diff --git a/build/source/actors/file_access_actor/output_structure.f90 b/build/source/actors/file_access_actor/output_structure.f90
index 8cf218d7e7fd36d00aa13db83cd17b1ff80af334..54db360ba1057b8dad0f7a3eba91930ab9431b06 100644
--- a/build/source/actors/file_access_actor/output_structure.f90
+++ b/build/source/actors/file_access_actor/output_structure.f90
@@ -689,9 +689,9 @@ subroutine allocateDat_rkind_nSteps(metadata,varData,nSnow, nSoil, &
case(iLookVarType%midSnow); allocate(varData%var(iVar)%tim(iStep)%dat(nSnow),stat=err)
case(iLookVarType%midSoil); allocate(varData%var(iVar)%tim(iStep)%dat(nSoil),stat=err)
case(iLookVarType%midToto); allocate(varData%var(iVar)%tim(iStep)%dat(nLayers),stat=err)
- case(iLookVarType%ifcSnow); allocate(varData%var(iVar)%tim(iStep)%dat(0:nSnow),stat=err)
- case(iLookVarType%ifcSoil); allocate(varData%var(iVar)%tim(iStep)%dat(0:nSoil),stat=err)
- case(iLookVarType%ifcToto); allocate(varData%var(iVar)%tim(iStep)%dat(0:nLayers),stat=err)
+ case(iLookVarType%ifcSnow); allocate(varData%var(iVar)%tim(iStep)%dat((nLayers-nSoil)+1),stat=err)
+ case(iLookVarType%ifcSoil); allocate(varData%var(iVar)%tim(iStep)%dat(nSoil+1),stat=err)
+ case(iLookVarType%ifcToto); allocate(varData%var(iVar)%tim(iStep)%dat(nLayers+1),stat=err)
case(iLookVarType%parSoil); allocate(varData%var(iVar)%tim(iStep)%dat(nSoil),stat=err)
case(iLookVarType%routing); allocate(varData%var(iVar)%tim(iStep)%dat(nTimeDelay),stat=err)
case(iLookVarType%outstat); allocate(varData%var(iVar)%tim(iStep)%dat(maxvarfreq*2),stat=err)
@@ -731,9 +731,9 @@ subroutine allocateDat_rkind(metadata,varData,nSnow,nSoil,err,message)
case(iLookVarType%midSnow); allocate(varData%var(iVar)%dat(nSnow),stat=err)
case(iLookVarType%midSoil); allocate(varData%var(iVar)%dat(nSoil),stat=err)
case(iLookVarType%midToto); allocate(varData%var(iVar)%dat(nLayers),stat=err)
- case(iLookVarType%ifcSnow); allocate(varData%var(iVar)%dat(0:nSnow),stat=err)
- case(iLookVarType%ifcSoil); allocate(varData%var(iVar)%dat(0:nSoil),stat=err)
- case(iLookVarType%ifcToto); allocate(varData%var(iVar)%dat(0:nLayers),stat=err)
+ case(iLookVarType%ifcSnow); allocate(varData%var(iVar)%dat((nLayers-nSoil)+1),stat=err)
+ case(iLookVarType%ifcSoil); allocate(varData%var(iVar)%dat(nSoil+1),stat=err)
+ case(iLookVarType%ifcToto); allocate(varData%var(iVar)%dat(nLayers+1),stat=err)
case(iLookVarType%parSoil); allocate(varData%var(iVar)%dat(nSoil),stat=err)
case(iLookVarType%routing); allocate(varData%var(iVar)%dat(nTimeDelay),stat=err)
case(iLookVarType%outstat); allocate(varData%var(iVar)%dat(maxvarfreq*2),stat=err)
@@ -773,9 +773,9 @@ subroutine allocateDat_int(metadata,varData,nSnow, nSoil, &
case(iLookVarType%midSnow); allocate(varData%var(iVar)%tim(iStep)%dat(nSnow),stat=err)
case(iLookVarType%midSoil); allocate(varData%var(iVar)%tim(iStep)%dat(nSoil),stat=err)
case(iLookVarType%midToto); allocate(varData%var(iVar)%tim(iStep)%dat(nLayers),stat=err)
- case(iLookVarType%ifcSnow); allocate(varData%var(iVar)%tim(iStep)%dat(0:nSnow),stat=err)
- case(iLookVarType%ifcSoil); allocate(varData%var(iVar)%tim(iStep)%dat(0:nSoil),stat=err)
- case(iLookVarType%ifcToto); allocate(varData%var(iVar)%tim(iStep)%dat(0:nLayers),stat=err)
+ case(iLookVarType%ifcSnow); allocate(varData%var(iVar)%tim(iStep)%dat((nLayers-nSoil)+1),stat=err)
+ case(iLookVarType%ifcSoil); allocate(varData%var(iVar)%tim(iStep)%dat(nSoil+1),stat=err)
+ case(iLookVarType%ifcToto); allocate(varData%var(iVar)%tim(iStep)%dat(nLayers+1),stat=err)
case(iLookVarType%parSoil); allocate(varData%var(iVar)%tim(iStep)%dat(nSoil),stat=err)
case(iLookVarType%routing); allocate(varData%var(iVar)%tim(iStep)%dat(nTimeDelay),stat=err)
case(iLookVarType%outstat); allocate(varData%var(iVar)%tim(iStep)%dat(maxvarfreq*2),stat=err)
diff --git a/config/configuration.py b/config/configuration.py
deleted file mode 100644
index 3faa35edf3e278dd5776660acad98d73225d64c8..0000000000000000000000000000000000000000
--- a/config/configuration.py
+++ /dev/null
@@ -1,215 +0,0 @@
-from distutils.command.config import config
-import json
-import os
-import math
-from os.path import exists
-from datetime import date
-
-"""
-Function to create the inital summa_actors_settings file
-"""
-def create_init_config():
- Settings_file = {
- "Configuration": {
- "controlVersion": "",
- "simStartTime": "",
- "simEndTime": "",
- "tmZoneInfo": "",
- "settingsPath": "",
- "forcingPath": "",
- "outputPath": "",
- "forcingFreq": "",
- "forcingStart": "",
- "decisionsFile": "",
- "outputControlFile": "",
- "globalHruParamFile": "",
- "globalGruParamFile": "",
- "attributeFile": "",
- "trialParamFile": "",
- "forcingListFile": "",
- "initConditionFile": "",
- "outFilePrefix": "",
- "vegTableFile": "",
- "soilTableFile": "",
- "generalTableFile": "",
- "noahmpTableFile": ""
- },
-
- "JobSubmissionParams": {
- "cpus-per-task": 1,
- "memory": "",
- "job-name": "",
- "account": "",
- "numHRUs": 1,
- "maxNumberOfJobs": 1,
- "maxGRUsPerSubmission": 1,
- "executablePath": ""
- },
-
- "SummaActor": {
- "OuputStructureSize": 1,
- "maxGRUPerJob": 1
- },
-
- "FileAccessActor": {
- "num_vectors_in_output_manager": 1
- },
-
- "JobActor": {
- "FileManagerPath": "",
- "outputCSV": "",
- "csvPath": ""
- },
-
- "HRUActor": {
- "printOutput": "",
- "outputFrequency": 1
- }
- }
- with open('Summa_Actors_Settings.json', 'w') as outfile:
- json.dump(Settings_file, outfile, indent=2)
-
-"""
-Function that creates the paths for the slurm output and the netCDF data
-"""
-def create_output_path(outputPath):
- print("The output path exists, now seperating this run by today's date")
- today = date.today()
- todays_date = today.strftime("%b-%d-%Y")
- outputPath += "{}/".format(todays_date)
- if not exists(outputPath):
- os.mkdir(outputPath)
- print("Directory Created. Now Creating sub directories for SLURM Data and NetCDF data")
- outputNetCDF = outputPath + "netcdf/"
- outputSlurm = outputPath + "slurm/"
- outputCSV = outputPath + "csv/"
- if not exists(outputNetCDF):
- os.mkdir(outputNetCDF)
- if not exists(outputSlurm):
- os.mkdir(outputSlurm)
- if not exists(outputCSV):
- os.mkdir(outputCSV)
-
- # need to add the file name to outputSlurm
- # The job will not be submitted without a file name
- outputSlurm += "slurm-%A_%a.out"
-
- return outputNetCDF, outputSlurm, outputCSV
-
-
-"""
-Function to create the file manager for SummaActors,
-THis is a text file that is created from the settings in the Configuration section
-in the JSON file.
-"""
-def create_file_manager():
- json_file = open("Summa_Actors_Settings.json")
- fileManagerSettings = json.load(json_file)
- json_file.close()
-
- # add the date for the run
- outputPath = fileManagerSettings["Configuration"]["outputPath"]
- if exists(outputPath):
- outputNetCDF, outputSlurm, outputCSV = create_output_path(outputPath)
- fileManagerSettings["Configuration"]["outputPath"] = outputNetCDF
- else:
- print("Output path does not exist, Ensure it exists before running this setup")
- return -1
-
- fileManager = open("fileManager.txt", "w")
- for key,value in fileManagerSettings["Configuration"].items():
- fileManager.write(key + " \'{}\'\n".format(value))
- fileManager.close()
-
- with open("Summa_Actors_Settings.json") as settings_file:
- data = json.load(settings_file)
- data["JobActor"]["FileManagerPath"] = os.getcwd() + "/" + "fileManager.txt"
- data["JobActor"]["csvPath"] = outputCSV
-
- with open("Summa_Actors_Settings.json", "w") as updated_settings:
- json.dump(data, updated_settings, indent=2)
-
-
- print("File Manager for this job has been created")
- return outputSlurm
-
-
-def create_caf_config():
- json_file = open("Summa_Actors_Settings.json")
- SummaSettings = json.load(json_file)
- json_file.close()
-
- numCPUs = SummaSettings["JobSubmissionParams"]["cpus-per-task"]
-
-
- caf_config_name = "caf-application.conf"
- caf_config = open(caf_config_name, "w")
- caf_config.write("caf {{ \n scheduler {{\n max-threads = {}\n }}\n}}".format(numCPUs))
- caf_config.close()
-
- caf_config_path = os.getcwd()
- caf_config_path += "/"
- caf_config_path += caf_config_name
- return caf_config_path
-
-
-def create_sbatch_file(outputSlurm, configFile):
- json_file = open("Summa_Actors_Settings.json")
- SummaSettings = json.load(json_file)
- json_file.close()
-
- numCPUs = SummaSettings["JobSubmissionParams"]["cpus-per-task"]
- memory = SummaSettings["JobSubmissionParams"]["memory"]
- jobName = SummaSettings["JobSubmissionParams"]["job-name"]
- account = SummaSettings["JobSubmissionParams"]["account"]
- numberOfTasks = SummaSettings["JobSubmissionParams"]["numHRUs"]
- GRUPerJob = SummaSettings["JobSubmissionParams"]["maxGRUsPerSubmission"]
- executablePath = SummaSettings["JobSubmissionParams"]["executablePath"]
-
- jobCount = math.ceil(numberOfTasks / GRUPerJob - 1)
-
- configPath = os.getcwd()
-
- sbatch = open("run_summa.sh", "w")
- sbatch.write("#!/bin/bash\n")
- sbatch.write("#SBATCH --cpus-per-task={}\n".format(numCPUs))
- sbatch.write("#SBATCH --time=24:00:00\n")
- sbatch.write("#SBATCH --mem={}\n".format(memory))
- sbatch.write("#SBATCH --job-name={}\n".format(jobName))
- sbatch.write("#SBATCH --account={}\n".format(account))
- sbatch.write("#SBATCH --output={}\n".format(outputSlurm))
- sbatch.write("#SBATCH --array=0-{}\n\n".format(jobCount))
- sbatch.write("gruMax={}\n".format(numberOfTasks))
- sbatch.write("gruCount={}\n".format(GRUPerJob))
- sbatch.write("offset=$SLURM_ARRAY_TASK_ID\n")
- sbatch.write("gruStart=$(( 1 + gruCount*offset ))\n")
- sbatch.write("check=$(( $gruStart + $gruCount ))\n")
- sbatch.write("if [ $check -gt $gruMax ]\n")
- sbatch.write("then\n")
- sbatch.write(" gruCount=$(( gruMax-gruStart+1 ))\n")
- sbatch.write("fi\n\n")
- sbatch.write("{} -g ${{gruStart}} -n ${{gruCount}} -c {} --config-file={}".format(executablePath, configPath, configFile))
-
-
-
-"""
-Funciton checks if the Summa_Actors_Settings.json file exists.
-If yes:
- move on
-If no:
- create it
-"""
-def init_run():
- Summa_Settings_Path = './Summa_Actors_Settings.json'
- if exists('./Summa_Actors_Settings.json'):
- print("File Exists, What do we do next")
- outputSlurm = create_file_manager()
- configFile = create_caf_config()
- create_sbatch_file(outputSlurm, configFile)
-
-
- else:
- print("File Does not Exist and we need to create it")
- create_init_config()
-
-init_run()
\ No newline at end of file
diff --git a/config/create_client_config.py b/config/create_client_config.py
deleted file mode 100644
index 2de8f83a63e399a05cc58b827ca006eccae4eee8..0000000000000000000000000000000000000000
--- a/config/create_client_config.py
+++ /dev/null
@@ -1,27 +0,0 @@
-import json
-import sys
-
-def distributed_settings(hostname, port):
- distributed_settings = {
- "distributed_mode": True,
- "hostname":hostname,
- "port":port,
- "total_hru_count": 5,
- "num_hru_per_batch": 1,
- "heartbeat_interval": 20,
- "lost_node_threshold": 3
- }
- return distributed_settings
-
-
-settings_dict = {
- "Distributed_Settings": {}
-}
-
-hostname = sys.argv[1]
-port = sys.argv[2]
-
-
-settings_dict['Distributed_Settings'] = distributed_settings(hostname, int(port))
-with open('Summa_Actors_Settings.json', 'w') as summa_actors_settings_file:
- json.dump(settings_dict, summa_actors_settings_file, indent=2)
\ No newline at end of file
diff --git a/config/create_summa_actors_config.py b/config/create_summa_actors_config.py
deleted file mode 100644
index 32ff9f448ba0ed994f8058d90fae89cc7d368589..0000000000000000000000000000000000000000
--- a/config/create_summa_actors_config.py
+++ /dev/null
@@ -1,97 +0,0 @@
-import json
-
-def distributed_settings():
- distributed_settings = {
- "distributed-mode": False,
- "host":"localhost",
- "port":4444,
- "total_hru_count": 5,
- "num_hru_per_batch": 1,
- "heartbeat_interval": 20,
- "lost_node_threshold": 3
- }
- return distributed_settings
-
-def simulation_settings():
- simulation_settings = {
- "total_hru_count": 0,
- "num_hru_per_batch": 0
- }
- return simulation_settings
-
-def summa_actor_settings():
- summa_actor_settings = {
- "OutputStructureSize": 250,
- "maxGRUPerJob": 250
- }
- return summa_actor_settings
-
-def file_access_actor_settings():
- file_access_actor_settings = {
- "num_vectors_in_output_manager": 1
- }
- return file_access_actor_settings
-
-def job_actor_settings():
- job_actor_settings = {
- "FileManagerPath" : "",
- "controlVersion" : "",
- "simStartTime" : "",
- "simEndTime" : "",
- "tmZoneInfo" : "",
- "settingsPath" : "",
- "forcingPath" : "",
- "outputPath" : "",
- "forcingFreq" : "",
- "forcingStart" : "",
- "decisionsFile" : "",
- "outputControlFile" : "",
- "globalHruParamFile" : "",
- "globalGruParamFile" : "",
- "attributeFile" : "",
- "trialParamFile" : "",
- "forcingListFile" : "",
- "initConditionFile" : "",
- "outFilePrefix" : "",
- "vegTableFile" : "",
- "soilTableFile" : "",
- "generalTableFile" : "",
- "noahmpTableFile" : "",
- "outputCSV": False,
- "csvPath": ""
- }
- return job_actor_settings
-
-def hru_actor_settings():
- hru_actor_settings = {
- "printOutput": True,
- "outputFrequency": 1
- }
- return hru_actor_settings
-
-
-
-
-
-def create_config():
- settings_dict = {
- "DistributedSettings": {},
- "SimulationSettings" : {},
- "SummaActor" : {},
- "FileAccessActor" : {},
- "JobActor" : {},
- "HRUActor" : {}
- }
- settings_dict['DistributedSettings'] = distributed_settings()
- settings_dict['SimulationSettings'] = simulation_settings()
- settings_dict['SummaActor'] = summa_actor_settings()
- settings_dict['FileAccessActor'] = file_access_actor_settings()
- settings_dict['JobActor'] = job_actor_settings()
- settings_dict['HRUActor'] = hru_actor_settings()
- with open('Summa_Actors_Settings.json', 'w') as summa_actors_settings_file:
- json.dump(settings_dict, summa_actors_settings_file, indent=2)
-
-
-
-
-create_config()
\ No newline at end of file
diff --git a/config/summa-distributed/launch_client.sh b/config/summa-distributed/launch_client.sh
deleted file mode 100755
index 67d92e5bdbb896b83874454daa523696068a1301..0000000000000000000000000000000000000000
--- a/config/summa-distributed/launch_client.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-
-nohup apptainer exec --bind /gladwell:/gladwell \
- --bind /scratch:/scratch \
- --bind /home/kck540/Summa-Actors:/Summa-Actors \
- /gladwell/kck540/container_files/summa_actors.sif \
- /Summa-Actors/config/summa-distributed/run_client.sh 2>&1 > \
- /scratch/kck540/Summa_Distributed_test/logs/`hostname`-client.out &
\ No newline at end of file
diff --git a/config/summa-distributed/launch_remote_clients.sh b/config/summa-distributed/launch_remote_clients.sh
deleted file mode 100755
index d517fd3bb77222323913d3221e0a628f297ea11b..0000000000000000000000000000000000000000
--- a/config/summa-distributed/launch_remote_clients.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/bash
-
-ssh kck540@simlab01.usask.ca /home/kck540/Summa-Actors/config/summa-distributed/launch_client.sh &
-ssh kck540@simlab05.usask.ca /home/kck540/Summa-Actors/config/summa-distributed/launch_client.sh &
-ssh kck540@simlab17.usask.ca /home/kck540/Summa-Actors/config/summa-distributed/launch_client.sh &
-ssh kck540@simlab18.usask.ca /home/kck540/Summa-Actors/config/summa-distributed/launch_client.sh &
\ No newline at end of file
diff --git a/config/summa-distributed/launch_server.sh b/config/summa-distributed/launch_server.sh
deleted file mode 100755
index 36859162dca095f19d954a7f28c2eebf979928fb..0000000000000000000000000000000000000000
--- a/config/summa-distributed/launch_server.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-
-apptainer exec --bind /gladwell:/gladwell \
- --bind /scratch:/scratch \
- --bind /home/kck540/Summa-Actors:/Summa-Actors \
- /gladwell/kck540/container_files/summa_actors.sif \
- /Summa-Actors/config/summa-distributed/run_server.sh > /scratch/kck540/Summa_Distributed_test/logs/`hostname`-server.out
\ No newline at end of file
diff --git a/config/summa-distributed/run_client.sh b/config/summa-distributed/run_client.sh
deleted file mode 100755
index a73b81cf42968cabb9ebd7b8749869695bfa8be6..0000000000000000000000000000000000000000
--- a/config/summa-distributed/run_client.sh
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/bin/bash
-export LD_LIBRARY_PATH=/Summa-Actors/bin/:/usr/local/lib
-cd /Summa-Actors/config/
-python3 create_client_config.py "simlab03" 4444
-cd /Summa-Actors/build
-make
-/Summa-Actors/bin/summaMain -c /Summa-Actors/config/Summa_Actors_Settings.json
\ No newline at end of file
diff --git a/config/summa-distributed/run_server.sh b/config/summa-distributed/run_server.sh
deleted file mode 100755
index c8d21db9ee5cf574a1b296d730f80de3b95c0f66..0000000000000000000000000000000000000000
--- a/config/summa-distributed/run_server.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-# !/bin/bash
-export LD_LIBRARY_PATH=/Summa-Actors/bin/:/usr/local/lib
-cd /Summa-Actors/build
-make
-/Summa-Actors/bin/summaMain -s -c /Summa-Actors/config/Summa_Actors_Settings.json
\ No newline at end of file
diff --git a/utils/Summa_Actors_Settings_backup.json b/utils/Summa_Actors_Settings_backup.json
deleted file mode 100644
index b6f659b78b9656388f1096c34e198aaeb978a2ce..0000000000000000000000000000000000000000
--- a/utils/Summa_Actors_Settings_backup.json
+++ /dev/null
@@ -1,32 +0,0 @@
-{
- "DistributedSettings": {
- "distributed-mode": true,
- "host": "simlab03",
- "port": 4444
- },
-
- "SimulationSettings": {
- "total_hru_count": 100,
- "num_hru_per_batch": 20
- },
-
- "SummaActor": {
- "OuputStructureSize": 250,
- "maxGRUPerJob": 20
- },
-
- "FileAccessActor": {
- "num_vectors_in_output_manager": 1
- },
-
- "JobActor": {
- "FileManagerPath": "/gladwell/SummaActorsSettings/fileManager.txt",
- "outputCSV": false,
- "csvPath": ""
- },
-
- "HRUActor": {
- "printOutput": true,
- "outputFrequency": 500
- }
- }
\ No newline at end of file