SoftwareMogulWrapper

mogul wrapper using 2013 mogul with 2014 CSD to work around NFS (particularly v3) issue

N.B., Please contact buster-develop@globalphasing.com before trying to use this page. CCDC can now issue licence/database to enable users to run the 2013 mogul

• N.B., This method may not apply correct filters to mogul results

• There are issues using the latest 2014 mogul from a CSDS installation accessed from a NFS-mounted file system. For details see SoftwareMogulRelease2014NFSissues and GradeErrorMessageMogulKilledCPULimit

• It is possible to use a wrapper that uses local directories for copies of the csd and data directories see SoftwareMogulWrapperLocal

• The alternative described here uses 2013 mogul (that works fine with NFS v3) but with the 2014 CSD

• The method works fine with tests at Global Phasing using the standard (non-research partner) 2013 mogul and 2014 CSDS (once again non-research partner). Please note that if you are a research-partner Dave Bardwell at the CCDC says:

• It was written for a Consortium Member but it turned out they were happier with a full local installation of the 2014 CSDS.

• To use the wrapper download the tar ball containing wrapper script from mogul2013mogulwith2014csd.tar.gz
• Once this is downloaded unpack the tar ball:

          % tar xvf mogul2013mogulwith2014csd.tar.gz
          mogul2013mogulwith2014csd.bash

• the script will now need to edited, altering lines 8 and 12 to give the locations of the mogul executable and the two data directories on your site.

• Once you have done the editing, test that mogul2013mogulwith2014csd.bash works:
• If you are on workstation that can support mogul running in graphical mode check that the wrapper launches interactive mogul.
• for an extensive test see GradeErrorMessageMogulKilledCPULimit

• To use mogul2013mogulwith2014csd.bash with grade and buster-report simply set the environment variable BDG_TOOL_MOGUL to the full location of the wrapper on your system. For example

          % setenv BDG_TOOL_MOGUL /home/software/GPhL/extras/mogul2013mogulwith2014csd.bash

• this can be done either as part of the normal Global Phasing Software configuration (in $BDG_home/setup_local.csh / $BDG_home/setup_local.sh) or afterwards as a user.

Page by Oliver Smart. Original version 19th April 2014, last modified 1st May 2014. Address problems, corrections and clarifications to buster-develop@globalphasing.com