknown argument is passed directly to the docker run
call, and
thus can be any normal Docker argument. If ,copy
is included in the
--mount
command options, the directory will be copied before
mounting. This may be useful if the directory is on a network mount
which the root docker can't access. It is recommended to always use
the form of options with =
, such as --option=X
, rather than
separating them with a space, to avoid problems with argument/option
detection.
Singularity
Singularity is a containerization system somewhat similar to Docker, but designed for user-mode usage without root, and with a mindset of using user software instead of system services.
Singularity example
envkernel singularity --name=NAME --contain --bind /m/jh/coursedata/:/coursedata /path/to/image.simg
Singularity mode arguments
General invocation:
envkernel singularity --name=NAME [envkernel options] [singularity options] [image]
-
image
: Required positional argument: name of singularity image to run. -
--pwd
: Bind-mount the current working directory and use it as the current working directory inside the notebook. This may happen by default if you don't--contain
.
Any unknown argument is passed directly to the singularity exec
call, and thus can be any normal Singularity arguments. It is
recommended to always use the form of options with =
, such as
--bind=X
, rather than separating them with a space, to avoid
problems with argument/option detection. The most useful Singularity
options are (nothing envkernel specific here):
-
--contain
or-c
: Don't share any filesystems by default. -
--bind src:dest[:ro]
: Bind mountsrc
from the host todest
in the container.:ro
is optional, and defaults torw
. -
--cleanenv
: Clean all environment before executing. -
--net
or-n
: Run in new network namespace. This does NOT work with Jupyter kernels, because localhost must currently be shared. So don't use this unless we create proper net gateway.
Lmod
The Lmod envkernel will load/unload Lmod modules before running a normal IPython kernel.
Using envkernel is better than the naive (but functional) method of modifying a kernel to invoke a particular Python binary, because that will invoke the right Python interpreter but not set relevant other environment variables (so, for example, subprocesses won't be in the right environment).
Lmod example
This will run module purge
and then module load anaconda3
before
invoking an IPython kernel using the name python
, which will
presumably be the one inside the anaconda3
environment.
envkernel lmod --name=anaconda3 --purge anaconda3
Lmod mode arguments
General invocation:
envkernel lmod --name=NAME [envkernel options] [module ...]
-
module ...
: Modules to load (positional argument). Note that if the module is prefixed with-
, it is actually unloaded (this is a Lmod feature). -
--purge
: Purge all modules before loading the new modules. This can be safer, because sometimes users may automatically load modules from their.bashrc
which will cause failures if you try to load conflicting ones.
Other kernels
Envkernel isn't specific to the IPython kernel. It defaults to
ipykernel, but by using the --kernel-template
option you can make it
work with any other kernel without having to understand the internals.
First, you install your other kernel normally, with some name (in this
case, R-3.6.1
). Then, you run envkernel with
--kernel-template=R-3.6.1
, which clones that (with all its support
files from the kernel directory, argv, and so on), and (in this case)
saves it to the same name with the --name=R-3.6.1
option.
# Load modules and install the IRKernel normally, without envkernel
module load r-irkernel/1.1-python3
module load jupyterhub/live
Rscript -e "library(IRkernel); IRkernel::installspec(name='R-3.6.1', displayname='R 3.6 module')"
# Use envkernel --kernel-template
# - Do the normal Lmod envkernel setup
# - copy the existing kernel, incuding argv, kernel.js, icon, and display name
# - Save it again, to the same name, with envkernel wrapper.
envkernel lmod --user --kernel-template=R-3.6.1 --name=R-3.6.1 r-irkernel/1.1-python3
This way, you can wrap any arbitrary kernel to run under envkernel.
Also, you can always use --kernel-cmd
to explicitly set your kernel
command to whatever is needed for any other kernel (but you have to
figure out that command yourself...).
How it works
When envkernel first runs, it sets up a kernelspec that will re-invoke envkernel when it runs. Some options are when firs run (kernelspec name and options), while usually most are passed through straight to the kernelspec. When the kernel is started, envkernel is re-invoked
Example envkernel setup command. This makes a new Jupyter kernel
(envkernel singularity
means singularity create mode) named
testcourse-0.5.9
out of the image /l/simg/0.5.9.simg
with the
Singularity options --contain
(contain, on default mounts) and
--bind
(bind a dir).`
envkernel singularity --sys-prefix --name=testcourse-0.5.9 /l/simg/0.5.9.simg --contain --bind /m/jh/coursedata/:/coursedata
That will create this kernelspec. Note that most of the arguments are passed through:
{
"argv": [
"/opt/conda-nbserver-0.5.9/bin/envkernel",
"singularity",
"run",
"--connection-file",
"{connection_file}",
"--contain",
"--bind",
"/m/jh/coursedata/:/coursedata",
"/l/simg/0.5.9.simg",
"--",
"python",
"-m",
"ipykernel_launcher",
"-f",
"{connection_file}"
],
"display_name": "Singularity with /l/simg/0.5.9.simg",
"language": "python"
}
When this runs, it runs singularity --contain --bind /m/jh/coursedata/:/coursedata /l/simg/0.5.9.simg
. Inside the image,
it runs python -m ipykernel_launcher -f {connection_file}
.
envkernel parses and manipulates these arguments however is needed.
Running multiple modes
envkernel doesn't support running multiple modes - for example,
conda
and lmod
at the same time. But, because of the general
nature, you should be able to layer it yourself. The following
example uses the conda
mode to create an envkernel. Then, it uses
--kernel-template
to re-read that kernel and wrap it in lmod
:
envkernel conda --name=test1 conda_path
envkernel lmod --name=test1 --kernel-template=test1 lmod_module
There is nothing really special here, it is layering one envkernel execution on top of another. If you notice problems with this, please try to debug a bit and then send feedback/improvements, this is a relatively new feature.
Use with nbgrader
envkernel was orginally inspired by the need for nbgrader to securely
contain student's code while autograding. To do this, set up a
contained kernel as above - it's up to you to figure out how to do
this properly with your chosen method (docker or singularity). Then
autograde like normal, but add the --ExecutePreprocessor.kernel_name
option.
Set up a kernel:
envkernel docker --user --name=testcourse-0.5.9 --pwd aaltoscienceit/notebook-server:0.5.9 --bind /mnt/jupyter/course/testcourse/data/:/coursedata
Run the autograding:
nbgrader autograde --ExecutePreprocessor.kernel_name=testcourse-0.5.9 R1_Introduction
Kernel quick reference
jupyter kernelspec list
jupyter kernelspec remove NAME
See also
-
General
- a2km, "Assistant to the kernel manager" is a command line tool for dealing with kernels, including making kernels which activate conda/venv kernels. And some other handy kernel manipulations stuff. Unfortunately written in Ruby.
- https://github.com/Anaconda-Platform/nb_conda_kernels - automatically create kernels from conda environments. Uses a KernelSpecManager so possibly overrides everything at once, and also defaults to all kernels.
- The direct way to make a conda/virtualenv available in Jupyter is to activate the environment, then run
python -m ipykernel install [--user|--prefix=/path/to/other/env/]
. But this does not set upPATH
, so calling other executables doesn't work... thus the benefit of envkernel. - This thread was the clue to getting a kernel inside Docker working.
-
The following commands are essential for kernel management
jupyter kernelspec list
jupyter --paths
- each$data_path/kernels
dir is searched for kernels.
Development and contributions
Developed at Aalto University Science-IT. Primary contact: Richard Darst. Contributions welcome from anyone. As of early 2019, it is mid 2019, it's usable but there may be bugs as it gets used in more sites.
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