Major improvements, workable version

I cleaned up the noweb template through a round of debugging and development.

I added an example directory that shows one with things filled in that work on the HPCC.

examples/test_template/input/test_input.txt

@@ -0,0 +1 @@
+This is the test input file

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/43144464.mgr-04.i.SC

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+#!/bin/sh -login
+
+#PBS -N test_template
+#PBS -l walltime=5:00
+#PBS -l mem=4gb
+#PBS -l nodes=1:ppn=1
+
+
+#PBS -e pbs.err
+#PBS -o pbs.out
+#PBS -M samuel.lotz@gmail.com
+#PBS -m abe
+
+# ------------------------------
+# Script for running the task test_template with PBS on hpcc
+
+# task name, this is the name of the directory for the task
+TASK="test_template"
+# directory path for this task
+TASKDIR="$MY_DICKSON_LAB/pbs_templates/examples/$TASK"
+
+# the directory with all of the input
+INPUTDIR=$TASKDIR/input
+# directory to put job results in
+JOBSDIR=$TASKDIR/jobs
+# 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
+
+# the job name
+JOBNAME=${TASK}-${PBS_JOBID}
+# the directory for the output of this job
+JOBDIR=$JOBSDIR/$JOBNAME
+# the directory output will be put into after completion
+OUTPUTDIR=$JOBDIR/output
+# log files
+LOG=$JOBDIR/log
+# directories to copy the stdout and stderr from scripts
+STDOUT=$JOBDIR/pbs.out
+STDERR=$JOBDIR/pbs.err
+
+# directory to execute code in
+# EXECDIR=$TMPDIR
+# EXECDIR=$MY_DICKSON_SCRATCH/$JOBNAME
+# Problems with Scratch so I will just run in the jobs dir
+# TODO make an if for different options
+EXECDIR=$JOBDIR/exec
+
+# make these directories if they do not exist
+mkdir -p $JOBDIR
+mkdir -p $EXECDIR
+mkdir -p $PBS_STDOUT
+mkdir -p $PBS_STDERR
+
+# Starting the LOG file
+echo "Starting Log file" 1> $LOG 2> $LOG
+echo "----------------------------------------" 1>> $LOG 2>> $LOG
+echo ""   1>> $LOG 2>> $LOG
+
+# write out explicitly the run parameters
+echo "----------------------------------------"  1>> $LOG 2>> $LOG
+echo "PBS Resource requests" 1>> $LOG 2>> $LOG
+echo "----------------------------------------" 1>> $LOG 2>> $LOG
+
+echo "" 1>> $LOG 2>> $LOG
+echo "walltime 5:00" 1>> $LOG 2>> $LOG
+echo "memory 4gb" 1>> $LOG 2>> $LOG
+echo "num-nodes 1" 1>> $LOG 2>> $LOG
+echo "num-processors 1" 1>> $LOG 2>> $LOG
+echo "num-gpus " 1>> $LOG 2>> $LOG
+echo "feature " 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+# print the paths for all the variables constructed in this script
+echo "----------------------------------------"  1>> $LOG 2>> $LOG
+echo "Check Paths"  1>> $LOG 2>> $LOG
+echo "----------------------------------------"  1>> $LOG 2>> $LOG
+
+echo "" 1>> $LOG 2>> $LOG
+echo "LOG $LOG" 1>> $LOG 2>> $LOG
+echo "PBS_JOBID $PBS_JOBID" 1>> $LOG 2>> $LOG
+echo "TASK $TASK" 1>> $LOG 2>> $LOG
+echo "TASKDIR $TASKDIR" 1>> $LOG 2>> $LOG
+echo "INPUTDIR $INPUTDIR" 1>> $LOG 2>> $LOG
+echo "JOBSDIR $JOBSDIR" 1>> $LOG 2>> $LOG
+echo "JOBNAME $JOBNAME" 1>> $LOG 2>> $LOG
+echo "JOBDIR $JOBDIR" 1>> $LOG 2>> $LOG
+echo "OUTPUTDIR $OUTPUTDIR" 1>> $LOG 2>> $LOG
+echo "EXECDIR $EXECDIR" 1>> $LOG 2>> $LOG
+echo "STDOUT $STDOUT" 1>> $LOG 2>> $LOG
+echo "STDERR $STDERR" 1>> $LOG 2>> $LOG
+echo "PBS_STDOUT $PBS_STDOUT" 1>> $LOG 2>> $LOG
+echo "PBS_STDERR $PBS_STDERR" 1>> $LOG 2>> $LOG
+echo "PBS_NODEFILE" 1>> $LOG 2>> $LOG
+cat $PBS_NODEFILE 1>> $LOG 2>> $LOG
+echo ""  1>> $LOG 2>> $LOG
+
+# saving PBS environmental variables
+echo "----------------------------------------"  1>> $LOG 2>> $LOG
+echo "PBS Environmental Variables" 1>> $LOG 2>> $LOG
+echo "----------------------------------------" 1>> $LOG 2>> $LOG
+
+echo ""   1>> $LOG 2>> $LOG
+# PBS env vars
+echo "PBS ENV:"  1>> $LOG 2>> $LOG
+env | grep PBS  1>> $LOG 2>> $LOG
+
+# PBS JOBID number
+echo "PBS_JOBID number"  1>> $LOG 2>> $LOG
+PBS_JOBID_NUM=(${PBS_JOBID//./ })
+echo "PBS_JOBID_NUM: $PBS_JOBID_NUM" 1>> $LOG 2>> $LOG
+
+# PBS stdout and stderr file paths
+PBS_JOB_STDOUT="$PBS_STDOUT/$TASK.o$PBS_JOBID_NUM"
+PBS_JOB_STDERR="$PBS_STDERR/$TASK.e$PBS_JOBID_NUM"
+
+# NODEFILE
+echo "PBS_NODEFILE:"  1>> $LOG 2>> $LOG
+cat $PBS_NODEFILE  1>> $LOG 2>> $LOG
+# GPUFILE
+echo "PBS_GPUFILE:"  1>> $LOG 2>> $LOG
+cat $PBS_GPUFILE  1>> $LOG 2>> $LOG
+# MICFILE
+echo "PBS_MICFILE:"  1>> $LOG 2>> $LOG
+cat $PBS_MICFILE  1>> $LOG 2>> $LOG
+echo ""  1>> $LOG 2>> $LOG
+
+# initial
+echo ""  1>> $LOG 2>> $LOG
+echo "----------------------------------------" 1>> $LOG 2>> $LOG
+echo "Initialization" 1>> $LOG 2>> $LOG
+echo "----------------------------------------" 1>> $LOG 2>> $LOG
+
+# load profile
+echo "------------" 1>> $LOG 2>> $LOG
+echo "RUNNING: source /etc/profile" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+source /etc/profile 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+# load hpcc modules
+echo "------------" 1>> $LOG 2>> $LOG
+echo "RUNNING: source /opt/software/modulefiles/setup_modules.sh" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+source /opt/software/modulefiles/setup_modules.sh 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+# load specific library modules
+# GNU Compilers
+echo "------------" 1>> $LOG 2>> $LOG
+echo "RUNNING: module load GNU/4.8.3" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+module load GNU/4.8.3 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+# CUDA compilers
+echo "------------" 1>> $LOG 2>> $LOG
+echo "RUNNING: module load CUDA/7.0" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+module load CUDA/7.0 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+
+# set environmental variables and other local variables that are used for 
+# many types of scripts
+# ===============================================================================
+echo "------------" 1>> $LOG 2>> $LOG
+echo "Setting environmental variables"  1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+
+# scratch directory
+export SCRATCHDIR=/mnt/ls15/scratch
+# your home scratch
+export SCRATCH_HOME=$SCRATCH
+
+# the Dickson lab directory
+export DICKSON_LAB=/mnt/research/DicksonLab
+# your Dickson lab dir
+export MY_DICKSON_LAB=$DICKSON_LAB/$USER
+# locally installed programs
+export DICKSON_LAB_PROGS=${DICKSON_LAB}/programs
+# the installed binaries for Dickson lab
+export DICKSON_LAB_BIN=${DICKSON_LAB_PROGS}/bin
+# directory with installed libraries
+export DICKSON_LAB_LIB=${DICKSON_LAB_PROGS}/lib
+# Dickson lab scratch directory
+export DICKSON_SCRATCH=$SCRATCHDIR/groups/DicksonLab
+# your Dickson lab scratch dir
+export MY_DICKSON_SCRATCH=$DICKSON_SCRATCH/$USER
+
+# set environmental variables to programs needed
+#----------------------------------------
+# charmm executables
+export CHARMM_DIR=${DICKSON_LAB_PROGS}/charmm
+export CHARMM=${CHARMM_DIR}/exec/gnu/charmm
+export MPICHARMM=${CHARMM_DIR}/exec/gnu_M/charmm
+export OPENMMCHARMM=${CHARMM_DIR}/exec/gnu/charmm_OpenMM6.3
+
+# charmm data
+export CHARMMDATA=${DICKSON_LAB}/toppar
+
+# set the path for mmtsb
+export MMTSBDIR=$DICKSON_LAB_PROGS/mmtsb
+
+# OpenMM
+export OPENMM_ROOT_DIR=/mnt/research/DicksonLab/programs/OpenMM6.3
+export OPENMM_PLUGIN_DIR=$OPENMM_ROOT_DIR/lib/plugins
+export OPENMM_PLATFORM=CUDA
+unset OPENMM_DEVICE
+
+
+# Anaconda Python paths
+export ANACONDA_DIR=$DICKSON_LAB_PROGS/anaconda2
+export ANACONDA_BIN=$ANACONDA_DIR/bin
+export PYTHONHOME=$ANACONDA_DIR
+
+# Library paths
+export LD_LIBRARY_PATH=${DICKSON_LAB_LIB}:${CUDADIR}/lib:${OPENMM_ROOT_DIR}/lib:${OPENMM_PLUGIN_DIR}:${LD_LIBRARY_PATH}
+
+# PATH
+export PATH=$ANACONDA_BIN:${DICKSON_LAB_BIN}:${OPENMM_ROOT_DIR}/bin:${MMTSBDIR}/perl:${DICKSON_LAB_PROGS}/charmm/exec/gnu:${PATH}
+
+# ===============================================================================
+
+# change to the exec dir
+echo "------------" 1>> $LOG 2>> $LOG
+echo "moving to EXECDIR: $EXECDIR" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+cd $EXECDIR 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+# remove current contents of the execdir, useful for if running
+# interactive job which writes to same dir, harmless if not
+echo "------------" 1>> $LOG 2>> $LOG
+echo "Removing existing files if they exist in EXECDIR: $EXECDIR" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+rm -rf $EXECDIR/* 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+# copy the input files to the execution directory
+echo "------------" 1>> $LOG 2>> $LOG
+echo "Copying input files from INPUTDIR: $INPUTDIR to EXECDIR: $EXECDIR" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+cp -rf $INPUTDIR/* $EXECDIR/ 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+# copy the actual submission script used
+echo "------------" 1>> $LOG 2>> $LOG
+echo "Copying submission script ${TASKDIR}/${PBS_JOBNAME} to EXECDIR: $EXECDIR" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+cp "${0}" $EXECDIR/ 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+# write file names in $EXECDIR to log
+echo "------------" 1>> $LOG 2>> $LOG
+echo "listing of EXECDIR: $EXECDIR" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+ls $EXECDIR 1>> $LOG 2>> $LOG
+echo "" 1>> $LOG 2>> $LOG
+
+# print out the environmental variables after modifications
+echo "------------" 1>> $LOG 2>> $LOG
+echo "Environmental variables before execution:"  1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+env 1>> $LOG 2>> $LOG
+echo ""   1>> $LOG 2>> $LOG
+
+# ------------------------------
+# set the parameters that will be used in this script
+# ===============================================================================
+echo "------------" 1>> $LOG 2>> $LOG
+echo "Setting Script parameters"  1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+echo ""   1>> $LOG 2>> $LOG
+
+TEST_PARAM="HELLO"
+TEST_VAL=8
+TEST_FILE="test_input.txt"
+
+echo ""   1>> $LOG 2>> $LOG
+# ===============================================================================
+
+
+# ------------------------------
+# The code for this script
+# ===============================================================================
+echo "------------" 1>> $LOG 2>> $LOG
+echo "Running script" 1>> $LOG 2>> $LOG
+echo "===============================================================================" 1>> $LOG 2>> $LOG
+
+echo "HELLO beginning the script body"
+cat $TEST_FILE 1>> $LOG 2>> $LOG
+for ((x=0; x<=${TEST_VAL}; x++)); do
+    echo ${TEST_PARAM} > "file_${x}.txt" 2>> $LOG;
+done
+
+echo "===============================================================================" 1>> $LOG 2>> $LOG
+echo "done with script" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+echo ""   1>> $LOG 2>> $LOG
+
+# ===============================================================================
+
+# move the output files in EXECDIR back to the job output dir
+echo "------------" 1>> $LOG 2>> $LOG
+echo "moving EXECDIR $EXECDIR to OUTPUTDIR $OUTPUTDIR" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+mv $EXECDIR $OUTPUTDIR  1>> $LOG 2>> $LOG
+echo ""   1>> $LOG 2>> $LOG
+
+
+# move the PBS stdout and stderr files to the jobdir
+echo "------------" 1>> $LOG 2>> $LOG
+echo "PBS STDOUT is in $PBS_JOB_STDOUT" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG
+echo ""   1>> $LOG 2>> $LOG
+
+echo "------------" 1>> $LOG 2>> $LOG
+echo "PBS STDERR $PBS_JOB_STDERR" 1>> $LOG 2>> $LOG
+echo "------------" 1>> $LOG 2>> $LOG

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/file_0.txt

@@ -0,0 +1 @@
+HELLO

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/file_1.txt

@@ -0,0 +1 @@
+HELLO

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/file_2.txt

@@ -0,0 +1 @@
+HELLO

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/file_3.txt

@@ -0,0 +1 @@
+HELLO

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/file_4.txt

@@ -0,0 +1 @@
+HELLO

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/file_5.txt

@@ -0,0 +1 @@
+HELLO

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/file_6.txt

@@ -0,0 +1 @@
+HELLO

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/file_7.txt

@@ -0,0 +1 @@
+HELLO

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/file_8.txt

@@ -0,0 +1 @@
+HELLO

examples/test_template/jobs/test_template-43144464.mgr-04.i/output/test_input.txt

@@ -0,0 +1 @@
+This is the test input file

examples/test_template/pbs.out/test_template.o43144464

@@ -0,0 +1 @@
+HELLO beginning the script body