Merge pull request #18 from Bai-Chiang/micromamba

Add micromamba support and various fix and improvements.

.gitignore

@@ -0,0 +1,3 @@
+tmpfs
+log_*
+toast_test_output

config/binary/packages_conda.txt

@@ -0,0 +1,7 @@
+# Adjust the default python version
+python=3.10.*
+#
+jupyterlab
+wurlitzer
+plotly
+plotly-resampler

config/binary/packages_pip.txt

@@ -0,0 +1,17 @@
+pixell
+quaternionarray
+pysm3
+# Uncomment here if installing wheel, and comment out
+# line in packages_local.txt
+posix-ipc
+toast==3.0.0a20
+pysqlite3-wheels
+qpoint
+so3g
+#
+# Latest tag
+https://github.com/simonsobs/sotodlib/archive/master.tar.gz
+#
+# The mapsims package has hard-coded versions of pysm3 and
+# pixell, which un-installs our versions of those packages.
+#https://github.com/galsci/mapsims/archive/main.tar.gz

config/binary/post_install.sh

@@ -0,0 +1,15 @@
+# This script is sourced in the main `soconda.sh` script.
+# Any commands placed here will be executed within that shell
+# and have access to all environment variables defined there.
+# There are 2 variables defined here which control the optional
+# creation of a modulefile to load the environment and also
+# which create a small script that installs a jupyter kernel
+# for the environment into a user's home directory.
+
+# Install a module file?
+install_module=yes
+
+# Install jupyter kernel setup script?
+install_jupyter_setup=yes
+
+# Add any other shell commands here for this system...

config/common.txt

@@ -5,6 +5,7 @@
 # and parse pip dependencies with pipgrip.
 #
 conda-build
+conda-verify
 compilers
 setuptools
 pip

config/minimal/packages_conda.txt

@@ -1,3 +1,3 @@
 # Adjust the default python version
-python=3.10.*
+python=3.11.*
 #

config/minimal/packages_local.txt

@@ -1,13 +0,0 @@
-# This config skips all the ACT tools and just installs
-# binary packages for everything.
-#qpoint
-#pixell
-#libactpol_deps
-#libactpol
-#moby2
-# Remove next line once toast-3.0 is on conda-forge,
-# and move to packages_conda.txt
-#toast
-# Uncomment next line to build so3g from source, and
-# comment out line in packages_pip.txt.
-#so3g

config/minimal/packages_pip.txt

@@ -3,12 +3,14 @@ quaternionarray
 pysm3
 # Uncomment here if installing wheel, and comment out
 # line in packages_local.txt
-pysqlite3-wheels
+posix-ipc
 toast==3.0.0a20
+pysqlite3-wheels
+qpoint
 so3g
 #
 # Latest tag
-https://github.com/simonsobs/sotodlib/archive/refs/master.tar.gz
+https://github.com/simonsobs/sotodlib/archive/master.tar.gz
 #
 # The mapsims package has hard-coded versions of pysm3 and
 # pixell, which un-installs our versions of those packages.

config/minimal/post_install.sh

@@ -7,9 +7,9 @@
 # for the environment into a user's home directory.
 
 # Install a module file?
-install_module=no
+install_module=yes
 
 # Install jupyter kernel setup script?
-install_jupyter_setup=no
+install_jupyter_setup=yes
 
 # Add any other shell commands here for this system...

config/perlmutter/packages_pip.txt

@@ -7,7 +7,7 @@ pysm3
 #so3g
 #
 # Latest tag
-https://github.com/simonsobs/sotodlib/archive/refs/master.tar.gz
+https://github.com/simonsobs/sotodlib/archive/master.tar.gz
 #
 # The mapsims package has hard-coded versions of pysm3 and
 # pixell, which un-installs our versions of those packages.

config/site/module_init

@@ -0,0 +1 @@
+-- No module dependencies

config/site/packages_conda.txt

@@ -0,0 +1,6 @@
+# Adjust the default python version
+python=3.10.*
+#
+wurlitzer
+plotly
+plotly-resampler

config/site/packages_local.txt

@@ -0,0 +1,11 @@
+qpoint
+pixell
+libactpol_deps
+libactpol
+moby2
+# Remove next line once toast-3.0 is on conda-forge,
+# and move to packages_conda.txt
+toast
+# Uncomment next line to build so3g from source, and
+# comment out line in packages_pip.txt.
+so3g

config/site/packages_pip.txt

@@ -0,0 +1,14 @@
+quaternionarray
+pysm3
+#
+# Uncomment here if installing wheel, and comment out
+# line in packages_local.txt
+#pysqlite3-wheels
+#so3g
+#
+# Latest tag
+https://github.com/simonsobs/sotodlib/archive/master.tar.gz
+#
+# The mapsims package has hard-coded versions of pysm3 and
+# pixell, which un-installs our versions of those packages.
+#https://github.com/galsci/mapsims/archive/main.tar.gz

config/site/post_install.sh

@@ -0,0 +1,15 @@
+# This script is sourced in the main `soconda.sh` script.
+# Any commands placed here will be executed within that shell
+# and have access to all environment variables defined there.
+# There are 2 variables defined here which control the optional
+# creation of a modulefile to load the environment and also
+# which create a small script that installs a jupyter kernel
+# for the environment into a user's home directory.
+
+# Install a module file?
+install_module=yes
+
+# Install jupyter kernel setup script?
+install_jupyter_setup=yes
+
+# Add any other shell commands here for this system...

docs/docs/install.md

@@ -5,7 +5,7 @@ The install script takes options to specify the location of the base environment
 to create. It also allows specifying a central location to install the
 modulefile:
 
-    $> ./soconda.sh -h
+    ./soconda.sh -h
         Usage:  ./soconda.sh
         [-c <directory in config to use for options>]
         [-e <environment, either name or full path>]
@@ -25,22 +25,20 @@ clutter.
 
 ## Base Conda Environment
 
-If you already have a conda-forge base environment, then you can skip this
+If you already have a conda-forge or micromamba base environment, then you can skip this
 step. However, you should consider setting the "solver" in the base environment
-to use libmamba. This will greatly speed up the dependency resolution
-calculation. Once you decide on the install prefix for your overall conda
-environment you can use the included bootstrap script. For this example, we
-will use `/opt/conda` as the path to the conda base installation. Now run the
-bootstrap script:
+to use `libmamba`. To use `libmamba` solver see
+[this](https://www.anaconda.com/blog/a-faster-conda-for-a-growing-community) article.
+This will greatly speed up the dependency resolution
+calculation.
 
-    $> ./tools/bootstrap_base "/opt/conda"
+For new installation run following script to install miniforge
 
-This bootstrap will install a base system with the conda-forge channel set to
-the default and using the libmamba solver. You can now source the conda
-initialization file and activate this base environment:
+    ./tools/bootstrap_base "$HOME/miniforge3"
 
-    $> source /opt/conda/etc/profile.d/conda.sh
-    $> conda activate base
+This will intall conda to `$HOME/miniforge3` directory.
+It will set conda-forge as default channel and use `libmamba` as default solver.
+After the installation you need to re-login or start a new terminal to initialize conda.
 
 After installing an `soconda` environment below, you will not need this step
 since it is done by the generated modulefile.
@@ -53,34 +51,69 @@ customized MPI compiler, then set the `MPICC` environment variable to the MPI C
 compiler before running `soconda.sh`. That will cause the mpi4py package to
 be built using your system MPI compiler.
 
-## Example:  Local System
+## Install soconda
+### Example:  Local System
+This installation could install `soconda` to your local computer and any cluster.
 
-Starting from scratch, bootstrap a small conda-forge base environment in `~/conda`:
+Clone soconda repo
 
-    $> ./tools/bootstrap_base.sh ~/conda
-    $> source ~/conda/etc/profile.d/conda.sh
-    $> conda activate base
+    git clone [email protected]:simonsobs/soconda.git
+    cd soconda
 
-Create an `soconda` environment with default name and version. However, we
-decide to put all the modulefiles into a central location in the root of the
-base conda install:
+Run the `soconda.sh` script
 
-    $> ./soconda.sh -b ~/conda -m ~/conda/modulefiles
+    export MAKEFLAGS='-j 4'
+    bash soconda.sh -e soconda -c default
 
-Now we can load the module:
+This will create a new environment `soconda_xxx.x.x` with version number as suffix
+using `default` configuration. [More details on configuration.](#customizing-an-environment)
+(The `MAKEFLAGS` doesn't seem to have any effect.)
+If you want to specify a conda base directory add `-b "$HOME/miniforge3"` argument to `soconda.sh`.
 
-    $> module use ~/conda/modulefiles
-    $> module avail
-    $> module load soconda/XXXXXX
+You could find out the name of new created environment with
 
-## Example:  NERSC
+    conda env list
+
+Then you can now activate the environment with
+
+    conda activate soconda_xxx.x.x
+
+
+If running on a Linux desktop that uses wayland, you also need to install the `qt-wayland` package
+
+    conda install qt-wayland
+
+
+If running on server, start jupyterlab listening on port `12345` with command
+
+    cd /path/to/project
+    nohup jupyter-lab --no-browser --port=12345 &> jupyter.log &
+
+
+To list current running jupyter server:
+
+    jupyter server list
+
+
+To connect to jupyterlab running on server, start SSH tunnel from your laptop/desktop:
+
+    ssh -N -L 12345:localhost:12345 server_domain_or_ip
+
+Then you can connect to jupyterlab with link provided by command `jupyter server list`.
+
+To stop jupyterlab listenging on port 12345:
+
+    jupyter server stop 12345
+
+
+### Example:  NERSC
 
 At NERSC, the default provided python is from Anaconda, and does not work well
 for our needs. Instead, we have a conda-forge base system installed in our
 project software directory:
 
-    $> source /global/common/software/sobs/perlmutter/conda/etc/profile.d/conda.sh
-    $> conda activate base
+    source /global/common/software/sobs/perlmutter/conda/etc/profile.d/conda.sh
+    conda activate base
 
 Now we can either install a shared software environment or use this base
 environment to build a conda environment in a personal directory. If you are
@@ -89,29 +122,29 @@ account and follow a specific naming convention which is beyond the scope of
 this document. If you wanted to install these tools to your home directory you
 could do:
 
-    $> mkdir -p ~/conda_envs
-    $> ./soconda.sh -e ~/conda_envs/soconda -m ~/conda_envs/modulefiles
+    mkdir -p ~/conda_envs
+    ./soconda.sh -e ~/conda_envs/soconda -m ~/conda_envs/modulefiles
 
 And then load the module:
 
-    $> module use ~/conda_envs/modulefiles
-    $> module avail
-    $> module load soconda/XXXXXX
+    module use ~/conda_envs/modulefiles
+    module avail
+    module load soconda/XXXXXX
 
 ## Running Tests
 
 After loading an `soconda` environment, you can run some tests with:
 
-    $> ./run_tests.sh
+    ./run_tests.sh
 
-## Installing a Jupyter Kernel
+## Installing a Jupyter Kernel for external Jupyter server
 
-After loading an soconda module the first time, you can run (once) the included script:
+After loading an soconda module or activate socond conda environment the first time, you can run (once) the included script:
 
-    $> soconda_jupyter.sh
+    soconda_jupyter.sh
 
-This will install a kernel file so that jupyter knows how to launch a kernel
-using this python stack.
+This will install a kernel file to `~/.local/share/jupyter/kernels/soconda-xxxxx` so that external jupyter server
+knows how to launch a kernel using this python stack.
 
 ## Customizing an Environment
 
@@ -127,9 +160,15 @@ Then install it as usual.
 ## Deleting an Environment
 
 The `soconda` environments are self contained and you can delete them by
-removing the path or (if using a name), removing the `<base dir>/envs/<name of
-env>` directory. You can optionally delete the modulefile and the versioned pip
+running command `conda remove --name envname --all` or `conda remove -p /base_dir/envs/name --all`.
+Or directly removing the `<base dir>/envs/<name of env>` directory.
+You can optionally delete the modulefile and the versioned pip
 local directory in your home directory.
+If you installed a jupyter kernel, remove kernel file in `~/.local/share/jupyter/kernels/`
+with matching soconda version.
+If you have multiple soconda environment and deleted wrong kernel file, you can always
+[recreate it](#installing-a-jupyter-kernel).
+
 
 ## Advanced Details
 

pkgs/so3g/meta.yaml

@@ -1,5 +1,5 @@
 {% set version = "0.1.10" %}
-{% set sha256 = "4cabc243acf6a18bb8b63572f468b303c3bc4cb4e0e901e3fbe222a8ff094e11" %}
+{% set sha256 = "5367cdd24ac7eff70b482ede2c32df8e1acd16e582a24e489467ec2c4760c31b" %}
 
 {% set build = 0 %}
 

pkgs/toast/meta.yaml

@@ -1,6 +1,6 @@
 
-{% set version = "3980cbb579de56a379df000df76e69a1c1ac73ae" %}
-{% set sha256 = "e2713145f758631cd6bb24b89a87f2522322a72a29400f8ba51d5144e9afe54d" %}
+{% set version = "3.0.0a20" %}
+{% set sha256 = "4d5ad584bf0d2e851009beb17a4ec96677b36b9c9e18893910014581bc22bb4c" %}
 
 {% set build = 0 %}
 
@@ -9,7 +9,7 @@ package:
   version: {{ version }}
 
 source:
-  url: https://github.com/hpc4cmb/toast/archive/{{ version }}.tar.gz
+  url: https://github.com/hpc4cmb/toast/archive/refs/tags/{{ version }}.tar.gz
   sha256: {{ sha256 }}
   # patches:
   #   - debug_lapack.patch

run_tests.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 
 # Pixell Tests
-OMP_NUM_THREADS=4 test_pixell.py
+#OMP_NUM_THREADS=4 test_pixell.py
 
 # Serial TOAST Tests
 OMP_NUM_THREADS=4 MPI_DISABLED=1 python -c 'import toast.tests; toast.tests.run()'
 
 # MPI-enabled tests
-OMP_NUM_THREADS=2 mpirun -np 4 python -c 'import toast.tests; toast.tests.run()'
+OMP_NUM_THREADS=2 mpirun -np 2 python -c 'import toast.tests; toast.tests.run()'