bug: switch from mpich to openmpi for auto-tests

.fprettify.rc

@@ -9,7 +9,7 @@ i: 2
 recursive
 # Excluded files:
 # Anything compiled, src/venus.f90 (it's incomplete), old fortran files, makefiles, template files
-exclude: ["*.exe","*.o","Venus.f90","*.f","Makef*","*emplate.f90"]
+exclude: ["*.exe","*.o","Venus.f90","*.f","Makef*","*emplate.f90","*Msis*"]
 
 # Whitespace option 2 (check fprettify -h for info):
 whitespace: 2

.github/workflows/Format-Doc-Test.yml

@@ -27,6 +27,7 @@ jobs:
       - name: Clone GITM
         uses: actions/checkout@v4
         with: 
+          ref: ${{ github.event.pull_request.head.sha }}
           path:
             GITM
       - name: Format check entire GITM repository
@@ -74,7 +75,7 @@ jobs:
     needs: [Format, Documentation]
     steps:
       - name: Install MPI (mpich)
-        run: sudo apt update && sudo apt install -y mpich
+        run: sudo apt update && sudo apt install -y libopenmpi-dev
       - name: Clone GITM repository
         uses: actions/checkout@v4
       - name: Run tests in srcTests/auto_test

src/read_MHDIMF_Indices_new.f90

@@ -154,8 +154,8 @@ subroutine read_MHDIMF_Indices_new(iOutputError, StartTime, EndTime)
             ! This means that the GITM time is all BEFORE the first
             ! line in the file!
             if (EndTime < IndexTimes_TV(iIMF, imf_bx_) .and. iIMF == 1) then
-               iIMF = iIMF + 1
-               iSW = iSW + 1
+              iIMF = iIMF + 1
+              iSW = iSW + 1
             endif
 
           endif
@@ -176,38 +176,37 @@ subroutine read_MHDIMF_Indices_new(iOutputError, StartTime, EndTime)
 
   iIMF = iIMF - 2
   iSW = iSW - 2
-  
+
   ! There is sometimes a problem where the end time is in the middle of
   ! a data gap. Let's check this:
   if (iIMF > 2) then
-     if (IndexTimes_TV(iIMF, imf_bx_) < EndTime) then
-        ! Copy the last index into the next index and assign times
-        iIMF = iIMF + 1
-        IndexTimes_TV(iIMF, imf_bx_) = EndTime
-        IndexTimes_TV(iIMF, imf_by_) = EndTime
-        IndexTimes_TV(iIMF, imf_bz_) = EndTime
-        Indices_TV(iIMF, imf_bx_) = Indices_TV(iIMF - 1, imf_bx_)
-        Indices_TV(iIMF, imf_by_) = Indices_TV(iIMF - 1, imf_by_)
-        Indices_TV(iIMF, imf_bz_) = Indices_TV(iIMF - 1, imf_bz_)
-
-        IndexTimes_TV(iSW, sw_vx_) = EndTime
-        IndexTimes_TV(iSW, sw_vy_) = EndTime
-        IndexTimes_TV(iSW, sw_vz_) = EndTime
-        IndexTimes_TV(iSW, sw_v_) = EndTime
-        IndexTimes_TV(iSW, sw_n_) = EndTime
-        IndexTimes_TV(iSW, sw_t_) = EndTime
-
-        Indices_TV(iSW, sw_vx_) = Indices_TV(iSW - 1, sw_vx_)
-        Indices_TV(iSW, sw_vy_) = Indices_TV(iSW - 1, sw_vy_)
-        Indices_TV(iSW, sw_vz_) = Indices_TV(iSW - 1, sw_vz_)
-        Indices_TV(iSW, sw_v_) = Indices_TV(iSW - 1, sw_v_)
-        Indices_TV(iSW, sw_n_) = Indices_TV(iSW - 1, sw_n_)
-        Indices_TV(iSW, sw_t_) = Indices_TV(iSW - 1, sw_t_)
-        
-     endif
+    if (IndexTimes_TV(iIMF, imf_bx_) < EndTime) then
+      ! Copy the last index into the next index and assign times
+      iIMF = iIMF + 1
+      IndexTimes_TV(iIMF, imf_bx_) = EndTime
+      IndexTimes_TV(iIMF, imf_by_) = EndTime
+      IndexTimes_TV(iIMF, imf_bz_) = EndTime
+      Indices_TV(iIMF, imf_bx_) = Indices_TV(iIMF - 1, imf_bx_)
+      Indices_TV(iIMF, imf_by_) = Indices_TV(iIMF - 1, imf_by_)
+      Indices_TV(iIMF, imf_bz_) = Indices_TV(iIMF - 1, imf_bz_)
+
+      IndexTimes_TV(iSW, sw_vx_) = EndTime
+      IndexTimes_TV(iSW, sw_vy_) = EndTime
+      IndexTimes_TV(iSW, sw_vz_) = EndTime
+      IndexTimes_TV(iSW, sw_v_) = EndTime
+      IndexTimes_TV(iSW, sw_n_) = EndTime
+      IndexTimes_TV(iSW, sw_t_) = EndTime
+
+      Indices_TV(iSW, sw_vx_) = Indices_TV(iSW - 1, sw_vx_)
+      Indices_TV(iSW, sw_vy_) = Indices_TV(iSW - 1, sw_vy_)
+      Indices_TV(iSW, sw_vz_) = Indices_TV(iSW - 1, sw_vz_)
+      Indices_TV(iSW, sw_v_) = Indices_TV(iSW - 1, sw_v_)
+      Indices_TV(iSW, sw_n_) = Indices_TV(iSW - 1, sw_n_)
+      Indices_TV(iSW, sw_t_) = Indices_TV(iSW - 1, sw_t_)
+
+    endif
   endif
 
-
   nIndices_V(imf_bx_) = iIMF
   nIndices_V(imf_by_) = iIMF
   nIndices_V(imf_bz_) = iIMF

src/read_sme.f90

@@ -276,8 +276,8 @@ subroutine read_sme(iOutputError, StartTime, EndTime, doUseAeForHp)
 
   ! Need to update the number of hemispheric power indices:
   if (doUseAeForHp) then
-     nIndices_V(hpi_) = iAE - 2
-     nIndices_V(hpi_norm_) = iAE - 2
+    nIndices_V(hpi_) = iAE - 2
+    nIndices_V(hpi_norm_) = iAE - 2
   endif
 
   ! If we have gotten to this point and we have no data,

src/set_inputs.f90

@@ -1968,7 +1968,7 @@ subroutine set_inputs
     if (iError == 0) then
       call check_all_indices(EndTime, iError)
       if (iError /= 0) &
-          write(*, *) 'Error with End Time and check_all_indices'
+        write(*, *) 'Error with End Time and check_all_indices'
     else
       write(*, *) 'Error with Current Time and check_all_indices'
     endif

src/set_vertical_bcs.Earth.f90

@@ -182,8 +182,8 @@ subroutine set_vertical_bcs(LogRho, LogNS, Vel_GD, Temp, LogINS, iVel, VertVel)
     ! run (i.e. MSIS-flat).  So, we can then assume that we can simply
     ! perturb the MSIS density.
     NS(0, 1:nSpecies) = &
-         NS(0, 1:nSpecies) * &
-         TidesRhoRat(iLon1D, iLat1D, 2, iBlock1D)
+      NS(0, 1:nSpecies)* &
+      TidesRhoRat(iLon1D, iLat1D, 2, iBlock1D)
     LogNS(0, 1:nSpecies) = alog(NS(0, 1:nSpecies))
 
   endif

srcTests/auto_test/run_all_tests.sh

@@ -94,7 +94,7 @@ do_tests(){
         cp $test_uam UAM.in
 
         # Run GITM, stop if error.
-        mpirun -np 4 ./GITM.exe
+        mpirun -np 4 --oversubscribe ./GITM.exe
         if [ $? -eq 0 ]; then
             printf "\n\n>>> $test_uam ran successfully! <<< \n\n"
             mv $test_uam $test_uam.success
@@ -164,6 +164,7 @@ while [[ $# -gt 0 ]]; do
 
 done
 
+lscpu
 
 do_tests
-done
+done

util/DATAREAD/srcIndices/indices_library.f90

@@ -21,30 +21,30 @@ subroutine check_all_indices(TimeIn, iOutputError)
     if (nIndices_V(iIndex) > 1) then
       if ((IndexTimes_TV(1, iIndex) - TimeIn) > &
           5.0*(IndexTimes_TV(2, iIndex) - IndexTimes_TV(1, iIndex))) then
-         iOutputError = 3
-         write(*, *) 'Error in index file times, before start :'
-         write(*, *) 'index, first time, time in : '
-         write(*, *) iIndex, IndexTimes_TV(1, iIndex), TimeIn
-         call time_real_to_int(IndexTimes_TV(1, iIndex), iTime)
-         write(*, *) 'First Index Time : ', iTime
-         call time_real_to_int(TimeIn, iTime)
-         write(*, *) 'TimeIn : ', iTime
-      end if
+        iOutputError = 3
+        write(*, *) 'Error in index file times, before start :'
+        write(*, *) 'index, first time, time in : '
+        write(*, *) iIndex, IndexTimes_TV(1, iIndex), TimeIn
+        call time_real_to_int(IndexTimes_TV(1, iIndex), iTime)
+        write(*, *) 'First Index Time : ', iTime
+        call time_real_to_int(TimeIn, iTime)
+        write(*, *) 'TimeIn : ', iTime
+      endif
 
       if ((TimeIn - IndexTimes_TV(nIndices_V(iIndex), iIndex)) > &
           5.0*(IndexTimes_TV(2, iIndex) - IndexTimes_TV(1, iIndex))) then
         iOutputError = 4
-         write(*, *) 'Error in index file times, after end :'
-         write(*, *) 'index, last time, time in : '
-         write(*, *) iIndex, IndexTimes_TV(nIndices_V(iIndex), iIndex), TimeIn
-         write(*, *) 'Number of values : ', nIndices_V(iIndex)
-         call time_real_to_int(IndexTimes_TV(nIndices_V(iIndex), iIndex), iTime)
-         write(*, *) 'Last Index Time : ', iTime
-         call time_real_to_int(TimeIn, iTime)
-         write(*, *) 'TimeIn : ', iTime
-      end if
-    end if
-  end do
+        write(*, *) 'Error in index file times, after end :'
+        write(*, *) 'index, last time, time in : '
+        write(*, *) iIndex, IndexTimes_TV(nIndices_V(iIndex), iIndex), TimeIn
+        write(*, *) 'Number of values : ', nIndices_V(iIndex)
+        call time_real_to_int(IndexTimes_TV(nIndices_V(iIndex), iIndex), iTime)
+        write(*, *) 'Last Index Time : ', iTime
+        call time_real_to_int(TimeIn, iTime)
+        write(*, *) 'TimeIn : ', iTime
+      endif
+    endif
+  enddo
 
   return
 end subroutine check_all_indices