Condense environment file activations (#194)

This is related to running the IMI at Harvard on Cannon. For @laestrada and I, the combination of first sourcing the GEOS-Chem environment file and then activating the conda environment (an alias for micromamba in our case) results in GEOS-Chem not being able to run (./gcclassic: error while loading shared libraries: libnetcdf.so.18: cannot open shared object file: No such file or directory).

This order was introduced in 7c57d91. This PR is a fix that makes sure the Conda environment and GEOS-Chem environment file are only activated a single time each (now in run_imi.sh) and than the order is Conda then GEOS-Chem environment file.

run_imi.sh

@@ -65,6 +65,12 @@ if ! "$isAWS"; then
 	printf "\nLoading GEOS-Chem environment: ${GEOSChemEnv}\n"
         source ${GEOSChemEnv}
     fi
+else
+    # Source Conda environment file
+    source $CondaFile
+
+    # Activate Conda environment
+    conda activate ${CondaEnv}
 fi
 
 # Check all necessary config variables are present

src/components/inversion_component/inversion.sh

@@ -67,12 +67,6 @@ run_inversion() {
         cd ${RunDirs}/inversion
     fi
 
-    if ! "$isAWS"; then
-        # Activate Conda environment
-        printf "\nActivating conda environment: ${CondaEnv}\n"
-        conda activate $CondaEnv
-    fi
-
     # Execute inversion driver script
     sbatch --mem $SimulationMemory \
            -c $SimulationCPUs \

src/components/jacobian_component/jacobian.sh

@@ -186,11 +186,6 @@ run_jacobian() {
 
         cd ${RunDirs}/jacobian_runs
 
-        if ! "$isAWS"; then
-            # Load environment with modules for compiling GEOS-Chem Classic
-            source ${GEOSChemEnv} 
-        fi
-
         # Submit job to job scheduler
         source submit_jacobian_simulations_array.sh
 
@@ -213,11 +208,6 @@ run_jacobian() {
 
         # Run the prior simulation
         cd ${JacobianRunsDir}
-
-        if ! "$isAWS"; then
-            # Load environment with modules for compiling GEOS-Chem Classic
-            source ${GEOSChemEnv}
-        fi
 
         # Submit prior simulation to job scheduler
         printf "\n=== SUBMITTING PRIOR SIMULATION ===\n"

src/components/posterior_component/posterior.sh

@@ -94,11 +94,6 @@ setup_posterior() {
 run_posterior() {
     posterior_start=$(date +%s)
     cd ${RunDirs}/posterior_run
-
-    if ! "$isAWS"; then
-        # Load environment with modules for compiling GEOS-Chem Classic
-        source ${GEOSChemEnv}
-    fi
 
     if "$OptimizeBCs"; then
         if "$KalmanMode"; then

src/components/setup_component/setup.sh

@@ -22,29 +22,7 @@ setup_imi() {
     SpinupEnd=${StartDate}
 
     # Use global boundary condition files for initial conditions
-    UseBCsForRestart=true
-
-    printf "\nActivating conda environment: ${CondaEnv}\n"
-    if "$isAWS"; then
-        # Get max process count for spinup, production, and run_inversion scripts
-        output=$(echo $(slurmd -C))
-        array=($output)
-        cpu_str=$(echo ${array[1]})
-        cpu_count=$(echo ${cpu_str:5})
-
-        # With sbatch reduce cpu_count by 1 to account for parent sbatch process 
-        # using 1 core 
-        if "$UseSlurm"; then 
-            cpu_count="$((cpu_count-1))"
-        fi
-
-        # Source Conda environment file
-        source $CondaFile
-
-    fi
-
-    # Activate Conda environment
-    conda activate $CondaEnv
+    UseBCsForRestart=true    
 
     ##=======================================================================
     ## Download Boundary Conditions files if requested