From 6aee9efbccc68b91849dd61ea8d83e4f7df98e75 Mon Sep 17 00:00:00 2001
From: T-Britton <tbritton@jlab.org>
Date: Wed, 13 Dec 2017 10:42:31 -0500
Subject: [PATCH 01/13] completed a bulk of the error checking/handling.  Fixed
 a bug with requesting just TagOnly background.  Cleaned up some spurious
 warnings/errors.  Brought bash version up to par

---
 MCwrapper/MakeMC.csh         | 111 +++++++++++++++++++++++++---------
 MCwrapper/MakeMC.sh          | 114 +++++++++++++++++++++++++----------
 MCwrapper/examples/MC.config |   6 +-
 MCwrapper/gluex_MC.py        |   6 +-
 4 files changed, 172 insertions(+), 65 deletions(-)

diff --git a/MCwrapper/MakeMC.csh b/MCwrapper/MakeMC.csh
index 9d7f26a9..477ba5c6 100755
--- a/MCwrapper/MakeMC.csh
+++ b/MCwrapper/MakeMC.csh
@@ -93,13 +93,13 @@ if ( "$BATCHRUN" != "0" ) then
     mkdir -p $OUTDIR/log
 endif
 
-if (! -d $RUNNING_DIR) then
+if ( ! -d $RUNNING_DIR ) then
 	mkdir $RUNNING_DIR
 endif
 
 cd $RUNNING_DIR
 
-if(! -d $RUNNING_DIR/${RUN_NUMBER}_${FILE_NUMBER}) then
+if ( ! -d $RUNNING_DIR/${RUN_NUMBER}_${FILE_NUMBER} ) then
 	mkdir $RUNNING_DIR/${RUN_NUMBER}_${FILE_NUMBER}
 endif
 
@@ -362,7 +362,7 @@ endif
 
 set bkglocstring=""
 set bkgloc_pre=`echo $BKGFOLDSTR | cut -c 1-4`
-
+echo $BKGFOLDSTR
 if ( "$BKGFOLDSTR" == "DEFAULT" || "$bkgloc_pre" == "loc:" || "$BKGFOLDSTR" == "Random" ) then
    #find file and run:1
     echo "Finding the right file to fold in during MCsmear step"
@@ -380,7 +380,7 @@ if ( "$BKGFOLDSTR" == "DEFAULT" || "$bkgloc_pre" == "loc:" || "$BKGFOLDSTR" == "
 
     if ( $RUN_NUMBER < 10000 ) then
 		echo "Warning: random triggers do not exist for this run"
-		exit
+		exit 1
     endif
 	
 	if ( "$bkgloc_pre" == "loc:" ) then
@@ -389,10 +389,10 @@ if ( "$BKGFOLDSTR" == "DEFAULT" || "$bkgloc_pre" == "loc:" || "$BKGFOLDSTR" == "
 	else
     	set bkglocstring="/cache/halld/""$runperiod""/sim/random_triggers/""run$formatted_runNumber""_random.hddm"
 	endif
-
+	
     if ( ! -f $bkglocstring ) then
 		echo "Could not find mix-in file "$bkglocstring
-		exit
+		exit 1
     endif
 endif
 
@@ -400,8 +400,10 @@ endif
 set recon_pre=`echo $CUSTOM_PLUGINS | cut -c1-4`
 set jana_config_file=`echo $CUSTOM_PLUGINS | sed -r 's/^.{5}//'`
 
-if ( -f $jana_config_file ) then
-    cp $jana_config_file ./jana_config.cfg
+if ( $recon_pre == "file" ) then
+	if ( -f $jana_config_file ) then
+    	cp $jana_config_file ./jana_config.cfg
+	endif
 endif
 
 set gen_pre=""
@@ -411,7 +413,7 @@ if ( "$GENR" != "0" ) then
     if ( "$gen_pre" != "file" && "$GENERATOR" != "genr8" && "$GENERATOR" != "bggen" && "$GENERATOR" != "genEtaRegge" && "$GENERATOR" != "gen_2pi_amp" && "$GENERATOR" != "gen_pi0" && "$GENERATOR" != "gen_2pi_primakoff" && "$GENERATOR" != "gen_omega_3pi" && "$GENERATOR" != "gen_2k" && "$GENERATOR" != "bggen_jpsi" && "$GENERATOR" != "gen_ee" && "$GENERATOR" != "gen_ee_hb" && "$GENERATOR" != "particle_gun" ) then
 		echo "NO VALID GENERATOR GIVEN"
 		echo "only [genr8, bggen, genEtaRegge, gen_2pi_amp, gen_pi0, gen_omega_3pi, gen_2k, bggen_jpsi, gen_ee , gen_ee_hb, particl_gun] are supported"
-		exit
+		exit 1
     endif
 
     if ( "$gen_pre" == "file" ) then
@@ -422,7 +424,7 @@ if ( "$GENR" != "0" ) then
 	    	cp $gen_in_file ./$STANDARD_NAME.hddm
 		else
 	    	echo "cannot find file: "$gen_in_file
-	    	exit
+	    	exit 1
 		endif
 	else if ( "$GENERATOR" == "particle_gun") then
 		echo "bypassing generation" 
@@ -433,7 +435,7 @@ if ( "$GENR" != "0" ) then
 			echo "Config file not applicable"
 		else
 	    	echo $CONFIG_FILE" does not exist"
-	    	exit
+	    	exit 1
     	endif
     endif
 
@@ -507,6 +509,7 @@ if ( "$GENR" != "0" ) then
 		sed -i 's/TEMPCOHERENT/'$COHERENT_PEAK'/' $STANDARD_NAME.conf
 		# RUN genr8 and convert
 		genr8 -r$formatted_runNumber -M$EVT_TO_GEN -A$STANDARD_NAME.ascii < $STANDARD_NAME.conf #$config_file_name
+		set generator_return_code=$status
 		genr8_2_hddm $STANDARD_NAME.ascii
     else if ( "$GENERATOR" == "bggen" ) then
 		set RANDOMnum=`bash -c 'echo $RANDOM'`
@@ -524,6 +527,7 @@ if ( "$GENR" != "0" ) then
 	
 		ln -s $STANDARD_NAME.conf fort.15
 		bggen
+		set generator_return_code=$status
 		mv bggen.hddm $STANDARD_NAME.hddm
     else if ( "$GENERATOR" == "genEtaRegge" ) then
 		echo "RUNNING GENETAREGGE" 	
@@ -534,7 +538,8 @@ if ( "$GENR" != "0" ) then
 		sed -i 's/TEMPMINGENE/'$GEN_MIN_ENERGY'/' $STANDARD_NAME.conf
 		sed -i 's/TEMPMAXGENE/'$GEN_MAX_ENERGY'/' $STANDARD_NAME.conf
 		genEtaRegge -N$EVT_TO_GEN -O$STANDARD_NAME.hddm -I$STANDARD_NAME.conf
-    else if ( "$GENERATOR" == "gen_2pi_amp" ) then
+	    set generator_return_code=$status
+	else if ( "$GENERATOR" == "gen_2pi_amp" ) then
 		echo "RUNNING GEN_2PI_AMP" 
     	set optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
 
@@ -549,6 +554,7 @@ if ( "$GENR" != "0" ) then
 		echo $optionals_line
 		echo gen_2pi_amp -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
 		gen_2pi_amp -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
+		set generator_return_code=$status
 	else if ( "$GENERATOR" == "gen_omega_3pi" ) then
 		echo "RUNNING GEN_OMEGA_3PI" 
     	set optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
@@ -564,24 +570,28 @@ if ( "$GENR" != "0" ) then
 		echo $optionals_line
 		echo gen_omega_3pi -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -m $eBEAM_ENERGY -p $COHERENT_PEAK $optionals_line
 		gen_omega_3pi -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -m $eBEAM_ENERGY -p $COHERENT_PEAK $optionals_line
-    else if ( "$GENERATOR" == "gen_2pi_primakoff" ) then
+		set generator_return_code=$status
+	else if ( "$GENERATOR" == "gen_2pi_primakoff" ) then
 		echo "RUNNING GEN_2PI_PRIMAKOFF" 
         set optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
 		echo $optionals_line
 		echo gen_2pi_primakoff -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER  -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
 		gen_2pi_primakoff -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
-    else if ( "$GENERATOR" == "gen_pi0" ) then
+		set generator_return_code=$status
+	else if ( "$GENERATOR" == "gen_pi0" ) then
 		echo "RUNNING GEN_PI0" 
         set optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
 		echo $optionals_line
 		gen_pi0 -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -s $formatted_fileNumber -m $eBEAM_ENERGY $optionals_line
-    else if ( "$GENERATOR" == "gen_2k" ) then
+		set generator_return_code=$status
+	else if ( "$GENERATOR" == "gen_2k" ) then
 		echo "RUNNING GEN_2K" 
     	set optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
 		#set RANDOMnum=`bash -c 'echo $RANDOM'`
 		echo $optionals_line
 		echo gen_2k -c $STANDARD_NAME.conf -o $STANDARD_NAME.hddm -hd $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
 		gen_2k -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
+		set generator_return_code=$status
 	else if ( "$GENERATOR" == "bggen_jpsi" ) then
 		set RANDOMnum=`bash -c 'echo $RANDOM'`
 		echo Random Number used: $RANDOMnum
@@ -598,16 +608,19 @@ if ( "$GENR" != "0" ) then
 	
 		ln -s $STANDARD_NAME.conf fort.15
 		bggen_jpsi
+		set generator_return_code=$status
 		mv bggen.hddm $STANDARD_NAME.hddm
 	else if ( "$GENERATOR" == "gen_ee" ) then
 		set RANDOMnum=`bash -c 'echo $RANDOM'`
 		echo "Random number used: "$RANDOMnum
 		echo ee_mc -n$EVT_TO_GEN -R2 -b2 -l$GEN_MIN_ENERGY -u$GEN_MAX_ENERGY -t2 -r$RANDOMnum -omc_ee.hddm
 		ee_mc -n$EVT_TO_GEN -R2 -b2 -l$GEN_MIN_ENERGY -u$GEN_MAX_ENERGY -t2 -r$RANDOMnum -omc_ee.hddm
+		set generator_return_code=$status
 		mv mc_ee.hddm $STANDARD_NAME.hddm
 	else if ( "$GENERATOR" == "gen_ee_hb" ) then
 		echo ee_mc_hb -N$RUN_NUMBER -n$EVT_TO_GEN
 		ee_mc_hb -N$RUN_NUMBER -n$EVT_TO_GEN
+		set generator_return_code=$status
 		mv genOut.hddm $STANDARD_NAME.hddm
 	endif
 
@@ -617,7 +630,13 @@ if ( "$GENR" != "0" ) then
 		exit 11
 	endif
 
-
+	if ( $generator_return_code != 0 ) then
+				echo
+				echo
+				echo "Something went wrong with " "$GENERATOR"
+				echo "status code: "$generator_return_code
+				exit $generator_return_code
+	endif
 #GEANT/smearing
 
     if ( "$GEANT" != "0" ) then
@@ -639,7 +658,8 @@ if ( "$GENR" != "0" ) then
 		if ( "$polarization_angle" == "-1" ) then
 			sed -i 's/TEMPCOHERENT/'0'/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
 		else
-			sed -i 's/TEMPCOHERENT/'$COHERENT_PEAK'/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
+			set Fortran_COHERENT_PEAK=`echo $COHERENT_PEAK | cut -c -7`
+			sed -i 's/TEMPCOHERENT/'$Fortran_COHERENT_PEAK'/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
 		endif
 
 		sed -i 's/TEMPIN/'$STANDARD_NAME.hddm'/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
@@ -687,16 +707,26 @@ if ( "$GENR" != "0" ) then
 	
 		if ( "$GEANTVER" == "3" ) then
 	    	hdgeant 
+			set geant_return_code=$status
 		else if ( "$GEANTVER" == "4" ) then
 	    	#make run.mac then call it below
 	    	rm -f run.mac
 	    	echo "/run/beamOn $EVT_TO_GEN" > run.mac
 	    	echo "exit" >>! run.mac
 	    	hdgeant4 -t$NUMTHREADS run.mac
+			set geant_return_code=$status
 	    	rm run.mac
 		else
 	    	echo "INVALID GEANT VERSION"
-	    	exit
+	    	exit 1
+		endif
+
+		if ( $geant_return_code != 0 ) then
+				echo
+				echo
+				echo "Something went wrong with hdgeant(4)"
+				echo "status code: "$geant_return_code
+				exit $geant_return_code
 		endif
 
 		if ( ! -f ./$STANDARD_NAME'_geant'$GEANTVER'.hddm' ) then
@@ -707,20 +737,33 @@ if ( "$GENR" != "0" ) then
 		if ( "$SMEAR" != "0" ) then
 	    	echo "RUNNING MCSMEAR"
 	    
-	    	if ( "$BKGFOLDSTR" == "BeamPhotons" || "$BKGFOLDSTR" == "None" ) then
+	    	if ( "$BKGFOLDSTR" == "BeamPhotons" || "$BKGFOLDSTR" == "None" || "$BKGFOLDSTR" == "TagOnly" ) then
 				echo "running MCsmear without folding in random background"
 				mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' $STANDARD_NAME'_geant'$GEANTVER'.hddm'
+				set mcsmear_return_code=$status
 	    	else if ( "$BKGFOLDSTR" == "DEFAULT" || "$BKGFOLDSTR" == "Random" ) then
 				echo "mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1"
 				mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1
+				set mcsmear_return_code=$status
 			else if ( "$bkgloc_pre" == "loc:" ) then
 				echo "mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1"
 				mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1
+				set mcsmear_return_code=$status
 	    	else
 				#trust the user and use their string
 				echo 'mcsmear -PTHREAD_TIMEOUT=300 -o'$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm'' '$STANDARD_NAME'_geant'$GEANTVER'.hddm'' '$BKGFOLDSTR
 				mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' $STANDARD_NAME'_geant'$GEANTVER'.hddm' $BKGFOLDSTR
+				set mcsmear_return_code=$status
 	    	endif
+
+			if ( $mcsmear_return_code != 0 ) then
+				echo
+				echo
+				echo "Something went wrong with mcsmear"
+				echo "status code: "$mcsmear_return_code
+				exit $mcsmear_return_code
+			endif
+
 		else
 			cp $STANDARD_NAME'_geant'$GEANTVER'.hddm' $STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' 
 		endif
@@ -739,6 +782,8 @@ if ( "$GENR" != "0" ) then
 			else if ( "$GENERATOR" == "gen_ee_hb" ) then
 				rm CFFs_DD_Feb2012.dat 
 				rm ee.ascii
+				rm cobrems.root
+				rm tcs_gen.root
 			endif	
 			if ( "$GENERATOR" != "particle_gun" && "$gen_pre" != "file" ) then	
 				rm $STANDARD_NAME.hddm
@@ -752,14 +797,18 @@ if ( "$GENR" != "0" ) then
     
 	    if ( "$RECON" != "0" ) then
 			echo "RUNNING RECONSTRUCTION"
-		
+
 			if ( "$recon_pre" == "file" ) then
 		   		echo "using config file: "$jana_config_file
+				
 		   		hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' --config=jana_config.cfg -PNTHREADS=$NUMTHREADS
+				set hd_root_return_code=$status
+				echo "STATUS: " $hd_root_return_code
 				rm jana_config.cfg
 			else
+				
 		   		set pluginlist=("danarest" "monitoring_hists")
-	     
+
 		   		if ( "$CUSTOM_PLUGINS" != "None" ) then
 					set pluginlist=( "$pluginlist" "$CUSTOM_PLUGINS" )
 		   		endif	
@@ -773,13 +822,18 @@ if ( "$GENR" != "0" ) then
 		   		echo "Running hd_root with:""$PluginStr"
 		   		echo "hd_root ""$STANDARD_NAME"'_geant'"$GEANTVER"'_smeared.hddm'" -PPLUGINS=""$PluginStr ""-PNTHREADS=""$NUMTHREADS"
 		   		hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' -PPLUGINS=$PluginStr -PNTHREADS=$NUMTHREADS
-		    
+		    	set hd_root_return_code=$status
+				
+			endif
+			
+			if ( $hd_root_return_code != 0 ) then
+				echo
+				echo
+				echo "Something went wrong with hd_root"
+				echo "Status code: "$hd_root_return_code
+				exit $hd_root_return_code
 			endif
-			#set hd_root_return_code=$?
-			#if ( hd_root_return_code != 0 ) then
-			#	echo "Something went wrong with hd_root"
-			#	exit hd_root_return_code
-			#endif
+
 			if ( -f dana_rest.hddm ) then
 				mv dana_rest.hddm dana_rest_$STANDARD_NAME.hddm
 			endif
@@ -812,6 +866,7 @@ if ( "$GENR" != "0" ) then
 				set filecheck=`echo $current_files | grep -c $filetomv`
 
 				if ( "$filecheck" == "0" ) then
+
 		   			mv $filetomv $filename_root\_$STANDARD_NAME.root
 		   			mv $PWD/$filename_root\_$STANDARD_NAME.root $OUTDIR/root/
 				endif
@@ -823,7 +878,7 @@ endif
 rm -rf ccdb.sqlite
 rm -rf rcdb.sqlite
 
-if ( "$gen_pre" != "file" ) then
+if ( "$gen_pre" != "file" && "$GENERATOR" != "gen_ee_hb" && "$GENERATOR" != "gen_ee" ) then
     mv $PWD/*.conf $OUTDIR/configurations/generation/
 endif
 
diff --git a/MCwrapper/MakeMC.sh b/MCwrapper/MakeMC.sh
index f2046744..c6c1443e 100755
--- a/MCwrapper/MakeMC.sh
+++ b/MCwrapper/MakeMC.sh
@@ -127,8 +127,6 @@ echo "Detected bash shell"
 
 current_files=`find . -maxdepth 1 -type f`
 
-BGRATE_toUse=$BGRATE
-
 radthick="50.e-6"
 
 if [[ "$RADIATOR_THICKNESS" != "rcdb" || "$VERSION" != "mc" ]]; then
@@ -140,7 +138,7 @@ else
 		if [[ "$word" != "number" ]]; then
 			if [[ "$word" == "3x10-4" ]]; then
 				radthick="30e-6"
-				done
+				break
 			else	
 			removedum=`echo $word | sed 's/um/ /g'`
 			if [[ $removedum != $word ]]; then
@@ -247,7 +245,7 @@ else
 	if [[ $BGTAGONLY_OPTION == "1" || $BKGFOLDSTR=="BeamPhotons" ]]; then
 		echo "Calculating BGRate.  This process takes a minute..."
 		BGRATE_toUse=`BGRate_calc --runNo $RUN_NUMBER --coherent_peak $COHERENT_PEAK --beam_on_current $beam_on_current --beam_energy $eBEAM_ENERGY --collimator_diameter 0.00$colsize --radiator_thickness $radthick --endpoint_energy_low $GEN_MIN_ENERGY --endpoint_energy_high $GEN_MAX_ENERGY`
-		echo BGRATE Is: $BGRATE_toUse
+
 		if [[ $BGRATE_toUse == "" ]]; then
 			echo "BGrate_calc is not built or inaccessible.  Please check your build and/or specify a BGRate to be used."
 			exit 12
@@ -368,13 +366,13 @@ if [[ "$BKGFOLDSTR" == "DEFAULT" || "$bkgloc_pre" == "loc:" || "$BKGFOLDSTR" ==
 		    
 			runperiod="RunPeriod-2017-01"
 
-		    if [[ $RUN_NUMBER >= 40000 ]]; then
+		    if [[ $RUN_NUMBER -gt 40000 || $RUN_NUMBER == 40000 ]]; then
 				runperiod="RunPeriod-2018-01"
-			elif [[ $RUN_NUMBER >= 30000 ]]; then
+			elif [[ $RUN_NUMBER -gt 30000 || $RUN_NUMBER == 30000 ]]; then
 				runperiod="RunPeriod-2017-01"
-			elif [[ $RUN_NUMBER >= 20000 ]]; then
+			elif [[ $RUN_NUMBER -gt 20000 || $RUN_NUMBER == 20000 ]]; then
 				runperiod="RunPeriod-2016-10"
-			elif [[ $RUN_NUMBER >= 10000 ]]; then
+			elif [[ $RUN_NUMBER -gt 10000 || $RUN_NUMBER == 10000 ]]; then
 				runperiod="RunPeriod-2016-02"
 		    fi
 
@@ -401,11 +399,12 @@ fi
 recon_pre=`echo $CUSTOM_PLUGINS | cut -c1-4`
 jana_config_file=`echo $CUSTOM_PLUGINS | sed -r 's/^.{5}//'`
 
-if [[ -f $jana_config_file ]]; then
-echo "gathering jana config file"
-cp $jana_config_file ./jana_config.cfg
+if [[ $recon_pre == "file" ]]; then
+	if [[ -f $jana_config_file ]]; then
+	echo "gathering jana config file"
+	cp $jana_config_file ./jana_config.cfg
+	fi
 fi
-
 gen_pre=""
 
 if [[ "$GENR" != "0" ]]; then
@@ -508,6 +507,7 @@ if [[ "$GENR" != "0" ]]; then
 	sed -i 's/TEMPCOHERENT/'$COHERENT_PEAK'/' $STANDARD_NAME.conf
 	# RUN genr8 and convert
 	genr8 -r$formatted_runNumber -M$EVT_TO_GEN -A$STANDARD_NAME.ascii < $STANDARD_NAME.conf #$config_file_name
+	generator_return_code=$?
 	genr8_2_hddm $STANDARD_NAME.ascii
     elif [[ "$GENERATOR" == "bggen" ]]; then
 	RANDOMnum=`bash -c 'echo $RANDOM'`
@@ -525,6 +525,7 @@ if [[ "$GENR" != "0" ]]; then
 	
 	ln -s $STANDARD_NAME.conf fort.15
 	bggen
+	generator_return_code=$?
 	mv bggen.hddm $STANDARD_NAME.hddm
     elif [[ "$GENERATOR" == "genEtaRegge" ]]; then
 	echo "RUNNING GENETAREGGE" 
@@ -536,7 +537,8 @@ if [[ "$GENR" != "0" ]]; then
 	sed -i 's/TEMPMINGENE/'$GEN_MIN_ENERGY'/' $STANDARD_NAME.conf
 	sed -i 's/TEMPMAXGENE/'$GEN_MAX_ENERGY'/' $STANDARD_NAME.conf
 	genEtaRegge -N$EVT_TO_GEN -O$STANDARD_NAME.hddm -I$STANDARD_NAME.conf
-    elif [[ "$GENERATOR" == "gen_2pi_amp" ]]; then
+    generator_return_code=$?
+	elif [[ "$GENERATOR" == "gen_2pi_amp" ]]; then
 	echo "RUNNING GEN_2PI_AMP" 
     optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
 	echo $optionals_line
@@ -550,6 +552,7 @@ if [[ "$GENR" != "0" ]]; then
 		
 	echo gen_2pi_amp -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY  $optionals_line
 	gen_2pi_amp -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
+	generator_return_code=$?
 	elif [[ "$GENERATOR" == "gen_omega_3pi" ]]; then
 	echo "RUNNING GEN_OMEGA_3PI" 
     optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
@@ -565,24 +568,28 @@ if [[ "$GENR" != "0" ]]; then
 	echo $optionals_line
 	echo gen_omega_3pi -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -m $eBEAM_ENERGY -p $COHERENT_PEAK $optionals_line
 	gen_omega_3pi -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -m $eBEAM_ENERGY -p $COHERENT_PEAK $optionals_line
-    elif [[ "$GENERATOR" == "gen_2pi_primakoff" ]]; then
+    generator_return_code=$?
+	elif [[ "$GENERATOR" == "gen_2pi_primakoff" ]]; then
 	echo "RUNNING GEN_2PI_PRIMAKOFF" 
-        optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
+    optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
 	echo $optionals_line
 	echo gen_2pi_primakoff -c $STANDARD_NAME.conf -o  $STANDARD_NAME.hddm -hd  $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
 	gen_2pi_primakoff -c $STANDARD_NAME.conf -hd  $STANDARD_NAME.hddm -o  $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
-    elif [[ "$GENERATOR" == "gen_pi0" ]]; then
+    generator_return_code=$?
+	elif [[ "$GENERATOR" == "gen_pi0" ]]; then
 	echo "RUNNING GEN_PI0" 
-        optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
+    optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
 	echo $optionals_line
 	gen_pi0 -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK  -s $formatted_fileNumber -m $eBEAM_ENERGY $optionals_line
-    elif [[ "$GENERATOR" == "gen_2k" ]]; then
+    generator_return_code=$?
+	elif [[ "$GENERATOR" == "gen_2k" ]]; then
 	echo "RUNNING GEN_2K" 
     set optionals_line=`head -n 1 $STANDARD_NAME.conf | sed -r 's/.//'`
 	#set RANDOMnum=`bash -c 'echo $RANDOM'`
 	echo $optionals_line
 	echo gen_2k -c $STANDARD_NAME.conf -o $STANDARD_NAME.hddm -hd $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
 	gen_2k -c $STANDARD_NAME.conf -hd $STANDARD_NAME.hddm -o $STANDARD_NAME.root -n $EVT_TO_GEN -r $RUN_NUMBER -a $GEN_MIN_ENERGY -b $GEN_MAX_ENERGY -p $COHERENT_PEAK -m $eBEAM_ENERGY $optionals_line
+	generator_return_code=$?
 	elif [[ "$GENERATOR" == "bggen_jpsi" ]]; then
 	RANDOMnum=`bash -c 'echo $RANDOM'`
 	echo "Random number used: "$RANDOMnum
@@ -599,15 +606,18 @@ if [[ "$GENR" != "0" ]]; then
 	
 	ln -s $STANDARD_NAME.conf fort.15
 	bggen_jpsi
+	generator_return_code=$?
 	mv bggen.hddm $STANDARD_NAME.hddm
 	elif [[ "$GENERATOR" == "gen_ee" ]]; then
 	set RANDOMnum=`bash -c 'echo $RANDOM'`
 	echo "Random number used: "$RANDOMnum
 	ee_mc -n$EVT_TO_GEN -R2 -b2 -l$GEN_MIN_ENERGY -u$GEN_MAX_ENERGY -t2 -r$RANDOMnum -omc_ee.hddm
+	generator_return_code=$?
 	mv mc_ee.hddm $STANDARD_NAME.hddm
 	elif [[ "$GENERATOR" == "gen_ee_hb" ]]; then
 		echo ee_mc_hb -N$RUN_NUMBER -n$EVT_TO_GEN
 		ee_mc_hb -N$RUN_NUMBER -n$EVT_TO_GEN
+		generator_return_code=$?
 		mv genOut.hddm $STANDARD_NAME.hddm
 	elif [[ "$GENERATOR" == "particle_gun" ]]; then
 		echo "configuring the particle gun"
@@ -615,6 +625,15 @@ if [[ "$GENR" != "0" ]]; then
 		cp $CONFIG_FILE ./$STANDARD_NAME.conf
 	fi
     
+
+	if [[ $generator_return_code != 0 ]]; then
+				echo
+				echo
+				echo "Something went wrong with " "$GENERATOR"
+				echo "status code: "$generator_return_code
+				exit $generator_return_code
+	fi
+
 	if [[ ! -f ./$STANDARD_NAME.hddm && "$GENERATOR" != "particle_gun" && "$gen_pre" != "file" ]]; then
 		echo "An hddm file was not found after generation step.  Terminating MC production.  Please consult logs to diagnose"
 		exit 11
@@ -639,7 +658,8 @@ if [[ "$GENR" != "0" ]]; then
 	if [[ "$polarization_angle" == "-1" ]]; then
 		sed -i 's/TEMPCOHERENT/'0'/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
 	else
-		sed -i 's/TEMPCOHERENT/'$COHERENT_PEAK'/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
+		Fortran_COHERENT_PEAK=`echo $COHERENT_PEAK | cut -c -7`
+		sed -i 's/TEMPCOHERENT/'$Fortran_COHERENT_PEAK'/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
 	fi
 	sed -i 's/TEMPIN/'$STANDARD_NAME.hddm'/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
 	sed -i 's/TEMPRUNG/'$RUN_NUMBER'/' control'_'$formatted_runNumber'_'$formatted_fileNumber.in
@@ -684,19 +704,29 @@ if [[ "$GENR" != "0" ]]; then
 	mv $PWD/control'_'$formatted_runNumber'_'$formatted_fileNumber.in $PWD/control.in
 	
 	if [[ "$GEANTVER" == "3" ]]; then
-	    hdgeant 
+	    hdgeant
+		geant_return_code=$?
 	elif [[ "$GEANTVER" == "4" ]]; then
 	    #make run.mac then call it below
 	    rm -f run.mac
 	    echo "/run/beamOn $EVT_TO_GEN" > run.mac
 	    echo "exit" >>! run.mac
 	    hdgeant4 -t$NUMTHREADS run.mac
+		geant_return_code=$?
 	    rm run.mac
 	else
 	    echo "INVALID GEANT VERSION"
-	    exit
+	    exit 1
 	fi
 	
+	if [[ $geant_return_code != 0 ]]; then
+			echo
+			echo
+			echo "Something went wrong with hdgeant(4)"
+			echo "status code: "$geant_return_code
+			exit $geant_return_code
+	fi
+
 	if [[ ! -f ./$STANDARD_NAME'_geant'$GEANTVER'.hddm' ]]; then
 		echo "An hddm file was not created by Geant.  Terminating MC production.  Please consult logs to diagnose"
 		exit 12
@@ -705,21 +735,34 @@ if [[ "$GENR" != "0" ]]; then
 	if [[ "$SMEAR" != "0" ]]; then
 	    echo "RUNNING MCSMEAR"
 	    
-	    if [[ "$BKGFOLDSTR" == "BeamPhotons" || "$BKGFOLDSTR" == "None" ]]; then
+	    if [[ "$BKGFOLDSTR" == "BeamPhotons" || "$BKGFOLDSTR" == "None" || "$BKGFOLDSTR" == "TagOnly" ]]; then
 		echo "running MCsmear without folding in random background"
 		mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' $STANDARD_NAME'_geant'$GEANTVER'.hddm'
+		mcsmear_return_code=$?
 	    elif [[ "$BKGFOLDSTR" == "DEFAULT" || "$BKGFOLDSTR" == "Random" ]]; then
 		echo "mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1"
 		mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1
+		mcsmear_return_code=$?
 		elif [[ "$bkgloc_pre" == "loc:" ]]; then
 		echo "mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1"
 		mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1
+		mcsmear_return_code=$?
 		else
 		    #trust the user and use their string
 		    echo 'mcsmear -PTHREAD_TIMEOUT=300 -o'$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm'' '$STANDARD_NAME'_geant'$GEANTVER'.hddm'' '$BKGFOLDSTR
 		    mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' $STANDARD_NAME'_geant'$GEANTVER'.hddm' $BKGFOLDSTR
+			mcsmear_return_code=$?
 
 	    fi
+		
+			if [[ $mcsmear_return_code != 0 ]]; then
+				echo
+				echo
+				echo "Something went wrong with mcsmear"
+				echo "status code: "$mcsmear_return_code
+				exit $mcsmear_return_code
+			fi
+
 	else
 			cp $STANDARD_NAME'_geant'$GEANTVER'.hddm' $STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm'
 	fi
@@ -736,6 +779,8 @@ if [[ "$GENR" != "0" ]]; then
 		elif [[ "$GENERATOR" == "gen_ee_hb" ]]; then
 				rm CFFs_DD_Feb2012.dat 
 				rm ee.ascii
+				rm cobrems.root
+				rm tcs_gen.root
 		fi
 		if [[ "$GENERATOR" != "particle_gun" && "$gen_pre" != "file" ]]; then
 			rm $STANDARD_NAME.hddm
@@ -753,16 +798,16 @@ if [[ "$GENR" != "0" ]]; then
 		if [[ "$recon_pre" == "file" ]]; then
 			echo "using config file: "$jana_config_file
 			hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' --config=jana_config.cfg -PNTHREADS=$NUMTHREADS
+			hd_root_return_code=$?
 			rm jana_config.cfg
 		else
 		
 			declare -a pluginlist=("danarest" "monitoring_hists")
-			echo ${pluginlist[@]}
-			echo $CUSTOM_PLUGINS
+			
             if [[ "$CUSTOM_PLUGINS" != "None" ]]; then
 				pluginlist=("${pluginlist[@]}" $CUSTOM_PLUGINS)
             fi
-			echo ${pluginlist[@]}
+
 
 			PluginStr=""
 		
@@ -771,15 +816,20 @@ if [[ "$GENR" != "0" ]]; then
             done
 		
 			PluginStr=`echo $PluginStr | sed -r 's/.{1}$//'`
-            echo "Running hd_root with:""$PluginStr"
+            echo "Running hd_root with: ""$PluginStr"
 			echo "hd_root ""$STANDARD_NAME"'_geant'"$GEANTVER"'_smeared.hddm'" -PPLUGINS=""$PluginStr ""-PNTHREADS=""$NUMTHREADS"
 			hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' -PPLUGINS=$PluginStr -PNTHREADS=$NUMTHREADS
+			hd_root_return_code=$?
 		fi
-		#if [[ hd_root_return_code != 0 ]]; then
-		#		echo "Something went wrong with hd_root"
-	#			exit hd_root_return_code
-	#	fi
-
+		
+		if [[ $hd_root_return_code != 0 ]]; then
+				echo
+				echo
+				echo "Something went wrong with hd_root"
+				echo "Status code: "$hd_root_return_code
+				exit $hd_root_return_code
+		fi
+		
 		if [[ -f dana_rest.hddm ]]; then
                     mv dana_rest.hddm dana_rest_$STANDARD_NAME.hddm
         fi
@@ -824,7 +874,7 @@ fi
 rm -rf ccdb.sqlite
 rm -rf rcdb.sqlite
 
-if [[ "$gen_pre" != "file" ]]; then
+if [[ "$gen_pre" != "file" && "$GENERATOR" != "gen_ee_hb" && "$GENERATOR" != "gen_ee" ]]; then
 	mv $PWD/*.conf $OUTDIR/configurations/generation/
 fi
 hddmfiles=$(ls | grep .hddm)
diff --git a/MCwrapper/examples/MC.config b/MCwrapper/examples/MC.config
index 974dda12..28e06a88 100755
--- a/MCwrapper/examples/MC.config
+++ b/MCwrapper/examples/MC.config
@@ -21,9 +21,9 @@ GENERATOR=generator-to-use #or you may specifile file:/.../file-to-use.hddm
 GENERATOR_CONFIG=config file for generator
 
 #common parameters for generators
-#eBEAM_ENERGY=12 #either use =rcdb or do not set to pull the value for the chosen run number from the rcdb
-#RADIATOR_THICKNESS=50.e-06#either use =rcdb or do not set to pull the value for the chosen run number from the rcdb
-#COHERENT_PEAK=9 #either use =rcdb or do not set to pull the value for the chosen run number from the rcdb
+#eBEAM_ENERGY=12 #either use rcdb or do not set to pull the value for the chosen run number from the rcdb
+#RADIATOR_THICKNESS=50.e-06#either use rcdb or do not set to pull the value for the chosen run number from the rcdb
+#COHERENT_PEAK=9 #either use rcdb or do not set to pull the value for the chosen run number from the rcdb
 #GEN_MIN_ENERGY=4
 #GEN_MAX_ENERGY=12
 
diff --git a/MCwrapper/gluex_MC.py b/MCwrapper/gluex_MC.py
index e688d7c1..b74285c8 100755
--- a/MCwrapper/gluex_MC.py
+++ b/MCwrapper/gluex_MC.py
@@ -195,8 +195,8 @@ def main(argv):
         #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
         print "*********************************"
-        print "Welcome to v1.11 of the MCwrapper"
-        print "Thomas Britton 12/7/17"
+        print "Welcome to v1.12 of the MCwrapper"
+        print "Thomas Britton 12/12/17"
         print "*********************************"
 
 	#load all argument passed in and set default options
@@ -337,6 +337,8 @@ def main(argv):
                                         return
                                 if subparts[0].upper() == "TAGONLY":
                                         BGTAGONLY=1
+                                        if BGFOLD == "DEFAULT":
+                                                BGFOLD="TagOnly"
                                         if len(subparts)==2:
                                                 BGRATE=subparts[1]
 

From d79aef37defb1b105c8cbf9b8d18a193bc669507 Mon Sep 17 00:00:00 2001
From: T-Britton <tbritton@jlab.org>
Date: Fri, 15 Dec 2017 08:19:25 -0500
Subject: [PATCH 02/13] now with less stable jpsi

---
 MCwrapper/Generators/bggen_jpsi/particle.dat | 1 +
 1 file changed, 1 insertion(+)

diff --git a/MCwrapper/Generators/bggen_jpsi/particle.dat b/MCwrapper/Generators/bggen_jpsi/particle.dat
index 309fc4b5..e36d3db9 100644
--- a/MCwrapper/Generators/bggen_jpsi/particle.dat
+++ b/MCwrapper/Generators/bggen_jpsi/particle.dat
@@ -19,3 +19,4 @@
  44    0.7755    0.      0  0  0      0 
  80    0.7755    0.151   9  8  0      1
  82    1.232     0.118  14  8  0      0
+ 83    3.097     0.      2  3  0      2

From be26ef61b5dbe6abe25b24d1e3ebadbb36371f27 Mon Sep 17 00:00:00 2001
From: T-Britton <tbritton@jlab.org>
Date: Mon, 18 Dec 2017 11:24:26 -0500
Subject: [PATCH 03/13] touch ups

---
 MCwrapper/MakeMC.csh | 8 +++++---
 MCwrapper/MakeMC.sh  | 7 ++++++-
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/MCwrapper/MakeMC.csh b/MCwrapper/MakeMC.csh
index 477ba5c6..d2a06990 100755
--- a/MCwrapper/MakeMC.csh
+++ b/MCwrapper/MakeMC.csh
@@ -106,13 +106,13 @@ endif
 cd $RUNNING_DIR/${RUN_NUMBER}_${FILE_NUMBER}
 
 if ( "$ccdbSQLITEPATH" != "no_sqlite" ) then
-        #cp $ccdbSQLITEPATH ./ccdb.sqlite
+        cp $ccdbSQLITEPATH ./ccdb.sqlite
         setenv CCDB_CONNECTION sqlite:///$ccdbSQLITEPATH
         setenv JANA_CALIB_URL ${CCDB_CONNECTION}
 endif
 
 if ( "$rcdbSQLITEPATH" != "no_sqlite" ) then
-        #cp $rcdbSQLITEPATH ./rcdb.sqlite
+        cp $rcdbSQLITEPATH ./rcdb.sqlite
         setenv RCDB_CONNECTION sqlite:///$rcdbSQLITEPATH
 endif
 
@@ -419,6 +419,7 @@ if ( "$GENR" != "0" ) then
     if ( "$gen_pre" == "file" ) then
 		set gen_in_file=`echo $GENERATOR | sed -r 's/^.{5}//'`
 		echo "bypassing generation"
+		set generator_return_code=0
 		if ( -f $gen_in_file ) then
 	    	echo "using pre-generated file: "$gen_in_file
 	    	cp $gen_in_file ./$STANDARD_NAME.hddm
@@ -426,8 +427,9 @@ if ( "$GENR" != "0" ) then
 	    	echo "cannot find file: "$gen_in_file
 	    	exit 1
 		endif
-	else if ( "$GENERATOR" == "particle_gun") then
+	else if ( "$GENERATOR" == "particle_gun" ) then
 		echo "bypassing generation" 
+		set generator_return_code=0
     else 
 		if ( -f $CONFIG_FILE ) then
 		    echo "input file found"
diff --git a/MCwrapper/MakeMC.sh b/MCwrapper/MakeMC.sh
index c6c1443e..661eb332 100755
--- a/MCwrapper/MakeMC.sh
+++ b/MCwrapper/MakeMC.sh
@@ -418,6 +418,7 @@ if [[ "$GENR" != "0" ]]; then
 	if [[ "$gen_pre" == "file" ]]; then
 		gen_in_file=`echo $GENERATOR | sed -r 's/^.{5}//'`
 		echo "bypassing generation"
+		
 		if [[ -f $gen_in_file ]]; then
 			echo "using pre-generated file: "$gen_in_file
 			cp $gen_in_file ./$STANDARD_NAME.hddm
@@ -425,7 +426,11 @@ if [[ "$GENR" != "0" ]]; then
 			echo "cannot find file: "$gen_in_file
 			exit
 		fi
-				
+			generator_return_code=0	
+
+	else if [[ "$GENERATOR" == "particle_gun" ]]; then
+		echo "bypassing generation" 
+		generator_return_code=0
 	else 
 		if [[ -f $CONFIG_FILE ]]; then
 	    	echo "input file found"

From b8e065fbc48a8d91d8a6c0fdeed20b919bbea4d2 Mon Sep 17 00:00:00 2001
From: T-Britton <tbritton@jlab.org>
Date: Wed, 20 Dec 2017 11:23:16 -0500
Subject: [PATCH 04/13] First commit pre OSG testing

---
 .../Generators/genEtaRegge/examples/eta548.in |  3 --
 MCwrapper/MakeMC.csh                          | 14 ++++---
 MCwrapper/MakeMC.sh                           |  4 +-
 MCwrapper/gluex_MC.py                         | 42 ++++++++++++++++++-
 MCwrapper/osg-container.csh                   | 41 ++++++++++++++++++
 MCwrapper/osg-container.sh                    | 41 ++++++++++++++++++
 6 files changed, 134 insertions(+), 11 deletions(-)
 create mode 100644 MCwrapper/osg-container.csh
 create mode 100644 MCwrapper/osg-container.sh

diff --git a/MCwrapper/Generators/genEtaRegge/examples/eta548.in b/MCwrapper/Generators/genEtaRegge/examples/eta548.in
index da33b5f4..ed68aaeb 100644
--- a/MCwrapper/Generators/genEtaRegge/examples/eta548.in
+++ b/MCwrapper/Generators/genEtaRegge/examples/eta548.in
@@ -10,6 +10,3 @@ TEMPELECE TEMPCOHERENT TEMPCOLD TEMPRADTHICK
 3
 #GEANT ids of decay particles (1=gamma,7=pi0, 8=pi+, 9=pi-, 17=eta).
 1 2 3
-
-
-   
diff --git a/MCwrapper/MakeMC.csh b/MCwrapper/MakeMC.csh
index d2a06990..37beeb25 100755
--- a/MCwrapper/MakeMC.csh
+++ b/MCwrapper/MakeMC.csh
@@ -744,12 +744,16 @@ if ( "$GENR" != "0" ) then
 				mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' $STANDARD_NAME'_geant'$GEANTVER'.hddm'
 				set mcsmear_return_code=$status
 	    	else if ( "$BKGFOLDSTR" == "DEFAULT" || "$BKGFOLDSTR" == "Random" ) then
-				echo "mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1"
-				mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1
+				set fold_skip_num=`echo "$FILE_NUMBER * $PER_FILE" | bc`
+				#set bkglocstring="/w/halld-scifs17exp/halld2/home/tbritton/MCwrapper_Development/converted.hddm"
+				echo "mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1""+"$fold_skip_num
+				mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1\+$fold_skip_num
 				set mcsmear_return_code=$status
 			else if ( "$bkgloc_pre" == "loc:" ) then
-				echo "mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1"
-				mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1
+				set fold_skip_num=`echo "$FILE_NUMBER * $PER_FILE" | bc`
+				
+				echo "mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1""+"$fold_skip_num
+				mcsmear -PTHREAD_TIMEOUT=300 -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1\+$fold_skip_num
 				set mcsmear_return_code=$status
 	    	else
 				#trust the user and use their string
@@ -805,7 +809,7 @@ if ( "$GENR" != "0" ) then
 				
 		   		hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' --config=jana_config.cfg -PNTHREADS=$NUMTHREADS
 				set hd_root_return_code=$status
-				echo "STATUS: " $hd_root_return_code
+				#echo "STATUS: " $hd_root_return_code
 				rm jana_config.cfg
 			else
 				
diff --git a/MCwrapper/MakeMC.sh b/MCwrapper/MakeMC.sh
index 661eb332..bea6bea5 100755
--- a/MCwrapper/MakeMC.sh
+++ b/MCwrapper/MakeMC.sh
@@ -111,13 +111,13 @@ fi
 cd $RUNNING_DIR/${RUN_NUMBER}_${FILE_NUMBER}
 
 if [[ "$ccdbSQLITEPATH" != "no_sqlite" ]]; then
-        #cp $ccdbSQLITEPATH ./ccdb.sqlite
+        cp $ccdbSQLITEPATH ./ccdb.sqlite
         export CCDB_CONNECTION=sqlite:///$ccdbSQLITEPATH
         export JANA_CALIB_URL=$CCDB_CONNECTION
 fi
 
 if [[ "$rcdbSQLITEPATH" != "no_sqlite" ]]; then
-        #cp $rcdbSQLITEPATH ./rcdb.sqlite
+        cp $rcdbSQLITEPATH ./rcdb.sqlite
         export RCDB_CONNECTION=sqlite:///$rcdbSQLITEPATH
 fi
 
diff --git a/MCwrapper/gluex_MC.py b/MCwrapper/gluex_MC.py
index b74285c8..cdb3884d 100755
--- a/MCwrapper/gluex_MC.py
+++ b/MCwrapper/gluex_MC.py
@@ -153,6 +153,42 @@ def  condor_add_job(VERBOSE, WORKFLOW, RUNNUM, FILENUM, indir, COMMAND, NCORES,
         status = subprocess.call(add_command, shell=True)
         status = subprocess.call("rm MCcondor.submit", shell=True)
 
+def  OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, FILENUM, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE ):
+        STUBNAME = str(RUNNUM) + "_" + str(FILENUM)
+	JOBNAME = WORKFLOW + "_" + STUBNAME
+
+        f=open('MCOSG.submit','w')
+        f.write("universe = vanilla"+"\n")
+        f.write("Executable = osg-container.sh""\n") 
+        f.write("Arguments  = "+indir+" "+COMMAND+"\n")
+        f.write("Requirements = (HAS_SINGULARITY == TRUE) && (HAS_CVMFS_oasis_opensciencegrid_org == True)"+"\n") 
+        f.write('+SingularityImage = "/cvmfs/singularity.opensciencegrid.org/rjones30/gluex:latest"'+"\n") 
+        f.write('+SingularityBindCVMFS = True'+"\n") 
+        f.write('+SingularityAutoLoad = True'+"\n") 
+        f.write('should_transfer_files = IF_NEEDED'+"\n")
+        f.write('when_to_transfer_output = ON_EXIT'+"\n")
+        f.write('x509userproxy = /tmp/user_proxy'+"\n")
+        f.write('concurrency_limits = GluexProduction'+"\n")
+        f.write('on_exit_remove = true'+"\n")
+        f.write('on_exit_hold = false'+"\n")
+        f.write("Error      = "+DATA_OUTPUT_BASE_DIR+"/log/"+"error_"+JOBNAME+".log\n")
+        f.write("Log      = "+DATA_OUTPUT_BASE_DIR+"/log/"+"out_"+JOBNAME+".log\n")
+        f.write("output = <logdir>/$(CLUSTER).$(PROCESS).out\n")
+        f.write("initialdir = "+RUNNING_DIR+"\n")
+        f.write("transfer_input_files = "+ENVFILE+"\n")
+        f.write("transfer_output_files = "+DATA_OUTPUT_BASE_DIR+"\n")
+
+        f.write("queue\n")
+        f.close()
+        
+        add_command="condor_submit -name "+JOBNAME+" MCOSG.submit"
+        if add_command.find(';')!=-1 or add_command.find('&')!=-1 or mkdircom.find(';')!=-1 or mkdircom.find('&')!=-1:#THIS CHECK HELPS PROTEXT AGAINST A POTENTIAL HACK VIA CONFIG FILES
+                print "Nice try.....you cannot use ; or &"
+                exit(1)
+
+        status = subprocess.call(add_command, shell=True)
+        status = subprocess.call("rm MCOSG.submit", shell=True)
+
 
 def showhelp():
         helpstring= "variation=%s where %s is a valid jana_calib_context variation string (default is \"mc\")\n"
@@ -196,7 +232,7 @@ def main(argv):
 
         print "*********************************"
         print "Welcome to v1.12 of the MCwrapper"
-        print "Thomas Britton 12/12/17"
+        print "Thomas Britton 12/19/17"
         print "*********************************"
 
 	#load all argument passed in and set default options
@@ -594,6 +630,8 @@ def main(argv):
                                                 qsub_add_job(VERBOSE, WORKFLOW, runs[0], BASEFILENUM+FILENUM_this_run+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, RAM, QUEUENAME, LOG_DIR )
                                         elif BATCHSYS.upper()=="CONDOR":
                                                 condor_add_job(VERBOSE, WORKFLOW, runs[0], BASEFILENUM+FILENUM_this_run+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR )
+                                        elif BATCHSYS.upper()=="OSG":
+                                                condor_add_job(VERBOSE, WORKFLOW, runs[0], BASEFILENUM+FILENUM_this_run+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE )
                         #print "----------------"
                 
         else:
@@ -622,6 +660,8 @@ def main(argv):
                                         qsub_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, RAM, QUEUENAME, LOG_DIR )
                                 elif BATCHSYS.upper()=="CONDOR":
                                         condor_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR )
+                                 elif BATCHSYS.upper()=="OSG":
+                                        condor_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE )
 
                                         
         if BATCHRUN == 1 and BATCHSYS.upper() == "SWIF":
diff --git a/MCwrapper/osg-container.csh b/MCwrapper/osg-container.csh
new file mode 100644
index 00000000..81b854de
--- /dev/null
+++ b/MCwrapper/osg-container.csh
@@ -0,0 +1,41 @@
+#!/bin/sh
+#
+# osg-container.sh - gluex job wrapper script for osg jobs
+#
+# This script contains GENERIC (non-job-specific) steps for getting
+# set up inside the gluex container on an osg worker node and launching
+# the job script. It should not normally be modified by the user.
+#
+# Usage: osg-container.sh <job script> [job script arguments]
+#
+# Author: Richard.T.Jones at uconn.edu
+# Version: June 8, 2017
+
+set container="/cvmfs/singularity.opensciencegrid.org/rjones30/gluex:latest"
+#oasismount="/cvmfs/oasis.opensciencegrid.org"
+set oasismount="/cvmfs"
+set dockerimage="docker://rjones30/gluex:latest"
+set userproxy=x509up_u$UID
+
+# define the container context for running on osg workers
+
+if ( -f /environment ) then
+    echo "Job running on" `hostname`
+    ( -r .$userproxy ) && mv .$userproxy /tmp/$userproxy
+    source /environment
+    unset CCDB_CONNECTION
+    unset RCDB_CONNECTION
+    $* && retcode=$?
+    echo "Job finished with exit code" $retcode
+    rm -rf *.sqlite
+    exit $retcode
+
+else if ( -f $container/environment ) then
+    echo "Starting up container on" `hostname`
+    ( -r /tmp/$userproxy ) && cp /tmp/$userproxy .$userproxy
+    exec singularity exec --containall --bind ${oasismount} --home `pwd`:/srv --pwd /srv --scratch /tmp,/var/tmp ${container} \
+    bash $0 $*
+
+else
+    echo "Job container not found on" `hostname`
+endif
\ No newline at end of file
diff --git a/MCwrapper/osg-container.sh b/MCwrapper/osg-container.sh
new file mode 100644
index 00000000..d6572188
--- /dev/null
+++ b/MCwrapper/osg-container.sh
@@ -0,0 +1,41 @@
+#!/bin/sh
+#
+# osg-container.sh - gluex job wrapper script for osg jobs
+#
+# This script contains GENERIC (non-job-specific) steps for getting
+# set up inside the gluex container on an osg worker node and launching
+# the job script. It should not normally be modified by the user.
+#
+# Usage: osg-container.sh <job script> [job script arguments]
+#
+# Author: Richard.T.Jones at uconn.edu
+# Version: June 8, 2017
+
+container="/cvmfs/singularity.opensciencegrid.org/rjones30/gluex:latest"
+#oasismount="/cvmfs/oasis.opensciencegrid.org"
+oasismount="/cvmfs"
+dockerimage="docker://rjones30/gluex:latest"
+userproxy=x509up_u$UID
+
+# define the container context for running on osg workers
+
+if [[ -f /environment ]]; then
+    echo "Job running on" `hostname`
+    [ -r .$userproxy ] && mv .$userproxy /tmp/$userproxy
+    source /environment
+    unset CCDB_CONNECTION
+    unset RCDB_CONNECTION
+    $* && retcode=$?
+    echo "Job finished with exit code" $retcode
+    rm -rf *.sqlite
+    exit $retcode
+
+elif [[ -f $container/environment ]]; then
+    echo "Starting up container on" `hostname`
+    [ -r /tmp/$userproxy ] && cp /tmp/$userproxy .$userproxy
+    exec singularity exec --containall --bind ${oasismount} --home `pwd`:/srv --pwd /srv --scratch /tmp,/var/tmp ${container} \
+    bash $0 $*
+
+else
+    echo "Job container not found on" `hostname`
+fi
\ No newline at end of file

From 741231c2ac7f8f9f55e4f58e3bebd069dc145ae7 Mon Sep 17 00:00:00 2001
From: T-Britton <tbritton@jlab.org>
Date: Thu, 21 Dec 2017 10:19:48 -0500
Subject: [PATCH 05/13] step 1 of OSG

---
 MCwrapper/gluex_MC.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/MCwrapper/gluex_MC.py b/MCwrapper/gluex_MC.py
index cdb3884d..af87ecfa 100755
--- a/MCwrapper/gluex_MC.py
+++ b/MCwrapper/gluex_MC.py
@@ -173,7 +173,7 @@ def  OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, FILENUM, indir, COMMAND, NCORES, DAT
         f.write('on_exit_hold = false'+"\n")
         f.write("Error      = "+DATA_OUTPUT_BASE_DIR+"/log/"+"error_"+JOBNAME+".log\n")
         f.write("Log      = "+DATA_OUTPUT_BASE_DIR+"/log/"+"out_"+JOBNAME+".log\n")
-        f.write("output = <logdir>/$(CLUSTER).$(PROCESS).out\n")
+        f.write("output = "+DATA_OUTPUT_BASE_DIR+"/log/"+"OSGout_"+JOBNAME+".log\n")
         f.write("initialdir = "+RUNNING_DIR+"\n")
         f.write("transfer_input_files = "+ENVFILE+"\n")
         f.write("transfer_output_files = "+DATA_OUTPUT_BASE_DIR+"\n")
@@ -181,13 +181,13 @@ def  OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, FILENUM, indir, COMMAND, NCORES, DAT
         f.write("queue\n")
         f.close()
         
-        add_command="condor_submit -name "+JOBNAME+" MCOSG.submit"
-        if add_command.find(';')!=-1 or add_command.find('&')!=-1 or mkdircom.find(';')!=-1 or mkdircom.find('&')!=-1:#THIS CHECK HELPS PROTEXT AGAINST A POTENTIAL HACK VIA CONFIG FILES
-                print "Nice try.....you cannot use ; or &"
-                exit(1)
+        #add_command="condor_submit -name "+JOBNAME+" MCOSG.submit"
+        #if add_command.find(';')!=-1 or add_command.find('&')!=-1 or mkdircom.find(';')!=-1 or mkdircom.find('&')!=-1:#THIS CHECK HELPS PROTEXT AGAINST A POTENTIAL HACK VIA CONFIG FILES
+        #        print "Nice try.....you cannot use ; or &"
+        #        exit(1)
 
-        status = subprocess.call(add_command, shell=True)
-        status = subprocess.call("rm MCOSG.submit", shell=True)
+        #status = subprocess.call(add_command, shell=True)
+        #status = subprocess.call("rm MCOSG.submit", shell=True)
 
 
 def showhelp():
@@ -631,7 +631,7 @@ def main(argv):
                                         elif BATCHSYS.upper()=="CONDOR":
                                                 condor_add_job(VERBOSE, WORKFLOW, runs[0], BASEFILENUM+FILENUM_this_run+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR )
                                         elif BATCHSYS.upper()=="OSG":
-                                                condor_add_job(VERBOSE, WORKFLOW, runs[0], BASEFILENUM+FILENUM_this_run+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE )
+                                                OSG_add_job(VERBOSE, WORKFLOW, runs[0], BASEFILENUM+FILENUM_this_run+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE )
                         #print "----------------"
                 
         else:
@@ -660,8 +660,8 @@ def main(argv):
                                         qsub_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, RAM, QUEUENAME, LOG_DIR )
                                 elif BATCHSYS.upper()=="CONDOR":
                                         condor_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR )
-                                 elif BATCHSYS.upper()=="OSG":
-                                        condor_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE )
+                                elif BATCHSYS.upper()=="OSG":
+                                        OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE )
 
                                         
         if BATCHRUN == 1 and BATCHSYS.upper() == "SWIF":

From 06c2308da6333839f12cb4d87d4981250e0d1b64 Mon Sep 17 00:00:00 2001
From: T-Britton <tbritton@jlab.org>
Date: Thu, 21 Dec 2017 10:49:39 -0500
Subject: [PATCH 06/13] added a dummy script to test OSG execution

---
 MCwrapper/MakeHelloWorld.csh | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100755 MCwrapper/MakeHelloWorld.csh

diff --git a/MCwrapper/MakeHelloWorld.csh b/MCwrapper/MakeHelloWorld.csh
new file mode 100755
index 00000000..fcf19a70
--- /dev/null
+++ b/MCwrapper/MakeHelloWorld.csh
@@ -0,0 +1,3 @@
+#!/bin/csh -f
+
+echo "Hello" >& HelloWorld.txt
\ No newline at end of file

From 7d8f4a4359e93d72219fa02b3c788fc7f5b8d71c Mon Sep 17 00:00:00 2001
From: tbritton <tbritton@jlab.org>
Date: Tue, 2 Jan 2018 15:34:06 -0500
Subject: [PATCH 07/13] beta osg implementation

---
 MCwrapper/MakeMC.csh  |   6 +--
 MCwrapper/MakeMC.sh   |   4 +-
 MCwrapper/gluex_MC.py | 100 ++++++++++++++++++++++++++++++++++--------
 3 files changed, 86 insertions(+), 24 deletions(-)

diff --git a/MCwrapper/MakeMC.csh b/MCwrapper/MakeMC.csh
index 37beeb25..2281a16b 100755
--- a/MCwrapper/MakeMC.csh
+++ b/MCwrapper/MakeMC.csh
@@ -85,7 +85,7 @@ setenv BGRATE $1
 
 
 #necessary to run swif, uses local directory if swif=0 is used
-if ( "$BATCHRUN" != "0" ) then
+if ( "$BATCHRUN" != "0"  ) then
 # ENVIRONMENT
 	echo $ENVIRONMENT
     echo pwd=$PWD
@@ -107,13 +107,13 @@ cd $RUNNING_DIR/${RUN_NUMBER}_${FILE_NUMBER}
 
 if ( "$ccdbSQLITEPATH" != "no_sqlite" ) then
         cp $ccdbSQLITEPATH ./ccdb.sqlite
-        setenv CCDB_CONNECTION sqlite:///$ccdbSQLITEPATH
+        setenv CCDB_CONNECTION sqlite:///$PWD/ccdb.sqlite #$ccdbSQLITEPATH
         setenv JANA_CALIB_URL ${CCDB_CONNECTION}
 endif
 
 if ( "$rcdbSQLITEPATH" != "no_sqlite" ) then
         cp $rcdbSQLITEPATH ./rcdb.sqlite
-        setenv RCDB_CONNECTION sqlite:///$rcdbSQLITEPATH
+        setenv RCDB_CONNECTION sqlite:///$PWD/rcdb.sqlite #$rcdbSQLITEPATH
 endif
 
 echo ""
diff --git a/MCwrapper/MakeMC.sh b/MCwrapper/MakeMC.sh
index bea6bea5..afe555cc 100755
--- a/MCwrapper/MakeMC.sh
+++ b/MCwrapper/MakeMC.sh
@@ -112,13 +112,13 @@ cd $RUNNING_DIR/${RUN_NUMBER}_${FILE_NUMBER}
 
 if [[ "$ccdbSQLITEPATH" != "no_sqlite" ]]; then
         cp $ccdbSQLITEPATH ./ccdb.sqlite
-        export CCDB_CONNECTION=sqlite:///$ccdbSQLITEPATH
+        export CCDB_CONNECTION=sqlite:///$PWD/ccdb.sqlite
         export JANA_CALIB_URL=$CCDB_CONNECTION
 fi
 
 if [[ "$rcdbSQLITEPATH" != "no_sqlite" ]]; then
         cp $rcdbSQLITEPATH ./rcdb.sqlite
-        export RCDB_CONNECTION=sqlite:///$rcdbSQLITEPATH
+        export RCDB_CONNECTION=sqlite:///$PWD/rcdb.sqlite
 fi
 
 echo ""
diff --git a/MCwrapper/gluex_MC.py b/MCwrapper/gluex_MC.py
index af87ecfa..8c1dec11 100755
--- a/MCwrapper/gluex_MC.py
+++ b/MCwrapper/gluex_MC.py
@@ -153,41 +153,101 @@ def  condor_add_job(VERBOSE, WORKFLOW, RUNNUM, FILENUM, indir, COMMAND, NCORES,
         status = subprocess.call(add_command, shell=True)
         status = subprocess.call("rm MCcondor.submit", shell=True)
 
-def  OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, FILENUM, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE ):
+def  OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, FILENUM, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE, LOG_DIR ):
         STUBNAME = str(RUNNUM) + "_" + str(FILENUM)
 	JOBNAME = WORKFLOW + "_" + STUBNAME
 
+        mkdircom="mkdir -p "+DATA_OUTPUT_BASE_DIR+"/log/"
+
+        indir_parts=indir.split("/")
+        script_to_use=indir_parts[len(indir_parts)-1]
+
+        ENVFILE_parts=ENVFILE.split("/")
+        envfile_to_source="/srv/"+ENVFILE_parts[len(ENVFILE_parts)-1]
+
+        
+        COMMAND_parts=COMMAND.split(" ")
+        COMMAND_parts[1]=envfile_to_source
+        
+        COMMAND_parts[3]="./"
+        COMMAND_parts[30]="./"
+
+        additional_passins=""
+        if COMMAND_parts[2][:5] == "file:":
+                gen_config_parts=COMMAND_parts[2].split("/")
+                gen_config_to_use=gen_config_parts[len(gen_config_parts)-1]
+                additional_passins+=COMMAND_parts[2][5:]+", "
+                COMMAND_parts[2]="file:/srv/"+gen_config_to_use
+        else:
+                gen_config_parts=COMMAND_parts[2].split("/")
+                gen_config_to_use=gen_config_parts[len(gen_config_parts)-1]
+                additional_passins+=COMMAND_parts[2]+", "
+                COMMAND_parts[2]="/srv/"+gen_config_to_use
+
+        if COMMAND_parts[28] != "None" and COMMAND_parts[28][:5]=="file:" :
+                janaconfig_parts=COMMAND_parts[28].split("/")
+                janaconfig_to_use=janaconfig_parts[len(janaconfig_parts)-1]
+                additional_passins+=COMMAND_parts[28][5:]+", "
+                COMMAND_parts[28]="file:/srv/"+janaconfig_to_use
+
+        if COMMAND_parts[31] != "no_sqlite" :
+                ccdbsqlite_parts=COMMAND_parts[31].split("/")
+                ccdbsqlite_to_use=ccdbsqlite_parts[len(ccdbsqlite_parts)-1]
+                additional_passins+=COMMAND_parts[31]+", "
+                COMMAND_parts[31]="/srv/"+ccdbsqlite_to_use
+
+        if COMMAND_parts[32] != "no_sqlite" :
+                rcdbsqlite_parts=COMMAND_parts[32].split("/")
+                rcdbsqlite_to_use=rcdbsqlite_parts[len(rcdbsqlite_parts)-1]
+                additional_passins+=COMMAND_parts[32]+", "
+                COMMAND_parts[32]="/srv/"+rcdbsqlite_to_use
+
+        if additional_passins != "":
+                additional_passins=", "+additional_passins
+                additional_passins=additional_passins[:-2]
+
+        modified_COMMAND=""
+
+        for com in COMMAND_parts:
+                modified_COMMAND=modified_COMMAND+com+" "
+        
+        modified_COMMAND=modified_COMMAND[:-1]
+
         f=open('MCOSG.submit','w')
         f.write("universe = vanilla"+"\n")
-        f.write("Executable = osg-container.sh""\n") 
-        f.write("Arguments  = "+indir+" "+COMMAND+"\n")
+        f.write("Executable = "+os.environ.get('MCWRAPPER_CENTRAL')+"/osg-container.sh"+"\n") 
+        #f.write("Arguments  = "+indir+" "+COMMAND+"\n")
+        f.write("Arguments  = "+"./"+script_to_use+" "+modified_COMMAND+"\n")
         f.write("Requirements = (HAS_SINGULARITY == TRUE) && (HAS_CVMFS_oasis_opensciencegrid_org == True)"+"\n") 
         f.write('+SingularityImage = "/cvmfs/singularity.opensciencegrid.org/rjones30/gluex:latest"'+"\n") 
         f.write('+SingularityBindCVMFS = True'+"\n") 
         f.write('+SingularityAutoLoad = True'+"\n") 
-        f.write('should_transfer_files = IF_NEEDED'+"\n")
+        f.write('should_transfer_files = YES'+"\n")
         f.write('when_to_transfer_output = ON_EXIT'+"\n")
-        f.write('x509userproxy = /tmp/user_proxy'+"\n")
+        
         f.write('concurrency_limits = GluexProduction'+"\n")
         f.write('on_exit_remove = true'+"\n")
         f.write('on_exit_hold = false'+"\n")
-        f.write("Error      = "+DATA_OUTPUT_BASE_DIR+"/log/"+"error_"+JOBNAME+".log\n")
-        f.write("Log      = "+DATA_OUTPUT_BASE_DIR+"/log/"+"out_"+JOBNAME+".log\n")
-        f.write("output = "+DATA_OUTPUT_BASE_DIR+"/log/"+"OSGout_"+JOBNAME+".log\n")
+        f.write("Error      = "+LOG_DIR+"/log/"+"error_"+JOBNAME+".log\n")
+        f.write("Log      = "+LOG_DIR+"/log/"+"out_"+JOBNAME+".log\n")
+        f.write("output = "+LOG_DIR+"OSGout_"+JOBNAME+".log\n")
         f.write("initialdir = "+RUNNING_DIR+"\n")
-        f.write("transfer_input_files = "+ENVFILE+"\n")
-        f.write("transfer_output_files = "+DATA_OUTPUT_BASE_DIR+"\n")
+        #f.write("transfer_input_files = "+ENVFILE+"\n")
+        f.write("transfer_input_files = "+indir+", "+ENVFILE+additional_passins+"\n")
+        f.write("transfer_output_files = "+RUNNUM+"_"+str(FILENUM)+"\n")
+        f.write("transfer_output_remaps = "+"\""+RUNNUM+"_"+str(FILENUM)+"="+DATA_OUTPUT_BASE_DIR+"\""+"\n")
 
         f.write("queue\n")
         f.close()
         
-        #add_command="condor_submit -name "+JOBNAME+" MCOSG.submit"
-        #if add_command.find(';')!=-1 or add_command.find('&')!=-1 or mkdircom.find(';')!=-1 or mkdircom.find('&')!=-1:#THIS CHECK HELPS PROTEXT AGAINST A POTENTIAL HACK VIA CONFIG FILES
-        #        print "Nice try.....you cannot use ; or &"
-        #        exit(1)
+        add_command="condor_submit -name "+JOBNAME+" MCOSG.submit"
+        if add_command.find(';')!=-1 or add_command.find('&')!=-1 :#THIS CHECK HELPS PROTEXT AGAINST A POTENTIAL HACK VIA CONFIG FILES
+                print "Nice try.....you cannot use ; or &"
+                exit(1)
 
-        #status = subprocess.call(add_command, shell=True)
-        #status = subprocess.call("rm MCOSG.submit", shell=True)
+        status = subprocess.call(mkdircom, shell=True)
+        status = subprocess.call(add_command, shell=True)
+        status = subprocess.call("rm MCOSG.submit", shell=True)
 
 
 def showhelp():
@@ -232,7 +292,7 @@ def main(argv):
 
         print "*********************************"
         print "Welcome to v1.12 of the MCwrapper"
-        print "Thomas Britton 12/19/17"
+        print "Thomas Britton 1/2/18"
         print "*********************************"
 
 	#load all argument passed in and set default options
@@ -520,6 +580,8 @@ def main(argv):
 	indir=os.environ.get('MCWRAPPER_CENTRAL')
         
         script_to_use = "/MakeMC.csh"
+        #script_to_use = "/MakeHelloWorld.csh"
+        
         if environ['SHELL']=="/bin/bash" :
                 script_to_use = "/MakeMC.sh"
         
@@ -631,7 +693,7 @@ def main(argv):
                                         elif BATCHSYS.upper()=="CONDOR":
                                                 condor_add_job(VERBOSE, WORKFLOW, runs[0], BASEFILENUM+FILENUM_this_run+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR )
                                         elif BATCHSYS.upper()=="OSG":
-                                                OSG_add_job(VERBOSE, WORKFLOW, runs[0], BASEFILENUM+FILENUM_this_run+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE )
+                                                OSG_add_job(VERBOSE, WORKFLOW, runs[0], BASEFILENUM+FILENUM_this_run+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE, LOG_DIR )
                         #print "----------------"
                 
         else:
@@ -661,7 +723,7 @@ def main(argv):
                                 elif BATCHSYS.upper()=="CONDOR":
                                         condor_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR )
                                 elif BATCHSYS.upper()=="OSG":
-                                        OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE )
+                                        OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, BASEFILENUM+FILENUM+-1, indir, COMMAND, NCORES, DATA_OUTPUT_BASE_DIR, TIMELIMIT, RUNNING_DIR, ENVFILE, LOG_DIR )
 
                                         
         if BATCHRUN == 1 and BATCHSYS.upper() == "SWIF":

From 0220e05e778d8720d4df85d670c8ebd8a0e8dcf4 Mon Sep 17 00:00:00 2001
From: T-Britton <tbritton@jlab.org>
Date: Wed, 3 Jan 2018 08:22:29 -0500
Subject: [PATCH 08/13] Delete MakeHelloWorld.csh

---
 MCwrapper/MakeHelloWorld.csh | 3 ---
 1 file changed, 3 deletions(-)
 delete mode 100755 MCwrapper/MakeHelloWorld.csh

diff --git a/MCwrapper/MakeHelloWorld.csh b/MCwrapper/MakeHelloWorld.csh
deleted file mode 100755
index fcf19a70..00000000
--- a/MCwrapper/MakeHelloWorld.csh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/csh -f
-
-echo "Hello" >& HelloWorld.txt
\ No newline at end of file

From c3a184a3a4a93f98c3aad9be64d94b6296af1b96 Mon Sep 17 00:00:00 2001
From: T-Britton <tbritton@jlab.org>
Date: Wed, 3 Jan 2018 08:22:50 -0500
Subject: [PATCH 09/13] Delete osg-container.csh

---
 MCwrapper/osg-container.csh | 41 -------------------------------------
 1 file changed, 41 deletions(-)
 delete mode 100644 MCwrapper/osg-container.csh

diff --git a/MCwrapper/osg-container.csh b/MCwrapper/osg-container.csh
deleted file mode 100644
index 81b854de..00000000
--- a/MCwrapper/osg-container.csh
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/bin/sh
-#
-# osg-container.sh - gluex job wrapper script for osg jobs
-#
-# This script contains GENERIC (non-job-specific) steps for getting
-# set up inside the gluex container on an osg worker node and launching
-# the job script. It should not normally be modified by the user.
-#
-# Usage: osg-container.sh <job script> [job script arguments]
-#
-# Author: Richard.T.Jones at uconn.edu
-# Version: June 8, 2017
-
-set container="/cvmfs/singularity.opensciencegrid.org/rjones30/gluex:latest"
-#oasismount="/cvmfs/oasis.opensciencegrid.org"
-set oasismount="/cvmfs"
-set dockerimage="docker://rjones30/gluex:latest"
-set userproxy=x509up_u$UID
-
-# define the container context for running on osg workers
-
-if ( -f /environment ) then
-    echo "Job running on" `hostname`
-    ( -r .$userproxy ) && mv .$userproxy /tmp/$userproxy
-    source /environment
-    unset CCDB_CONNECTION
-    unset RCDB_CONNECTION
-    $* && retcode=$?
-    echo "Job finished with exit code" $retcode
-    rm -rf *.sqlite
-    exit $retcode
-
-else if ( -f $container/environment ) then
-    echo "Starting up container on" `hostname`
-    ( -r /tmp/$userproxy ) && cp /tmp/$userproxy .$userproxy
-    exec singularity exec --containall --bind ${oasismount} --home `pwd`:/srv --pwd /srv --scratch /tmp,/var/tmp ${container} \
-    bash $0 $*
-
-else
-    echo "Job container not found on" `hostname`
-endif
\ No newline at end of file

From 80e053580d6c6ecbc8e5fb864b703f638c442684 Mon Sep 17 00:00:00 2001
From: tbritton <tbritton@jlab.org>
Date: Wed, 3 Jan 2018 08:31:05 -0500
Subject: [PATCH 10/13] text touchups

---
 MCwrapper/osg-container.sh | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)
 mode change 100644 => 100755 MCwrapper/osg-container.sh

diff --git a/MCwrapper/osg-container.sh b/MCwrapper/osg-container.sh
old mode 100644
new mode 100755
index d6572188..44ecf9fd
--- a/MCwrapper/osg-container.sh
+++ b/MCwrapper/osg-container.sh
@@ -20,22 +20,22 @@ userproxy=x509up_u$UID
 # define the container context for running on osg workers
 
 if [[ -f /environment ]]; then
-    echo "Job running on" `hostname`
-    [ -r .$userproxy ] && mv .$userproxy /tmp/$userproxy
-    source /environment
-    unset CCDB_CONNECTION
-    unset RCDB_CONNECTION
-    $* && retcode=$?
-    echo "Job finished with exit code" $retcode
-    rm -rf *.sqlite
-    exit $retcode
+    echo "Job running on" `hostname`
+    [ -r .$userproxy ] && mv .$userproxy /tmp/$userproxy
+    source /environment
+    unset CCDB_CONNECTION
+    unset RCDB_CONNECTION
+    eval $*; retcode=$?
+    echo "Job finished with exit code" $retcode
+    rm -rf *.sqlite
+    exit $retcode
 
 elif [[ -f $container/environment ]]; then
-    echo "Starting up container on" `hostname`
-    [ -r /tmp/$userproxy ] && cp /tmp/$userproxy .$userproxy
-    exec singularity exec --containall --bind ${oasismount} --home `pwd`:/srv --pwd /srv --scratch /tmp,/var/tmp ${container} \
-    bash $0 $*
+    echo "Starting up container on" `hostname`
+    [ -r /tmp/$userproxy ] && cp /tmp/$userproxy .$userproxy
+    exec singularity exec --containall --bind ${oasismount} --home `pwd`:/srv --pwd /srv --scratch /tmp,/var/tmp ${container} \
+    bash $0 $*
 
 else
-    echo "Job container not found on" `hostname`
-fi
\ No newline at end of file
+    echo "Job container not found on" `hostname`
+fi

From bf3a88da83e3ca1bd8d8a064d63a9d468420ee83 Mon Sep 17 00:00:00 2001
From: tbritton <tbritton@jlab.org>
Date: Wed, 3 Jan 2018 08:31:18 -0500
Subject: [PATCH 11/13] text touchups

---
 MCwrapper/examples/MC.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/MCwrapper/examples/MC.config b/MCwrapper/examples/MC.config
index 28e06a88..32799b72 100755
--- a/MCwrapper/examples/MC.config
+++ b/MCwrapper/examples/MC.config
@@ -3,7 +3,7 @@
 #CUSTOM_GCONTROL=use-this-Gcontrol-instead
 #========================================================================
 
-#VARIATION=mc calibtime=timegoes here #set your jana calib context here with or without calibtime Default is variation=mc
+#VARIATION=mc calibtime=timegoeshere #set your jana calib context here with or without calibtime Default is variation=mc
 
 #RUNNING_DIRECTORY=/run/in/this/directory #where the code should run.  This is defaulted to ./
 

From 2915fb2d7f252ec559ab0bdd512d6d8aa6fa71c4 Mon Sep 17 00:00:00 2001
From: tbritton <tbritton@jlab.org>
Date: Wed, 3 Jan 2018 09:56:03 -0500
Subject: [PATCH 12/13] changed osg log location

---
 MCwrapper/gluex_MC.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/MCwrapper/gluex_MC.py b/MCwrapper/gluex_MC.py
index 8c1dec11..2ddc6adf 100755
--- a/MCwrapper/gluex_MC.py
+++ b/MCwrapper/gluex_MC.py
@@ -230,7 +230,7 @@ def  OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, FILENUM, indir, COMMAND, NCORES, DAT
         f.write('on_exit_hold = false'+"\n")
         f.write("Error      = "+LOG_DIR+"/log/"+"error_"+JOBNAME+".log\n")
         f.write("Log      = "+LOG_DIR+"/log/"+"out_"+JOBNAME+".log\n")
-        f.write("output = "+LOG_DIR+"OSGout_"+JOBNAME+".log\n")
+        f.write("output = "+LOG_DIR+"/log/"+"OSGout_"+JOBNAME+".log\n")
         f.write("initialdir = "+RUNNING_DIR+"\n")
         #f.write("transfer_input_files = "+ENVFILE+"\n")
         f.write("transfer_input_files = "+indir+", "+ENVFILE+additional_passins+"\n")
@@ -292,7 +292,7 @@ def main(argv):
 
         print "*********************************"
         print "Welcome to v1.12 of the MCwrapper"
-        print "Thomas Britton 1/2/18"
+        print "Thomas Britton 1/3/18"
         print "*********************************"
 
 	#load all argument passed in and set default options

From bf76792b00a8dfa6dc500c338b02bc69963e2870 Mon Sep 17 00:00:00 2001
From: tbritton <tbritton@jlab.org>
Date: Wed, 3 Jan 2018 10:37:16 -0500
Subject: [PATCH 13/13] better osg log naming scheme

---
 MCwrapper/gluex_MC.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/MCwrapper/gluex_MC.py b/MCwrapper/gluex_MC.py
index 2ddc6adf..8846dcc4 100755
--- a/MCwrapper/gluex_MC.py
+++ b/MCwrapper/gluex_MC.py
@@ -229,8 +229,8 @@ def  OSG_add_job(VERBOSE, WORKFLOW, RUNNUM, FILENUM, indir, COMMAND, NCORES, DAT
         f.write('on_exit_remove = true'+"\n")
         f.write('on_exit_hold = false'+"\n")
         f.write("Error      = "+LOG_DIR+"/log/"+"error_"+JOBNAME+".log\n")
-        f.write("Log      = "+LOG_DIR+"/log/"+"out_"+JOBNAME+".log\n")
-        f.write("output = "+LOG_DIR+"/log/"+"OSGout_"+JOBNAME+".log\n")
+        f.write("output      = "+LOG_DIR+"/log/"+"out_"+JOBNAME+".log\n")
+        f.write("log = "+LOG_DIR+"/log/"+"OSG_"+JOBNAME+".log\n")
         f.write("initialdir = "+RUNNING_DIR+"\n")
         #f.write("transfer_input_files = "+ENVFILE+"\n")
         f.write("transfer_input_files = "+indir+", "+ENVFILE+additional_passins+"\n")