Merge pull request #187 from HPSCTerrSys/release_candidate

Setting the release candidate as the new master

LICENSE.txt → LICENSE

@@ -1,9 +1,11 @@
 MIT License
 
-Copyright 2010-2020 Prabhakar SHRESTHA, Mauro SULIS, Stefan KOLLET, 
+Copyright 2010-2023 Prabhakar SHRESTHA, Mauro SULIS, Stefan KOLLET, 
 Fabian GASPER, Wolfgang KURTZ, Jessica KEUNE, Ketan KULKARNI, Slavko BRDAR,
 Niklas WAGNER, Mukund PONDKULE, Lukas STREBEL, Tobias SCHRUFF, Tim HOAR, 
-Cunbo HAN, Markus UEBEL, Guowei HE, Haojin ZHAO, Klaus GOERGEN, Abouzar Ghasemi
+Cunbo HAN, Markus UEBEL, Guowei HE, Haojin ZHAO, Klaus GOERGEN, Abouzar GHASEMI,
+Stefan POLL, Johannes KELLER, Paul RIGOR, Daniel CAVIEDES-VOULLIEME, Ilya ZHUKOV,
+Joerg BENKE, Carl HARTICK
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of 
 this software and associated documentation files (the "Software"), to deal in 

README.md

@@ -27,7 +27,7 @@ TSMP development has been driven by groups within the [Center for High-Performan
 Please see [getting started section](https://hpscterrsys.github.io/TSMP/content/gettingstarted.html) for guided steps on how the model can be setup and configured for *one* specific experiment, which we use as one of the default test cases. To get an overview on possible TSMP applications refer to the [TSMP website](https://www.terrsysmp.org) and the [TSMP documention](https://hpscterrsys.github.io/TSMP/index.html).
 
 ## TSMP version history
-The model components used in TSMP are OASIS3-MCT v2, COSMO v5.01, CLM v3.5, ParFlow 3.2 for TSMP versions v1.2.1, v1.2.2 and v1.2.3, and ParFlow 3.9 for version v1.3.3. TSMP supports ParFlow 3.7 onwards from version v1.3.3 onward.
+The model components used in TSMP are OASIS3-MCT v2, COSMO v5.01, CLM v3.5, ParFlow 3.2 for TSMP versions v1.2.1, v1.2.2 and v1.2.3, ParFlow 3.9 for version v1.3.3 and ParFlow 3.12 for version v1.4.0. TSMP supports ParFlow 3.7 onwards from version v1.3.3 onward. 
 
 Those who need to work with ParFlow 3.2, should use the branch `TSMP_pdaf`.
 
@@ -39,8 +39,8 @@ If you use TSMP in a publication, please cite the these papers that describe the
 * Gasper, F., Goergen, K., Kollet, S., Shrestha, P., Sulis, M., Rihani, J., and Geimer, M. (2014). Implementation and scaling of the fully coupled Terrestrial Systems Modeling Platform (TerrSysMP) in a massively parallel supercomputing environment – a case study on JUQUEEN (IBM Blue Gene/Q). Geoscientific Model Development, 7(5), 2531-2543. doi:[10.5194/gmd-7-2531-2014](https://dx.doi.org/10.5194/gmd-7-2531-2014).
 
 ## License
-TSMP is open source software and is licensed under the [MIT-License](https://github.com/HPSCTerrSys/TSMP/blob/master/LICENSE.txt).
+TSMP is open source software and is licensed under the [MIT-License](https://github.com/HPSCTerrSys/TSMP/blob/master/LICENSE).
 
 ## To come
 
-HPSC-TerrSys will also stage run control scripts for different usage scenarios such as long climate runs, and a variety of pre- and postprocessing tools we developed specifically for TSMP. Documented test case experiments also encompass convection permitting simulations at 1km for COSMO and 0.5km for CLM and ParFlow, idealized experiments, a data assimilation experiment based on the TSMP-PDAF version. We will also update the generic machinefiles to make an adjustment of the built system more straightforward for external users.
+HPSC-TerrSys will also stage run control scripts for different usage scenarios such as long climate runs, and a variety of pre- and postprocessing tools we developed specifically for TSMP. Documented test case experiments also encompass convection permitting simulations at 1km for COSMO and 0.5km for CLM and ParFlow, idealized experiments, a data assimilation experiment based on the TSMP-PDAF version. We will also update the generic machinefiles to make an adjustment of the built system more straightforward for external users.

VERSION.txt

@@ -1 +1 @@
-v1.3.3
+v1.4.0

bldsva/build_tsmp.ksh

@@ -32,6 +32,7 @@ getDefaults(){
   def_mode="0" #0: let flags decide, 1:batch, 2:interactive
   def_cplscheme="true"
   def_readCLM="false"
+  def_maxpft="1" # (CLM default is 4)
   def_freeDrain="false"
 
   #compiler optimization
@@ -65,9 +66,9 @@ getDefaults(){
 setDefaults(){
   #load the default values
   platform=$def_platform
-  if [[ $platform == "" ]] then ; platform="CLUMA2" ; fi #We need a hard default here
-  version=$def_version
-  if [[ $version == "" ]] then ; version="1.1.0MCT" ; fi #We need a hard default here
+  if [[ $platform == "" ]] then ; platform="JUWELS" ; fi #We need a hard default here
+  version=$def_combination
+  if [[ $version == "" ]] then ; version="" ; fi #We need a hard default here
   rootdir=$def_rootdir
   bindir=$def_bindir
   optComp=$def_optComp
@@ -94,6 +95,7 @@ setDefaults(){
 
   freeDrain=$def_freeDrain
   readCLM=$def_readCLM
+  maxpft=${def_maxpft}
   cplscheme=$def_cplscheme
   mode=$def_mode
 
@@ -174,15 +176,45 @@ check
 }
 
 setCombination(){
-  set -A mList ${modelVersion[$version]}
-  if [[ $oasdir == "" ]] then ;  oasdir=$rootdir/${mList[0]}_${platform}_${version}_${combination} ; fi
-  if [[ $cosdir == "" ]] then ;  cosdir=$rootdir/${mList[2]}_${platform}_${version}_${combination} ; fi
-  if [[ $icondir == "" ]] then ; icondir=$rootdir/${mList[2]}_${platform}_${version}_${combination} ; fi
-  if [[ $clmdir == "" ]] then ;  clmdir=$rootdir/${mList[1]}_${platform}_${version}_${combination} ; fi
-  if [[ $pfldir == "" ]] then ;  pfldir=$rootdir/${mList[3]}_${platform}_${version}_${combination} ; fi
+   if echo "$combination" | grep -q 'pdaf'; then
+	if echo "$combination" | grep -q 'cos4'; then
+	        mListgen="clm3-cos4-pfl-pdaf"
+	else
+                mListgen="clm3-cos5-pfl-pdaf"
+	fi
+   elif echo "$combination" | grep -q 'clm4' && echo "$combination" | grep -q 'cos4'; then
+	mListgen="clm4-cos4-pfl"
+   elif echo "$combination" | grep -q 'clm4'; then
+	mListgen="clm4-cos5-pfl"
+
+   elif echo "$combination" | grep -q 'icon21'; then
+	mListgen="clm3-icon21-pfl"
+   elif echo "$combination" | grep -q 'icon26'; then
+	mListgen="clm3-icon26-pfl"
+
+   elif echo "$combination" | grep -q 'eclm'; then
+	mListgen="eclm"
+   elif echo "$combination" | grep -q 'eclm-mct'; then
+	mListgen="eclm-mct"
+
+   else 
+	if echo "$combination" | grep -q 'cos4'; then
+		mListgen="clm3-cos4-pfl"
+	else
+		mListgen="clm3-cos5-pfl"
+	fi
+  fi 
+
+  version=$mListgen
+  set -A mList ${modelVersion[$mListgen]}
+  if [[ $oasdir == "" ]] then ;  oasdir=$rootdir/${mList[0]}_${platform}_${combination} ; fi
+  if [[ $cosdir == "" ]] then ;  cosdir=$rootdir/${mList[2]}_${platform}_${combination} ; fi
+  if [[ $icondir == "" ]] then ; icondir=$rootdir/${mList[2]}_${platform}_${combination} ; fi
+  if [[ $clmdir == "" ]] then ;  clmdir=$rootdir/${mList[1]}_${platform}_${combination} ; fi
+  if [[ $pfldir == "" ]] then ;  pfldir=$rootdir/${mList[3]}_${platform}_${combination} ; fi
 #DA
-  if [[ $dadir == "" ]] then ;  dadir=$rootdir/${mList[4]}_${platform}_${version}_${combination} ; fi  
-  if [[ $bindir == "" ]] then ;  bindir=$rootdir/bin/${platform}_${version}_${combination} ;  fi 
+  if [[ $dadir == "" ]] then ;  dadir=$rootdir/${mList[4]}_${platform}_${combination} ; fi  
+  if [[ $bindir == "" ]] then ;  bindir=$rootdir/bin/${platform}_${combination} ;  fi 
 
   withOAS="false"
   withCOS="false"
@@ -202,18 +234,18 @@ setCombination(){
   case "$combination" in *pfl*) withPFL="true" ;; esac
   if [[ $withCLM == "true" && ( $withCOS == "true" || $withICON == "true" || $withPFL == "true" )  ]]; then
     withOAS="true"
-    case "$version" in *MCT*) withOASMCT="true" ;; esac
+    withOASMCT="true"
   fi
 #DA
-  case "$version" in *PDAF*) withDA="true" ; withPDAF="true" ;; esac
+  case "$combination" in *pdaf*) withDA="true" ; withPDAF="true" ;; esac
 }
 
 
 compileClm(){
 route "${cyellow}> c_compileClm${cnormal}"
   comment "  source clm interface script"
-    comment "intf_oas3/${mList[1]}/arch/${platform}/build_interface_${mList[1]}_${platform}.ksh"
-    . ${rootdir}/bldsva/intf_oas3/${mList[1]}/arch/${platform}/build_interface_${mList[1]}_${platform}.ksh >> $log_file 2>> $err_file
+    comment "intf_oas3/${mList[1]}/arch/build_interface_${mList[1]}.ksh"
+    . ${rootdir}/bldsva/intf_oas3/${mList[1]}/arch/build_interface_${mList[1]}.ksh >> $log_file 2>> $err_file
   check
     always_clm
     if [[ ${options["clm"]} == "skip" ]] ; then ; route "${cyellow}< c_compileClm${cnormal}" ; return  ;fi 
@@ -244,7 +276,7 @@ route "${cyellow}< c_compileClm${cnormal}"
 compileIcon(){
 route "${cyellow}> c_compileIcon${cnormal}"
   comment "  source icon interface script"
-    . ${rootdir}/bldsva/intf_oas3/${mList[2]}/arch/${platform}/build_interface_${mList[2]}_${platform}.ksh >> $log_file 2>> $err_file
+    . ${rootdir}/bldsva/intf_oas3/${mList[2]}/arch/build_interface_${mList[2]}.ksh >> $log_file 2>> $err_file
   check
     always_icon
     if [[ ${options["icon"]} == "skip" ]] ; then ; route "${cyellow}< c_compileIcon${cnormal}" ;  return  ;fi 
@@ -272,7 +304,7 @@ route "${cyellow}< c_compileIcon${cnormal}"
 compileCosmo(){
 route "${cyellow}> c_compileCosmo${cnormal}"
   comment "  source cos interface script"
-    . ${rootdir}/bldsva/intf_oas3/${mList[2]}/arch/${platform}/build_interface_${mList[2]}_${platform}.ksh >> $log_file 2>> $err_file
+    . ${rootdir}/bldsva/intf_oas3/${mList[2]}/arch/build_interface_${mList[2]}.ksh >> $log_file 2>> $err_file
   check
     always_cos
     if [[ ${options["cos"]} == "skip" ]] ; then ; route "${cyellow}< c_compileCosmo${cnormal}" ;  return  ;fi 
@@ -300,7 +332,7 @@ route "${cyellow}< c_compileCosmo${cnormal}"
 compileOasis(){
 route "${cyellow}> c_compileOasis${cnormal}"
   comment "  source oas interface script"
-    . ${rootdir}/bldsva/intf_oas3/${mList[0]}/arch/${platform}/build_interface_${mList[0]}_${platform}.ksh >> $log_file 2>> $err_file
+    . ${rootdir}/bldsva/intf_oas3/${mList[0]}/arch/build_interface_${mList[0]}.ksh >> $log_file 2>> $err_file
   check
     always_oas
     if [[ ${options["oas"]} == "skip" ]] ; then ; route "${cyellow}< c_compileOasis${cnormal}" ; return  ;fi 
@@ -328,7 +360,7 @@ route "${cyellow}< c_compileOasis${cnormal}"
 compileParflow(){
 route "${cyellow}> c_compileParflow${cnormal}"
   comment "  source pfl interface script"
-    . ${rootdir}/bldsva/intf_oas3/${mList[3]}/arch/${platform}/build_interface_${mList[3]}_${platform}.ksh >> $log_file 2>> $err_file
+    . ${rootdir}/bldsva/intf_oas3/${mList[3]}/arch/build_interface_${mList[3]}.ksh >> $log_file 2>> $err_file
   check
     always_pfl
     if [[ ${options["pfl"]} == "skip" ]] ; then ; route "${cyellow}< c_compileParflow${cnormal}" ;return  ;fi 
@@ -427,7 +459,7 @@ interactive(){
 			print "Please type in your desired value..."
 			read platform
 			comment "  source machine build interface for $platform"
-                          . ${rootdir}/bldsva/machines/${platform}/build_interface_${platform}.ksh >> $log_file 2>> $err_file
+                          . ${rootdir}/bldsva/machines/config_${platform}.ksh >> $log_file 2>> $err_file
                         check
                         clearMachineSelection
                         getMachineDefaults
@@ -448,25 +480,6 @@ interactive(){
                         setCombination
                         setSelection 
 		  fi
-		  if [[ $numb == 2 ]] ; then 
-                        print "The following versions are available for $platform:"
-                        for a in ${availability[$platform]} ; do
-                                printf "%-20s #%s\n" "$a" "${versions[$a]} consisting of: "
-				for b in ${modelVersion[$a]} ; do
-				   printf "%-20s - %s\n" "" "$b"
-				done
-                        done		
-			print "Please type in your desired value..."
-			read version
-                        case "${combinations[$version]}" in  
-                                *" $combination "*);;
-                                *)
-                                set -A array ${combinations[$version]}
-                                combination=${array[0]} ;;
-                        esac
-			clearPathSelection
- 			setCombination
-		  fi
 		  if [[ $numb == 3 ]] ; then  
                         print "The following combinations are available for $version:"
                         for a in ${combinations[$version]} ; do
@@ -563,9 +576,10 @@ printState(){
   print "${cred}(25)${cnormal} profiling (default=$def_profiling): ${cgreen}$profiling ${cnormal}"
   print "${cred}(26)${cnormal} Couple-Scheme (default=$def_cplscheme): ${cgreen}$cplscheme ${cnormal}"
   print "${cred}(27)${cnormal} readCLM: Consistently read CLM-mask (default=$def_readCLM): ${cgreen}$readCLM ${cnormal}"
-  print "${cred}(28)${cnormal} Compiles ParFlow with free drainage feature (default=$def_freeDrain): ${cgreen}$freeDrain ${cnormal}"
-  print "${cred}(29)${cnormal} compiler (default=$defaultcompiler): ${cgreen}$compiler ${cnormal}"
-  print "${cred}(30)${cnormal} processor (default=$defaultprocessor): ${cgreen}$processor ${cnormal}"
+  print "${cred}(28)${cnormal} maxpft: Set maxpft per grid cell for CLM (default=$def_maxpft): ${cgreen}$maxpft ${cnormal}"
+  print "${cred}(29)${cnormal} Compiles ParFlow with free drainage feature (default=$def_freeDrain): ${cgreen}$freeDrain ${cnormal}"
+  print "${cred}(30)${cnormal} compiler (default=$defaultcompiler): ${cgreen}$compiler ${cnormal}"
+  print "${cred}(31)${cnormal} processor (default=$defaultprocessor): ${cgreen}$processor ${cnormal}"
 }
 
 check(){
@@ -618,17 +632,20 @@ warning(){
 
 hardSanityCheck(){
 
-  if [[ "${versions[${version}]}" == ""  ]] then
-      print "The selected version '${version}' is not available. run '$call --man' for help"
-      terminate
-  fi
-
   if [[ "${platforms[${platform}]}" == ""  ]] then
       print "The selected platform '${platform}' is not available. run '$call --man' for help"
       terminate
   fi
 
 }
+
+deprecatedVersion(){
+  if [[ "${version}" != ""  ]] then
+      print "The use of the internal version with -v is deprecated. Please provide your desired combination with -c including version numbers (clm3-cos5-pfl). "
+      terminate
+  fi
+}
+
 softSanityCheck(){
 
 
@@ -811,7 +828,13 @@ getGitInfo(){
     echo "Version (${mList[4]}):" >> $log_file
     comment "  Log version information (${mList[4]})"
       echo ${rootdir}/${mList[4]} >> $log_file
-      cat ${rootdir}/${mList[4]}/src/PDAF-D_print_version.F90 | grep +++ | grep Version | cut -c 50-65 >> $log_file
+      # PDAF-version >= v2.0
+      if [[ -f ${rootdir}/${mList[4]}/src/PDAF_print_version.F90 ]] ; then
+	cat ${rootdir}/${mList[4]}/src/PDAF_print_version.F90 | grep +++ | grep Version | cut -c 50-65 >> $log_file
+      # PDAF-version v1.*
+      else
+	cat ${rootdir}/${mList[4]}/src/PDAF-D_print_version.F90 | grep +++ | grep Version | cut -c 50-65 >> $log_file
+      fi
     check
     echo "" >> $log_file
   fi
@@ -853,7 +876,7 @@ getGitInfo(){
   USAGE+="[R:rootdir?Absolute path to TerrSysMP root directory.]:[path:='$def_rootdir']"
   USAGE+="[B:bindir?Absolute path to bin directory for the builded executables. bin/MACHINE_DATE will be taken if ''.]:[path:='$def_bindir']"
 
-  USAGE+="[v:version?Tagged TerrSysMP version. Note that not every version might be implemented on every machine. Run option -a, --avail to get a listing.]:[version:='$version']"
+  USAGE+="[v:version?Deprecated. Please specify your desired combination with the -c option.]"
   USAGE+="[m:machine?Target Platform. Run option -a, --avail to get a listing.]:[machine:='$def_platform']"
 
   USAGE+="[p:profiling?Makes necessary changes to compile with a profiling tool if available.]:[profiling:='$def_profiling']"
@@ -863,6 +886,7 @@ getGitInfo(){
   USAGE+="[c:combination? Combination of component models.]:[combination:='$def_combination']"
   USAGE+="[C:cplscheme? Couple-Scheme for CLM/COS coupling.]:[cplscheme:='$def_cplscheme']"
   USAGE+="[r:readclm? Flag to consistently read in CLM mask.]:[readclm:='$def_readCLM']"
+  USAGE+="[f:maxpft? Flag to control maxpft per grid cell in CLM.]:[maxpft:='$def_maxpft']"
   USAGE+="[d:freedrain? Compiles ParFlow with free drainage feature.]:[freedrain:='$def_freeDrain']"
 
   USAGE+="[W:optoas?Build option for Oasis.]:[optoas:='${def_options["oas"]}']{"
@@ -916,6 +940,7 @@ getGitInfo(){
     c)  combination="$OPTARG" ; args=1 ;;
     C)  cplscheme="$OPTARG" ; args=1 ;;
     r)  readCLM="$OPTARG" ; args=1 ;;
+    f)  maxpft="$OPTARG" ; args=1 ;;
     d)  freeDrain="$OPTARG" ; args=1 ;;
 #DA
     T)  options+=(["icon"]="$OPTARG") ; args=1 ;;
@@ -943,8 +968,7 @@ getGitInfo(){
     esac
   done
 
-
-
+deprecatedVersion
 
 comment "  source list with supported machines and configurations"
   . $rootdir/bldsva/supported_versions.ksh
@@ -966,11 +990,12 @@ check
 
   setCombination
   comment "  source machine build interface for $platform"
-    . ${rootdir}/bldsva/machines/${platform}/build_interface_${platform}.ksh >> $log_file 2>> $err_file
+    . ${rootdir}/bldsva/machines/config_${platform}.ksh >> $log_file 2>> $err_file
   check
   getMachineDefaults
   setSelection
 
+printf "$platform\n$profiling\n$optComp\n$compiler\n$version\n$rootdir$bindir\n$combination\n$readCLM" > build_info_${date}.txt
 
   # determine whether or not to run interactive session
   if [[ $mode == 0 ]] then
@@ -997,7 +1022,7 @@ check
   runCompilation
 
   echo "Patched files:  NOTE: sed substitutions are not listed" >> $log_file
-  cat $patchlog_file >> $log_file
+  #cat $patchlog_file >> $log_file
 
   echo "" >> $log_file
   echo "Git:" >> $log_file