Making fixed TMBTrees from non-fixed tmb's (on clued0)
------------------------------------------------------

Following Serban's instructions:

    69  7:35    mkdir serban_tmb_analyze
    70  7:35    cd serban_tmb_analyze
    71  7:36    cp -r /work/yaphank-clued0/serban/p16job .
    72  7:37    cd p16job
    73  7:37    setup D0RunII p16.00.00 -O SRT_QUAL=maxopt
    74  7:37    d0setwa
    77  7:39    ln -s /work/naia-clued0/bruce1/dimu_asym_2004/p140600/TMBTrees_155084_cosmicray/tmbfile1
    79  7:41    cp /work/yaphank-clued0/serban/p16job/Runme1.sh .

where Runme1.sh is

#!/bin/sh
. /etc/bashrc
# The next part sets the current directory to the work
  # directory as specified by the batch system
  # $WORKDIR is set by sourcing /usr/local/etc/pbssetup.sh
  # Some error checking is done.
  WORKDIR="NONE"
  if [ -r /usr/local/etc/pbssetup.sh ]; then
      . /usr/local/etc/pbssetup.sh
      echo "Found pbssetup.sh"
      echo "Workdir is now:"
      echo $WORKDIR
  else
      echo "ERROR: Could not find /usr/local/etc/pbssetup.sh"
      echo "ERROR: Maybe the partition is not mounted correctly"
      echo "ERROR: Exiting..."
      exit 1
  fi
  if [ $WORKDIR = "NONE" ]; then
      echo "ERROR: WORKDIR is not defined, problem with batch system!"
      echo "ERROR: Exiting..."
      exit 1
  fi
  if [ $WORKDIR = $HOME ]; then
      echo "ERROR: WORKDIR is defined to be your homedir"
      echo "ERROR: This means there is a problem with setting WORKDIR!"
      echo "ERROR: Exiting..."
      exit 1
  fi
# cd /work/yaphank-clued0/serban/d0correct_with_TMBAnalyze/
cd /work/naia-clued0/bruce1/dimu_asym_2004/p140600/serban_tmb_analyze/p16job
setup D0RunII p14.06.00
srt_setup SRT_QUAL=maxopt
d0setwa


  # Go to working directory on executing machine
cd $WORKDIR

# cp -r /work/yaphank-clued0/serban/d0correct_with_TMBAnalyze/bin/Linux2.4-KCC_4_0-maxopt/job1/* .
cp -r /work/naia-clued0/bruce1/dimu_asym_2004/p140600/serban_tmb_analyze/p16job/bin/Linux2.4-KCC_4_0-maxopt/job1/* .
TMBAnalyze_x -rcp runTMBTreeMaker.rcp -log test.log -input_file "tmbfile1"
# cp test.log /work/yaphank-clued0/serban/d0correct_with_TMBAnalyze/bin/Linux2.4-KCC_4_0-maxopt/job1/
cp test.log /work/naia-clued0/bruce1/dimu_asym_2004/p140600/serban_tmb_analyze/p16job/bin/Linux2.4-KCC_4_0-maxopt/job1/

*****
To submit the job:

cluesow -l cput=12:00:00 -l mem=500M Runme1.sh
******

The preceeding Runme1.sh did not work for me, so I submitted
the job with this rsubmit.sh:

#!/bin/sh
. /etc/bashrc
cd /work/naia-clued0/bruce1/dimu_asym_2004/p140600/serban_tmb_analyze/p16job
setup D0RunII p16.00.00 -O SRT_QUAL=maxopt
d0setwa
# first:  ln -s your_input_file inputfile
TMBAnalyze_x -rcp runTMBTreeMaker.rcp -log test.log -input_file "tmbfile3"
#
# to submit:
# cluesow -l cput=12:00:00 -l mem=500M rsubmit.sh
# to check status:
# qstat -u bruce1
*******************************************

Making TMBTrees (without fixing) from tmb's
-------------------------------------------

cd /work/naia-clued0/bruce1/dimu_asym_2004/p140600
setup D0RunII p14.06.00
setup d0cvs
setenv SCRATCH /work/naia-clued0/bruce1/scratch
newrel -t p14.06.00 wa_tmb_analyze
cd wa_tmb_analyze
addpkg tmb_analyze
gmake all
d0setwa
cp tmb_analyze/rcp/runTMBTreeMaker.rcp .

To run interactively:

TMBAnalyze_x -rcp runTMBTreeMaker.rcp -log tmb.log -input_file "<yourfile>"

To run in batch:

edit a file "rsubmit.sh" and put the following lines in it:

#!/bin/sh
. /etc/bashrc
cd /work/naia-clued0/bruce1/dimu_asym_2004/p140600/wa_tmb_analyze
setup D0RunII p14.06.00
d0setwa
TMBAnalyze_x -rcp runTMBTreeMaker.rcp -log tmb.log -input_file "<yourfile>"
#

and make "rsubmit" executable; then submit the file

cluesow -l cput=12:00:00 -l mem=500M rsubmit.sh