Merged in hiddenHelpers (pull request #57)

HiddenHelpers

Approved-by: ksorathia
Approved-by: Eric Winter

src/voltron/mpi/voltapp_mpi.F90

@@ -391,6 +391,25 @@ module voltapp_mpi
             call Toc("GCM2MIX")
         end if
 
+        ! tubes are only done after spinup
+        if(vApp%doDeep .and. vApp%time >= 0) then
+            if(vApp%useHelpers) call vhReqStep(vApp)
+
+            !Update i-shell to trace within in case rTrc has changed
+            vApp%iDeep = vApp%gApp%Grid%ie-1
+
+            !Pull in updated fields to CHIMP
+            call Tic("G2C")
+            call convertGameraToChimp(vApp%mhd2chmp,vApp%gApp,vApp%ebTrcApp)
+            call Toc("G2C")
+
+            if(vApp%useHelpers .and. vApp%doTubeHelp) then
+                call Tic("VoltTubes",.true.)
+                call VhReqTubeStart(vApp)
+                call Toc("VoltTubes",.true.)
+            endif
+        endif
+
         ! run remix
         call Tic("ReMIX", .true.)
         call runRemix(vApp)
@@ -405,19 +424,11 @@ module voltapp_mpi
 
         ! only do imag after spinup
         if(vApp%doDeep .and. vApp%time >= 0) then
-            if(vApp%useHelpers) call vhReqStep(vApp)
-
             ! instead of PreDeep, use Tube Helpers and replicate other calls
-            !Update i-shell to trace within in case rTrc has changed
-            vApp%iDeep = vApp%gApp%Grid%ie-1
 
-            !Pull in updated fields to CHIMP
-            call Tic("G2C")
-            call convertGameraToChimp(vApp%mhd2chmp,vApp%gApp,vApp%ebTrcApp)
-            call Toc("G2C")
             call Tic("VoltTubes",.true.)
             if(vApp%useHelpers .and. vApp%doTubeHelp) then
-                call VhReqTubeStart(vApp)
+                ! Tubes were started earlier
                 call vhReqTubeEnd(vApp)
                 ! Now pack into tubeShell
                 call Tic("Tube2Shell")

testingScripts/weeklyDash-template.pbs

@@ -20,19 +20,26 @@ echo 'The currently loaded modules are:'
 module list
 
 echo 'Loading python environment.'
-mage_miniconda3="${HOME}/miniconda3"
-mage_conda="${mage_miniconda3}/bin/conda"
-__conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
-if [ $? -eq 0 ]; then
-    eval "$__conda_setup"
-else
-    if [ -f "$mage_miniconda3/etc/profile.d/conda.sh" ]; then
-        . "$mage_miniconda3/etc/profile.d/conda.sh"
+mage_test_root=$HOME
+if [ -d "${mage_test_root}/miniconda3" ]; then
+    echo 'Loading local miniconda3'
+    mage_miniconda3="${mage_test_root}/miniconda3"
+    mage_conda="${mage_miniconda3}/bin/conda"
+    __conda_setup="$($mage_conda 'shell.bash' 'hook' 2> /dev/null)"
+    if [ $? -eq 0 ]; then
+        eval "$__conda_setup"
     else
-        export PATH="$mage_miniconda3/bin:$PATH"
+        if [ -f "$mage_miniconda3/etc/profile.d/conda.sh" ]; then
+            . "$mage_miniconda3/etc/profile.d/conda.sh"
+        else
+            export PATH="$mage_miniconda3/bin:$PATH"
+        fi
     fi
+    unset __conda_setup
+else
+    echo 'Loading conda module'
+    module load conda
 fi
-unset __conda_setup
 conda activate {{ conda_environment }}
 echo "The current conda environment is ${CONDA_PREFIX}."