Merge branch 'development' into localdashfix

CMakeLists.txt

@@ -1,5 +1,6 @@
 cmake_minimum_required(VERSION 3.20.2)
-project(Kaiju Fortran)
+project(Kaiju Fortran C)
+#K: Adding C to project to deal w/ issues w/ most recent HDF (10/13/25)
 
 # add and search for pfunit (fingers crossed)
 list(APPEND CMAKE_PREFIX_PATH "./external")

cmake/compilers.cmake

@@ -83,7 +83,12 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
 	#Base
 	string(APPEND CMAKE_Fortran_FLAGS " -fPIC -fpconstant")
 	#Production
-    set(PROD "-align array64byte -align rec32byte -no-prec-div -fast-transcendentals")
+    set(PROD "-align array64byte -align rec32byte -no-prec-div")
+    if (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 23.1)
+    	#Fast transcendentals removed in ifx
+    	string(APPEND PROD " -fast-transcendentals")
+    endif()
+    	
     #Production with Debug Info
     set(PRODWITHDEBUGINFO "-traceback -debug all -align array64byte -align rec32byte -no-prec-div -fast-transcendentals")
 	#Debug
@@ -123,11 +128,24 @@ if(CMAKE_Fortran_COMPILER_ID MATCHES Intel)
 		endif()
 		string(APPEND PROD " -march=core-avx2")
 		string(APPEND PRODWITHDEBUGINFO " -march=core-avx2")
+	elseif (HOST MATCHES stampede3)
+		message("You're on Stampede3!")
+		if (ENABLE_MKL)
+			string(APPEND CMAKE_Fortran_FLAGS " -qmkl")
+		endif()
+		string(APPEND PROD " -xCORE-AVX512")
+		string(APPEND PRODWITHDEBUGINFO " -xCORE-AVX512")
 	endif()
 
+
 	#Check Intel Fortran version
-	if(NOT ALLOW_INVALID_COMPILERS AND CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER "2021.9")
-		message(FATAL_ERROR "Intel Fortran compilers newer than 2023 (version 2021.8) are not supported. Set the ALLOW_INVALID_COMPILERS variable to ON to force compilation at your own risk.")
+	if(NOT ALLOW_INVALID_COMPILERS AND CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER "2021.9" AND CMAKE_Fortran_COMPILER_VERSION VERSION_LESS "2025.1")
+		message(FATAL_ERROR "Intel OneAPI compilers between 2022-2024 have compiler bugs which cause weird numerical errors in our code. You can set the ALLOW_INVALID_COMPILERS variable to ON to force compilation at your own risk. You'll probably get what you deserve.")
+	endif()
+
+	#Check for MKL + intel25
+	if (ENABLE_MKL AND (CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER "2024"))
+		message(WARNING "Intel OneAPI MKL has been found to fail in weird ways and should probably be avoided. But hey, do what you want. I'm a warning message, not a cop.")
 	endif()
 
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES GNU)

src/gamera/ringutils.F90

@@ -491,8 +491,9 @@ module ringutils
         !Map i to itself
         ip = i
 
-        !Next do k, map via periodicity
-        !NOTE: This is assuming you have all
+        !Next do k, map via periodicity. Have to do k first otherwise have to deal w/ right hand becoming left
+
+        !NOTE: This is assuming you have all k cells (ie, no mpi decomp in KDIR)
         if (k < Grid%ks) then
             kp = k + Np
         elseif (k > Grid%ke) then
@@ -501,18 +502,19 @@ module ringutils
             kp = k
         endif
 
-        !Finally do j
+        !Now handle ip,j,kp => ip,jp,kp
+        
         jp = j ! default value
         if ( Model%Ring%doS .and. (j<Grid%js) ) then
             !js-1 => js
             jp = Grid%js + (Grid%js-j) - 1
-            kp = WrapK(k,Np)
+            kp = WrapK(kp,Np)
         endif
 
         if ( Model%Ring%doE .and. (j>Grid%je) ) then
             !je+1 => je
             jp = Grid%je - (j-Grid%je) + 1
-            kp = WrapK(k,Np)
+            kp = WrapK(kp,Np)
         endif
 
     end subroutine lfmIJKcc

src/voltron/modelInterfaces/imag2mhd_interface.F90

@@ -79,13 +79,11 @@ module imag2mhd_interface
                             !Below inner boundary, do dipole projection
                             isGoodCC(i,j,k) = .true.
                             xyz = Gr%xyzcc(i,j,k,:) !Gamera grid center
-                            call Proj2Rad(xyz,Rion,x1,x2)
-                            Gr%Gas0(i,j,k,PROJLAT) = x1
+                            call NHProj(xyz,x1,x2)
+                            Gr%Gas0(i,j,k,PROJLAT) = x1 !Must project to NH
                             Gr%Gas0(i,j,k,PROJLON) = x2
-
                         else
                             !Get value from xyzsquish
-
                             if ( all(vApp%chmp2mhd%isGood(i:i+1,j:j+1,k:k+1)) ) then
                                 !All values are good, so just do this thing
                                 call SquishCorners(vApp%chmp2mhd%xyzSquish(i:i+1,j:j+1,k:k+1,1),Qs)
@@ -123,7 +121,7 @@ module imag2mhd_interface
                         if (i < Gr%is) then
                             !Use dipole projection
                             xyz = Gr%xyz(i,j,k,:) !Gamera grid corner
-                            call Proj2Rad(xyz,Rion,x1,x2)
+                            call NHProj(xyz,x1,x2)
                             isG = .true.
                         else
                             x1  = vApp%chmp2mhd%xyzSquish(i,j,k,1)
@@ -284,41 +282,43 @@ module imag2mhd_interface
                 real(rp), intent(inout) :: Q(Gr%isg:Gr%ieg,Gr%jsg:Gr%jeg,Gr%ksg:Gr%keg)
 
                 integer :: i,j,k,ip,jp,kp
-                logical :: isActive
 
-                !!$OMP PARALLEL DO default(shared) collapse(2) &
-                !!$OMP private(i,j,k,isActive,ip,jp,kp)
-                ! this causes a race condition copying values between ghost cells
-                ! probably a false positive since some of the cells are just copying
-                ! values onto themselves, but easier to remove for now
+                !$OMP PARALLEL DO default(shared) collapse(2) &
+                !$OMP private(i,j,k,ip,jp,kp)
                 do k=Gr%ksg,Gr%keg
                     do j=Gr%jsg,Gr%jeg
                         do i=Gr%isg,Gr%ieg
-                            isActive = (j >= Gr%js) .and. (j <= Gr%je) .and. &
-                                       (k >= Gr%ks) .and. (k <= Gr%ks)
-                            if(.not. isActive) then
-                                !If still here map this ghost to active and set value based on active
+                            if (.not. isPhysical(Model,Gr,i,j,k)) then
+                                !This is a geometric ghost so we can map it to a physical cell
                                 call lfmIJKcc(Model,Gr,i,j,k,ip,jp,kp)
                                 Q(i,j,k) = Q(ip,jp,kp)
-                            endif
+                            endif !isPhys
                         enddo
                     enddo !j
                 enddo !k
 
             end subroutine FillGhostsCC
 
-            !Project xyz along dipole to R0 and return lat (x1) and lon (x2)
-            subroutine Proj2Rad(xyz,R0,x1,x2)
-                real(rp), intent(in ) :: xyz(NDIM), R0
+            !Checks if cell is "physical" as opposed to "geometric". 
+            !Ie, i ghosts are physical but j/k ghosts are geometric (they point to other physical cells)
+            function isPhysical(Model,Gr,i,j,k)
+                type(Model_T), intent(in) :: Model
+                type(Grid_T) , intent(in) :: Gr
+                integer, intent(in) :: i,j,k
+                logical :: isPhysical       
+
+                isPhysical = (j >= Gr%js) .and. (j <= Gr%je) .and. &
+                             (k >= Gr%ks) .and. (k <= Gr%ke)
+            end function isPhysical
+
+            !Get azimuth and invariant latitude
+            subroutine NHProj(xyz,x1,x2)
+                real(rp), intent(in ) :: xyz(NDIM)
                 real(rp), intent(out) :: x1,x2
-
-                real(rp), dimension(NDIM) :: xyz0
-
-                xyz0 = DipoleShift(xyz,R0)
-                x1 = asin(xyz0(ZDIR)/R0) !Lat
-                x2 = katan2(xyz0(YDIR),xyz0(XDIR)) !katan => [0,2pi] instead of [-pi,pi]
-
-            end subroutine Proj2Rad 
+               
+               x1 = InvLatitude(xyz)
+               x2 = katan2(xyz(YDIR),xyz(XDIR)) !katan => [0,2pi] instead of [-pi,pi]
+            end subroutine NHProj
 
     end subroutine
 

src/voltron/mpi/modelInterfaces/gamCouple_mpi_G2V.F90

@@ -86,7 +86,7 @@ module gamCouple_mpi_G2V
 
         ! initialize F08 MPI objects
         App%couplingComm = MPI_COMM_NULL
-        App%zeroArraytypes = (/ MPI_DATATYPE_NULL /)
+        App%zeroArraytypes(:) = (/ MPI_INTEGER /) ! = (/ MPI_DATATYPE_NULL /)
 
         ! split voltron helpers off of the communicator
         ! split couplingPoolComm into a communicator with only the non-helper voltron rank

src/voltron/mpi/modelInterfaces/gamCouple_mpi_V2G.F90

@@ -559,13 +559,13 @@ module gamCouple_mpi_V2G
 
     subroutine sendGameraCplDataMpi(gCplApp, CouplingTargetT)
         class(gamCouplerMpi_volt_T), intent(inout) :: gCplApp
-        real(rp), intent(in) :: CouplingTargetT
+        real(rp), intent(inout) :: CouplingTargetT
 
         call sendShallowCplDataMpi(gCplApp)
         if(gCplApp%doDeep) call sendDeepCplDataMpi(gCplApp)
         call sendCplTimeMpi(gCplApp, CouplingTargetT)
 
-    end subroutine
+    end subroutine sendGameraCplDataMpi
 
     subroutine sendShallowCplDataMpi(gCplApp)
         class(gamCouplerMpi_volt_T), intent(inout) :: gCplApp
@@ -628,14 +628,14 @@ module gamCouple_mpi_V2G
 
     subroutine sendCplTimeMpi(gCplApp, CouplingTargetT)
         class(gamCouplerMpi_volt_T), intent(inout) :: gCplApp
-        real(rp), intent(in) :: CouplingTargetT
+        real(rp), intent(inout) :: CouplingTargetT
 
         integer :: ierr
 
         ! Send Target Time for next coupling
         call mpi_bcast(CouplingTargetT,1,MPI_MYFLOAT, gCplApp%myRank, gCplApp%couplingComm, ierr)
 
-    end subroutine
+    end subroutine sendCplTimeMpi
 
 end module
 

src/voltron/mpi/volthelpers_mpi.F90

@@ -107,7 +107,7 @@ module volthelpers_mpi
     ! chimp data update functions
 
     subroutine sendChimpStateData(ebState, vHelpComm)
-        type(ebState_T), intent(in) :: ebState
+        type(ebState_T), intent(inout) :: ebState
         type(MPI_Comm), intent(in) :: vHelpComm
 
         integer :: ierr, length
@@ -195,7 +195,7 @@ module volthelpers_mpi
             call mpi_Abort(MPI_COMM_WORLD, 1, ierr)
         end if
 
-    end subroutine
+    end subroutine sendChimpStateData
 
     subroutine recvChimpStateData(ebState, vHelpComm)
         type(ebState_T), intent(inout) :: ebState
@@ -272,7 +272,7 @@ module volthelpers_mpi
     end subroutine
 
     subroutine sendChimpUpdate(vApp)
-        type(voltAppMpi_T), intent(in) :: vApp
+        type(voltAppMpi_T), intent(inout) :: vApp
 
         integer :: ierr, length
         character( len = MPI_MAX_ERROR_STRING) :: message
@@ -317,7 +317,7 @@ module volthelpers_mpi
             call mpi_Abort(MPI_COMM_WORLD, 1, ierr)
         end if
 
-    end subroutine
+    end subroutine sendChimpUpdate
 
     subroutine recvChimpUpdate(vApp)
         type(voltAppMpi_T), intent(inout) :: vApp
@@ -374,14 +374,15 @@ module volthelpers_mpi
         type(voltAppMpi_T), intent(in) :: vApp
         integer, intent(in) :: rType
 
-        integer :: ierr
+        integer :: ierr,wtf
         type(MPI_Request) :: helpReq
 
+        wtf = rType
         ! async to match waiting helper nodes
-        call mpi_Ibcast(rType, 1, MPI_INTEGER, 0, vApp%vHelpComm, helpReq, ierr)
+        call mpi_Ibcast(wtf, 1, MPI_INTEGER, 0, vApp%vHelpComm, helpReq, ierr)
         call mpi_wait(helpReq, MPI_STATUS_IGNORE, ierr)
 
-    end subroutine
+    end subroutine vhRequestType
 
     subroutine vhReqStep(vApp)
         type(voltAppMpi_T), intent(inout) :: vApp

testingScripts/build_mage-template.pbs

@@ -9,8 +9,6 @@
 #PBS -j oe
 #PBS -m abe
 
-# This script just builds the MAGE software.
-
 echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
 
 echo 'Loading modules.'

testingScripts/send_slack_message.py

@@ -0,0 +1,152 @@
+#!/usr/bin/env python
+
+"""Send a message to Slack.
+
+Send a message to Slack.
+
+Authors
+-------
+Eric Winter
+"""
+
+
+# Import standard modules.
+import datetime
+# import glob
+import os
+import sys
+
+# # Import 3rd-party modules.
+
+# Import project modules.
+import common
+
+
+# Program constants
+
+# Program description.
+DESCRIPTION = "Send a message to Slack."
+
+# # Root of directory tree for this set of tests.
+# MAGE_TEST_SET_ROOT = os.environ['MAGE_TEST_SET_ROOT']
+
+# # Directory for unit tests
+# UNIT_TEST_DIRECTORY = os.path.join(MAGE_TEST_SET_ROOT, 'unitTest')
+
+# # glob pattern for naming unit test directories
+# UNIT_TEST_DIRECTORY_GLOB_PATTERN = 'unitTest_*'
+
+# # Name of build subdirectory containing binaries
+# BUILD_BIN_DIR = 'bin'
+
+# # Name of file containing job IDs for each unit test directory.
+# JOB_ID_LIST_FILE = 'jobs.txt'
+
+
+def create_command_line_parser():
+    """Create the command-line argument parser.
+
+    Create the parser for command-line arguments.
+
+    Parameters
+    ----------
+    None
+
+    Returns
+    -------
+    parser : argparse.ArgumentParser
+        Command-line argument parser for this script.
+
+    Raises
+    ------
+    None
+    """
+    parser = common.create_command_line_parser(DESCRIPTION)
+    parser.add_argument(
+        "message",
+        default="",
+        help="Message to send to Slack (default: %(default)s)"
+    )
+    return parser
+
+
+def send_slack_message(args: dict = None):
+    """Send a message to Slack.
+
+    Send a message to Slack.
+
+    Parameters
+    ----------
+    args : dict
+        Dictionary of program options.
+
+    Returns
+    -------
+    None
+
+    Raises
+    ------
+    None
+    """
+    # Local convenience variables.
+    debug = args["debug"]
+    be_loud = args["loud"]
+    slack_on_fail = args["slack_on_fail"]
+    is_test = args["test"]
+    verbose = args["verbose"]
+    message = args["message"]
+
+    # ------------------------------------------------------------------------
+
+    if debug:
+        print(f"Starting {sys.argv[0]} at {datetime.datetime.now()}")
+        print(f"Current directory is {os.getcwd()}")
+
+    # ------------------------------------------------------------------------
+
+    # Create the Slack client.
+    slack_client = common.slack_create_client()
+    slack_response_summary = common.slack_send_message(
+        slack_client, message, is_test=is_test
+    )
+
+    # ------------------------------------------------------------------------
+
+    if debug:
+        print(f"Ending {sys.argv[0]} at {datetime.datetime.now()}")
+
+
+def main():
+    """Begin main program.
+
+    This is the main program code.
+
+    Parameters
+    ----------
+    None
+
+    Returns
+    -------
+    None
+
+    Raises
+    ------
+    None
+    """
+    # Set up the command-line parser.
+    parser = create_command_line_parser()
+
+    # Parse the command-line arguments.
+    args = parser.parse_args()
+    if args.debug:
+        print(f"args = {args}")
+
+    # ------------------------------------------------------------------------
+
+    # Call the main program logic. Note that the Namespace object (args)
+    # returned from the option parser is converted to a dict using vars().
+    send_slack_message(vars(args))
+
+
+if __name__ == "__main__":
+    main()

testingScripts/unitTest-build-template.pbs

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+#PBS -N {{ job_name }}
+#PBS -A {{ account }}
+#PBS -q {{ queue }}
+#PBS -l job_priority={{ job_priority }}
+#PBS -l select=1:ncpus=128
+#PBS -l walltime={{ walltime }}
+#PBS -j oe
+#PBS -m abe
+
+# Abort script on any error.
+set -e
+
+echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
+
+echo 'Loading modules.'
+module --force purge
+{%- for module in modules %}
+module load {{ module }}
+{%- endfor %}
+echo 'The currently loaded modules are:'
+module list
+
+echo 'The active environment variables are:'
+printenv
+
+echo 'Copying pFUnit binaries.'
+pfunit_dir="{{ mage_test_root }}/pfunit/pFUnit-4.2.0/ifort-23-mpich-derecho"
+kaiju_external_dir="{{ kaijuhome }}/external"
+cp -rp "${pfunit_dir}/FARGPARSE-1.1" "${kaiju_external_dir}/"
+cp -rp "${pfunit_dir}/GFTL-1.3" "${kaiju_external_dir}/"
+cp -rp "${pfunit_dir}/GFTL_SHARED-1.2" "${kaiju_external_dir}/"
+cp -rp "${pfunit_dir}/PFUNIT-4.2" "${kaiju_external_dir}/"
+
+# Build the code.
+cmd="{{ cmake_cmd }} >& cmake.out"
+echo $cmd
+eval $cmd
+cmd="{{ make_cmd }} >& make.out"
+echo $cmd
+eval $cmd
+
+echo "Job $PBS_JOBID ended at `date` on `hostname` in directory `pwd`."

testingScripts/unitTestReport.py

@@ -111,8 +111,7 @@ def main():
             print(f"Checking unit test results in {unit_test_directory}.")
 
         # Move to the directory containing the unit test results.
-        path = os.path.join(UNIT_TEST_DIRECTORY, unit_test_directory,
-                            BUILD_BIN_DIR)
+        path = os.path.join(UNIT_TEST_DIRECTORY, unit_test_directory)
         if debug:
             print(f"path = {path}")
         os.chdir(path)
@@ -136,19 +135,27 @@ def main():
         # NOTE: This needs to be reorganized.
 
         # Compute the names of the job log files.
-        job_file_0 = f"genTestData.o{job_ids[0]}"  # 0 OKs
-        job_file_1 = f"runCaseTests.o{job_ids[1]}" # 2 OKs
-        job_file_2 = f"runNonCaseTests1.o{job_ids[2]}"  # 6 OKs
-        job_file_3 = f"runNonCaseTests2.o{job_ids[3]}"  # 1 OK
-        if debug:
-            print(f"job_file_0 = {job_file_0}")
-            print(f"job_file_1 = {job_file_1}")
-            print(f"job_file_2 = {job_file_2}")
-            print(f"job_file_3 = {job_file_3}")
+        # 0 OKs
+        job_file_build = f"../unitTest-build.o{job_ids[0]}"
+        # 0 OKs
+        job_file_genTestData = f"../unitTest-genTestData.o{job_ids[1]}"
+        # 2 OKs
+        job_file_caseTests = f"../unitTest-caseTests.o{job_ids[2]}"
+        # 6 OKs
+        job_file_noncaseTests1 = f"../unitTest-noncaseTests1.o{job_ids[3]}"
+        # 1 OK
+        job_file_noncaseTests2 = f"../unitTest-noncaseTests2.o{job_ids[4]}"
 
         # Combine the results of each test log file.
+        os.chdir("bin")
         bigFile = []
-        job_files = [job_file_0, job_file_1, job_file_2, job_file_3]
+        job_files = [
+            job_file_build,
+            job_file_genTestData,
+            job_file_caseTests,
+            job_file_noncaseTests1,
+            job_file_noncaseTests2,
+        ]
         for job_file in job_files:
             with open(job_file, 'r', encoding='utf-8') as f:
                 bigFile += f.readlines()
@@ -234,12 +241,14 @@ def main():
         )
         if debug:
             print(f"slack_response_summary = {slack_response_summary}")
-    
+
     # Also write a summary file to the root folder of this test
-    with open(os.path.join(MAGE_TEST_SET_ROOT,'testSummary.out'), 'w', encoding='utf-8') as f:
+    with open(os.path.join(
+        MAGE_TEST_SET_ROOT, 'testSummary.out'), 'w', encoding='utf-8'
+    ) as f:
         f.write(test_report_details_string)
         f.write('\n')
-    
+
     # ------------------------------------------------------------------------
 
     if debug:

tests/genTestData-template.pbs

@@ -9,6 +9,9 @@
 #PBS -j oe
 #PBS -m abe
 
+# Abort script on any error.
+set -e
+
 echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
 
 echo 'Loading modules.'
@@ -28,6 +31,16 @@ export KMP_STACKSIZE=128M
 echo 'The active environment variables are:'
 printenv
 
+# Move to the directory containing the compiled code.
+cd bin
+
+echo 'Copying input files.'
+test_inputs_dir="{{ mage_test_root }}/unit_test_inputs"
+cp "${test_inputs_dir}/bcwind.h5" .
+cp "${test_inputs_dir}/geo_mpi.xml" .
+cp "${test_inputs_dir}/lfmD.h5" .
+cp "${test_inputs_dir}/raijuconfig.h5" .
+
 echo 'Generating data for testing.'
 MPICOMMAND="mpiexec $KAIJUHOME/scripts/preproc/pinCpuCores.sh"
 $MPICOMMAND ./voltron_mpi.x cmiD_deep_8_genRes.xml >& cmiD_deep_8_genRes.out

tests/runCaseTests-template.pbs

@@ -9,6 +9,9 @@
 #PBS -j oe
 #PBS -m abe
 
+# Abort script on any error.
+set -e
+
 echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
 
 echo 'Loading modules.'
@@ -28,6 +31,9 @@ export KMP_STACKSIZE=128M
 echo 'The active environment variables are:'
 printenv
 
+# Move to the directory containing the compiled code.
+cd bin
+
 echo 'Running non-MPI test cases.'
 ./caseTests >& caseTests.out
 echo 'Non-MPI test cases complete.'

tests/runNonCaseTests1-template.pbs

@@ -9,6 +9,9 @@
 #PBS -j oe
 #PBS -m abe
 
+# Abort script on any error.
+set -e
+
 echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
 
 echo 'Loading modules.'
@@ -28,6 +31,9 @@ export KMP_STACKSIZE=128M
 echo 'The active environment variables are:'
 printenv
 
+# Move to the directory containing the compiled code.
+cd bin
+
 echo 'Running GAMERA tests.'
 date
 ./gamTests >& gamTests.out

tests/runNonCaseTests2-template.pbs

@@ -9,6 +9,9 @@
 #PBS -j oe
 #PBS -m abe
 
+# Abort script on any error.
+set -e
+
 echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
 
 echo 'Loading modules.'
@@ -28,6 +31,9 @@ export KMP_STACKSIZE=128M
 echo 'The active environment variables are:'
 printenv
 
+# Move to the directory containing the compiled code.
+cd bin
+
 echo 'Running VOLTRON MPI tests.'
 date
 MPICOMMAND="mpiexec $KAIJUHOME/scripts/preproc/pinCpuCores.sh"

tests/unitTestReport-template.pbs

@@ -9,6 +9,9 @@
 #PBS -j oe
 #PBS -m abe
 
+# Abort script on any error.
+set -e
+
 echo "Job $PBS_JOBID started at `date` on `hostname` in directory `pwd`."
 
 echo 'Loading modules.'
@@ -40,6 +43,7 @@ else
     module load conda
 fi
 conda activate {{ conda_environment }}
+echo "The active conda environment is ${CONDA_DEFAULT_ENV}."
 
 echo 'Setting up MAGE environment.'
 source {{ kaijuhome }}/scripts/setupEnvironment.sh
@@ -51,6 +55,13 @@ export BRANCH_OR_COMMIT={{ branch_or_commit }}
 echo 'The active environment variables are:'
 printenv
 
+# Move to the directory containing the compiled code.
+cd bin
+if [[ $? -eq 1 ]]; then
+    python $KAIJUHOME/testingScripts/send_slack_message.py "Unit test build failed in `pwd`!"
+    exit 1
+fi
+
 echo 'Generating unit test report.'
 python $KAIJUHOME/testingScripts/unitTestReport.py {{ report_options }} >& unitTestReport.out