updated slurm for reservoir container

Dockerfile.base

@@ -0,0 +1,30 @@
+FROM rocker/geospatial:4.3.0
+MAINTAINER "Noam Ross" [email protected]
+
+ENV PYTHON_VENV_PATH=/opt/venv/reticulate
+RUN /rocker_scripts/install_python.sh
+
+COPY scripts/install_system_tools.sh /reservoir_scripts/install_system_tools.sh
+RUN /reservoir_scripts/install_system_tools.sh
+
+COPY scripts/install_eigen_stan_inla.sh /reservoir_scripts/install_eigen_stan_inla.sh
+RUN /reservoir_scripts/install_eigen_stan_inla.sh
+
+COPY scripts/install_r_pkgs_compiled.sh /reservoir_scripts/install_r_pkgs_compiled.sh
+RUN /reservoir_scripts/install_r_pkgs_compiled.sh
+
+COPY scripts/install_r_pkgs_other.sh /reservoir_scripts/install_r_pkgs_other.sh
+RUN /reservoir_scripts/install_r_pkgs_other.sh
+
+ENV TZ=America/New_York
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
+  && echo $TZ > /etc/timezone \
+  && dpkg-reconfigure --frontend noninteractive tzdata
+
+COPY /scripts/server_config.sh /reservoir_scripts/server_config.sh
+COPY config /reservoir_config
+RUN /reservoir_scripts/server_config.sh
+
+RUN locale-gen en_US.UTF-8
+
+EXPOSE 22 8787

Reservoir /Dockerfile.gpu → Dockerfile.gpu

@@ -4,13 +4,6 @@ MAINTAINER "Noam Ross" [email protected]
 ENV CUDAToolkit_ROOT=/usr/local/cuda
 ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64
 
-# Install SLURM client
-RUN apt-get update && apt-get install -y slurm-client
-
-# Add SLURM configuration file
-ADD slurm.conf /etc/slurm-llnl/slurm.conf
-
-# All your previous installation scripts and configurations
 COPY scripts/install_xgboost.sh /reservoir_scripts/install_xgboost.sh
 RUN /reservoir_scripts/install_xgboost.sh
 

README.md

@@ -1,2 +1,19 @@
-# slurm-containerized-hpc-environment
-The goal of this project is to outline the strategies for integrating Simple Linux Utility for Resource Management(SLURM) into our existing High-Performance Computing(HPC) platform.
+# Reservoir: The EHA Data Science Container
+
+A docker image for EHA's modeling and analytics work servers.
+
+[![GitHub Actions CI](https://github.com/ecohealthalliance/reservoir/actions/workflows/build-containers.yml/badge.svg)](https://github.com/ecohealthalliance/reservoir/actions/workflows/build-containers.yml)
+[![license](https://img.shields.io/badge/license-GPLv2-blue.svg)](https://opensource.org/licenses/GPL-2.0)
+
+
+
+*reservoir* is an image built for the modeling and analytics workflow at [EcoHealth Alliance](ecohealthalliance.org).  It build on top of the [rocker project](https://www.rocker-project.org/) `geospatial` and GPU-enabled `ml-verse` images and adds commonly used other R packages, system tools, SSH and mosh access, and GPU-compiled tools.
+
+Get the images at
+
+```
+docker pull ghcr.io/ecohealthalliance/reservoir:base # The primary image
+
+docker pull ghcr.io/ecohealthalliance/reservoir:gpu # for hosts with GPUs
+```
+

build-and-push.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+set -e
+set -x
+
+for tag in base gpu
+do
+  image=ecohealthalliance/reservoir:$tag
+  time docker pull $image > /dev/null
+  time docker build -f Dockerfile.$tag --cache-from $image -t $image .
+  docker push $image > /dev/null
+done

build.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+set -e 
+set -x
+
+for tag in base gpu
+do
+  image=ecohealthalliance/reservoir:$tag
+ # time docker pull $image > /dev/null
+  time docker build -f Dockerfile.$tag --cache-from $image -t $image .
+done

config/Makevars.site

@@ -0,0 +1,13 @@
+NPROC=$(shell nproc)
+NPROC_MIN=$(shell $(($NPROC>4?4:$NPROC)))
+MAKE=nice -n 10 make
+MAKEFLAGS+="-j $(NPROC_MIN)"
+VER=
+CCACHE=
+CC=$(CCACHE) gcc$(VER)
+CXX=$(CCACHE) g++$(VER)
+CXX11=$(CCACHE) g++$(VER)
+CXX14=$(CCACHE) g++$(VER)
+FC=$(CCACHE) gfortran$(VER)
+F77=$(CCACHE) gfortran$(VER)
+

config/Renviron.site

@@ -0,0 +1,3 @@
+IS_RESERVOIR=true
+TEMPDIR=~/.tmp
+R_LIBS_USER=~/R/%p-library/%v

config/Rprofile.site

@@ -0,0 +1,52 @@
+# R Startup configuration
+
+## Set CRAN mirror
+options(repos = c(
+  CRAN = "https://packagemanager.rstudio.com/all/__linux__/jammy/latest"
+))
+
+## Reduce raster tempfile generation
+options(rasterTmpTime = 1, rasterMaxMemory = 1e10)
+
+## Set temp directory inside user folders
+if(!dir.exists(path.expand("~/tmp"))) dir.create(path.expand("~/tmp"))
+
+if("unixtools" %in% utils::installed.packages()) {
+  unixtools::set.tempdir(path.expand("~/tmp"))
+}
+
+## Make sure users have home R libraries
+if(!dir.exists(Sys.getenv("R_LIBS_USER"))) dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)
+.libPaths(Sys.getenv("R_LIBS_USER"))
+
+# Configure httr to perform out-of-band authentication if HTTR_LOCALHOST
+# is not set since a redirect to localhost may not work depending upon
+# where this Docker container is running.
+if(is.na(Sys.getenv("HTTR_LOCALHOST", unset=NA))) {
+  options(httr_oob_default = TRUE)
+}
+
+## Set to single threaded unless user has environment variables
+##    set to the contrary
+
+local({
+  if(require("RhpcBLASctl", quietly=TRUE)) {
+    if(Sys.getenv("OPENBLAS_NUM_THREADS")=="" &&
+       Sys.getenv("OMP_NUM_THREADS")=="") {
+       RhpcBLASctl::blas_set_num_threads(1)
+    }
+  }
+})
+
+## Startup message
+#.First <- function() {
+#  ("\014")
+#  message("Welcome to *reservoir*, the EcoHealth Alliance Modeling &\n",
+#      "Analytics machine image. Please read our users' guide at\n",
+#      "https://github.com/ecohealthalliance/eha-servers.\n",
+#      "\n",
+#      R.version$version.string, "\n",
+#      "Cores available: ", parallel::detectCores(),"\n"
+#      )
+#
+#}

config/bash_settings.sh

@@ -0,0 +1,54 @@
+# set a fancy prompt (non-color, overwrite the one in /etc/profile)
+#PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
+
+# Commented out, don't overwrite xterm -T "title" -n "icontitle" by default.
+# If this is an xterm set the title to user@host:dir
+#case "$TERM" in
+#xterm*|rxvt*)
+#    PROMPT_COMMAND='echo -ne "\033]0;${USER}@${HOSTNAME}: ${PWD}\007"'
+#    ;;
+#*)
+#    ;;
+#esac
+
+# enable bash completion in interactive shells
+if ! shopt -oq posix; then
+  if [ -f /usr/share/bash-completion/bash_completion ]; then
+    . /usr/share/bash-completion/bash_completion
+  elif [ -f /etc/bash_completion ]; then
+    . /etc/bash_completion
+  fi
+fi
+
+# if the command-not-found package is installed, use it
+if [ -x /usr/lib/command-not-found -o -x /usr/share/command-not-found/command-not-found ]; then
+        function command_not_found_handle {
+                # check because c-n-f could've been removed in the meantime
+                if [ -x /usr/lib/command-not-found ]; then
+                   /usr/lib/command-not-found -- "$1"
+                   return $?
+                elif [ -x /usr/share/command-not-found/command-not-found ]; then
+                   /usr/share/command-not-found/command-not-found -- "$1"
+                   return $?
+                else
+                   printf "%s: command not found\n" "$1" >&2
+                   return 127
+                fi
+        }
+fi
+
+# Show a color prompt with path and git status
+parse_git_branch() {
+     git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/ (\1)/'
+}
+export PS1="\u@\h \[\033[32m\]\w\[\033[33m\]\$(parse_git_branch)\[\033[00m\]$ "
+
+# Auto-login to byobu by default
+#export LC_BYOBU=1
+
+# Essential gurobi variables
+export GUROBI_HOME="/opt/gurobi752/linux64"
+export PATH="${PATH}:${GUROBI_HOME}/bin"
+export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${GUROBI_HOME}/lib"
+export EDITOR=/usr/bin/micro
+export GPG_TTY=$(tty)

config/byobu_status

@@ -0,0 +1,37 @@
+#    status - Byobu's default status enabled/disabled settings
+#
+#      Override these in $BYOBU_CONFIG_DIR/status
+#      where BYOBU_CONFIG_DIR is XDG_CONFIG_HOME if defined,
+#      and $HOME/.byobu otherwise.
+#
+#    Copyright (C) 2009-2011 Canonical Ltd.
+#
+#    Authors: Dustin Kirkland <[email protected]>
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, version 3 of the License.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# Status beginning with '#' are disabled.
+
+# Screen has two status lines, with 4 quadrants for status
+screen_upper_left="color"
+screen_upper_right="color whoami hostname ip_address menu"
+screen_lower_left="color logo distro release #arch session"
+screen_lower_right="color network #disk_io custom #entropy raid reboot_required updates_available #apport #services #mail users uptime #ec2_cost #rcs_cost #fan_speed #cpu_temp battery wifi_quality #processes load_average cpu_count cpu_freq memory #swap #disk #time_utc date time"
+
+# Tmux has one status line, with 2 halves for status
+tmux_left=" #logo #distro #release #arch session"
+# You can have as many tmux right lines below here, and cycle through them using Shift-F5
+#tmux_right=" #network disk_io #custom #entropy raid #reboot_required #updates_available #apport #services #mail users #uptime #ec2_cost #rcs_cost #fan_speed cpu_temp #battery #wifi_quality processes load_average cpu_count cpu_freq memory swap #disk whoami #hostname #ip_address #time_utc date time"
+tmux_right=" #network #disk_io #custom #entropy #raid #reboot_required #updates_available #apport #services #mail users #uptime #ec2_cost #rcs_cost #fan_speed #cpu_temp #battery #wifi_quality #processes cpu_count load_average #cpu_freq memory #swap disk whoami hostname #ip_address #time_utc date time"
+#tmux_right="network #disk_io custom #entropy raid reboot_required updates_available #apport #services #mail users uptime #ec2_cost #rcs_cost #fan_speed #cpu_temp battery wifi_quality #processes load_average cpu_count cpu_freq memory #swap #disk #whoami #hostname ip_address #time_utc date time"
+#tmux_right="#network disk_io #custom entropy #raid #reboot_required #updates_available #apport #services #mail #users #uptime #ec2_cost #rcs_cost fan_speed cpu_temp #battery #wifi_quality #processes #load_average #cpu_count #cpu_freq #memory #swap whoami hostname ip_address #time_utc disk date time"

config/byobu_statusrc

@@ -0,0 +1,78 @@
+#    statusrc - Byobu's default status configurations
+#
+#      Override these in $BYOBU_CONFIG_DIR/statusrc
+#      where BYOBU_CONFIG_DIR is XDG_CONFIG_HOME if defined,
+#      and $HOME/.byobu otherwise.
+#
+#    Copyright (C) 2009-2011 Canonical Ltd.
+#
+#    Authors: Dustin Kirkland <[email protected]>
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, version 3 of the License.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# Configurations that you can override; if you leave these commented out,
+# Byobu will try to auto-detect them.
+
+# This should be auto-detected for most distro, but setting it here will save
+# some call to lsb_release and the like.
+#BYOBU_DISTRO=Ubuntu
+
+# Default: depends on the distro (which is either auto-detected, either set
+# via $DISTRO)
+#LOGO="\o/"
+
+# Abbreviate the release to N characters
+# By default, this is disabled.  But if you set RELEASE_ABBREVIATED=1
+# and your lsb_release is "precise", only "p" will be displayed
+#RELEASE_ABBREVIATED=1
+
+# Default: /
+MONITORED_DISK=/home
+
+# Minimum disk throughput that triggers the notification (in kB/s)
+# Default: 50
+#DISK_IO_THRESHOLD=50
+
+# Default: eth0
+#MONITORED_NETWORK=eth0
+
+# Unit used for network throughput (either bits per second or bytes per second)
+# Default: bits
+#NETWORK_UNITS=bytes
+
+# Minimum network throughput that triggers the notification (in kbit/s)
+# Default: 20
+#NETWORK_THRESHOLD=20
+
+# You can add an additional source of temperature here
+#MONITORED_TEMP=/proc/acpi/thermal_zone/THM0/temperature
+
+# Default: C
+#TEMP=F
+
+#SERVICES="eucalyptus-nc|NC eucalyptus-cloud|CLC eucalyptus-walrus eucalyptus-cc|CC eucalyptus-sc|SC"
+
+#FAN=$(find /sys -type f -name fan1_input | head -n1)
+
+# You can set this to 1 to report your external/public ip address
+# Default: 0
+#IP_EXTERNAL=0
+
+# The users notification normally counts ssh sessions; set this configuration to '1'
+# to instead count number of distinct users logged onto the system
+# Default: 0
+#USERS_DISTINCT=0
+
+# Set this to zero to hide seconds int the time display
+# Default 1
+#TIME_SECONDS=0

config/byoburc

@@ -0,0 +1,29 @@
+###############################################################################
+#    Load:
+#     * the stock byobu profile
+#     * any windows
+#     * and the local byoburc (instead of .screenrc)
+#    Used at startup but not profile refresh
+#
+#    Copyright (C) 2009-2011 Canonical Ltd.
+#
+#    Authors: Dustin Kirkland <[email protected]>
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, version 3 of the License.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+###############################################################################
+
+set -g mouse on
+
+source $BYOBU_CONFIG_DIR/profile
+source $BYOBU_WINDOWS
+source $BYOBU_CONFIG_DIR/.screenrc

config/ccache.conf

@@ -0,0 +1,6 @@
+max_size = 5.0G
+# important for R CMD INSTALL *.tar.gz as tarballs are expanded freshly -> fresh ctime
+sloppiness = include_file_ctime
+# also important as the (temp.) directory name will differ
+hash_dir = false
+# cache_dir = /shared/ccache_shared_cache

config/motd.sh

@@ -0,0 +1,11 @@
+#!/bin/sh
+
+B="\033[34m"
+R="\033[31m"
+S="\033[34;1m"
+N="\033[0m"
+
+echo "$B Welcome to$S reservoir$N$B, the EcoHealth Alliance Modeling &"
+echo "$B Analytics machine image. Please read our users' guide at"
+echo "$B https://github.com/ecohealthalliance/eha-servers."
+echo "$N"

config/rserver.conf

@@ -0,0 +1,4 @@
+# R Studio server configuration file. Put in /etc/rstudio/rserver.conf
+
+auth-timeout-minutes=0
+auth-stay-signed-in-days=30