Running Rincondor Pool

See also RstatJobs (Eventually that page should be merged into this one.)

Running R in a HTCondor Pool

It works very well to move the R runtime in either Windows or Linux with the job. Then one actually runs a wrapper script to set up the runtime and place things as needed. The only moderately tricky part is handling non-included R Packages.

Though the commands are the same in both a Wiindows R developement location(One where a matching RTools is installed and R was built using those tools) the environment settings to have a local Package store found is a bit different.

I make sure that the directory RR/library exists and then I run this command and tar up the RR directory afRLIBSter:

  R CMD INSTALL --preclean -l ./RR/library package.tar.gx
  tar -zcvf RLIBS.tar.gz RR

With windows I ship cygwin tools for tar and gzip and associated DLLs so there is some similarity between extractions by the wrapper scripts.

Under Linux using perl I drop R into current directory and set these two things:

  $ENV{R_HOME} = "$Rlocation";
  $ENV{LD_LIBRARY_PATH} = "$Rlocation/lib";

If there is a library tar ball as mentioned above, the following is done:

  # do we have prebuilt libraries?
  my $renviron;
  if(-f "RLIBS.tar.gz") {
    system("tar -zxvf RLIBS.tar.gz");
    $ENV{HOME} = $location;
    $renviron = "$location/.Renviron";
    open(RLIB,">$renviron") or die "Can not create <$renviron>:$!\n";
    print RLIB "R_LIBS_USER=$location/RR/library\n";
    close(RLIB);
  }

Once that is done, the following starts R:

  $cmdtorun = "$Rlocation/bin/Rscript --no-save ./$scripts $realarg";
  print "about to execute <<$cmdtorun>>\n";
  $res = system("$cmdtorun");

Windows is similar but wrapper is a .bat script. Here is what we use in the Center for High Throughput Computing for packages, shared files for sets up jobs, job specific input, the runtime etc.

  dir
  time /t
  if not exist built-win32-R-2.10.1.tar.gz goto noruntime
  set R_LIBS_USER=RLIBS
  tar.exe -zxvf built-win32-R-2.10.1.tar.gz
  if not exist RLIBS.tar.gz goto nolibs
  tar.exe -zxvf RLIBS.tar.gz
  set R_LIBS_USER=RLIBS
  :nolibs
  if not exist %2.tar.gz goto nojobfiles
  tar -xvf %2.tar
  :nojobfiles
  if not exist sharedfiles.tar.gz goto nosharedfiles
  tar -zxvf sharedfiles.tar.gz
  :nosharedfiles
  mkdir tmp
  set PATH=%path%;.\bin
  dir
  dir .\bin
  echo Try job now
  Rscript.exe soartest.R
  dir
  echo Job completed
  :noruntime
  echo Failed to find runtime. This is bad!