Updated submit.org

Made it a bit more sane.

Cam up with a concept of a 'task' which is the directory in which the
submission script is run. Then renamed variables to reflect this.

Also simplified the path variables and did away with it being
dependent on your $HOME or whatever. Now the user does that in the
noweb.org file and just gives the preceeding path.

Also moved out the whole environmental variable section to another
noweb insertion point, this makes the script much shorter and comprehendable.

submit.org

@@ -1,159 +1,117 @@
 * Fill in these fields here:
+** task name
 
-#+name: job-name
+When running PBS scripts you might want to run something multiple
+times or have to deal with debugging which can become messy.
+We organize by "task", which is a unit of something we want to get
+done, and then organize all the outputs it produces in a sane way.
+
+The task name must (and should) also be the name of the directory the
+task is set up in.
+
+#+name: task-name
 #+BEGIN_SRC bash
-  test-job-name
+  test-task-name
 #+END_SRC
 
+** task dir
+
+Task directories should be organized in some way. This variable is the
+path preceeding your task dir.
+
+For instance if you working in `$HOME/this_project/task1` then your
+task dir would be `$HOME/this_project`.
+
+#+name: task-dir-path
+#+BEGIN_SRC bash
+  $MY_DICKSON_LAB
+#+END_SRC
+
+
+** wall time
 
 #+name: walltime
 #+BEGIN_SRC bash
-  168:00:00
+  5:00
 #+END_SRC
 
+** memory
 #+name: memory
 #+BEGIN_SRC bash
-  64gb
+  4gb
 #+END_SRC
 
+** number of nodes
 #+name: num-nodes
 #+BEGIN_SRC bash
-  2
+  1
 #+END_SRC
 
+** number of processors
 #+name: num-processors
 #+BEGIN_SRC bash
-  8
+  1
 #+END_SRC
 
+** number of GPUs
+
 #+name: num-gpus
 #+BEGIN_SRC bash
-  8
+  0
 #+END_SRC
 
+** feature
+
+One use for this is to put in 'gpgpu:intel16'.
+
 #+name: feature
 #+BEGIN_SRC bash
-  'gpgpu:intel16'
+  ''
 #+END_SRC
 
+** email
 #+name: email
 #+BEGIN_SRC bash
   samuel.lotz@gmail.com
 #+END_SRC
 
-#+name: base-name
-#+BEGIN_SRC bash
-  test-job-name
-#+END_SRC
-
-#+name: proj-dir-name
-#+BEGIN_SRC bash
-  test-project
-#+END_SRC
-
+** GNU module
 #+name: gnu-module
 #+BEGIN_SRC bash
   GNU/4.8.3
 #+END_SRC
 
+** CUDA module
 #+name: cuda-module
 #+BEGIN_SRC bash
   CUDA/7.0
 #+END_SRC
 
+** script parameters
 #+name: script-parameters
 #+BEGIN_SRC bash
   TEST_PARAM="HELLO"
   TEST_VAL=8
 #+END_SRC
 
+** script
 #+name: script
 #+BEGIN_SRC bash
   for ((x=0; x<=${TEST_VAL}; x++)); do
       echo $TEST_PARAM > "file_$TEST_VAL.txt" 2> $LOG;
   done
 #+END_SRC
 
-* Noweb Template
-#+BEGIN_SRC bash :tangle submit.pbs :noweb yes :shebang #!/bin/sh -login
-  #PBS -N <<job-name>>
-  #PBS -l walltime=<<walltime>>
-  #PBS -l mem=<<memory>>
-  #PBS -l nodes=<<num-nodes>>:ppn=<<num-processors>>:gpus=<<num-gpus>>
-  #PBS -l feature=<<feature>>
-  #PBS -e pbs.err
-  #PBS -o pbs.out
-  #PBS -M <<email>>
-  #PBS -m abe
 
-  #------------------------------
+* Additional Tweaks
 
-  # script for running jobs on HPCC
+These are things that change less often but are particular to a
+particular place and user.
 
+** Environmental Variables
 
-  ## set the base name for this script
-  ################################################################################
-  # base directory for this script
-  BASE="<<base-name>>"
-  PROJDIR="<<proj-dir>>"
-  BASEDIR="$PROJDIR/$BASE"
-
-  ################################################################################
-
-  # the job name
-  JOBNAME=${BASE}-${PBS_JOBID}
-  # directories, keep these named the same as this is a common pattern
-  # the main development directory
-  DEVDIR=$MY_DICKSON_LAB/$BASEDIR
-  # the directory with all of the input
-  INPUTDIR=$DEVDIR/input
-  # directory to put job results in
-  JOBSDIR=$DEVDIR/jobs
-  # the directory for the output of this job
-  JOBDIR=$JOBSDIR/$PBS_JOBID
-  # the directory output will be put into after completion
-  OUTPUTDIR=$JOBDIR/output
-  # directory to execute code in
-  # EXECDIR=$TMPDIR
-  # EXECDIR=$MY_DICKSON_SCRATCH/$JOBNAME
-  ###### README Problems with Scratch so I will just run in the jobs dir
-  EXECDIR=$JOBDIR
-  # directory to put temporary output in
-  EXECOUTPUTDIR=$EXECDIR/output
-  # directories to copy the stdout and stderr from scripts
-  STDOUT=$JOBDIR/stdout
-  STDERR=$JOBDIR/stderr
-  # we should redirect our own output streams but we will catch the PBS
-  # files as well
-  PBS_STDOUT=$PBS_O_WORKDIR/pbs.out
-  PBS_STDERR=$PBS_O_WORKDIR/pbs.err
-  # log files
-  LOG=$JOBDIR/log
-
-  # make these directories if they do not exist
-  mkdir -p $EXECDIR
-  mkdir -p $EXECOUTPUTDIR
-  mkdir -p $JOBDIR
-  mkdir -p $OUTPUTDIR
-  mkdir -p $STDOUT
-  mkdir -p $STDERR
-  mkdir -p $PBS_STDOUT
-  mkdir -p $PBS_STDERR
-  echo "Starting Log file" 1> $LOG 2> $LOG
-
-  # initial
-  #----------------------------------------
-  # load profile
-  source /etc/profile
-  # load hpcc modules
-  source /opt/software/modulefiles/setup_modules.sh
-  # load specific library modules
-  module load <<gnu-module>>
-  module load <<cuda-module>>
-
-  # general paths
-  #----------------------------------------
-
+#+name: env-vars
+#+BEGIN_SRC bash
   # scratch directory
   export SCRATCHDIR=/mnt/ls15/scratch
   # your home scratch
@@ -206,21 +164,13 @@
   # PATH
   export PATH=$ANACONDA_BIN:${DICKSON_LAB_BIN}:${OPENMM_ROOT_DIR}/bin:${MMTSBDIR}/perl:${DICKSON_LAB_PROGS}/charmm/exec/gnu:${PATH}
 
-  # check to make sure all these paths are correct
-  echo "" 1>> $LOG 2>> $LOG
-  echo "LOG $LOG" 1>> $LOG 2>> $LOG
-
-  # change to the exec dir
-  cd $EXECDIR
-
   # check to make sure all these paths for the job are correct
   echo "" 1>> $LOG 2>> $LOG
   echo "LOG $LOG" 1>> $LOG 2>> $LOG
   echo "PBS_JOBID $PBS_JOBID" 1>> $LOG 2>> $LOG
-  echo "BASE $BASE" 1>> $LOG 2>> $LOG
-  echo "BASEDIR $BASEDIR" 1>> $LOG 2>> $LOG
+  echo "TASK $TASK" 1>> $LOG 2>> $LOG
+  echo "TASKDIR $TASKDIR" 1>> $LOG 2>> $LOG
   echo "JOBNAME $JOBNAME" 1>> $LOG 2>> $LOG
-  echo "DEVDIR $DEVDIR" 1>> $LOG 2>> $LOG
   echo "JOBSDIR $JOBSDIR" 1>> $LOG 2>> $LOG
   echo "JOBDIR $JOBDIR" 1>> $LOG 2>> $LOG
   echo "OUTPUTDIR $OUTPUTDIR" 1>> $LOG 2>> $LOG
@@ -233,6 +183,103 @@
   cat $PBS_NODEFILE 1>> $LOG 2>> $LOG
   echo ""  1>> $LOG 2>> $LOG
 
+#+END_SRC
+
+
+
+
+* Noweb Template
+
+When you export/tangle this script the named code blocks will be
+inserted into their targets marked by `<<my-target>>` for a target
+called `my-target`.
+
+#+BEGIN_SRC bash :tangle submit.pbs :noweb yes :shebang #!/bin/sh -login
+  #PBS -N <<task-dir>>
+  #PBS -l walltime=<<walltime>>
+  #PBS -l mem=<<memory>>
+  #PBS -l nodes=<<num-nodes>>:ppn=<<num-processors>>:gpus=<<num-gpus>>
+  #PBS -l feature=<<feature>>
+  #PBS -e pbs.err
+  #PBS -o pbs.out
+  #PBS -M <<email>>
+  #PBS -m abe
+
+  #------------------------------
+
+  # script for running jobs on HPCC
+
+
+  ## set the base name for this script
+  ################################################################################
+  # base directory for this script
+  TASK="<<task-name>>"
+  TASKDIR="<<task-dir-path>>/$TASK"
+
+  ################################################################################
+
+  # the job name
+  JOBNAME=${TASK}-${PBS_JOBID}
+  # the directory with all of the input
+  INPUTDIR=$TASKDIR/input
+  # directory to put job results in
+  JOBSDIR=$TASKDIR/jobs
+  # the directory for the output of this job
+  JOBDIR=$JOBSDIR/$JOBNAME
+  # the directory output will be put into after completion
+  OUTPUTDIR=$JOBDIR/output
+
+  # directory to execute code in
+  # EXECDIR=$TMPDIR
+  # EXECDIR=$MY_DICKSON_SCRATCH/$JOBNAME
+  ###### README Problems with Scratch so I will just run in the jobs dir
+  EXECDIR=$JOBDIR
+  # directory to put temporary output in
+  EXECOUTPUTDIR=$EXECDIR/output
+
+  # directories to copy the stdout and stderr from scripts
+  STDOUT=$JOBDIR/stdout
+  STDERR=$JOBDIR/stderr
+  # we should redirect our own output streams but we will catch the PBS
+  # files as well
+  PBS_STDOUT=$TASKDIR/pbs.out
+  PBS_STDERR=$TASKDIR/pbs.err
+
+  # log files
+  LOG=$JOBDIR/log
+
+  # make these directories if they do not exist
+  mkdir -p $EXECDIR
+  mkdir -p $EXECOUTPUTDIR
+  mkdir -p $JOBDIR
+  mkdir -p $OUTPUTDIR
+  mkdir -p $STDOUT
+  mkdir -p $STDERR
+  mkdir -p $PBS_STDOUT
+  mkdir -p $PBS_STDERR
+  echo "Starting Log file" 1> $LOG 2> $LOG
+
+  # initial
+  #----------------------------------------
+  # load profile
+  source /etc/profile
+  # load hpcc modules
+  source /opt/software/modulefiles/setup_modules.sh
+  # load specific library modules
+  module load <<gnu-module>>
+  module load <<cuda-module>>
+
+  echo "" 1>> $LOG 2>> $LOG
+  echo "LOG $LOG" 1>> $LOG 2>> $LOG
+
+  ## general paths
+  ################################################################################
+  <<env-vars>>
+  ################################################################################
+
+  # change to the exec dir
+  cd $EXECDIR
+
   # remove current contents of the execdir, useful for if running
   # interactive job which writes to same dir, harmless if not
   echo "Removing existing files if they exist in $EXECDIR" 1>> $LOG 2>> $LOG