Updates from cloudinfra

guide.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+
 # Color definitions
 BBlack='\033[1;30m'
 BRed='\033[1;31m'
@@ -21,6 +22,7 @@ Color_Off='\033[0m'
 set -e
 
 CONFIG_FILE="$HOME/.host_data_path.conf"
+TETHYS_SCRIPT="./viewOnTethys.sh"
 
 echo -e "\n========================================================="
 echo -e "${UWhite} Welcome to CIROH-UA:NextGen National Water Model App! ${Color_Off}"
@@ -46,6 +48,12 @@ else
     read -erp "Enter your input data directory path (use absolute path): " HOST_DATA_PATH
 fi
 
+# Check the directory exists
+if [ ! -d "$HOST_DATA_PATH" ]; then
+  echo -e "${BRed}Directory does not exist. Exiting the program.${Color_Off}"
+  exit 0
+fi
+
 # Save the new path to the config file
 echo "$HOST_DATA_PATH" > "$CONFIG_FILE"
 echo -e "The Directory you've given is:\n$HOST_DATA_PATH\n"
@@ -56,7 +64,7 @@ validate_directory() {
     local color=$3
 
     if [ -d "$dir" ]; then
-        local count=$(ls "$dir" | wc -l)
+        local count=$(find $dir -type f | uniq | wc -l)
         echo -e "${color}${name}${Color_Off} exists. $count ${name} found."
     else
         echo -e "Error: Directory $dir does not exist."
@@ -74,7 +82,7 @@ cleanup_folder() {
     local folder_name="$3"
 
     # Construct the find command
-    local find_cmd="find \"$folder_path\" -maxdepth 1 -type f \( $file_types \)"
+    local find_cmd="find \"$folder_path\" -maxdepth 2 -type f \( $file_types \)"
 
     # Execute the find command and count the results
     local file_count=$(eval "$find_cmd" 2> /dev/null | wc -l)
@@ -98,7 +106,7 @@ choose_option() {
                 echo "Cleaning folder for fresh run"
 
                 # Construct the find delete command
-                local find_delete_cmd="find \"$folder_path\" -maxdepth 1 -type f \( $file_types \) -delete"
+                local find_delete_cmd="find \"$folder_path\" -maxdepth 2 -type f \( $file_types \) -delete"
 
                 # Execute the find delete command
                 eval "$find_delete_cmd"
@@ -122,25 +130,26 @@ choose_option() {
 # Cleanup Process for Outputs Folder
 cleanup_folder "$HOST_DATA_PATH/outputs/" "-name '*' " "Outputs"
 
-# Cleanup Process for ngen/data Folder
-cleanup_folder "$HOST_DATA_PATH/" "-name '*.parquet' -o -name '*.csv' -o -name '*.cn'" "ngen/data"
+# Cleanup Process for restarts Folder
+cleanup_folder "$HOST_DATA_PATH/restarts/" "-name '*' " "Restarts"
+
 
 
 # File discovery
 echo -e "\nLooking in the provided directory gives us:"
 find_files() {
     local path=$1
     local name=$2
-    local color=$3
+    local regex=$3
+    local color=$4
 
-    local files=$(find "$path" -iname "*$name*.*")
+    local files=$(find "$path" -iname "$regex")
     echo -e "${color}Found these $name files:${Color_Off}"
     echo "$files" || echo "No $name files found."
 }
 
-find_files "$HOST_DATA_PATH" "datastream" "$UGreen"
-find_files "$HOST_DATA_PATH" "datastream" "$UGreen"
-find_files "$HOST_DATA_PATH" "realization" "$UGreen"
+find_files "$HOST_DATA_PATH" "hydrofabric" "*.gpkg" "$UGreen"
+find_files "$HOST_DATA_PATH" "realization" "realization.json" "$UGreen"
 
 # Detect Arch and Singularity
 echo -e "\nDetected ISA = $(uname -a)"
@@ -157,41 +166,50 @@ if uname -a | grep arm64 || uname -a | grep aarch64 ; then
     IMAGE_NAME=ciroh-ngen-singularity_latest.sif
 else
     ARCH=amd64
-    IMAGE_URL=library://trupeshkumarpatel/awiciroh/ciroh-ngen-singularity:latest_x86
+    IMAGE_URL=library://awiciroh/ngiab/ciroh-ngen-singularity:latest
     IMAGE_NAME=ciroh-ngen-singularity_latest.sif
 fi
 
-
 # Model run options
 echo -e "${UYellow}Select an option (type a number): ${Color_Off}"
-options=("Run NextGen Model using local singularity image" "Run Nextgen using remote singularity image" "Exit")
+options=("Run NextGen using existing local singularity image" "Run NextGen after updating to latest singularity image" "Exit")
 select option in "${options[@]}"; do
     case $option in
-        "Run NextGen Model using local singularity image")
+        "Run NextGen using existing local singularity image")
             echo "running the model"
             break
             ;;
-        "Run Nextgen using remote singularity image")
+        "Run NextGen after updating to latest singularity image")
             echo "pulling container and running the model"
-            singularity pull --arch $ARCH $IMAGE_NAME $IMAGE_URL
+            singularity pull -F --arch $ARCH $IMAGE_NAME $IMAGE_URL
             break
             ;;
         Exit)
             echo "Have a nice day!"
             exit 0
             ;;
-        *) echo "Invalid option $REPLY, 1 to continue and 2 to exit"
+        *) echo "Invalid option $REPLY, 1 to continue with existing local image, 2 to update and run, and 3 to exit"
             ;;
     esac
 done
 
+
 echo -e "\nRunning NextGen singularity container..."
 echo -e "Mounting local host directory $HOST_DATA_PATH to /ngen/ngen/data within the container."
 singularity run --bind $HOST_DATA_PATH:/ngen/ngen/data $IMAGE_NAME /ngen/ngen/data
 
 # Final output count
-Final_Outputs_Count=$(ls "$HOST_DATA_PATH/outputs" | wc -l)
+Final_Outputs_Count=$(ls "$HOST_DATA_PATH/outputs/*/*" | wc -l)
 echo -e "$Final_Outputs_Count new outputs created."
 echo -e "Any copied files can be found here: $HOST_DATA_PATH/outputs"
+
+# visualize with Tethys
+if [ $Final_Outputs_Count -gt 0 ]; then
+    ARG1="$HOST_DATA_PATH"
+    if ! "$TETHYS_SCRIPT" "$ARG1"; then
+        printf "Failed to visualize outputs in Tethys:"
+    fi
+fi
+
 echo -e "Thank you for running NextGen In A Box: National Water Model! Have a nice day!"
 exit 0

singularity/singularity_ngen.def

@@ -23,6 +23,8 @@ From: rockylinux:9.2
      dnf install libstdc++ libstdc++-devel glibc glibc-devel libgfortran openmpi openmpi-devel -y
      dnf --enablerepo=devel install texinfo -y
      dnf install netcdf netcdf-devel netcdf-fortran netcdf-fortran-devel netcdf-openmpi netcdf-openmpi-devel netcdf-fortran-openmpi netcdf-fortran-openmpi-devel -y 
+
+     # Boost installation
      curl -L -o boost_1_79_0.tar.bz2 https://sourceforge.net/projects/boost/files/boost/1.79.0/boost_1_79_0.tar.bz2/download
      tar -xjf boost_1_79_0.tar.bz2 -C /tmp/
      cp -r /tmp/boost_1_79_0/boost /usr/include/
@@ -34,6 +36,8 @@ From: rockylinux:9.2
      /tmp/t-route/install_t_route.sh
      /tmp/ngen/install_ngen.sh
 
+     cp -R /usr/share/modulefiles/mpi /usr/share/lmod/lmod/modulefiles/Core/
+
      rm -rf /tmp/ngen /tmp/t-route /tmp/netcdf /tmp/extern /tmp/guide
 
 %runscript

singularity/templates/extern/install_extern_libraries.sh

@@ -27,7 +27,7 @@ echo "-- Now Installing External Library noah-owp-modular ..."
 echo "-----------------------------------------------------------"
 cd /ngen/extern/noah-owp-modular
 # cmake -B cmake_build -S .
-cmake -DnetCDF_MOD_PATH=/usr/include/openmpi-x86_64/ -B cmake_build -S .
+cmake -DNETCDF_MODULE_DIR=/usr/lib64/gfortran/modules/openmpi/ -B cmake_build -S .
 cmake --build cmake_build --target surfacebmi -- -j 2
 
 echo "==========================================================="
@@ -87,7 +87,9 @@ cp /tmp/guide/HelloNGEN.sh /ngen/HelloNGEN.sh
 chown -R root /dmod /ngen /root
 chmod a+x /dmod/bin/* /ngen/HelloNGEN.sh /root
 find /ngen/extern/ -name "*.so*" -exec ln -s "{}" /dmod/shared_libs/ \;
-
+find /ngen/extern/noah-owp-modular -type f -iname "*.TBL" -exec cp '{}' /dmod/datasets/static  \; 
 ls -ahl /dmod/shared_libs
 echo "==========================================================="
+ls -ahl /dmod/datasets/static
+echo "==========================================================="
 echo "==========================================================="

singularity/templates/guide/HelloNGEN.sh

@@ -9,7 +9,7 @@ CYAN='\e[36m'
 RESET='\e[0m'
 
 # Increasing `ulimit` to Open files
-ulimit -n 1000000
+ulimit -n 500000
 
 # Loading Lmod
 source /etc/profile.d/modules.sh
@@ -24,6 +24,8 @@ echo -e "${CYAN}Working directory is:${RESET}"
 pwd
 echo -e "\n"
 
+
+
 # Function to automatically select file if only one is found
 auto_select_file() {
   local files=($1)
@@ -35,8 +37,8 @@ auto_select_file() {
 }
 
 # Finding files
-HYDRO_FABRIC_CATCHMENTS=$(find . -name "*datastream*.gpkg")
-HYDRO_FABRIC_NEXUS=$(find . -name "*datastream*.gpkg")
+HYDRO_FABRIC_CATCHMENTS=$(find . -name "*.gpkg")
+HYDRO_FABRIC_NEXUS=$(find . -name "*.gpkg")
 NGEN_REALIZATIONS=$(find . -name "*realization*.json")
 
 # Auto-selecting files if only one is found
@@ -78,8 +80,7 @@ if [ "$2" == "auto" ]
     echo "Run completed successfully, exiting, have a nice day!"
     exit 0
   else
-    echo "Entering Interactive Mode"
-    continue
+    echo "Entering Interactive Mode"    
 fi
 
 echo -e "${YELLOW}Select an option (type a number): ${RESET}"
@@ -91,20 +92,22 @@ select option in "${options[@]}"; do
       n1=${selected_catchment:-$(read -p "Enter the hydrofabric catchment file path: " n1; echo "$n1")}
       n2=${selected_nexus:-$(read -p "Enter the hydrofabric nexus file path: " n2; echo "$n2")}
       n3=${selected_realization:-$(read -p "Enter the Realization file path: " n3; echo "$n3")}
-      
+
       echo -e "${GREEN}Selected files:\nCatchment: $n1\nNexus: $n2\nRealization: $n3${RESET}\n"
 
       if [ "$option" == "Run NextGen model framework in parallel mode" ]; then
         procs=$(nproc)
-        procs=2 # Temporary fixed value
+        num_catchments=$(find forcings -name *.csv | wc -l)
+        if [ $num_catchments -lt $procs ]; then
+                procs=$num_catchments
+        fi
         generate_partition "$n1" "$n2" "$procs"
         run_command="mpirun -n $procs /dmod/bin/ngen-parallel $n1 all $n2 all $n3 $(pwd)/partitions_$procs.json"
       else
         run_command="/dmod/bin/ngen-serial $n1 all $n2 all $n3"
       fi
 
       echo -e "${YELLOW}Your NGEN run command is $run_command${RESET}"
-      sleep 3
       break
       ;;
     "Run Bash shell")
@@ -114,7 +117,7 @@ select option in "${options[@]}"; do
     "Exit")
       exit 0
       ;;
-    *) 
+    *)
       echo -e "${RED}Invalid option $REPLY${RESET}"
       ;;
   esac
@@ -159,9 +162,9 @@ select option in "${options[@]}"; do
       echo -e "${GREEN}Have a nice day.${RESET}"
       break
       ;;
-    *) 
+    *)
       echo -e "${RED}Invalid option $REPLY${RESET}"
       ;;
   esac
 done
-exit
+exit

singularity/templates/ngen/install_ngen.sh

@@ -46,7 +46,9 @@ echo "-- Now Building NGen at /ngen/serialbuild ..."
 echo "-----------------------------------------------------------"
 cd /ngen
 # cmake -B /ngen/mpibuild -S . -DNGEN_WITH_MPI=ON -DNGEN_WITH_PYTHON=ON -DNGEN_WITH_ROUTING=ON -DNGEN_WITH_NETCDF=ON -DNGEN_QUIET=ON
-cmake -B $current_path/ngen/serialbuild -S . -DNGEN_WITH_MPI:BOOL=OFF -DNGEN_WITH_NETCDF:BOOL=ON -DNGEN_WITH_SQLITE:BOOL=ON -DNGEN_WITH_UDUNITS:BOOL=ON -DNGEN_WITH_BMI_FORTRAN:BOOL=ON -DNGEN_WITH_BMI_C:BOOL=ON -DNGEN_WITH_PYTHON:BOOL=ON -DNGEN_WITH_ROUTING:BOOL=ON -DNGEN_WITH_TESTS:BOOL=ON -DNGEN_QUIET:BOOL=ON -DNETCDF_CXX_INCLUDE_DIR=/usr/local/include -DNETCDF_CXX_LIBRARY=/usr/local/lib64/libnetcdf-cxx4.so # -DNETCDF_INCLUDE_DIR=/usr/include -DNETCDF_LIBRARY=/usr/lib64/libnetcdf.so
+cmake -B $current_path/ngen/serialbuild -S . -DCMAKE_INSTALL_PREFIX=/ngen/ngen -DNGEN_WITH_EXTERN_ALL=ON -DNGEN_WITH_MPI:BOOL=OFF -DNGEN_WITH_NETCDF:BOOL=ON -DNGEN_WITH_SQLITE:BOOL=ON -DNGEN_WITH_UDUNITS:BOOL=ON -DNGEN_QUIET:BOOL=ON -DNGEN_WITH_BMI_FORTRAN:BOOL=ON -DNGEN_WITH_BMI_C:BOOL=ON -DNGEN_WITH_PYTHON:BOOL=ON -DNGEN_WITH_ROUTING:BOOL=ON -DNGEN_WITH_TESTS:BOOL=ON -DNETCDF_CXX_INCLUDE_DIR=/usr/local/include -DNETCDF_CXX_LIBRARY=/usr/local/lib64/libnetcdf-cxx4.so
+# -DNETCDF_INCLUDE_DIR=/usr/include -DNETCDF_LIBRARY=/usr/lib64/libnetcdf.so
+
 echo "==========================================================="
 echo "==========================================================="
 
@@ -65,7 +67,7 @@ echo "-- Now Building NGen at /ngen/parallelbuild ..."
 echo "-----------------------------------------------------------"
 cd /ngen
 # cmake -B /ngen/mpibuild -S . -DNGEN_WITH_MPI=ON -DNGEN_WITH_PYTHON=ON -DNGEN_WITH_ROUTING=ON -DNGEN_WITH_NETCDF=ON -DNGEN_QUIET=ON
-cmake -B $current_path/ngen/parallelbuild -S . -DNGEN_WITH_MPI:BOOL=ON -DNGEN_WITH_NETCDF:BOOL=ON -DNGEN_WITH_SQLITE:BOOL=ON -DNGEN_WITH_UDUNITS:BOOL=ON -DNGEN_WITH_BMI_FORTRAN:BOOL=ON -DNGEN_WITH_BMI_C:BOOL=ON -DNGEN_WITH_PYTHON:BOOL=ON -DNGEN_WITH_ROUTING:BOOL=ON -DNGEN_WITH_TESTS:BOOL=ON -DNGEN_QUIET:BOOL=ON -DNETCDF_CXX_INCLUDE_DIR=/usr/local/include -DNETCDF_CXX_LIBRARY=/usr/local/lib64/libnetcdf-cxx4.so # -DNETCDF_INCLUDE_DIR=/usr/include -DNETCDF_LIBRARY=/usr/lib64/libnetcdf.so
+cmake -B $current_path/ngen/parallelbuild -S . -DCMAKE_INSTALL_PREFIX=/ngen/ngen -DNGEN_WITH_EXTERN_ALL=ON -DNGEN_WITH_MPI:BOOL=ON -DNGEN_WITH_NETCDF:BOOL=ON -DNGEN_WITH_SQLITE:BOOL=ON -DNGEN_WITH_UDUNITS:BOOL=ON -DNGEN_QUIET:BOOL=ON -DNGEN_WITH_BMI_FORTRAN:BOOL=ON -DNGEN_WITH_BMI_C:BOOL=ON -DNGEN_WITH_PYTHON:BOOL=ON -DNGEN_WITH_ROUTING:BOOL=ON -DNGEN_WITH_TESTS:BOOL=ON -DNETCDF_CXX_INCLUDE_DIR=/usr/local/include -DNETCDF_CXX_LIBRARY=/usr/local/lib64/libnetcdf-cxx4.so # -DNETCDF_INCLUDE_DIR=/usr/include -DNETCDF_LIBRARY=/usr/lib64/libnetcdf.so
 echo "==========================================================="
 echo "==========================================================="
 

singularity/templates/t-route/install_t_route.sh

@@ -19,6 +19,8 @@ echo "-----------------------------------------------------------"
 export FC=gfortran NETCDF=/usr/include
 git clone --progress --single-branch --branch master https://github.com/NOAA-OWP/t-route
 cd t-route
+git submodule update --init
+
 ./compiler.sh no-e
 
 cd /t-route/src/troute-network
@@ -27,10 +29,15 @@ python setup.py --use-cython bdist_wheel
 cd /t-route/src/troute-routing
 python setup.py --use-cython bdist_wheel
 
+# troute-config doesn't use setup.py, use build to make the wheel
+cd /t-route/src/troute-config
+python -m build . \
+
 cd /t-route/src/troute-nwm
 python setup.py bdist_wheel
 
 cd /t-route
 cp /t-route/src/troute-network/dist/*.whl /t-route/wheels
 cp /t-route/src/troute-routing/dist/*.whl /t-route/wheels
+cp /t-route/src/troute-config/dist/*.whl /t-route/wheels
 cp /t-route/src/troute-nwm/dist/*.whl /t-route/wheels