Ruby Installation on Hyak
Get an interactive compute node
Depends on rights to access of your account (only use one command). The compute node is required to install, check loaded modules and list of available modules.
- Have access to chem account:
salloc -A chem -p compute -N 1 -c 4 --mem=10G --time=1:00:00 - Have access to stf account:
salloc -A stf -p compute -N 1 -c 4 --mem=10G --time=1:00:00
Install rvm
1. Signature verification [2]
gpg --keyserver keyserver.ubuntu.com --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3 7D2BAF1CF37B13E2069D6956105BD0E739499BDB
2. Install the exact version (the latest version doesn’t support Ruby <2.0 [3])
curl -sSL https://get.rvm.io | bash -s -- --version 1.29.3
3. Activate rvm:
source /mmfs1/home/UW_net_ID/.rvm/scripts/rvm
4. Check the .bash_profile file and load:
- The following information should be added into the ~/.bash_profile if not, add it manually.
- View the file:
vi ~/.bash_profile - Add
[[ -s "$HOME/.rvm/scripts/rvm" ]] && source "$HOME/.rvm/scripts/rvm" # Load RVM into a shell session *as a function*
- View the file:
- Activate: source
~/.bash_profile
5. Check rvm version: the “rvm” command should work and the version should be 1.29.3
rvm -v
Install ruby [4]
1. disable auto dependency installation
rvm autolibs disable
2. install open ssl
rvm pkg install openssl
3. install ruby with specific version
rvm install ruby-1.9.3-p551 --force --with-openssl-dir=$HOME/.rvm/usr
4. check the default version
ruby -v
Note
- If anything wrong, you can delete the rvm package and redo it again by
rvm implode. - If the version is not 1.9.3, set the default version:
rvm --default use 1.9.3. - You may see there’s a warning called “It seems your ruby installation is missing psych (for YAML output). To eliminate this warning, please install libyaml and reinstall your ruby.” You will see this warning at the beginning of the LOG file after every run of PM6 or BOMD calculation. It’s fine and it won’t affect the results.