Merge branch 'master' of git.nilu.no:ignacio/flex_gen_input

Makefile_0

+options:
+	./define_default_run_0.sh	
+slfiles: 
+	./loop_on_pathnames_laptop.sh
+run:
+	./run_all_sl
+clean: this_is_a_run
+	rm -r options*
+cleanrun:
+	rm *.out rm *.err *.sl

README

+flex gen cases
+
+Generates flexpart run cases based on the current default options dir and pathnames file.
+(pathanmes can be edited at a later stage to accomodate different winds with the same options IMPLEMENT
+)
+files 
+- define_<runs>: Generates flexpart run cases (groups depending on _<runs>) 
+- export*: copy define* to a ifferent directory to build the run cases there.
+- (pathanmes could be edited here)
+- loop_on_pathnames*.sh: for a fived options-pathnames pair, create a run case (adding an executable and an output directory)
+- run_all_sl*: execute the run cases generating a set of flexpart outputs
+- read_joblist*.sh: verify that the runs finished properly.
+
+input:
+ options dir: 
+   default located repo in the same directory 
+   i.e. ../flexpart/options/
+ pathname: ../flexpart/pathnames
+ destinantion dir: 
+  default "../flex_cases" alongside in the same directory level
+  it is created every time. it it already exists from a previous run it will stop 
+  (add --force option ENHANCE)
+
+history
+repo flex_gen_input cloned to ~/repos
+
+how to run
+example
+
+./export_flexgen_0.sh
+
+generates ../flex_cases 
+
+containing 
+
+Makefile
+define_default_run_0.sh*
+loop_on_pathnames_laptop.sh*
+run_all_sl_laptop*
+
+this by itself or a s a copy can generate a list of flexpart run cases
+(only default FIXME)
+
+just running 
+make or
+define_default_run_0.sh
+
+generates: 
+pathnames 
+output
+options
+
+./loop_on_pathnames_laptop.sh*
+generates a file (e.g. batch_dry_pathnames*.sl) that associates the executable with that patnames in a FLEXPART_run_string
+(the executable is by default FLEXPART_8d70e43)
+in can be configured with exporting variable $FLEXPARTvar
+
+now all batch_dry_pathnames*.sl
+can be run by
+
+./run_all_sl_*
+
+the stdout of flexpart is tee'd to stdoutbatch_dry_pathnames*.sl
+
+the output* directory(es) is(are) ready to be read by flex_read
+
+
+
+
+
+
+
+

define_default_run_0.sh

+#!/bin/bash
+# Ignacio Pisso 2018-03-29
+# generate FLEXPART variations on the default for parameter sweep hello world tests
+
+#define input options
+options_repo=~/repos/flexpart/options
+#define winds
+pathnames_local=~/repos/flexpart/pathnames
+
+#copy default
+cp -r  $options_repo options
+#sed -i '/IOUT=/c\ IOUT=    2,' options2/COMMAND
+mkdir output
+cp $pathnames_local pathnames
+#sed -i "s/\boptions\b/options2/g" pathnames2
+#sed -i "s/\boutput\b/output2/g" pathnames2

export_flexgen_0.sh

+#!/bin/bash
+#OUTPUT=${OUTPUTvar:-$OUTPUTdefault}
+#target=$1 #/Users/ignacio/todo/doing/flexpart/flex_gen_input/2018-07-03
+target_default='../flex_cases'
+target_in=$1
+target=${target_in:-$target_default} 
+echo target=$target
+
+#[ -e $target ] && (echo WARNING: target=$target exists as file)
+#echo post -e
+
+#[ -d $target ] || mkdir $target
+#echo post -d
+
+if [ -d $target ] 
+then
+  echo  WARNING: target=$target exists as dir, exit
+  exit
+else
+  if [ -e $target ] 
+  then
+     echo WARNING: target=$target exists as file, exit
+     exit
+  else
+    mkdir $target
+    echo $target created
+  fi
+fi
+
+listoffiles=(define_default_run_0.sh Makefile loop_on_pathnames_laptop.sh run_all_sl_laptop) 
+echo copy ${listoffiles[*]} to $target
+cp ${listoffiles[*]}  $target
+
+#exit
+#cp define_default_run_0.sh $target
+cp Makefile_0 $target/Makefile
+#cp loop_on_pathnames_laptop.sh $target
+#cp run_all_sl_laptop $target
+
+#echo "created by $(basename \"$0\") on $(date) from $(pwd)" > $target/README
+echo "created by $(basename "$0") on $(date) from $(pwd)" > $target/README

run_all_sl

 #!/bin/bash
 
 #OUTPUT="$(ls -1 *.sl)"
-OUTPUdefaultT="$(ls -1 *.sl)"
+OUTPUTdefault="$(ls -1 *.sl)"
 OUTPUT=${OUTPUTvar:-$OUTPUTdefault}
 
 rm joblist