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:

You will need a valid 2014 licence key that the 2013 software understands... as research partners you have a run anywhere version of the 2014 software, but its licence key will not be understood by the older 2013 software as that was created prior to the run anywhere licensing changes. So we would need to create a valid key for you. The simplest type of key to generate would be an IP based one, so we would need to know the IP keys of the computers that would be running these searches.

• 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.

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