Some Grid Engine is a fork of Son of Grid Engine at University of Liverpool, with SOME improvement.
We have been using and maintaining this software at Michigan Neuroscience Institute, University of Michigan for over a decade. It is stable and good enough for a small HPC cluster. Here we share it on github, hoping more peoples can benefit from it.
- Support for submitting jobs via SystemD which also allows to enforce memory/cpu limitations via kernel cgroups. Many thanks to fretn:master and ondrejv2:master!
- CMake compiling support. This paved the way for easier maintenance in future. It took 38 seconds to compile in parallel and install on an 8-core old machine, while it took 302 seconds with the legacy SGE way, and 377 seconds with makepkg.
- Fixed a permission error introduced since systemd 241 in 2019 during installation, if SGE is installed as non-root on production system
- Compatible with openssl-1.1.1
- All C compling warning are fixed on Arch Linux and Void Linux. Most of them were caused by 'smarter' gcc, new SSL, new GLIBC, obsolete function such 'sigignore', depreciated function such as 'readdir_r', etc.
- Underscore in port service name 'sge_qmaster/sge_execd' is changed to hyphen in all C files and shell scripts, saving us from modifying /etc/services each time
- Supports both systemd and runit on Void Linux
- Version is changed to the commit version of this github repo
- CMake
cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/opt/sge
cmake --build build -j
sudo cmake --install build
Please check the tested environment below in case of any compiling issue.
- Legacy SGE installation on modern Linux distributions, check the original source/README.BUILD for detail
make
sudo make install
- Legacy SGE installation on Arch Linux
cp PKGBUILD.in PKGBUILD
makepkg
sudo pacman -U sge-r*.pkg.tar.zst
- step 1, as root.
cd /opt/sge
yes "" | ./install_qmaster
yes "" | ./install_execd
source /opt/sge/default/common/settings.sh
qhost -q #you should be able to see five lines of output
qconf -as $HOSTNAME #add this node as submit host
please make sure there is no SGE process running with 'ps -ef |grep sge' and directory '/opt/sge/default' is removed if you want to run the commands above again
- step 2, as a regular account
source /opt/sge/default/common/settings.sh
echo hostname | qsub -cwd
watch qstat #check job status
ls STDIN.* #check job output
All SGE services are running under user 'sge' for security reason, as this is production system.
Tested with the latest Arch Linux on Oct 27, 2020, on two nodes created by daiker with command 'daiker run -PT 22 ...'
Assuming master node hostname is 'master-node', and execution node hostname is 'exec-node'. /etc/hosts on both nodes have these two entries
10.1.1.1 master-node
10.1.1.2 exec-node
- step 1, on both nodes as root
ping master-node
ping exec-node
pacman -Sy --needed git cmake make gcc openmotif hwloc vi inetutils
useradd -r -d /opt/sge sge
mkdir /opt/sge
chown sge /opt/sge
git clone https://github.com/daimh/sge.git
cd sge
cmake -S . -B build -DCMAKE_INSTALL_PREFIX=/opt/sge
cmake --build build -j
cmake --install build
- step 2, on master-node as root
cd /opt/sge
yes "" | ./install_qmaster
source /opt/sge/default/common/settings.sh
qconf -ah exec-node
qconf -as exec-node
- step 3, on exec-node as root
mkdir -p /opt/sge/default
chown -R sge /opt/sge/default
scp -pr master-node:/opt/sge/default/common /opt/sge/default/common
cd /opt/sge
yes "" | ./install_execd
source /opt/sge/default/common/settings.sh
qhost -q
su - sge
- step 4, on exec-node as sge
source /opt/sge/default/common/settings.sh
echo hostname | qsub -cwd
watch qstat
cat STDIN.*
- Arch Linux, 2021-06-21
pacman -Sy --needed git cmake make gcc openmotif hwloc vi inetutils
- Debian Buster, 2021-06-21, cmake 3.20.5 downloaded from cmake.org
apt install git build-essential libhwloc-dev libssl-dev libtirpc-dev libmotif-dev libxext-dev libncurses-dev libdb5.3-dev libpam0g-dev
- Ubuntu Server 20.04, 2021-06-21
apt install git build-essential libhwloc-dev libssl-dev libtirpc-dev libmotif-dev libxext-dev libncurses-dev libdb5.3-dev libpam0g-dev cmake
- CentOS 8.3, 2021-06-21, with SELinux set to permissive
dnf group install "Development Tools"
dnf --enablerepo=powertools install hwloc-devel openssl-devel libtirpc-devel motif-devel ncurses-devel libdb-devel pam-devel cmake
- Void Linux, 2021-06-21, x86_64, Glibc
xbps-install cmake make gcc openssl-devel motif-devel hwloc libhwloc-devel libtirpc-devel ncurses-devel pam-devel
Contributions are always welcome!
Written by Manhong Dai
Copyright © 2021 University of Michigan. License SISSL
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Thomas Wilson, M.D., Ph.D. Professor of Pathology, UMICH
Ruth Freedman, MPH, former administrator of MNI, UMICH
Fan Meng, Ph.D., Research Associate Professor, Psychiatry, UMICH
Huda Akil, Ph.D., Director of MNI, UMICH
Stanley J. Watson, M.D., Ph.D., Director of MNI, UMICH
Also thanks to https://arc.liv.ac.uk/trac/SGE, Sun, and Oracle