Reinstalling rocks

Question

I am new to using Rocks cluster. Recently, I tried to install a newer version of freetype. Before doing so, I did a yum remove freetype. On doing this all the softwares which were dependent on freetype were deleted including rocks. Later on, I found out that yum remove removes packages dependent on the packages to be deleted.

So now, on doing rocks list roll I get rocks: command not found. Whereas all data remains intact although the file system is not getting mounted on the compute nodes.

Also, when logging to the head node remotely I get

Last login: Wed Jun  3 20:04:59 2015 from 172.28.4.149
Rocks 6.0 (Mamba)
Profile built 09:16 19-Jun-2012
Kickstarted 15:10 19-Jun-2012
-bash: /opt/gridengine/util/arch: No such file or directory
-bash: /opt/gridengine/util/arch: No such file or directory
-bash: /opt/gridengine/util/arch: No such file or directory
-bash: /opt/gridengine/util/arch: No such file or directory
-bash: =/opt/gridengine/lib/:$: No such file or directory
declare -x ANT_HOME="/opt/rocks"
declare -x CVS_RSH="ssh"
declare -x G_BROKEN_FILENAMES="1"
declare -x HISTCONTROL="ignoredups"
declare -x HISTSIZE="1000"
declare -x HOME="/home/xyz"
declare -x HOSTNAME="hostname"
declare -x JAVA_HOME="/usr/java/latest"
declare -x LANG="en_IN"
declare -x LD_LIBRARY_PATH="/opt/openmpi/lib"
declare -x LESSOPEN="|/usr/bin/lesspipe.sh %s"
declare -x LOADEDMODULES="rocks-openmpi"
declare -x LOGNAME="xyz"
declare -x LS_COLORS="rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.tbz=01;31:*.tbz2=01;31:*.bz=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.rar=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:"
declare -x MAIL="/var/spool/mail/xyz"
declare -x MAVEN_HOME="/opt/maven"
declare -x MODULEPATH="/usr/share/Modules/modulefiles:/etc/modulefiles"
declare -x MODULESHOME="/usr/share/Modules"
declare -x MPIHOME="/opt/openmpi"
declare -x OLDPWD
declare -x PATH="/opt/openmpi/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/java/latest/bin:/opt/maven/bin:/opt/gridengine/bin/"
declare -x PWD="/home/xyz"
declare -x SGE_ARCH=""
declare -x SGE_CELL="default"
declare -x SGE_EXECD_PORT="537"
declare -x SGE_QMASTER_PORT="536"
declare -x SGE_ROOT="/opt/gridengine"
declare -x SHELL="/bin/bash"
declare -x SHLVL="1"
declare -x SSH_CLIENT="172.28.x.x 123 22"
declare -x SSH_CONNECTION="172.28.x.x 123 172.16.x.x 22"
declare -x SSH_TTY="/dev/pts/11"
declare -x TERM="xterm"
declare -x USER="xyz"
declare -x _LMFILES_="/usr/share/Modules/modulefiles/rocks-openmpi"

What do I do now? Please help!

Answer 1

It's probably easier and safer to start over and reinstall Rocks on your frontend.

That said, you could try one or more of the following with the understanding that they may not work and you'll have to reinstall...

• Parse the Yum log file (/var/log/yum.log) for dependant packages that were removed when you removed freetype and reinstall them, or...
• Parse the anaconda kickstart file (/root/anaconda-ks.cfg) for the packages and package groups installed during initial setup and reinstall them.

In the future, if you wish to update a specific RPM in the Rocks distro installed on your cluster you should follow the instructions in the Rocks User Guide.

For the current version of Rocks (6.2) this is in section 8.10.