diff --git a/Makefile.am b/Makefile.am
index 9254d916e5..42cd7edbd1 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -115,5 +115,16 @@ include $(top_srcdir)/mkmods.mk
 #	-rm -f FMSConfig.cmake FMSConfigVersion.cmake
 EXTRA_DIST = README.md #_package_init_cmake
 
+
+if COV
+check-code-coverage: check
+	-cd ${top_builddir}/test_fms && chmod +x intel_coverage.sh && ./intel_coverage.sh
+
+.PHONY: check-code-coverage
+
+clean-local:
+	-rm -rf .mods coverage-data coverage-report
+else
 clean-local:
 	-rm -rf .mods
+endif
diff --git a/configure.ac b/configure.ac
index cc1367ccb8..a552ae33bc 100644
--- a/configure.ac
+++ b/configure.ac
@@ -79,6 +79,12 @@ AC_ARG_ENABLE([setting-flags],
 AS_IF([test ${enable_setting_flags:-yes} = yes],
   [enable_setting_flags=yes],
   [enable_setting_flags=no])
+AC_ARG_ENABLE([code-coverage],
+  [AS_HELP_STRING([--enable-code-coverage],
+    [Allow configure to set flags and add check-code-coverage target for code coverage analysis (Default no)])])
+AS_IF([test ${enable_code_coverage:-no} = no],
+  [enable_code_coverage=no],
+  [enable_code_coverage=yes])
 
 # Does the user want to build documentation?
 AC_MSG_CHECKING([whether documentation should be build (requires doxygen)])
@@ -174,6 +180,16 @@ if test $with_mpi = yes; then
   GX_FC_CHECK_MOD([mpi], [], [], [AC_MSG_ERROR([Can't find the MPI Fortran module.  Set FC/CPPFLAGS/FCFLAGS])])
   AC_CHECK_FUNC([MPI_init], [], [AC_MSG_ERROR([Can't find the MPI Fortran library.  Set FC/LDFLAGS/LIBS])])
 fi
+# check intel compiler and coverage tools are avaiable if code coverage is enabled
+if test "$enable_code_coverage" = yes; then
+  if test ! -z "`$FC --version | grep ifort`"; then
+    AC_CHECK_PROGS([PROFMERGE],[profmerge])
+    AC_CHECK_PROGS([CODECOV], [codecov])
+  else
+    AC_MSG_ERROR([Intel compiler and coverage tools required for coverage report])
+  fi
+fi
+AM_CONDITIONAL(COV, [test "$enable_code_coverage" = yes])
 
 # Require netCDF
 GX_FC_CHECK_MOD([netcdf], [], [], [AC_MSG_ERROR([Can't find the netCDF Fortran module.  Set CPPFLAGS/FCFLAGS])])
@@ -238,6 +254,12 @@ if test $enable_setting_flags = yes; then
   if test ! -z "$OPENMP_FCFLAGS"; then
     FCFLAGS="$FCFLAGS $OPENMP_FCFLAGS"
   fi
+
+  # Add code coverage flags
+  if test $enable_code_coverage = yes; then
+    FCFLAGS="$FCFLAGS -prof-gen=srcpos"
+    CFLAGS="$CFLAGS -prof-gen=srcpos"
+  fi
 fi
 
 # Define an AM_CONDITIONAL to determine if you are on a CRAY
@@ -358,6 +380,7 @@ AC_CONFIG_FILES([
   docs/Makefile
   parser/Makefile
   test_fms/test_common.sh
+  test_fms/intel_coverage.sh
   test_fms/Makefile
   test_fms/diag_manager/Makefile
   test_fms/data_override/Makefile
diff --git a/mkmods.mk b/mkmods.mk
index e433f4a23b..1508528763 100644
--- a/mkmods.mk
+++ b/mkmods.mk
@@ -6,4 +6,4 @@ SUFFIXES = .$(FC_MODEXT) _mod.$(FC_MODEXT)
 	$(PPFCCOMPILE) -c $<
 	@cp $(MODDIR)/$@ .
 
-CLEANFILES = *.$(FC_MODEXT) $(BUILT_SOURCES:%=$(MODDIR)/%) *__genmod.$(FC_MODEXT) *__genmod.f90
+CLEANFILES = *.$(FC_MODEXT) $(BUILT_SOURCES:%=$(MODDIR)/%) *__genmod.$(FC_MODEXT) *__genmod.f90 *.dyn *.spi *.dpi *.spl
diff --git a/test_fms/Makefile.am b/test_fms/Makefile.am
index 639a69c5b0..b691ce9096 100644
--- a/test_fms/Makefile.am
+++ b/test_fms/Makefile.am
@@ -30,4 +30,4 @@ horiz_interp field_manager axis_utils affinity fms2_io parser
 
 # This input file must be distributed, it is turned into
 # test_common.sh by configure.
-EXTRA_DIST = test_common.sh.in
+EXTRA_DIST = test_common.sh.in intel_coverage.sh.in
diff --git a/test_fms/affinity/Makefile.am b/test_fms/affinity/Makefile.am
index 6d94e593f4..e5f4996a67 100644
--- a/test_fms/affinity/Makefile.am
+++ b/test_fms/affinity/Makefile.am
@@ -41,4 +41,4 @@ TESTS = test_affinity2.sh
 EXTRA_DIST = input_base.nml test_affinity2.sh
 
 # Clean up
-CLEANFILES = input.nml *.out*
+CLEANFILES = input.nml *.out* *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/axis_utils/Makefile.am b/test_fms/axis_utils/Makefile.am
index f514855e6d..2985efcbb1 100644
--- a/test_fms/axis_utils/Makefile.am
+++ b/test_fms/axis_utils/Makefile.am
@@ -41,4 +41,4 @@ TESTS = test_axis_utils2.sh
 EXTRA_DIST = test_axis_utils2.sh
 
 # Clean up
-CLEANFILES = input.nml *.out* *.nc*
+CLEANFILES = input.nml *.out* *.nc* *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/coupler/Makefile.am b/test_fms/coupler/Makefile.am
index 68411531a6..a6665be6e5 100644
--- a/test_fms/coupler/Makefile.am
+++ b/test_fms/coupler/Makefile.am
@@ -42,4 +42,4 @@ TESTS = test_coupler.sh
 EXTRA_DIST = test_coupler.sh
 
 # Clean up
-CLEANFILES = input.nml *.nc* *.out
+CLEANFILES = input.nml *.nc* *.out *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/data_override/Makefile.am b/test_fms/data_override/Makefile.am
index 7564bec265..23017e088b 100644
--- a/test_fms/data_override/Makefile.am
+++ b/test_fms/data_override/Makefile.am
@@ -44,4 +44,4 @@ EXTRA_DIST = input_base.nml diag_table_base data_table_base	\
 test_data_override2.sh
 
 # Clean up
-CLEANFILES = input.nml *.nc* *.out diag_table data_table data_table.yaml
+CLEANFILES = input.nml *.nc* *.out diag_table data_table data_table.yaml *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/diag_manager/Makefile.am b/test_fms/diag_manager/Makefile.am
index cf5d063e7b..a0429e49bb 100644
--- a/test_fms/diag_manager/Makefile.am
+++ b/test_fms/diag_manager/Makefile.am
@@ -40,4 +40,4 @@ TESTS = test_diag_manager2.sh
 # Copy over other needed files to the srcdir
 EXTRA_DIST = input.nml_base diagTables test_diag_manager2.sh
 
-CLEANFILES = input.nml *.nc *.out diag_table
+CLEANFILES = input.nml *.nc *.out diag_table *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/drifters/Makefile.am b/test_fms/drifters/Makefile.am
index 2addf4aad9..378658c29a 100644
--- a/test_fms/drifters/Makefile.am
+++ b/test_fms/drifters/Makefile.am
@@ -50,4 +50,4 @@ EXTRA_DIST = input_base.nml drifters_inp_test_3d.cdl	\
 test_drifters2.sh
 
 # Clean up
-CLEANFILES = *out *__genmod.mod *__genmod.f90 input.nml *.nc
+CLEANFILES = *out *__genmod.mod *__genmod.f90 input.nml *.nc *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/exchange/Makefile.am b/test_fms/exchange/Makefile.am
index ff7c05756b..e13c19fdd7 100644
--- a/test_fms/exchange/Makefile.am
+++ b/test_fms/exchange/Makefile.am
@@ -41,4 +41,4 @@ TESTS = test_xgrid2.sh
 EXTRA_DIST = input_base.nml test_xgrid2.sh
 
 # Clean up
-CLEANFILES = input.nml *.nc *.out
+CLEANFILES = input.nml *.nc *.out *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/field_manager/Makefile.am b/test_fms/field_manager/Makefile.am
index 6110149168..33beb1da33 100644
--- a/test_fms/field_manager/Makefile.am
+++ b/test_fms/field_manager/Makefile.am
@@ -41,4 +41,4 @@ TESTS = test_field_manager2.sh
 EXTRA_DIST = test_field_manager2.sh input_base.nml field_table_base
 
 # Clean up
-CLEANFILES = input.nml *.out* field_table
+CLEANFILES = input.nml *.out* field_table *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/fms/Makefile.am b/test_fms/fms/Makefile.am
index 3e60cfff6c..05594fb439 100644
--- a/test_fms/fms/Makefile.am
+++ b/test_fms/fms/Makefile.am
@@ -39,7 +39,7 @@ TESTS = test_fms2.sh
 # These will also be included in the distribution.
 EXTRA_DIST = test_fms2.sh
 
-CLEANFILES = input.nml logfile.*.out *.mod *.o
+CLEANFILES = input.nml logfile.*.out *.mod *.o *.dpi *.spi *.dyn *.spl
 
 clean-local:
 	rm -rf RESTART
diff --git a/test_fms/fms2_io/Makefile.am b/test_fms/fms2_io/Makefile.am
index a9624914ad..d6629dd6ad 100644
--- a/test_fms/fms2_io/Makefile.am
+++ b/test_fms/fms2_io/Makefile.am
@@ -63,4 +63,4 @@ TESTS = test_bc_restart.sh test_fms2_io.sh test_atmosphere_io.sh test_io_simple.
 # Set srcdir as evironment variable to be reference in the job script
 TESTS_ENVIRONMENT = srcdir="$(top_srcdir)";
 
-CLEANFILES = *.mod *.nc *.nc.* input.nml logfile.000000.out the_mask ascii_test1
+CLEANFILES = *.mod *.nc *.nc.* input.nml logfile.000000.out the_mask ascii_test1 *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/horiz_interp/Makefile.am b/test_fms/horiz_interp/Makefile.am
index d2bb8a8545..37141ebee6 100644
--- a/test_fms/horiz_interp/Makefile.am
+++ b/test_fms/horiz_interp/Makefile.am
@@ -41,4 +41,4 @@ TESTS = test_horiz_interp2.sh
 EXTRA_DIST = input_base.nml test_horiz_interp2.sh
 
 # Clean up
-CLEANFILES = input.nml *.out*
+CLEANFILES = input.nml *.out* *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/intel_coverage.sh.in b/test_fms/intel_coverage.sh.in
new file mode 100755
index 0000000000..bc452277be
--- /dev/null
+++ b/test_fms/intel_coverage.sh.in
@@ -0,0 +1,89 @@
+#!/usr/bin/sh
+#***********************************************************************
+#                   GNU Lesser General Public License
+#
+# This file is part of the GFDL Flexible Modeling System (FMS).
+#
+# FMS is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at
+# your option) any later version.
+#
+# FMS is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+# for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with FMS.  If not, see <http://www.gnu.org/licenses/>.
+#***********************************************************************
+# Produces a code coverage report for each subdirectory using intel's codecov tool
+# runs with `make check-code-coverage` after configuring with `--enable-code-coverage`
+
+# Ryan Mulhall 1/26/21
+
+merge_dpis () {
+
+  mkdir coverage-data
+
+  for dir in `find . -maxdepth 1 -mindepth 1 -type d -printf '%f\n' | grep -v test_fms`
+  do
+    cd $dir
+    if [ ! -z "`find . -type f -name "*.dyn" `" ]; then
+      profmerge -prof_dpi ${dir}.dpi
+      mv ${dir}.dpi ../coverage-data
+      echo ${1} ${dir} coverage data done.
+    fi
+    cd ..
+  done
+
+  cd coverage-data
+  profmerge -a -prof_dpi ${1}.dpi *.dpi
+  cd ..
+}
+
+# ensure working directory is at the top of the build directory
+top_builddir='@abs_top_builddir@'
+cd $top_builddir
+
+# remove previous runtime data/report
+rm -rf coverage-data
+rm -rf test_fms/coverage-data
+rm -rf coverage-report
+
+# combine runtime generated coverage data from src and tests
+merge_dpis src
+cd test_fms
+merge_dpis tests
+cd ..
+cp coverage-data/src.dpi ./
+cp test_fms/coverage-data/tests.dpi ./
+profmerge -a -prof_dpi fms-global-coverage.dpi src.dpi tests.dpi
+
+# basic html page to link the reports
+mkdir coverage-report
+cat <<_EOF > coverage-report/fms-coverage.html
+<!DOCTYPE html>
+<html>
+<head>
+  <title> FMS Code Coverage </title>
+  <h1>FMS Code Coverage</h1>
+</head>
+<body>
+_EOF
+
+# generate code coverage report and links for each (src) subdirectory
+for dir in `find . -maxdepth 1 -mindepth 1 -type d -printf '%f\n' | grep -v test_fms | sort`
+do
+  cd $dir
+  if [ ! -z "`find . -type f -name "*.spi"`" ] ; then
+    mkdir ../coverage-report/$dir
+    codecov -prj $dir -spi pgopti.spi -dpi ../fms-global-coverage.dpi
+    mv CODE_COVERAGE.HTML ../coverage-report/$dir
+    mv CodeCoverage ../coverage-report/$dir
+    echo "<p><a href=\"${dir}/CODE_COVERAGE.HTML\">${dir}</a></p>" >> ../coverage-report/fms-coverage.html
+  fi
+  cd ..
+done
+echo "</body>" >> coverage-report/fms-coverage.html
+echo "</html>" >> coverage-report/fms-coverage.html
diff --git a/test_fms/interpolator/Makefile.am b/test_fms/interpolator/Makefile.am
index ee6c42a34c..f0977e0a44 100644
--- a/test_fms/interpolator/Makefile.am
+++ b/test_fms/interpolator/Makefile.am
@@ -41,4 +41,4 @@ TESTS = test_interpolator2.sh
 EXTRA_DIST = test_interpolator2.sh input_base.nml diag_table_base
 
 # Clean up
-CLEANFILES = input.nml diag_table
+CLEANFILES = input.nml diag_table *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/monin_obukhov/Makefile.am b/test_fms/monin_obukhov/Makefile.am
index bb7772d693..b36be75a96 100644
--- a/test_fms/monin_obukhov/Makefile.am
+++ b/test_fms/monin_obukhov/Makefile.am
@@ -41,4 +41,4 @@ TESTS = test_monin_obukhov2.sh
 EXTRA_DIST = input_base.nml test_monin_obukhov2.sh
 
 # Clean up
-CLEANFILES = input.nml *.out
+CLEANFILES = input.nml *.out *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/mosaic/Makefile.am b/test_fms/mosaic/Makefile.am
index c1c438d715..1a8c324a7f 100644
--- a/test_fms/mosaic/Makefile.am
+++ b/test_fms/mosaic/Makefile.am
@@ -41,4 +41,4 @@ TESTS = test_mosaic2.sh
 EXTRA_DIST = test_mosaic2.sh
 
 # Clean up
-CLEANFILES = input.nml *.nc *.out
+CLEANFILES = input.nml *.nc *.out *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/mpp/Makefile.am b/test_fms/mpp/Makefile.am
index 30ab2d93ae..249d168f3d 100644
--- a/test_fms/mpp/Makefile.am
+++ b/test_fms/mpp/Makefile.am
@@ -215,4 +215,4 @@ test_mpp_domains.$(OBJEXT): compare_data_checksums.mod test_domains_utility_mod.
 
 # Clean up
 CLEANFILES = input.nml input_alternative.nml input_blank.nml empty.nml *.out* *.tst* \
-  ascii* test_numb* *.mod
+  ascii* test_numb* *.mod *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/mpp_io/Makefile.am b/test_fms/mpp_io/Makefile.am
index 8ccae6dd0a..219691b519 100644
--- a/test_fms/mpp_io/Makefile.am
+++ b/test_fms/mpp_io/Makefile.am
@@ -47,4 +47,4 @@ TESTS = test_mpp_io2.sh \
 EXTRA_DIST = test_mpp_io2.sh test_io_R4_R8.sh test_io_mosaic_R4_R8.sh input_base.nml
 
 # Clean up
-CLEANFILES = input.nml *.nc* *.out
+CLEANFILES = input.nml *.nc* *.out *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/parser/Makefile.am b/test_fms/parser/Makefile.am
index 469538ce11..29139ba4a8 100644
--- a/test_fms/parser/Makefile.am
+++ b/test_fms/parser/Makefile.am
@@ -51,4 +51,4 @@ endif
 
 TESTS_ENVIRONMENT = parser_skip=${skipflag}
 # Clean up
-CLEANFILES = input.nml *.nc* *.out *.yaml
+CLEANFILES = input.nml *.nc* *.out *.yaml *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/time_interp/Makefile.am b/test_fms/time_interp/Makefile.am
index b657481532..e556a0ad16 100644
--- a/test_fms/time_interp/Makefile.am
+++ b/test_fms/time_interp/Makefile.am
@@ -42,4 +42,4 @@ TESTS = test_time_interp2.sh
 EXTRA_DIST = test_time_interp2.sh
 
 # Clean up
-CLEANFILES = input.nml *.out*
+CLEANFILES = input.nml *.out* *.dpi *.spi *.dyn *.spl
diff --git a/test_fms/time_manager/Makefile.am b/test_fms/time_manager/Makefile.am
index 61c2dc5aa8..a6cf0efb3a 100644
--- a/test_fms/time_manager/Makefile.am
+++ b/test_fms/time_manager/Makefile.am
@@ -41,4 +41,4 @@ TESTS = test_time_manager2.sh
 EXTRA_DIST = test_time_manager2.sh input_base.nml
 
 # Clean up
-CLEANFILES = input.nml *.out*
+CLEANFILES = input.nml *.out* *.dpi *.spi *.dyn *.spl