diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 0000000..f04e101
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,6 @@
+.env
+.gitlab_ci.yaml
+*.log
+*.md
+docker-compose.yml
+hooks
diff --git a/.gitignore b/.gitignore
index 67a0b70..0906a4f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,17 @@ libjigsaw64r.so
 # Misc
 sediments-us
 
+# Common test output files
+# (Test directories may also have their own .gitignore files)
+model/tests/ems_test.log
+model/tests/**/alert.*
+model/tests/**/core.*
+model/tests/**/diag.txt
+model/tests/**/in*.nc
+model/tests/**/loc*.ts
+model/tests/**/obc_spec.txt
+model/tests/**/out*.nc
+model/tests/**/runlog
+model/tests/**/setup.txt
+model/tests/**/out/*
+!model/tests/**/out/.empty
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..14f9871
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,69 @@
+#------------------------------------------------------------------------------
+# CSIRO EMS Image Build Script
+#------------------------------------------------------------------------------
+# The recommended base image is one of the onaci/ereefs-netcdf-base variants,
+# as those have been designed to include all the EMS dependencies.
+# Allow it to be overridden in order to choose *which* variant, or even
+# something completely different.
+ARG BASE_IMAGE="onaci/ereefs-netcdf-base:python-3.11-slim-bullseye"
+FROM ${BASE_IMAGE}
+
+# Record the actual base image used from the FROM command as a label.
+ARG BASE_IMAGE
+LABEL org.opencontainers.image.base.name=${BASE_IMAGE}
+
+# Enable Bash in RUN commands, and ensure that any commands with
+# pipes exit on the first failure.
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+# Prepare a base directory for all the EMS code
+ARG EMS_BASE="/usr/local/src/ems"
+ENV EMS_BASE="${EMS_BASE}"
+WORKDIR ${EMS_BASE}
+
+# Install all the EMS Source Code
+COPY ./ ./
+
+# Selectively remove some subdirectories that we want to omit
+# (List can be overridden by a build argument)
+ARG EMS_RM_DIRS=""
+RUN if [ -n "${EMS_RM_DIRS}" ]; then for d in $EMS_RM_DIRS; do rm -rf "${EMS_BASE}/${d}"; done; fi
+
+# Compile the EMS components
+# We build with OpenMP support by default for use in a docker container
+# Different options can be specified by overriding the EMS_CONFIGURE_OPTS build argument
+# (The base image *does* include NetCDF and HDF5 with Open MPI support, so that is an option)
+ENV EMS_BUILD_LOG="${EMS_BASE}/ems_build.log"
+ARG EMS_CONFIGURE_OPTS="--enable-omp"
+RUN make distclean || true \
+    && conf/configure ${EMS_CONFIGURE_OPTS} 2>&1 | tee -a "${EMS_BUILD_LOG}"
+RUN make clean \
+    && make 2>&1 | tee -a "${EMS_BUILD_LOG}"
+RUN make check install 2>&1 | tee -a "${EMS_BUILD_LOG}"
+
+# Symlink the EMS executable(s) into the default path
+# (This will fail if the executable did not build for some reason)
+ENV SHOC="${EMS_BASE}/model/hd/shoc" \
+    COMPAS="${EMS_BASE}/model/hd-us/compas"
+RUN if [ -n "${SHOC}" ]; then chmod 0755 "${SHOC}" && ln -s "${SHOC}" /usr/local/bin/shoc; fi; \
+    if [ -n "${COMPAS}" ]; then chmod 0755 "${COMPAS}" && ln -s "${COMPAS}" /usr/local/bin/compas; fi; \
+    ln -s "${EMS_BASE}/model/tests/run-tests.sh" /usr/local/bin/run-ems-tests
+
+# Optionally run all available unit tests
+# (Override the EMS_TEST_RUN build argument to have a value of 0 to skip testing at build time)
+ARG EMS_TEST_RUN=1
+ARG EMS_TEST_INCLUDE="${EMS_BASE}/model/tests"
+ENV EMS_TEST_INCLUDE="${EMS_TEST_INCLUDE}"
+ARG EMS_TEST_EXCLUDE=""
+ENV EMS_TEST_EXCLUDE="${EMS_TEST_EXCLUDE}"
+ENV EMS_TEST_LOG="${EMS_BASE}/model/tests/ems_test.log"
+RUN if [ $EMS_TEST_RUN -eq 1 ]; then run-ems-tests; fi
+
+# Encode EMS metadata in labels
+LABEL au.csiro.ems.base=${EMS_BASE} \
+      au.csiro.ems.shoc=${SHOC} \
+      au.csiro.ems.compas=${COMPAS}
+
+# Configure the default entrypoint to be a default EMS executable
+ENTRYPOINT ["/bin/bash", "-c" ]
+CMD [ "${SHOC:-$COMPAS}", "-v"]
diff --git a/docker-compose.test.yml b/docker-compose.test.yml
new file mode 100644
index 0000000..a357702
--- /dev/null
+++ b/docker-compose.test.yml
@@ -0,0 +1,22 @@
+---
+#-------------------------------------------------------------------------------
+# Docker *test* environment composition for EMS
+# This exists to support the autotest option for a Dockerhub repository build
+# (See: https://docs.docker.com/docker-hub/builds/automated-testing/)
+#
+# If this repository and rbanch are configured as Dockerhub autotest
+# repositories, this will automatically build and test EMS with all default
+# settings every time a push is made to the repository.
+#
+# The resulting image is not automatically pushed to the DockerHub registry
+# unless the same respository is automatically configured for autobuild.
+#-------------------------------------------------------------------------------
+version: "3.8"
+
+services:
+  ems:
+    build:
+      context: .
+      args:
+        EMS_TEST_RUN: 0
+    command: "run-ems-tests"
diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 0000000..8bdb97c
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,23 @@
+---
+#-------------------------------------------------------------------------------
+# Docker development environment composition for ems
+# (Not for production use!)
+#
+# This default compose stack is designed for use on a local development host.
+#-------------------------------------------------------------------------------
+version: "3.8"
+
+services:
+  ems:
+    build:
+      context: .
+      args:
+        #EMS_RM_DIRS: "ext/swan model/lib/da model/lib/exchange"
+        EMS_TEST_RUN: 0
+    command: "run-ems-tests"
+    container_name: ems
+    environment:
+      EMS_TEST_INCLUDE: '/usr/local/src/ems/model/tests'
+    image: onaci/ereefs-ems-shoc:dev
+    volumes:
+      - ./model/tests/:/usr/local/src/ems/model/tests/
diff --git a/hooks/README.md b/hooks/README.md
new file mode 100644
index 0000000..c084349
--- /dev/null
+++ b/hooks/README.md
@@ -0,0 +1,7 @@
+# csiro-coasts/EMS/hooks
+
+The files in this directory are custom build phase hooks for the automated dockerhub builder,
+and are used to set up custom build configurations and docker registry push options for when
+this repository is set up as a DockerHub repository with autobuild enabled.
+
+See <https://docs.docker.com/docker-hub/builds/advanced/#custom-build-phase-hooks> for more information about how they work.
diff --git a/hooks/build b/hooks/build
new file mode 100644
index 0000000..df195fa
--- /dev/null
+++ b/hooks/build
@@ -0,0 +1,62 @@
+#!/bin/bash
+
+# Derive useful variables from the dockerhub build environment
+BUILD_TIMESTAMP="$(date --rfc-3339=seconds)"
+DOCKER_TAG="${DOCKER_TAG:-}"
+DOCKERFILE_PATH="${DOCKERFILE_PATH:-./Dockerfile}"
+IMAGE_NAME="${IMAGE_NAME:-csiro-coasts/ems}"
+SAFE_TIMESTAMP="$(echo $BUILD_TIMESTAMP | sed 's/ /T/g' | sed 's/:/-/g' | sed 's/\+.*//')"
+SOURCE_URL="$(git remote get-url origin || true)"
+VERSION_TAG="${SOURCE_BRANCH}_v${SAFE_TIMESTAMP}-${SOURCE_COMMIT}"
+
+# Ensure we have values for all required build arguments.
+# These can be configured as environment variables on the dockerhub build,
+# but if they are not, then we parse the defaults out of the Dockerfile.
+BASE_IMAGE="${BASE_IMAGE:-}"
+if [ -z "${BASE_IMAGE:-}" ]; then
+    BASE_IMAGE=$(grep 'ARG BASE_IMAGE=' ./Dockerfile | tr '"' ' ' | tr '=' ' ' | awk '{print $3}')
+fi
+EMS_CONFIGURE_OPTS="${EMS_CONFIGURE_OPTS:-}"
+if [ -z "${EMS_CONFIGURE_OPTS:-}" ]; then
+    EMS_CONFIGURE_OPTS=$(grep 'ARG EMS_CONFIGURE_OPTS=' ./Dockerfile | tr '"' ' ' | tr '=' ' ' | awk '{print $3}')
+fi
+EMS_RM_DIRS="${EMS_RM_DIRS:-}"
+if [ -z "${EMS_RM_DIRS:-}" ]; then
+    EMS_RM_DIRS=$(grep 'ARG EMS_RM_DIRS=' ./Dockerfile | tr '"' ' ' | tr '=' ' ' | awk '{print $3}')
+fi
+EMS_TEST_RUN="${EMS_TEST_RUN:-}"
+if [ -z "${EMS_TEST_RUN:-}" ]; then
+    EMS_TEST_RUN=$(grep 'ARG EMS_TEST_RUN=' ./Dockerfile | tr '"' ' ' | tr '=' ' ' | awk '{print $3}')
+fi
+
+# Treat most DOCKER_TAG values as overrides for the
+# BASE_IMAGE variable sourced from the .env file
+if [[ -n "${DOCKER_TAG}" ]] && [[ "${DOCKER_TAG}" != "latest" ]] && [[ "${DOCKER_TAG}" != "${SOURCE_BRANCH}" ]]; then
+    # Assume the custom docker tag is an override for the tag part of
+    # the BASE_IMAGE configured in the Dockerfile and any .env file.
+    BASE_IMAGE="$(echo $BASE_IMAGE | sed -E 's/^([^:]*):.*$/\1/'):${DOCKER_TAG}"
+
+    # Override the VERSION_TAG to include it there too.
+    VERSION_TAG="${SOURCE_BRANCH}_${DOCKER_TAG}_v${SAFE_TIMESTAMP}-${SOURCE_COMMIT}"
+fi
+
+# Build our customised docker image
+docker build --pull \
+    --build-arg "BASE_IMAGE=${BASE_IMAGE}" \
+    --build-arg "EMS_CONFIGURE_OPTS=${EMS_CONFIGURE_OPTS}" \
+    --build-arg "EMS_RM_DIRS=${EMS_RM_DIRS}" \
+    --build-arg "EMS_TEST_RUN=${EMS_TEST_RUN}" \
+    --label "org.opencontainers.image.authors=${BUILD_AUTHORS:-CSIRO Coastal Group}" \
+    --label "org.opencontainers.image.branch=${SOURCE_BRANCH}" \
+    --label "org.opencontainers.image.buildhost=${DOCKER_REPO}" \
+    --label "org.opencontainers.image.created=${BUILD_TIMESTAMP}" \
+    --label "org.opencontainers.image.licenses=https://github.com/csiro-coasts/EMS/blob/master/LICENSE.md" \
+    --label "org.opencontainers.image.revision=${SOURCE_COMMIT}" \
+    --label "org.opencontainers.image.source=${SOURCE_URL}" \
+    --label "org.opencontainers.image.title=${DOCKER_REPO:-csiro-coasts/EMS}" \
+    --label "org.opencontainers.image.url=https://github.com/csiro-coasts/EMS" \
+    --label "org.opencontainers.image.vendor=CSIRO" \
+    --label "org.opencontainers.image.version=${VERSION_TAG}" \
+    -f ${DOCKERFILE_PATH} \
+    -t ${IMAGE_NAME} \
+    .
diff --git a/hooks/post_push b/hooks/post_push
new file mode 100644
index 0000000..4cd9186
--- /dev/null
+++ b/hooks/post_push
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+VERSION_TAG="$(docker image inspect  --format '{{ index .Config.Labels "org.opencontainers.image.version"}}' $IMAGE_NAME || true)"
+if [ -n "${VERSION_TAG}" ]; then
+    IMAGE_TAGGED="${DOCKER_REPO}:${VERSION_TAG}"
+    docker tag $IMAGE_NAME $IMAGE_TAGGED
+    docker push $IMAGE_TAGGED
+fi
diff --git a/model/tests/hd-us/.gitignore b/model/tests/hd-us/.gitignore
new file mode 100644
index 0000000..a42fa18
--- /dev/null
+++ b/model/tests/hd-us/.gitignore
@@ -0,0 +1,18 @@
+boundary.txt
+closed*.nc
+closed*.txt
+closed*.us
+est.nc
+est_hex*.txt
+est_hex*.us
+est_quad*.nc
+est_quad*.txt
+plot_*_hex.m
+in1*.txt
+in1*.us
+points.txt
+pt.nc
+s_*_quad.nc
+segment.txt
+test2*.txt
+totals.ts
diff --git a/model/tests/hd-us/cetas/.gitignore b/model/tests/hd-us/cetas/.gitignore
new file mode 100644
index 0000000..367e1dc
--- /dev/null
+++ b/model/tests/hd-us/cetas/.gitignore
@@ -0,0 +1,10 @@
+*.msh
+*.txt
+*.us
+*.jig
+*.site
+in.nc
+in.prm
+outputs/*
+!outputs/.empty
+plot_auto.m
diff --git a/model/tests/hd-us/cetas/run_cetas b/model/tests/hd-us/cetas/run_cetas
index 36baa61..120de9b 100755
--- a/model/tests/hd-us/cetas/run_cetas
+++ b/model/tests/hd-us/cetas/run_cetas
@@ -1,15 +1,19 @@
-#!/bin/csh -f
+#!/bin/csh -exf
 
 echo "Testing COMPAS cetas..."
-rm *.msh
-rm *.txt
-rm *.us
-rm *.jig
-rm *.site
-rm in.nc
 
-../compas -ag auto.prm
+if (! $?COMPAS || "$COMPAS" == "") then
+    set COMPAS='../compas'
+endif
 
-echo "DONE"
+set nonomatch
+rm -f *.msh
+rm -f *.txt
+rm -f *.us
+rm -f *.jig
+rm -f *.site
+rm -f in.nc
 
+$COMPAS -ag auto.prm
 
+echo "DONE"
diff --git a/model/tests/hd-us/closed/run_closed b/model/tests/hd-us/closed/run_closed
index 48fd897..8d4cc86 100755
--- a/model/tests/hd-us/closed/run_closed
+++ b/model/tests/hd-us/closed/run_closed
@@ -1,8 +1,13 @@
 #!/bin/csh -ef
 
-# Set relative path to compas executable
-set COMPAS='../../../hd-us/compas'
-set SHOC='../../../hd/shoc'
+if (! $?COMPAS || "$COMPAS" == "") then
+    # Set relative path to compas executable
+    set COMPAS='../../../hd-us/compas'
+endif
+if (! $?SHOC || "$SHOC" == "") then
+    # Set relative path to shoc executable
+    set SHOC='../../../hd/shoc'
+endif
 
 echo "Testing SHOC..."
 rm -f closed.nc || true
@@ -14,7 +19,7 @@ if (-f $SHOC) then
 else
     echo "SHOC not found, skipping ..."
 endif
-    
+
 echo "DONE"
 
 echo "Testing COMPAS quad..."
@@ -42,6 +47,3 @@ $COMPAS -g closed_hex.prm closed_hex.nc
 $COMPAS -p closed_hex.prm
 
 echo "DONE"
-
-
-
diff --git a/model/tests/hd-us/est/run_est b/model/tests/hd-us/est/run_est
index 00aded8..c61eeff 100755
--- a/model/tests/hd-us/est/run_est
+++ b/model/tests/hd-us/est/run_est
@@ -1,47 +1,55 @@
-#!/bin/csh -f
+#!/bin/csh -ef
+
+if (! $?SHOC || "$SHOC" == "") then
+    set SHOC='../shoc'
+endif
+
+if (! $?COMPAS || "$COMPAS" == "") then
+    set COMPAS='../compas'
+endif
+
 
 echo "Testing SHOC..."
-rm est.nc
-rm out1.nc
+rm -f est.nc
+rm -f out1.nc
 
-../shoc -g est.prm est.nc
+$SHOC -g est.prm est.nc
 
-../shoc -p est.prm
+$SHOC -p est.prm
 
 echo "DONE"
 
 echo "Testing COMPAS quad..."
-rm est_quad.nc
-rm out1_quad.nc
+rm -f est_quad.nc
+rm -f out1_quad.nc
+rm -f s_est_quad.nc
 
-../compas -g est_quad.prm est_quad.nc
+$COMPAS -g est_quad.prm est_quad.nc
 
-../compas -p est_quad.prm
+$COMPAS -p est_quad.prm
 
 echo "DONE"
 
 echo "Testing COMPAS quad 5 window..."
-rm out1_quad5w.nc
+rm -f out1_quad5w.nc
 
-../compas -p est_quad5w.prm
+$COMPAS -p est_quad5w.prm
 
 echo "DONE"
 
 echo "Testing COMPAS hex..."
-rm est_hex.nc
-rm out1_hex.nc
+rm -f est_hex.nc
+rm -f out1_hex.nc
 
-../compas -g est_hex.prm est_hex.nc
+$COMPAS -g est_hex.prm est_hex.nc
 
-../compas -p est_hex.prm
+$COMPAS -p est_hex.prm
 
 echo "DONE"
 
 echo "Testing COMPAS hex 5 window..."
-rm out1_hex5w.nc
+rm -f out1_hex5w.nc
 
-../compas -p est_hex5w.prm
+$COMPAS -p est_hex5w.prm
 
 echo "DONE"
-
-
diff --git a/model/tests/hd-us/test2/closed/run_closed b/model/tests/hd-us/test2/closed/run_closed
index 96a47e5..f29b010 100755
--- a/model/tests/hd-us/test2/closed/run_closed
+++ b/model/tests/hd-us/test2/closed/run_closed
@@ -1,46 +1,55 @@
-#!/bin/csh -f
+#!/bin/csh -ef
+
+if (! $?SHOC || "$SHOC" == "") then
+    set SHOC='../../shoc'
+endif
+
+if (! $?COMPAS || "$COMPAS" == "") then
+    set COMPAS='../../compas'
+endif
 
 echo "Testing SHOC..."
-rm in1.nc
-rm out1.nc
+rm -f in1.nc
+rm -f out1.nc
 
-../../shoc -g test2.prm in1.nc
+$SHOC -g test2.prm in1.nc
 
-../../shoc -p test2.prm
+$SHOC -p test2.prm
 
 echo "DONE"
 
 echo "Testing COMPAS quad..."
-rm in1_quad.nc
-rm s_in1_quad.nc
-rm out1_quad.nc
+rm -f in1_quad.nc
+rm -f s_in1_quad.nc
+rm -f out1_quad.nc
 
-../../compas -g test2_quad.prm in1_quad.nc
+$COMPAS -g test2_quad.prm in1_quad.nc
 
-../../compas -p test2_quad.prm
+$COMPAS -p test2_quad.prm
 
 echo "DONE"
 
 echo "Testing COMPAS quad 2 window..."
-rm out1_quad2w.nc
-rm win2.nc
+rm -f out1_quad2w.nc
+rm -f win2.nc
 
-../../compas -p test2_quad2w.prm
+$COMPAS -p test2_quad2w.prm
 
 echo "DONE"
 
 echo "Testing COMPAS hex..."
-rm in1_hex.nc
-rm out1_hex.nc
+rm -f in1_hex.nc
+rm -f out1_hex.nc
 
-../../compas -g test2_hex.prm in1_hex.nc
+$COMPAS -g test2_hex.prm in1_hex.nc
 
-../../compas -p test2_hex.prm
+$COMPAS -p test2_hex.prm
 
 echo "DONE"
 
 echo "Testing COMPAS hex 2 window..."
-rm out1_hex2w.nc
+rm -f out1_hex2w.nc
 
-../../compas -p test2_hex2w.prm
+$COMPAS -p test2_hex2w.prm
 
+echo "DONE"
diff --git a/model/tests/hd-us/test2/open/run_open b/model/tests/hd-us/test2/open/run_open
index ae7847b..52086a9 100755
--- a/model/tests/hd-us/test2/open/run_open
+++ b/model/tests/hd-us/test2/open/run_open
@@ -1,41 +1,47 @@
-#!/bin/csh -f
+#!/bin/csh -ef
+
+if (! $?SHOC || "$SHOC" == "") then
+    set SHOC='../shoc'
+endif
+
+if (! $?COMPAS || "$COMPAS" == "") then
+    set COMPAS='../compas'
+endif
 
 echo "Testing SHOC..."
-rm in1.nc
-rm out1.nc
+rm -f in1.nc
+rm -f out1.nc
 
-../../shoc -g test2.prm in1.nc
+$SHOC -g test2.prm in1.nc
 
-../../shoc -p test2.prm
+$SHOC -p test2.prm
 
 echo "DONE"
 
 echo "Testing COMPAS quad..."
-rm in1_quad.nc
-rm s_in1_quad.nc
-rm out1_quad.nc
+rm -f in1_quad.nc
+rm -f s_in1_quad.nc
+rm -f out1_quad.nc
 
-../../compas -g test2_quad.prm in1_quad.nc
+$COMPAS -g test2_quad.prm in1_quad.nc
 
-../../compas -p test2_quad.prm
+$COMPAS -p test2_quad.prm
 
 echo "DONE"
 
 echo "Testing COMPAS quad 2 window..."
-rm out1_quad2w.nc
+rm -f out1_quad2w.nc
 
-../../compas -p test2_quad2w.prm
+$COMPAS -p test2_quad2w.prm
 
 echo "DONE"
 
 echo "Testing COMPAS hex..."
-rm in1_hex.nc
-rm out1_hex.nc
+rm -f in1_hex.nc
+rm -f out1_hex.nc
 
-../../compas -g test2_hex.prm in1_hex.nc
+$COMPAS -g test2_hex.prm in1_hex.nc
 
-../../compas -p test2_hex.prm
+$COMPAS -p test2_hex.prm
 
 echo "DONE"
-
-
diff --git a/model/tests/hd/.gitignore b/model/tests/hd/.gitignore
new file mode 100644
index 0000000..d9494a2
--- /dev/null
+++ b/model/tests/hd/.gitignore
@@ -0,0 +1,5 @@
+
+flushing.ts
+test7*_sed.prm
+totals*.ts
+zoom.points
diff --git a/model/tests/hd/test1/run_test1 b/model/tests/hd/test1/run_test1
index fedc91d..b653450 100755
--- a/model/tests/hd/test1/run_test1
+++ b/model/tests/hd/test1/run_test1
@@ -1,7 +1,9 @@
 #!/bin/csh -ef
 
-# Set relative path to shoc executable
-set SHOC='../../../hd/shoc'
+if (! $?SHOC || "$SHOC" == "") then
+    # Set relative path to shoc executable
+    set SHOC='../../../hd/shoc'
+endif
 
 echo "Testing 'z' model..."
 rm -f in1.nc || true
diff --git a/model/tests/hd/test2/run_test2 b/model/tests/hd/test2/run_test2
index d03f54b..0f7ed33 100755
--- a/model/tests/hd/test2/run_test2
+++ b/model/tests/hd/test2/run_test2
@@ -1,7 +1,9 @@
 #!/bin/csh -ef
 
-# Set relative path to shoc executable
-set SHOC='../../../hd/shoc'
+if (! $?SHOC || "$SHOC" == "") then
+    # Set relative path to shoc executable
+    set SHOC='../../../hd/shoc'
+endif
 
 echo "Testing 'z' model..."
 rm -f in2.nc || true
diff --git a/model/tests/hd/test3/run_test3 b/model/tests/hd/test3/run_test3
index 9b6ce43..b8ca014 100755
--- a/model/tests/hd/test3/run_test3
+++ b/model/tests/hd/test3/run_test3
@@ -1,7 +1,9 @@
 #!/bin/csh -ef
 
-# Set relative path to shoc executable
-set SHOC='../../../hd/shoc'
+if (! $?SHOC || "$SHOC" == "") then
+    # Set relative path to shoc executable
+    set SHOC='../../../hd/shoc'
+endif
 
 echo "Testing 'z' model..."
 rm -f in3.nc || true
diff --git a/model/tests/hd/test4/run_test4 b/model/tests/hd/test4/run_test4
index 377c3ec..7a369ea 100755
--- a/model/tests/hd/test4/run_test4
+++ b/model/tests/hd/test4/run_test4
@@ -1,7 +1,9 @@
 #!/bin/csh -ef
 
-# Set relative path to shoc executable
-set SHOC='../../../hd/shoc'
+if (! $?SHOC || "$SHOC" == "") then
+    # Set relative path to shoc executable
+    set SHOC='../../../hd/shoc'
+endif
 
 echo "Testing 'z' model..."
 rm -f in4.nc || true
diff --git a/model/tests/hd/test5/run_test5 b/model/tests/hd/test5/run_test5
index 0be889c..e8bb243 100755
--- a/model/tests/hd/test5/run_test5
+++ b/model/tests/hd/test5/run_test5
@@ -1,7 +1,9 @@
 #!/bin/csh -ef
 
-# Set relative path to shoc executable
-set SHOC='../../../hd/shoc'
+if (! $?SHOC || "$SHOC" == "") then
+    # Set relative path to shoc executable
+    set SHOC='../../../hd/shoc'
+endif
 
 echo "Testing 'z' model..."
 rm -f in5.nc || true
diff --git a/model/tests/hd/test6/run_test6 b/model/tests/hd/test6/run_test6
index bff17c0..7dbe63c 100755
--- a/model/tests/hd/test6/run_test6
+++ b/model/tests/hd/test6/run_test6
@@ -1,7 +1,9 @@
 #!/bin/csh -ef
 
-# Set relative path to shoc executable
-set SHOC='../../../hd/shoc'
+if (! $?SHOC || "$SHOC" == "") then
+    # Set relative path to shoc executable
+    set SHOC='../../../hd/shoc'
+endif
 
 echo "Testing 'z' model..."
 rm -f in6.nc || true
diff --git a/model/tests/hd/test7/run_test7 b/model/tests/hd/test7/run_test7
index c1ab1ac..6099b77 100755
--- a/model/tests/hd/test7/run_test7
+++ b/model/tests/hd/test7/run_test7
@@ -1,7 +1,9 @@
 #!/bin/csh -ef
 
-# Set relative path to shoc executable
-set SHOC='../../../hd/shoc'
+if (! $?SHOC || "$SHOC" == "") then
+    # Set relative path to shoc executable
+    set SHOC='../../../hd/shoc'
+endif
 
 echo "Testing 'z' model..."
 rm -f in7.nc || true
diff --git a/model/tests/hd/test7/test7_sed.prm b/model/tests/hd/test7/test7_sed.prm
index 97e0974..4c19750 100644
--- a/model/tests/hd/test7/test7_sed.prm
+++ b/model/tests/hd/test7/test7_sed.prm
@@ -1,16 +1,16 @@
-# Test 7 of model shoc: 50 by 27 by 24 closed basin with sloping 
-# bottom (southern hemisphere) is forced with wind stress in the 
+# Test 7 of model shoc: 50 by 27 by 24 closed basin with sloping
+# bottom (southern hemisphere) is forced with wind stress in the
 # e1 ditrection having positive curl. Anti-cyclonic circulation
 # is set up due to topographically induced conservation of potential
 # vorticity, where the centre of the gyre biased to the west.
-# Conservation of potential vorticity theory (e.g. Herzfeld & Tomczak 
+# Conservation of potential vorticity theory (e.g. Herzfeld & Tomczak
 # (1999), Aust. J. Marine Freshw. Res., 50, 613 - 627.) predicts that :
 # A poitive gradient of f/H (f < 0) results in an eastward biased gyre.
 # A poitive gradient of f/H (f > 0) results in an westward biased gyre.
 # Constant depth (BATHYMAX = 50) results in a gyre with no bias.
 # A change in sign of the wind curl (WIND_SPEED_SCALE = -1.0) results
 # in a cyclonic gyre with no change to the bias.
-   
+
 CODEHEADER           SHOC default version : leapfrog
 PARAMETERHEADER      Test 7 - closed basin with +ve wind curl
 DESCRIPTION          SHOC test 7
@@ -47,7 +47,7 @@ RAMPSTART            0 days
 RAMPEND              1 days
 MERGE_THIN           YES
 HMIN                 0.1400
-SLIP                 1.0   
+SLIP                 1.0
 SIGMA                NO
 COMPATIBLE           V4201
 
@@ -97,50 +97,50 @@ ALERT      	     NONE
 MOM_TEND	     YES
 CALC_FLUXES          NONE
 FLUSHING_TR          NO
-STERIC_HEIGHT        0.00  
+STERIC_HEIGHT        0.00
 TOTALS               YES Sand Silt Fine tss
 
 # Grid
 GRIDTYPE             GEOGRAPHIC_RECTANGULAR
 NCE1                 50
 NCE2                 27
-X00                  0.00000 
-Y00                  0.00000 
+X00                  0.00000
+Y00                  0.00000
 DX                   25000.000
 DY                   25000.000
-ROTATION             0.0   
+ROTATION             0.0
 
 # Vertical grid spacing
 LAYERFACES           24
--110.00 
--105.00 
--100.00 
--95.00  
--90.00  
--85.00  
--80.00  
--75.00  
--70.00  
--65.00  
--60.00  
--55.00  
--50.00  
--45.00  
--40.00  
--35.00  
--30.00  
--25.00  
--20.00  
--15.00  
--10.00  
--5.00   
--2.00   
-0.00    
+-110.00
+-105.00
+-100.00
+-95.00
+-90.00
+-85.00
+-80.00
+-75.00
+-70.00
+-65.00
+-60.00
+-55.00
+-50.00
+-45.00
+-40.00
+-35.00
+-30.00
+-25.00
+-20.00
+-15.00
+-10.00
+-5.00
+-2.00
+0.00
 
 # Bathymetry limits
-BATHYMIN             50.0  
-BATHYMAX             120.0 
-ETAMAX               10.0  
+BATHYMIN             50.0
+BATHYMAX             120.0
+ETAMAX               10.0
 MIN_CELL_THICKNESS   25%
 
 # Tracers
@@ -150,8 +150,8 @@ TRACER0.name         salt
 TRACER0.long_name    Salinity
 TRACER0.type         WATER SEDIMENT
 TRACER0.units        PSU
-TRACER0.fill_value   35.0  
-TRACER0.valid_range  0.0    40.0  
+TRACER0.fill_value   35.0
+TRACER0.valid_range  0.0    40.0
 TRACER0.advect       1
 TRACER0.diffuse      1
 TRACER0.diagn        0
@@ -161,8 +161,8 @@ TRACER1.name         temp
 TRACER1.long_name    Temperature
 TRACER1.type         WATER SEDIMENT
 TRACER1.units        degrees C
-TRACER1.fill_value   20.0  
-TRACER1.valid_range  0.0    40.0  
+TRACER1.fill_value   20.0
+TRACER1.valid_range  0.0    40.0
 TRACER1.advect       1
 TRACER1.diffuse      1
 TRACER1.diagn        0
@@ -277,7 +277,7 @@ TRACER5.cohesive        0
 TRACER6.name            depth_sed
 TRACER6.long_name       depth_sed
 TRACER6.type            BENTHIC
-TRACER6.units 
+TRACER6.units
 TRACER6.fill_value_wc   0.0
 TRACER6.fill_value_sed  0.0
 TRACER6.valid_range_wc  0 10
@@ -302,7 +302,7 @@ TRACER6.cohesive        0
 TRACER7.name            ustrcw_skin
 TRACER7.long_name       ustrcw_skin
 TRACER7.type            BENTHIC
-TRACER7.units 
+TRACER7.units
 TRACER7.fill_value_wc   0.0
 TRACER7.fill_value_sed  0.0
 TRACER7.valid_range_wc  0 30
@@ -327,11 +327,11 @@ TRACER7.cohesive        0
 # Forcing
 WIND_TS              wind_test7.nc
 WIND_INPUT_DT        10   days
-WIND_SPEED_SCALE     1.0   
-DRAG_LAW_V0          10.0  
-DRAG_LAW_V1          26.0  
-DRAG_LAW_CD0         0.00114 
-DRAG_LAW_CD1         0.00218 
+WIND_SPEED_SCALE     1.0
+DRAG_LAW_V0          10.0
+DRAG_LAW_V1          26.0
+DRAG_LAW_CD0         0.00114
+DRAG_LAW_CD1         0.00218
 
 # Time series
 TSPOINTS             1
@@ -385,7 +385,7 @@ CSS_ER            0.2
 
 # FLOCCULATION
 # Modes: FLOC0, FLOC1
-# Default: FLOC0 - no flocculation 
+# Default: FLOC0 - no flocculation
 FLOC_MODE        FLOC0
 FLOC_PRM1  0.01
 FLOC_PRM2  3
@@ -1800,5 +1800,5 @@ BATHY    1350
 
 
 ID_CODE SHOC grid|G1.0|H1.0|S|B
-�U
+�U
 |B0.00
diff --git a/model/tests/hd/test8/run_test8 b/model/tests/hd/test8/run_test8
index fd999be..e09177b 100755
--- a/model/tests/hd/test8/run_test8
+++ b/model/tests/hd/test8/run_test8
@@ -1,7 +1,9 @@
 #!/bin/csh -ef
 
-# Set relative path to shoc executable
-set SHOC='../../../hd/shoc'
+if (! $?SHOC || "$SHOC" == "") then
+    # Set relative path to shoc executable
+    set SHOC='../../../hd/shoc'
+endif
 
 echo "Testing 'z' model..."
 rm -f in8.nc || true
diff --git a/model/tests/run-tests.sh b/model/tests/run-tests.sh
new file mode 100755
index 0000000..675e944
--- /dev/null
+++ b/model/tests/run-tests.sh
@@ -0,0 +1,103 @@
+#!/bin/bash
+#
+# Runs the EMS test suite(s)
+#
+
+# Don't exit for errors: we will handle (and count) those.
+set +e
+
+# Send all output to a logfile as well as stdout / stderr
+EMS_TEST_LOG="${EMS_TEST_LOG:-ems_test.log}"
+if [ -f "${EMS_TEST_LOG}" ]; then
+    truncate -s 0 "${EMS_TEST_LOG}"
+fi
+exec > >(tee -a "${EMS_TEST_LOG}")
+exec 2> >(tee -a "${EMS_TEST_LOG}" >&2)
+
+# Dump some useful information about the test environment
+# (note: some of these vars are set by the base image)
+echo "Testing EMS at $(date --rfc-3339=seconds)"
+echo
+echo "SHOC = '${SHOC}' => '$(which shoc)'"
+echo "COMPAS = '${COMPAS}' => '$(which compas)'"
+echo
+echo "CURL_VERSION = '${CURL_VERSION:-}', curl binary = '$(which curl)' => $(curl --version | head -n 1)"
+echo "DAP_VERSION = '${DAP_VERSION:-}', getdap4 binary = '$(which getdap4)' => $(getdap4 -V 2>&1)"
+echo "GDAL_VERSION = '${GDAL_VERSION:-}', gdalinfo binary = '$(which gdalinfo)', => $(gdalinfo --version 2>&1)"
+echo "HDF5_VERSION = '${HDF5_VERSION:-}', h5dump binary = '$(which h5dump)' => $(h5dump --version)"
+echo "NETCDF_VERSION = '${NETCDF_VERSION:-}', ncdump binary = '$(which ncdump)' => $(ncdump 2>&1 | tail -n 1)"
+echo "NCO_VERSION = '${NCO_VERSION:-}', ncks binary = '$(which ncks)' => $(ncks --version 2>&1 | xargs)"
+echo "PROJ_VERSION = '${PROJ_VERSION:-}', proj binary = '$(which proj)' => $(proj 2>&1 | head -n 1)"
+echo
+
+# Initialise vars to hold test result statistics
+FAIL_LIST=""
+FAIL_COUNT=0
+SUCCESS_LIST=""
+SUCCESS_COUNT=0
+TEST_COUNT=0
+
+# Parse the include and exclude variables used to select target tests
+EMS_TEST_INCLUDE="${EMS_TEST_INCLUDE:-${EMS_BASE}/model/tests}"
+echo "EMS_TEST_INCLUDE = '${EMS_TEST_INCLUDE}'"
+
+EMS_TEST_EXCLUDE="${EMS_TEST_EXCLUDE:-} ${EMS_BASE}/model/tests/run-tests.sh '${EMS_BASE}/model/tests/hd/run_tests'"
+if [ ! -f "${COMPAS}" ]; then
+    # Valid scenario: skip the COMPAS tests
+    EMS_TEST_EXCLUDE="${EMS_TEST_EXCLUDE} '${EMS_BASE}/model/tests/hd-us/*'"
+else
+    EMS_TEST_EXCLUDE="${EMS_TEST_EXCLUDE} '${EMS_BASE}/model/tests/hd-us/run_tests'"
+fi
+echo "EMS_TEST_EXCLUDE = '${EMS_TEST_EXCLUDE}'"
+
+
+for ti in $EMS_TEST_INCLUDE; do
+    FIND_CMD="find ${ti} -type f \( -regex '^.*/run_test[0-9]*$' -o -name 'run_all.sh' -o -regex '^.*/run_[^\.]*$' \) ! -iname '.*'"
+    for te in $EMS_TEST_EXCLUDE; do
+        FIND_CMD="${FIND_CMD} ! -path ${te}"
+    done
+    echo "FIND_CMD = '${FIND_CMD}'"
+    TEST_FILES=$(eval "${FIND_CMD}")
+    if [ -z "${TEST_FILES}" ]; then
+        echo "There are no test files to run below include path '${ti}'"
+    else
+        echo "Test files to run below include path '${ti}':"
+        echo "${TEST_FILES}"
+        for tf in $TEST_FILES; do
+            chmod 0755 "${tf}"
+            cd $(dirname "${tf}")
+            echo
+            echo "#-----------------------------------------------------"
+            echo "# Running test file '${tf}'"
+            echo "# CWD = '$(pwd)'"
+            echo "#-----------------------------------------------------"
+            ${tf}
+            TEST_RESULT=$?
+            echo "#......................................................"
+            if [ $TEST_RESULT -eq 0 ]; then
+                echo "exitcode: ${TEST_RESULT} => Test SUCCEEDED"
+                SUCCESS_LIST="${SUCCESS_LIST} ${tf}"
+                SUCCESS_COUNT=$((SUCCESS_COUNT+1))
+            else
+                echo "exitcode: ${TEST_RESULT} => Test FAILED"
+                FAIL_LIST="${FAIL_LIST} ${tf}"
+                FAIL_COUNT=$((FAIL_COUNT+1))
+            fi
+            TEST_COUNT=$((TEST_COUNT+1))
+        done
+    fi
+done
+
+echo
+echo "#-----------------------------------------------------"
+echo
+echo "${SUCCESS_COUNT} of ${TEST_COUNT} tests passed:"
+echo "${SUCCESS_LIST}" | tr ' ' '\n'
+echo
+echo "${FAIL_COUNT} of ${TEST_COUNT} tests failed:"
+echo "${FAIL_LIST}" | tr ' ' '\n'
+if [ $TEST_COUNT -eq 0 ]; then
+    exit -1
+else
+    exit $FAIL_COUNT
+fi
diff --git a/model/tests/sediments/.gitignore b/model/tests/sediments/.gitignore
new file mode 100644
index 0000000..785f762
--- /dev/null
+++ b/model/tests/sediments/.gitignore
@@ -0,0 +1,4 @@
+test_trans*.nc
+sed_mass*.txt
+sedlog.txt
+trans.mnc
diff --git a/model/tests/sediments/test1/inputs/test_d.tran b/model/tests/sediments/test1/inputs/test_d.tran
index f678fdb..4c1e8e5 100644
--- a/model/tests/sediments/test1/inputs/test_d.tran
+++ b/model/tests/sediments/test1/inputs/test_d.tran
@@ -313,3 +313,5 @@ TS0.reference        msl
 # Open boundaries
 NBOUNDARIES           0
 
+
+ID_CODE SHOC grid|G1.0|H|S|B
diff --git a/model/tests/sediments/test1/run.sh b/model/tests/sediments/test1/run.sh
index 2f80ad6..80f38f6 100755
--- a/model/tests/sediments/test1/run.sh
+++ b/model/tests/sediments/test1/run.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 
 if [ $# == 0 ] 
 then
@@ -24,26 +24,29 @@ else
    echo "run './run.sh' for info"
 fi
 
+SHOC="${SHOC:-./shoc}"
+mkdir -p outputs tran_outputs
+
 if [ $# == 1 ] 
 then
    echo "Cleaning up"
-   rm outputs/*
-   rm tran_outputs/*
-   rm inputs/in_test.nc
-   rm inputs/test_trans_1990-01.nc
-   rm diag.txt runlog mass.txt sedlog.txt setup.txt trans.mnc sed_mass_*.txt
+   rm -f outputs/*
+   rm -f tran_outputs/*
+   rm -f inputs/in_test.nc
+   rm -f inputs/test_trans_1990-01.nc
+   rm -f diag.txt runlog mass.txt sedlog.txt setup.txt trans.mnc sed_mass_*.txt
    echo "Running $1: hd first and then sediment transport"
-  ./shoc -g inputs/test.prm inputs/in_test.nc
-  ./shoc -p inputs/test.prm
-  ./shoc -t inputs/$1.tran
+   $SHOC -g inputs/test.prm inputs/in_test.nc
+   $SHOC -p inputs/test.prm
+   $SHOC -t inputs/$1.tran
 fi
 
 if [ $# == 2 ] 
 then
    echo "Running $1: only sediment transport"
-   rm tran_outputs/*
-   rm mass.txt sedlog.txt sed_mass_*.txt
-  ./shoc -t inputs/$1.tran
+   rm -f tran_outputs/*
+   rm -f mass.txt sedlog.txt sed_mass_*.txt
+   $SHOC -t inputs/$1.tran
 fi
 
 # post-processing
@@ -51,4 +54,3 @@ cat ./vars sed_mass_end.txt > mass.txt
 rm sed_mass_*.txt
 #python plot.py
 echo "Done"
-
diff --git a/model/tests/sediments/test1/run_all.sh b/model/tests/sediments/test1/run_all.sh
index 8c09273..2695749 100755
--- a/model/tests/sediments/test1/run_all.sh
+++ b/model/tests/sediments/test1/run_all.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 
 if [ $# == 1 ] 
 then
@@ -14,31 +14,34 @@ else
   echo ""
 fi
   
+SHOC="${SHOC:-./shoc}"
+mkdir -p outputs tran_outputs
+
 echo "Cleaning up"
-rm outputs/*
-rm tran_outputs/*
-rm inputs/in_test.nc
-rm inputs/test_trans_1990-01.nc
-rm diag.txt runlog mass.txt sedlog.txt setup.txt trans.mnc sed_mass_*.txt
+rm -f outputs/*
+rm -f tran_outputs/*
+rm -f inputs/in_test.nc
+rm -f inputs/test_trans_1990-01.nc
+rm -f diag.txt runlog mass.txt sedlog.txt setup.txt trans.mnc sed_mass_*.txt
 echo ""
 
 echo "Running hd"
-./shoc -g inputs/test.prm inputs/in_test.nc
-./shoc -p inputs/test.prm
+$SHOC -g inputs/test.prm inputs/in_test.nc
+$SHOC -p inputs/test.prm
 echo "OK: HD forcing files complete"
 echo ""
 
 echo "Running Diffusion test"
-./shoc -t inputs/test_d.tran
+$SHOC -t inputs/test_d.tran
 awk 'BEGIN{a=0;} {if ($NR eq 3) a=$4;} END{if((a-$4)<0.1) \
 print("OK: mass conservation of dissolved tracer"); \
 else print("ERROR: mass conservation of dissolved tracer");}' sed_mass_end.txt
 echo ""
 
 echo "Running Resuspension test"
-rm tran_outputs/*   
-rm sedlog.txt sed_mass_*.txt
-./shoc -t inputs/test_r.tran
+rm -f tran_outputs/*   
+rm -f sedlog.txt sed_mass_*.txt
+$SHOC -t inputs/test_r.tran
 awk 'BEGIN{a=0;} {if ($NR eq 3) a=$5;} END{if((a-$5)<0.1) \
 print("OK: mass conservation of gravel"); \
 else print("ERROR: mass conservation of gravel");}' sed_mass_end.txt
@@ -51,9 +54,9 @@ else print("ERROR: mass conservationof mud");}' sed_mass_end.txt
 echo ""
 
 echo "Running Compaction test"
-rm tran_outputs/*   
-rm sedlog.txt sed_mass_*.txt
-./shoc -t inputs/test_c.tran
+rm -f tran_outputs/*   
+rm -f sedlog.txt sed_mass_*.txt
+$SHOC -t inputs/test_c.tran
 awk 'BEGIN{a=0;} {if ($NR eq 3) a=$4;} END{if((a-$4)<0.1) \
 print("OK: mass conservation of dissolved tracer"); \
 else print("ERROR: mass conservation of dissolved tracer");}' sed_mass_end.txt
@@ -63,18 +66,18 @@ else print("ERROR: mass conservation of mud");}' sed_mass_end.txt
 echo ""
 
 echo "Running Desorption of Pollutant test"
-rm tran_outputs/*   
-rm sedlog.txt sed_mass_*.txt
-./shoc -t inputs/test_p.tran
+rm -f tran_outputs/*   
+rm -f sedlog.txt sed_mass_*.txt
+$SHOC -t inputs/test_p.tran
 awk 'BEGIN{a=0;} {if ($NR eq 3) a=$4+$8;} END{if((a-$4-$8)<0.1) \
 print("OK: mass conservation of pollutant"); \
 else print("ERROR: mass conservation of pollutant");}' sed_mass_end.txt
 echo ""
 
 echo "Running Resuspension, Diffusion and Compaction together"
-rm tran_outputs/*
-rm sedlog.txt sed_mass_*.txt
-./shoc -t inputs/test_rcd.tran
+rm -f tran_outputs/*
+rm -f sedlog.txt sed_mass_*.txt
+$SHOC -t inputs/test_rcd.tran
 awk 'BEGIN{a=0;} {if ($NR eq 3) a=$4;} END{if((a-$4)<0.1) \
 print("OK: mass conservation of dissolved tracer"); \
 else print("ERROR: mass conservation of dissolved tracer");}' sed_mass_end.txt
diff --git a/model/tests/sediments/test2/inputs/test_flat.tran b/model/tests/sediments/test2/inputs/test_flat.tran
index b24c8cf..096f973 100644
--- a/model/tests/sediments/test2/inputs/test_flat.tran
+++ b/model/tests/sediments/test2/inputs/test_flat.tran
@@ -311,3 +311,6 @@ TS0.reference        msl
 # Open boundaries
 NBOUNDARIES           0
 
+
+ID_CODE SHOC grid|G1.0|H|S|B
+
diff --git a/model/tests/sediments/test2/run.sh b/model/tests/sediments/test2/run.sh
index 1ddbafd..44234bc 100755
--- a/model/tests/sediments/test2/run.sh
+++ b/model/tests/sediments/test2/run.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 
 if [ $# == 0 ] 
 then
@@ -16,26 +16,29 @@ else
    echo "run './run.sh' for info"
 fi
 
+SHOC="${SHOC:-./shoc}"
+mkdir -p outputs tran_outputs
+
 if [ $# == 1 ] 
 then
    echo "Cleaning up"
-   rm outputs/*
-   rm tran_outputs/*
-   rm inputs/in_test.nc
-   rm inputs/test_trans_1990-01.nc
-   rm diag.txt runlog mass.txt sedlog.txt setup.txt trans.mnc sed_mass_*.txt
+   rm -f outputs/*
+   rm -f tran_outputs/*
+   rm -f inputs/in_test.nc
+   rm -f inputs/test_trans_1990-01.nc
+   rm -f diag.txt runlog mass.txt sedlog.txt setup.txt trans.mnc sed_mass_*.txt
    echo "Running $1: hd first and then sediment transport"
-  ./shoc -g inputs/test.prm inputs/in_test.nc
-  ./shoc -p inputs/test.prm
-  ./shoc -t inputs/$1.tran
+   $SHOC -g inputs/test.prm inputs/in_test.nc
+   $SHOC -p inputs/test.prm
+   $SHOC -t inputs/$1.tran
 fi
 
 if [ $# == 2 ] 
 then
    echo "Running $1: only sediment transport"
-   rm tran_outputs/*
-   rm mass.txt sedlog.txt sed_mass_*.txt
-  ./shoc -t inputs/$1.tran
+   rm -f tran_outputs/*
+   rm -f mass.txt sedlog.txt sed_mass_*.txt
+   $SHOC -t inputs/$1.tran
 fi
 
 # post-processing
@@ -52,6 +55,5 @@ awk 'BEGIN{a=0;} {if ($NR eq 3) a=$7;} END{if((a-$7)<0.1) \
 print("OK: mass conservation of mud"); \
 else print("ERROR: mass conservation of mud");}' sed_mass_end.txt
 
-rm sed_mass_*.txt
+rm -f sed_mass_*.txt
 echo "Done"
-
diff --git a/model/tests/sediments/test2/run_all.sh b/model/tests/sediments/test2/run_all.sh
index be26607..d662ca3 100755
--- a/model/tests/sediments/test2/run_all.sh
+++ b/model/tests/sediments/test2/run_all.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 
 if [ $# == 1 ] 
 then
@@ -14,23 +14,26 @@ else
   echo ""
 fi
   
+SHOC="${SHOC:-./shoc}"
+mkdir -p outputs tran_outputs
+
 echo "Cleaning up"
-rm outputs/*
-rm tran_outputs/*
-rm inputs/in_test.nc
-rm inputs/test_trans_1990-01.nc
-rm diag.txt runlog mass.txt sedlog.txt setup.txt trans.mnc sed_mass_*.txt
+rm -f outputs/*
+rm -f tran_outputs/*
+rm -f inputs/in_test.nc
+rm -f inputs/test_trans_1990-01.nc
+rm -f diag.txt runlog mass.txt sedlog.txt setup.txt trans.mnc sed_mass_*.txt
 echo ""
 
 echo "Simulating hd in a wind driven, closed basin"
-./shoc -g inputs/test.prm inputs/in_test.nc
-./shoc -p inputs/test.prm
+$SHOC -g inputs/test.prm inputs/in_test.nc
+$SHOC -p inputs/test.prm
 echo "OK: HD forcing files complete"
 echo ""
 
 
 echo "Simulating transport of particulate and dissolver tracers"
-./shoc -t inputs/test_flat.tran
+$SHOC -t inputs/test_flat.tran
 awk 'BEGIN{a=0;} {if ($NR eq 3) a=$4;} END{if((a-$4)<0.1) \
 print("OK: mass conservation of dissolved tracer"); \
 else print("ERROR: mass conservation of dissolved tracer");}' sed_mass_end.txt
@@ -45,5 +48,5 @@ print("OK: mass conservation of mud"); \
 else print("ERROR: mass conservation of mud");}' sed_mass_end.txt
 
 echo ""
-rm  sed_mass_*.txt
+rm -f sed_mass_*.txt
 echo "3D TEST COMPLETE"
diff --git a/model/tests/sediments/test3/inputs/test_advanced.tran b/model/tests/sediments/test3/inputs/test_advanced.tran
index 1402ede..27cf50c 100644
--- a/model/tests/sediments/test3/inputs/test_advanced.tran
+++ b/model/tests/sediments/test3/inputs/test_advanced.tran
@@ -456,3 +456,5 @@ BOUNDARY1.POINTS        3
 1 13
 1 14
 
+
+ID_CODE SHOC grid|G1.0|H|S|B
diff --git a/model/tests/sediments/test3/inputs/test_basic.tran b/model/tests/sediments/test3/inputs/test_basic.tran
index ba1f986..91267c0 100644
--- a/model/tests/sediments/test3/inputs/test_basic.tran
+++ b/model/tests/sediments/test3/inputs/test_basic.tran
@@ -407,3 +407,5 @@ BOUNDARY1.POINTS        3
 1 13
 1 14
 
+
+ID_CODE SHOC grid|G1.0|H|S|B
diff --git a/model/tests/sediments/test3/run.sh b/model/tests/sediments/test3/run.sh
index 3976cd0..6c824ab 100755
--- a/model/tests/sediments/test3/run.sh
+++ b/model/tests/sediments/test3/run.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 
 if [ $# == 0 ] 
 then
@@ -22,27 +22,29 @@ else
    echo "run './run.sh' for info"
 fi
 
+SHOC="${SHOC:-./shoc}"
+mkdir -p outputs tran_outputs
+
 if [ $# == 1 ] 
 then
    echo "Cleaning up"
-   rm outputs/*
-   rm tran_outputs/*
-   rm inputs/in_test.nc
-   rm inputs/test_trans_1990-01.nc
-   rm diag.txt runlog sedlog.txt setup.txt trans.mnc
+   rm -f outputs/*
+   rm -f tran_outputs/*
+   rm -f inputs/in_test.nc
+   rm -f inputs/test_trans_1990-01.nc
+   rm -f diag.txt runlog sedlog.txt setup.txt trans.mnc
    echo "Running $1: hd first and then sediment transport"
-  ./shoc -g inputs/test.prm inputs/in_test.nc
-  ./shoc -p inputs/test.prm
-  ./shoc -t inputs/$1.tran
+  $SHOC -g inputs/test.prm inputs/in_test.nc
+  $SHOC -p inputs/test.prm
+  $SHOC -t inputs/$1.tran
 fi
 
 if [ $# == 2 ] 
 then
    echo "Running $1: only sediment transport"
-   rm tran_outputs/*
-   rm sedlog.txt
-  ./shoc -t inputs/$1.tran
+   rm -f tran_outputs/*
+   rm -f sedlog.txt
+   $SHOC -t inputs/$1.tran
 fi
 
 echo "Done"
-
diff --git a/model/tests/sediments/test3/run_all.sh b/model/tests/sediments/test3/run_all.sh
new file mode 100755
index 0000000..1a5c03e
--- /dev/null
+++ b/model/tests/sediments/test3/run_all.sh
@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+THIS_SCRIPT="${BASH_SOURCE[0]}"
+THIS_DIR=$( cd "$(dirname "${THIS_SCRIPT}")" && pwd)
+
+"${THIS_DIR}/run.sh" "test_basic"
+
+"${THIS_DIR}/run.sh" "test_advanced" "sedi"
diff --git a/model/tests/sediments/test4/inputs/test.prm b/model/tests/sediments/test4/inputs/test.prm
index 6acd496..dabb163 100644
--- a/model/tests/sediments/test4/inputs/test.prm
+++ b/model/tests/sediments/test4/inputs/test.prm
@@ -499,3 +499,5 @@ BATHY    100
  10.000
 
 
+
+ID_CODE SHOC grid|G1.0|H1.0|S|B
diff --git a/model/tests/sediments/test4/run_all.sh b/model/tests/sediments/test4/run_all.sh
index 4afd2a0..ac27756 100755
--- a/model/tests/sediments/test4/run_all.sh
+++ b/model/tests/sediments/test4/run_all.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -e
 
 if [ $# == 1 ] 
 then
@@ -13,16 +13,19 @@ then
 else
   echo ""
 fi
+
+SHOC="${SHOC:-./shoc}"
+mkdir -p outputs
   
 echo "Cleaning up"
-rm outputs/*
-rm inputs/in_test.nc
-rm diag.txt runlog sedlog.txt setup.txt sed_mass_*.txt
+rm -f outputs/*
+rm -f inputs/in_test.nc
+rm -f diag.txt runlog sedlog.txt setup.txt sed_mass_*.txt
 echo ""
 
 echo "Simulating coupled hd and sediment transport in a wind driven, closed basin"
-./shoc -g inputs/test.prm inputs/in_test.nc
-./shoc -p inputs/test.prm
+$SHOC -g inputs/test.prm inputs/in_test.nc
+$SHOC -p inputs/test.prm
 echo "OK: Run complete"
 echo ""
 
@@ -40,5 +43,5 @@ print("OK: mass conservation of mud"); \
 else print("ERROR: mass conservation of mud");}' sed_mass_end.txt
 
 echo ""
-rm  sed_mass_*.txt
+rm  -f sed_mass_*.txt
 echo "3D TEST COMPLETE"
diff --git a/model/tests/tracerstats/basic/run_test b/model/tests/tracerstats/basic/run_test
index 53d06e5..d04bdac 100755
--- a/model/tests/tracerstats/basic/run_test
+++ b/model/tests/tracerstats/basic/run_test
@@ -1,23 +1,25 @@
-#!/bin/csh -f
+#!/bin/csh -ef
 
 # Script to run test
 
+if (! $?SHOC || "$SHOC" == "") then
+    set SHOC='../../../hd/shoc'
+endif
+
 # check shoc
-if (! -e ../../../hd/shoc) then
+if (! -e $SHOC) then
     echo "cannot find the shoc executable, please build and try again"
     exit(0)
 endif
 
-# check output dir
-if (! -d out) then
-    mkdir out
-else
-    rm -r out/*
-endif
+# Ensure output dir is empty
+set nonomatch
+mkdir -p out
+rm -rf out/*
 
 # Kick off model
 echo "Starting model ..."
-../../../hd/shoc -p basic.prm
+$SHOC -p basic.prm
 
 if ($status) then
     echo ".... uh oh!"
@@ -26,4 +28,3 @@ else
     echo " "
     echo "Run out.m in Matlab to see results"
 endif
-