Merge pull request #270 from chrislxj/CoLM202X-CROP

Fix several bugs in vcmax and run scripts

main/MOD_Const_PFT.F90

@@ -375,7 +375,7 @@ MODULE MOD_Const_PFT
          , 57.0, 57.0, 57.0, 57.0, 57.0, 57.0, 57.0, 57.0&
          , 57.0, 57.0, 57.0, 57.0, 57.0, 57.0, 57.0  &
 #endif
-         /) * 0.3 * 1.e-6
+         /) * 1.e-6
 
    ! quantum efficiency
    real(r8), parameter :: effcon_p(0:N_PFT+N_CFT-1) &

run/copy_code

@@ -0,0 +1,113 @@
+#!/bin/bash
+
+Help()
+{
+#DISPLAY help
+   echo "-------------------- Usage ----------------------------------------------------"
+   echo "Descripion:clone CoLM simulation case from an existing case"
+
+   echo "-------------------------------------------------------------------------------"
+   echo 'Syntax: ./copy_code -s $SourcePath -d $DestinationPath'
+   echo !--------------------------------------------------------------------------------
+   echo
+   echo 'eg. ./copy_code -s ~/CoLM/cases/TEST1/bld -d /home/luxj/CoLM202X/cases/TEST2/bld'
+   echo '  which will copy the code under case ~/CoLM/cases/TEST1 to the code under the case '
+   echo "/home/luxj/CoLM202X/cases/TEST2"
+   echo
+   echo 'or  ./copy_code -s ~/CoLM/ -d /home/luxj/CoLM202X/cases/TEST2/bld'
+   echo '  which will copy the code under  ~/CoLM to the code under the case '
+   echo "/home/luxj/CoLM202X/cases/TEST2"
+   echo 
+   echo options:
+   echo "-s (optional) "'$SourcePath'" is the path of the source code, which location your"
+   echo " want to copy from (including case name and 'bld' folder, but without ''/'' at"
+   echo " end of case path)"
+   echo " if -s optioin is not present, copy source code from the ROOT"
+   echo
+   echo "-d The path of the destimation code, which location you want to copy to "
+   echo "(including case name and "'bld'" folder but without ''/'' at end of case path)"
+   echo
+   echo -h display command information
+}
+
+CopyCode()
+{ 
+
+   SourcePathName=$1
+   DestPathName=$2
+   mkdir -p $DestPathName
+   cd $SourcePathName
+
+   for files1 in *
+   do
+      if [ -f $files1 ];then
+         cp -p $files1 $DestPathName/
+      else
+         if [ -d $files1 ];then
+            mkdir -p $DestPathName/$files1
+            cd $SourcePathName/$files1
+            echo copy $files1
+            if [ $files1 = CaMa -o $files1 = include -o $files1 = run -o $files1 = preprocess ];then
+               cp -pr * $DestPathName/$files1/
+            else
+               if [ $files1 = cases ];then
+                  echo ignore cases directory
+               else
+                  if [ $files1 = postprocess ];then
+                     cp -p *F90 $DestPathName/$files1/
+                  else
+                     for files2 in *
+                     do 
+                        if [ -d $files2 ];then
+                           mkdir -p $DestPathName/$files1/$files2/
+                           cd $SourcePathName/$files1/$files2
+                           echo copy $files1/$files2
+                           for files3 in *
+                           do
+                              if echo $files3 | grep -q -E '.F90$'
+                              then
+                                 cp -p $files3 $DestPathName/$files1/$files2/
+                              fi
+                           done
+                           cd ../
+                        else 
+                           if echo $files2 | grep -q -E '.F90$'
+                           then
+                              cp -p $files2 $DestPathName/$files1/
+                           fi
+                        fi
+                     done
+                  fi
+               fi
+            fi
+            cd ..
+         fi
+      fi
+   done
+}
+
+
+while getopts ":hs:d:" options ;
+do
+    case $options in
+      s) Source="$OPTARG" ;;
+      d) Destination="$OPTARG"  ;;
+      h) Help; exit;;
+      *) echo "invalid option: $@";exit ;;
+    esac
+done
+
+if [ -z "${Source}" ] || [ -z "${Destination}" ]; then
+   echo
+   echo 'Error: either "-s" or "-d" is missing' 
+   echo
+   Help
+   exit
+else 
+   if [ ! -d "${Source}" ];then
+      echo Source folder does not exist or is not a folder
+   fi
+   echo "copy source code: $Source"
+   echo "to destimation: $Destination"
+   CopyCode $Source $Destination
+fi

run/create_header

@@ -59,4 +59,4 @@ CreateHeader()
    fi
 }
 
-CreateHeader Global_Grid_50km_PFT_VG mksrf.submit /data/sysu_daiyj_01/luxj/CoLM202X/run/jobs.config-earthlab /data/sysu_daiyj_01/luxj/CoLM202X/run/mpi.config
+CreateHeader Global_Grid_50km_PFT_VG mksrf.submit $ROOT/run/jobs.config-earthlab $ROOT/run/mpi.config

run/create_newcase

@@ -247,21 +247,23 @@ NdaysofYear()
 #FORCINGNML=$ROOT/run/forcing/GSWP3.nml
 
 #machine = baiduboat
-#ROOT=/share/home/dq010/CoLM/CoLM202X-CROP
-#RAWDATA=/share/home/dq010/CoLM/data/rawdata/CROP-NITRIF/CLMrawdata_updating/
-#RUNTIME=/share/home/dq010/CoLM/data/rawdata/CROP-NITRIF/CoLMruntime//
-#MAKEOPTION=$ROOT/include/Makeoptions-baiduboat-intel
-#FORCINGPATH=/share/home/dq010/CoLM/data/inputdata/atm/GSWP3/
-
-#machine = earthlab
-ROOT=/data/sysu_daiyj_01/luxj/CoLM202X/
-RAWDATA=/data/sysu_daiyj_01/data_mpi/CLMrawdata_igbp/
-RUNTIME=/data/sysu_daiyj_01/data_mpi/CoLMruntime/
-MAKEOPTION=$ROOT/include/Makeoptions-earthlab-par
-FORCINGPATH=/data/zhangh/data/lifang/GSWP-future/SSP126/
+ROOT=/share/home/dq010/CoLM/CoLM202X-CROP
+RAWDATA=/share/home/dq010/CoLM/data/rawdata/CROP-NITRIF/CLMrawdata_updating/
+RUNTIME=/share/home/dq010/CoLM/data/rawdata/CROP-NITRIF/CoLMruntime//
+MAKEOPTION=$ROOT/include/Makeoptions-baiduboat-intel
+FORCINGPATH=/share/home/dq010/CoLM/data/inputdata/atm/GSWP3/
 HEADER=$ROOT/run/jobs.config
 CONFIG=$ROOT/run/mpi.config
 
+#machine = earthlab
+#ROOT=/data/sysu_daiyj_01/luxj/CoLM202X/
+#RAWDATA=/data/sysu_daiyj_01/data_mpi/CLMrawdata_igbp/
+#RUNTIME=/data/sysu_daiyj_01/data_mpi/CoLMruntime/
+#MAKEOPTION=$ROOT/include/Makeoptions-earthlab-par
+#FORCINGPATH=/data/zhangh/data/lifang/GSWP-future/SSP126/
+#HEADER=$ROOT/run/jobs.config
+#CONFIG=$ROOT/run/mpi.config
+
 while getopts ":hbprlun:i:t:e:c:g:s:m:" options ;
 do
     case $options in
@@ -573,9 +575,11 @@ else
    fi
    if [ -z "$LuLCC" ];then
       IsDefLuLCC="#undef"
+      LandMask=False
    else
       if [ $LuLCC == True ];then
          IsDefLuLCC="#define"
+	 LandMask="DEF_file_mesh='$RAWDATA/landdata/landmask_igbp_10km_Guangdong-extended.nc'"
       else
 	 echo Error in LuLCC definition
 	 exit
@@ -717,6 +721,11 @@ else
 	    exit
 	    ;;
       esac
+   else
+      IsDefUSGS="#undef"
+      IsDefIGBP="#undef"
+      IsDefPFT="#define"
+      IsDefPC="#undef"
    fi
 
    if [ ! -z "$SoilModel" ];then

run/create_scripts

@@ -201,7 +201,7 @@ CreateScripts()
    RESTENDYR=`expr $ENDYR + 1`
    ILOOP='$iloop'
    LOOPPLUS='iloop=`expr $iloop + 1`'
-   SEQYR='`seq -w `'${STARTYR}' '${ENDYR}'`'
+   SEQYR='`seq -w '${STARTYR}' '${ENDYR}'`'
    SEQMO='`seq -w 1 12 `'
    YEARMON='${iyr}-${i}'
    NDAYSOFENDYR=`NdaysofYear ${endyr}`
@@ -393,6 +393,8 @@ if [ -z "${ENDYR}" ];then
    echo "Note: -e option is absent, set endyr 2000 as the default."
    echo
    ENDYR=2000
+else
+   ENDYR=`expr $ENDYR - 1`
 fi
 
 echo HEADER before check $HEADER

run/jobs.config

@@ -1,40 +1,54 @@
-#!/bin/bash
-
-#SBATCH -J <CASENAME>
-#SBATCH -p <QUEUE>
-#SBATCH -N <NNODES>
-#SBATCH -n <NPROCESSES>
-#SBATCH --ntasks-per-node=<NTASKSPERNODE>
-#SBATCH --mem=<MEMORY>
-#SBATCH -o colm.o%j
-#SBATCH -e colm.e%j
-#SBATCH --exclusive
-#SBATCH -t <WALLTIME>
+#------------------------------earthlab--------------------------------------------
+##!/bin/bash
+#
+##SBATCH -J <CASENAME>
+##SBATCH -p <QUEUE>
+##SBATCH -N <NNODES>
+##SBATCH -n <NPROCESSES>
+##SBATCH --ntasks-per-node=<NTASKSPERNODE>
+##SBATCH --mem=<MEMORY>
+##SBATCH -o colm.o%j
+##SBATCH -e colm.e%j
+##SBATCH --exclusive
+##SBATCH -t <WALLTIME>
+#
+#module purge
+#module load compiler/intel/2021.3.1
+#module load mpi/intelmpi/2018.4.274
+#module load mathlib/netcdf/intel/4.4.1
+#module load mathlib/hdf5/intel/1.8.20
+#
+#export I_MPI_FABRICS=shm:dapl
+#export I_MPI_DAPL_UD=1
+#export I_MPI_DAPL_UD_RDMA_MIXED=1
+#export I_MPI_LARGE_SCALE_THRESHOLD=8192
+#export I_MPI_DAPL_UD_ACK_SEND_POOL_SIZE=8704
+#export I_MPI_DAPL_UD_ACK_RECV_POOL_SIZE=8704
+#export I_MPI_DAPL_UD_RNDV_EP_NUM=2
+#
+#export DAPL_UCM_REP_TIME=8000 #  REQUEST timer, waiting for REPLY in millisecs
+#export DAPL_UCM_RTU_TIME=8000 #  REPLY timer, waiting for RTU in millisecs
+#export DAPL_UCM_RETRY=10 #  REQUEST and REPLY retries
+#export DAPL_UCM_CQ_SIZE=2000
+#export DAPL_UCM_QP_SIZE=2000
+#
+#export DAPL_UCM_DREQ_RETRY=4 #default == 1
+#export DAPL_UCM_DREP_TIME=200 #default == 200ms
+#export DAPL_UCM_WAIT_TIME=10000 #default == 60000ms
+#
+#ulimit -s unlimited
+#scontrol show hostname > nd
+#NP=$SLURM_NPROCS
 
-module purge
-module load compiler/intel/2021.3.1
-module load mpi/intelmpi/2018.4.274
-module load mathlib/netcdf/intel/4.4.1
-module load mathlib/hdf5/intel/1.8.20
 
-export I_MPI_FABRICS=shm:dapl
-export I_MPI_DAPL_UD=1
-export I_MPI_DAPL_UD_RDMA_MIXED=1
-export I_MPI_LARGE_SCALE_THRESHOLD=8192
-export I_MPI_DAPL_UD_ACK_SEND_POOL_SIZE=8704
-export I_MPI_DAPL_UD_ACK_RECV_POOL_SIZE=8704
-export I_MPI_DAPL_UD_RNDV_EP_NUM=2
-
-export DAPL_UCM_REP_TIME=8000 #  REQUEST timer, waiting for REPLY in millisecs
-export DAPL_UCM_RTU_TIME=8000 #  REPLY timer, waiting for RTU in millisecs
-export DAPL_UCM_RETRY=10 #  REQUEST and REPLY retries
-export DAPL_UCM_CQ_SIZE=2000
-export DAPL_UCM_QP_SIZE=2000
+#-------------------------------baiduboat------------------------------------------
+#!/bin/bash
 
-export DAPL_UCM_DREQ_RETRY=4 #default == 1
-export DAPL_UCM_DREP_TIME=200 #default == 200ms
-export DAPL_UCM_WAIT_TIME=10000 #default == 60000ms
+#BSUB -J <CASENAME>
+#BSUB -q <QUEUE>
+#BSUB -o colm.o%
+#BSUB -e colm.e%
+#BSUB -n <NPROCESSES>
+#BSUB -R rusage[mem=<MEMORY>]
+#BSUB -R span[ptile=<NTASKSPERNODE>]
 
-ulimit -s unlimited
-scontrol show hostname > nd
-NP=$SLURM_NPROCS

run/mpi.config

@@ -1,18 +1,18 @@
-NProcesses_mksrf	1000
-NNodes_mksrf		20
-NTasksPerNode_mksrf	50
-Memory_mksrf		512G
-Walltime_mksrf		7-24:00
-Queue_mksrf		bigmem
-NProcesses_mkini	50
+NProcesses_mksrf	672
+NNodes_mksrf		14
+NTasksPerNode_mksrf	48
+Memory_mksrf		150G
+Walltime_mksrf		24:00:00
+Queue_mksrf		normal
+NProcesses_mkini	48
 NNodes_mkini		1
-NTasksPerNode_mkini	50
-Memory_mkini		512G
-Walltime_mkini		7-24:00
+NTasksPerNode_mkini	48
+Memory_mkini		150G
+Walltime_mkini		24:00:00
 Queue_mkini		normal
-NProcesses_case		250
+NProcesses_case		240
 NNodes_case		5
-NTasksPerNode_case	50
-Memory_case		512G
-Walltime_case		7-24:00
+NTasksPerNode_case	48
+Memory_case		150G
+Walltime_case		24:00:00
 Queue_case		normal