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Xuesong (Steve)
338
runs/v8-02-01/geos5/run~
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338
runs/v8-02-01/geos5/run~
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#!/bin/bash
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####
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# Can insert bsub commands here:
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##BSUB -n 08 -W 02:00
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##BSUB -o outfile -e errfile # my default stdout, stderr files
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####
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#
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# This script runs succesive iterations of optimizing the cost function using
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# gradients that are either computed or read from *.gdt.* files. dkh, 02/05
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#
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# Notes:
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# - added comments (dkh, 04/11/05)
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# - make directory names shell variables (dkh, 10/06/06)
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# - Now make a tar file of aero.ave* and satave.bpch files at each iteration
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# - Add bsub commands for batch jobs on orion
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# - This script only seems to work from a tcsh.
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# - Improved diagnostics and output, added more comments. (dkh, 11/21/07)
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# - make default setup for running on prospero. (dkh, 11/18/10)
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# - comment out backup
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# - use echo instead of ex
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# - change number of threads
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# - append ctm.bpch and log with iteration number
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#############################################################################
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##################################################################
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# Set run parameters.
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# - X
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# - XSTOP
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# - RNAME
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#
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# These need to be set and checked before every run.
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# X = 0 creates observations. X_STOP < X only
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# creates a backup of the program directory.
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##################################################################
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# Set the start (or current ) iteration number
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X=0
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# Set the stopping iteration number
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XSTOP=0
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# Give every run a unique name (default is $PBS_JOBID)
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RNAME=gcadj_std_I_WC
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# Specify Type of Run "DEFAULT, HDF, SAT_NETCDF, LIDORT"
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TYPE=HDF_NETCDF
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# Set Compiler Options. For a list of all compiler options
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# type 'make help' on the code directory.
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# example IFORT_OPT="DEBUG=yes TRACEBACK=yes"
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IFORT_OPT=""
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# Recompile geos on every iteration.
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# NOTE: If you have IPO set to yes we recommend not to recompile.
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# IPO optimization make linking process slow.
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RECOMPILE=NO
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# Save packages to temporary storage before and after execution
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# Note: Need to set DSAVE below
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SAVE=NO
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# Archive packages to permanent storage after execution
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# Note: Need to set DARCHIVE below
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ARCHIVE=NO
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# Set compiler, if necessary
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#source /usr/projects/compilers/intel/9.1.043/bin/ifortvars.sh
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##################################################################
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#
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# File structure should be:
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# DRUN/DPACK/DRUNDIR
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# DRUN/DPACK/DCODE
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#
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# Definitions:
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# - DRUNDIR contains the input files, run script, log files, and
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# the optimization files.
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# - DCODE contains the source code.
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# - DPACK is the complete package of files and folders
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# - DRUN is the location where the user would like to place the
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# package during execution (usually a local scratch dive).
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# - DSAVE is the location where the packages are saved before
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# and after execution (usually a large NFS mounted storage
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# drive).
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#
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# You MUST set the following according to your filesystem:
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# - DRUNDIR
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# - DSAVE
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#
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# You MAY change the following:
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# - DPACK (default is to set equal to RNAME)
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##################################################################
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# Directory in the package where the executable runs
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DRUNDIR=runs/v8-02-01/geos5_tes_mls_0605
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# Directory in the package with the source code
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DCODE=code
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# Package directory name
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DPACK=$RNAME
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# Directory where run packages are unpacked and run
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DRUN=/users/jk/16/xzhang/
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# Directory where run packages are stored and saved (if not saved locally)
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DSAVE=
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# Directory where run packages are backed up (if not saved locally)
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DARCHIVE=
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# Get rid of old executables
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if [ -f geos ]; then
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rm geos
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fi
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# The optimization code will create this file to indicate completion. Remove it to start.
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#if [ -f done_with_opt ]; then
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# rm done_with_opt
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#fi
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# dkh debug unlimit core size and force core dump
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ulimit -c 5000
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decfort_dump_flag=y
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# Set number of threads
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export OMP_NUM_THREADS=24
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grep 'Xeon' /proc/cpuinfo
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# go to run direction
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cd $DRUN/$DPACK/$DRUNDIR
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##################################################################
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# For every iteration we edit ITER, recompile, execute geos
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# and save the results.
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##################################################################
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while [ $X -le $XSTOP ]
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do
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echo "ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss"
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echo " R U N F O R N _ C A L C _ S T O P = $X"
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echo " "
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# Clean out old files
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echo ' run: Removing old files'
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echo ' - checking for old core files'
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ls core.*
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if [ $? -eq 0 ]; then
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echo ' - removing old core files'
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rm -v core.*
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fi
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if [ -f ctm.bpch ]; then
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rm -v ctm.bpch
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fi
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echo ' - checking for *.chk.* file '
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ls adjtmp/*.chk.*
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if [ $? -eq 0 ]; then
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echo ' - removing old *.chk.* file '
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rm -v adjtmp/*.chk.*
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fi
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# Save a copy to temporary storage
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if [ $SAVE = 'YES' ]; then
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echo ' run: Backing up to temp storage:'
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echo ' Backup PATH: '$DSAVE
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cd $DRUN
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tar -cf $RNAME.tar $DPACK/*
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cp -v $DRUN/$RNAME.tar $DSAVE/$RNAME.tar
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fi
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echo "ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss"
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##################################################################
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# Now update the iteration number in ITER
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##################################################################
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cd $DRUN/$DPACK/$DRUNDIR
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echo " $X" > ITER
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echo " $XSTOP" >> ITER
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echo "ITER file updated"
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##################################################################
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# Compile geos, move it to the run directory and execute
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##################################################################
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cd $DRUN/$DPACK/$DCODE
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echo "$DRUN/$DPACK/$DRUNDIR" > INPUT_FOLDER
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./objects.sh $TYPE
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rm INPUT_FOLDER
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if [ $TYPE = 'DEFAULT' ]; then
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IFORT_OPT="$IFORT_OPT "
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elif [ $TYPE = 'HDF' ]; then
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IFORT_OPT="$IFORT_OPT HDF=yes"
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elif [ $TYPE = 'SAT_NETCDF' ]; then
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IFORT_OPT="$IFORT_OPT SAT_NETCDF=yes"
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elif [ $TYPE = 'HDF_NETCDF' ]; then
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IFORT_OPT="$IFORT_OPT SAT_NETCDF=yes HDF=yes"
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elif [ $TYPE = 'LIDORT' ]; then
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IFORT_OPT="$IFORT_OPT LIDORT=yes"
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fi
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LBFGS="$(grep 'Compute BFGS inverse Hessian : F' $DRUN/$DPACK/$DRUNDIR/input.gcadj)"
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OFFDIAG="$(grep ' => offdiagonal : F' $DRUN/$DPACK/$DRUNDIR/input.gcadj)"
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if [ -z "$OFFDIAG" ] || [ -z "$LBFGS" ] ; then
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IFORT_OPT="$IFORT_OPT USE_MKL=yes"
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fi
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make $IFORT_OPT
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if [ $RECOMPILE = 'YES' ]; then
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mv -f geos ../$DRUNDIR/
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else
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cp -f geos ../$DRUNDIR/
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fi
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cd ../$DRUNDIR/
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time ./geos
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Y=$X
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# make a copy of ctm.bpch for the current iteration
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cp -v ctm.bpch ctm.bpch.$X
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# Clean out old files
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echo ' run: Removing excess files'
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echo ' - checking for old core files'
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ls core.*
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if [ $? -eq 0 ]; then
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echo ' - removing core files'
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rm -v core.*
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fi
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echo ' - checking for *.chk.* file '
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ls adjtmp/*.chk.*
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if [ $? -eq 0 ]; then
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echo ' - removing old *.chk.* file '
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rm -v adjtmp/*.chk.*
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fi
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if [ -f done_with_opt ]; then
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X=$XSTOP
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fi
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# A succesful run will generate a gctm.sf.* file.
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if [ $X -le 9 ]; then
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echo ' run: checking if finished iteration ' $X
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if [ -f OptData/gctm.sf.0${X} ]; then
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echo ' - found ' gctm.sf.0$X
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XGOOD=0
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else
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echo ' - did not find ' gctm.sf.0$X
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XGOOD=1
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X=$XSTOP
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fi
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elif [ $X -gt 9 ]; then
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echo ' run: checking if finished iteration ' $X
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if [ -f OptData/gctm.sf.${X} ]; then
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echo ' - found ' gctm.sf.$X
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XGOOD=0
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else
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echo ' - did not find ' gctm.sf.$X
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XGOOD=1
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X=$XSTOP
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fi
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fi
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X=$((X+1))
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done
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##################################################################
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# Finish up.
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## Save program directories again.
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##################################################################
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echo "sssssssssssssssssssssssssssssssssssssssssssssssssssssss"
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# check to see if it even compiled
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if [ ! -f geos ]; then
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XGOOD=3
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fi
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if [ "$XGOOD" -eq 0 ]; then
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echo " ------------------------------------------------"
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echo " G E O S C H E M A D J O I N T E X I T E D "
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echo " N O R M A L L Y "
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echo " ------------------------------------------------"
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elif [ "$XGOOD" -eq 1 ]; then
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echo " ------------------------------------------------"
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echo " * * * E R R O R * * * "
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echo " G E O S C H E M A D J O I N T D I D "
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echo " N O T F I N I S H . "
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echo " ------------------------------------------------"
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elif [ "$XGOOD" -eq 2 ]; then
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echo " ------------------------------------------------"
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echo " G E O S C H E M F O R W A R D M O D E L "
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echo " ( check log file to see if OK ) "
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echo " ------------------------------------------------"
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elif [ "$XGOOD" -eq 3 ]; then
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echo " ------------------------------------------------"
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echo " * * * E R R O R * * * "
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echo " D I D N O T C O M P I L E "
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echo " ( check source code for errors ) "
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echo " ------------------------------------------------"
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fi
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## Clean out checkpoint files and creat a tarball
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if [[ $SAVE = 'YES' || $ARCHIVE = 'YES' ]]; then
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echo ' Creating run package tarball '
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if [ -f adjtmp/*.chk.* ]; then
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rm adjtmp/*.chk.*
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fi
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cd $DRUN
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tar -cf $RNAME.tar $DPACK/*
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fi
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## Save a copy to temp storage
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if [ $SAVE = 'YES' ]; then
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echo ' Backing up to temp storage: '
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echo ' Backup PATH: '$DSAVE
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cp -v $DRUN/$RNAME.tar $DSAVE/$RNAME.tar
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fi
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#
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## Save a copy to permanent storage
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if [ $ARCHIVE = 'YES' ]; then
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echo ' Backing up to permanent storage:'
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echo ' Backup PATH: '$DARCHIVE
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cp -v $DRUN/$RNAME.tar $DARCHIVE/runs/$RNAME.tar
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fi
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echo " N_CALC_STOP at $Y "
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echo " "
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echo " R U N S C R I P T E X I T E D O N : " $HOSTNAME
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echo "sssssssssssssssssssssssssssssssssssssssssssssssssssssss"
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