diff --git a/.github/workflows/cime-build.yml b/.github/workflows/cime-build.yml
index 907692d..2aedefe 100644
--- a/.github/workflows/cime-build.yml
+++ b/.github/workflows/cime-build.yml
@@ -2,11 +2,10 @@ name: Build and Push CIME Container
 
 on:
   workflow_dispatch:
-  pull_request:
-    branches: [main]
-    paths:
-      - 'unit-testing/Dockerfile'
-      - '.github/workflows/cime-build.yml'
+  # pull_request:
+  #   branches: [main]
+  #   paths:
+  #     - '.github/workflows/cime-build.yml'
 
 jobs:
   build-and-push:
@@ -41,6 +40,7 @@ jobs:
         uses: docker/build-push-action@v6
         with:
           context: ./unit-testing/
+          dockerfile: Dockerfile-CIME
           push: true
           tags: ghcr.io/${{ env.REPO_NAME}}/unit-testing:latest
           cache-from: type=gha
diff --git a/.github/workflows/ctsm-build.yml b/.github/workflows/ctsm-build.yml
new file mode 100644
index 0000000..36f8252
--- /dev/null
+++ b/.github/workflows/ctsm-build.yml
@@ -0,0 +1,49 @@
+name: Build and Push CTSM Container
+
+on:
+  # We could have ctsm send out a trigger for this workflow
+  # repository_dispatch:
+    # types: [new-tag]
+  workflow_dispatch:
+  pull_request:
+    branches: [main]
+    paths:
+      - '.github/workflows/ctsm-build.yml'
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+        with:
+          buildkitd-flags: --debug
+          
+      - name: Lowercase the github.repository name
+        # This step addresses https://github.com/orgs/community/discussions/25768 
+        run: |
+          echo "REPO_NAME=`echo ${{ github.repository }} | tr '[:upper:]' '[:lower:]'`" >> $GITHUB_ENV
+
+      - name: Build and push image
+        uses: docker/build-push-action@v6
+        with:
+          context: ./unit-testing/
+          push: true
+          tags: ghcr.io/${{ env.REPO_NAME}}/unit-test-ctsm:latest
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
\ No newline at end of file
diff --git a/unit-testing/Dockerfile b/unit-testing/Dockerfile
index ab7af74..39b057f 100644
--- a/unit-testing/Dockerfile
+++ b/unit-testing/Dockerfile
@@ -1,24 +1,26 @@
 FROM ghcr.io/ngeet/containers/spack-env:latest
 
-ARG CIME_VERSION=cime6.1.102
-ARG CCS_CONFIG_VERSION=ccs_config_cesm1.0.46
+# Manually update the ctsm version here
+ARG CTSM_VERSION=ctsm5.3.065
 
-# Install wget
-RUN apt-get update && apt-get install -y wget
+# Set runtime environment variables for branch name and URL
+ENV BRANCH_NAME=""
+ENV BRANCH_URL=""
 
-# Download and unpack CIME archive for tag cime6.1.102.  Rename the directory to cime.
-RUN wget -q https://github.com/ESMCI/cime/archive/refs/tags/${CIME_VERSION}.tar.gz \
-    && tar -xzf ${CIME_VERSION}.tar.gz \
-    && mv cime-${CIME_VERSION} cime \
-    && rm ${CIME_VERSION}.tar.gz
+# Install dependencies not associated with the spack environment
+RUN apt-get update && apt-get install -y wget git python3
 
-RUN wget -q https://github.com/ESMCI/ccs_config_cesm/archive/refs/tags/${CCS_CONFIG_VERSION}.tar.gz \
-    && tar -xzf ${CCS_CONFIG_VERSION}.tar.gz \
-    && mv ccs_config_cesm-${CCS_CONFIG_VERSION} ccs_config \
-    && rm ${CCS_CONFIG_VERSION}.tar.gz
+# Clone CTSM and checkout the specified version with git-fleximod
+RUN git clone https://github.com/ESCOMP/CTSM.git && \
+    cd CTSM && \
+    git checkout ${CTSM_VERSION} && \
+    ./bin/git-fleximod update
 
-# Copy the cime configuration files in the .cime directory in the container
-COPY cime/ /root/.cime/
+# Overwrite the container configuration files in ccs_config
+COPY container/ /ctsm/ccs_config/container/
+
+# Modify the .gitmodules file to take an environment variable from the container runtime command
+RUN sed -i '/\[submodule "fates"\]/,/\[submodule /{s|^\(url *= *\).*|url = '"\${BRANCH_URL}"'|; s|^\(fxtag *= *\).*|fxtag = '"\${BRANCH_NAME}"'|}' /CTSM/.gitmodules
 
 # Make sure that the entrypoint defined in the spack-env image is used
 ENTRYPOINT [ "/entrypoint.sh" ]
diff --git a/unit-testing/Dockerfile-CIME b/unit-testing/Dockerfile-CIME
new file mode 100644
index 0000000..ab7af74
--- /dev/null
+++ b/unit-testing/Dockerfile-CIME
@@ -0,0 +1,25 @@
+FROM ghcr.io/ngeet/containers/spack-env:latest
+
+ARG CIME_VERSION=cime6.1.102
+ARG CCS_CONFIG_VERSION=ccs_config_cesm1.0.46
+
+# Install wget
+RUN apt-get update && apt-get install -y wget
+
+# Download and unpack CIME archive for tag cime6.1.102.  Rename the directory to cime.
+RUN wget -q https://github.com/ESMCI/cime/archive/refs/tags/${CIME_VERSION}.tar.gz \
+    && tar -xzf ${CIME_VERSION}.tar.gz \
+    && mv cime-${CIME_VERSION} cime \
+    && rm ${CIME_VERSION}.tar.gz
+
+RUN wget -q https://github.com/ESMCI/ccs_config_cesm/archive/refs/tags/${CCS_CONFIG_VERSION}.tar.gz \
+    && tar -xzf ${CCS_CONFIG_VERSION}.tar.gz \
+    && mv ccs_config_cesm-${CCS_CONFIG_VERSION} ccs_config \
+    && rm ${CCS_CONFIG_VERSION}.tar.gz
+
+# Copy the cime configuration files in the .cime directory in the container
+COPY cime/ /root/.cime/
+
+# Make sure that the entrypoint defined in the spack-env image is used
+ENTRYPOINT [ "/entrypoint.sh" ]
+CMD [ "/bin/bash" ]
\ No newline at end of file
diff --git a/unit-testing/container/config_machines.xml b/unit-testing/container/config_machines.xml
new file mode 100644
index 0000000..7655eb7
--- /dev/null
+++ b/unit-testing/container/config_machines.xml
@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<config_machines>
+   <machine MACH="fatestestcontainer">
+      <DESC></DESC>
+      <OS>linux</OS>
+      <COMPILERS>gnu</COMPILERS>
+      <MPILIBS>openmpi,mpi-serial</MPILIBS>
+      <CIME_OUTPUT_ROOT>/output</CIME_OUTPUT_ROOT>
+      <DIN_LOC_ROOT>/inputdata</DIN_LOC_ROOT>
+      <DIN_LOC_ROOT_CLMFORC>/inputdata/atm/datm7</DIN_LOC_ROOT_CLMFORC>
+      <DOUT_S_ROOT>$CIME_OUTPUT_ROOT/archive/$CASE</DOUT_S_ROOT>
+      <BASELINE_ROOT>/baselines</BASELINE_ROOT>
+      <CCSM_CPRNC>$CIMEROOT/tools/cprnc/build/cprnc</CCSM_CPRNC>
+      <GMAKE>make</GMAKE>
+      <GMAKE_J>1</GMAKE_J>
+      <BATCH_SYSTEM>none</BATCH_SYSTEM>
+      <SUPPORTED_BY>glemieux at lbl dot gov</SUPPORTED_BY>
+      <MAX_TASKS_PER_NODE>4</MAX_TASKS_PER_NODE>
+      <MAX_MPITASKS_PER_NODE>1</MAX_MPITASKS_PER_NODE>
+      <PROJECT_REQUIRED>FALSE</PROJECT_REQUIRED>
+      <mpirun mpilib="mpi-serial">
+	<executable></executable>
+      </mpirun>
+      <mpirun mpilib="default">
+	<executable>mpirun</executable>
+	<arguments>
+	  <arg name="anum_tasks"> -np $TOTALPES</arg>
+	  <arg name="tasks_per_node"> -npernode $MAX_TASKS_PER_NODE</arg>
+	</arguments>
+      </mpirun>
+      <module_system type="none"/>
+   </machine>
+
+</config_machines>