From Earlham CS Department
Revision as of 11:52, 25 June 2019 by Craigje (talk | contribs)
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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/; 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

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