Torque

A hub for notes about torque.

Uninstalling Torque from modules

Torque should always be a system program, not a module. These are the steps for pollock, as done by Charlie. Substitute appropriate server names, and note that different systems have different ways of configuring software to launch on system start.

• uninstall torque from modules
  • Make a tarball of /mounts/pollock/software/torque and save it to the root or sysadmin directory (this will save you problems)
  • rm -rf /mounts/pollock/software/Modules/MODVER/modulefiles/torque
  • rm -rf /mounts/pollock/software/torque
  • check with “module avail”

• uninstall boost from modules
  • as above with s/torque/boost/

• install torque dependencies
  • yum install libxml2-devel openssl-devel gcc gcc-c++ boost boost-devel

• (aside, install locate, yum install mlocate and updatedb as root)

• (aside, fix modules install, cleanup /etc/bashrc, profile, and profile.d/modules.sh; this fixed the MANPATH problem too)

• (aside, fix the python 3.5 install, s/bronte/pollock in setup files, change to correct version (3.6), reset paths)

Installing torque

• • (references: https://www.webmo.net/support/torque.html, http://docs.adaptivecomputing.com/torque/6-0-1/help.htm#topics/hpcSuiteInstall/manual/1-installing/installingTorque.htm)
  • stop and disable the local firewalld (service stop and service disable)
  • download tarball from adaptive computing (v6.0.0.1), unpack, cd
  • ./configure && make && make install
  • check file contents of /var/spool/torque/server_name
  • add trqauthd to system startup and start
  • ./torque.setup root
  • setup /var/spool/torque/server_priv/nodes #see http://docs.adaptivecomputing.com/torque/6-0-1/help.htm#topics/torque/1-installConfig/specifyComputeNodes.htm
  • add pbs_server to system startup and start
  • add pbs_sched to system startup and start
  • build the client packages and install # both mom and clients as per the webmo link
  • qmgr -c “set server scheduling = True”
  • test with qsub -I
  • reboot server and test again

install mothur into modules

• • (aside, cleanup mess in /mounts/pollock/software/mothur*)
  • download latest version (1.41.3 as of this writing) in source form (NOT binary) into /mounts/pollock/software/mothur
  • unpack tarball, rename directory to use version (e.g. 1.41.3) (note this is the pattern to follow for all packages that we maintain multiple versions of) Leave tarball.
  • Edit the Makefile # for reference, `diff Makefile Makefile.original`
  • make (this takes a bit, -j 4 helps a bit)
  • quick test of the resulting binary ./mothur -v
  • either make /mounts/pollock/software/Modules/MODVER/modulefiles/mothur or add a version file to it as appropriate
  • test with module load mothur and mothur -v