Test py branch

.github/workflows/cmake.yml

@@ -13,7 +13,7 @@ jobs:
   container-test-job:
     runs-on: ubuntu-latest
     container:
-      image: scslab/coeus:0.9.1
+      image: scslab/coeus:0.9.3
     steps:
     - name: Check for dockerenv file
       run: (ls /.dockerenv && echo Found dockerenv) || (echo No dockerenv)

CI/jarvis-util/.coveragerc

@@ -0,0 +1,4 @@
+# .coveragerc
+[run]
+source = .
+omit = *test*

CI/jarvis-util/.gitignore

@@ -0,0 +1,139 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.idea
+hostfile.txt
+lcov.info
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+/.idea/jarvis-cd.iml
+/.idea/misc.xml
+/.idea/modules.xml
+/.idea/inspectionProfiles/profiles_settings.xml
+/.idea/inspectionProfiles/Project_Default.xml
+/.idea/vcs.xml
+/.idea/deployment.xml

CI/jarvis-util/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022-present Luke Logan and other contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

CI/jarvis-util/README.md

@@ -0,0 +1,118 @@
+# Jarvis UTIL
+
+Jarvis-util is a library which contains various utilities to aid with
+creating shell scripts within Python. This library contains wrappers
+for executing shell commands locally, SSH, SCP, MPI, argument parsing, 
+and various other random utilities.
+
+![Build](https://github.com/lukemartinlogan/jarvis-util/workflows/GitHub%20Actions/badge.svg)
+
+[![Coverage Status](https://coveralls.io/repos/github/lukemartinlogan/jarvis-util/badge.svg?branch=master)](https://coveralls.io/github/lukemartinlogan/jarvis-util?branch=master)
+
+## Installation
+
+For now, we only consider manual installation
+```bash
+cd jarvis-util
+python3 -m pip install -r requirements.txt
+python3 -m pip install -e .
+```
+
+## Executing a program
+
+The following code will execute a command on the local machine.
+The output will NOT be collected into an in-memory buffer.
+The output will be printed to the terminal as it occurs.
+
+```python
+from jarvis_util.shell.exec import Exec
+from jarvis_util.shell.local_exec import LocalExecInfo 
+
+node = Exec('echo hello', LocalExecInfo(collect_output=False))
+```
+
+Programs can also be executed asynchronously:
+```python
+from jarvis_util.shell.exec import Exec
+from jarvis_util.shell.local_exec import LocalExecInfo 
+
+node = Exec('echo hello', LocalExecInfo(collect_output=False,
+                                        exec_async=True))
+node.wait()
+```
+
+Various examples of outputs:
+```python
+from jarvis_util.shell.exec import Exec
+from jarvis_util.shell.local_exec import LocalExecInfo 
+
+# Will ONLY print to the terminal
+node = Exec('echo hello', LocalExecInfo(collect_output=False))
+# Will collect AND print to the terminal
+node = Exec('echo hello', LocalExecInfo(collect_output=True))
+# Will collect BUT NOT print to the terminal
+node = Exec('echo hello', LocalExecInfo(collect_output=True,
+                                        hide_output=True))
+# Will collect, pipe to file, and print to terminal
+node = Exec('echo hello', LocalExecInfo(collect_output=True,
+                                        pipe_stdout='/tmp/stdout.txt',
+                                        pipe_stderr='/tmp/stderr.txt'))
+```
+
+This is useful if you have a program which runs using a daemon mode.
+
+## Executing an MPI program
+
+The following code will execute the "hostname" command on the local
+machine 24 times using MPI.
+
+```python
+from jarvis_util.shell.exec import Exec
+from jarvis_util.shell.mpi_exec import MpiExecInfo 
+
+node = Exec('hostname', MpiExecInfo(hostfile=None,
+                                    nprocs=24,
+                                    ppn=None,
+                                    collect_output=False))
+```
+
+## Executing an SSH program
+
+The following code will execute the "hostname" command on all machines
+in the hostfile
+
+```python
+from jarvis_util.shell.exec import Exec
+from jarvis_util.shell.pssh_exec import PsshExecInfo 
+
+node = Exec('hostname', PsshExecInfo(hostfile="/tmp/hostfile.txt",
+                                     collect_output=False))
+```
+
+## The contents of a hostfile
+
+A hostfile can have the following syntax:
+```
+ares-comp-01
+ares-comp-[02-04]
+ares-comp-[05-09,11,12-14]-40g
+```
+
+These will be expanded internally by PSSH and MPI.
+
+# Unit tests
+
+We run our unit tests in a docker container, which is located underneath
+the CI directory. This is because we need to test multi-node functionality,
+without having multiple nodes. To setup unit testing, perform the following:
+
+1. Install Docker
+2. Setup our "ci" container
+3. Run the unit tests
+
+```
+```
+
+# Contributing
+
+We use the Google Python Style guide (pylintrc).

CI/jarvis-util/bin/jarvis-imports

@@ -0,0 +1,8 @@
+#!/usr/bin/env python3
+
+from jarvis_util.util.import_all import *
+import pathlib
+import os
+
+
+build_global_import_from_bin('jarvis_util')

CI/jarvis-util/ci/cluster/Dockerfile

@@ -0,0 +1,55 @@
+# Install ubuntu 20.04
+FROM ubuntu:20.04
+LABEL maintainer="[email protected]"
+LABEL version="0.0"
+LABEL description="An example docker image"
+
+# Disable Prompt During Packages Installation
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Update ubuntu
+RUN apt update && apt install
+
+# Install some basic packages
+RUN apt install -y \
+    openssh-server \
+    sudo git nano vim \
+    docker \
+    mpich \
+    gcc \
+    g++ \
+    gfortran \
+    libtool \
+    libtool-bin \
+    automake \
+    autoconf
+
+# Create a new user
+RUN useradd -m sshuser
+RUN usermod -aG sudo sshuser
+RUN passwd -d sshuser
+
+# Copy the host's SSH keys
+# Docker requires COPY be relative to the current working
+# directory. We cannot pass ~/.ssh/id_rsa unfortunately...
+ENV SSHDIR=/home/sshuser/.ssh
+RUN sudo -u sshuser mkdir ${SSHDIR}
+COPY id_rsa ${SSHDIR}/id_rsa
+COPY id_rsa.pub ${SSHDIR}/id_rsa.pub
+
+# Authorize host SSH keys
+RUN sudo -u sshuser touch ${SSHDIR}/authorized_keys
+RUN cat ${SSHDIR}/id_rsa.pub >> ${SSHDIR}/authorized_keys
+
+# Set SSH permissions
+RUN chmod 700 ${SSHDIR}
+RUN chmod 644 ${SSHDIR}/id_rsa.pub
+RUN chmod 600 ${SSHDIR}/id_rsa
+RUN chmod 600 ${SSHDIR}/authorized_keys
+
+# Enable passwordless SSH
+RUN sed -i 's/#PermitEmptyPasswords no/PermitEmptyPasswords yes/' /etc/ssh/sshd_config
+
+# Start SSHD and wait forever
+RUN mkdir /run/sshd
+CMD ["/usr/sbin/sshd", "-D"]

CI/jarvis-util/ci/cluster/docker-compose.yml

@@ -0,0 +1,24 @@
+version: "3"
+
+services:
+  node1:
+    build: .
+    links:
+      - node2
+    networks:
+      - net
+    hostname: node1
+    stdin_open: true
+    tty: true
+
+  node2:
+    build: .
+    networks:
+      - net
+    hostname: node2
+    stdin_open: true
+    tty: true
+
+networks:
+  net:
+    driver: bridge