diff --git a/.github/workflows/build-all.yml b/.github/workflows/build-all.yml
index 3912676..01e87f1 100644
--- a/.github/workflows/build-all.yml
+++ b/.github/workflows/build-all.yml
@@ -128,20 +128,33 @@ jobs:
 
           module test xsd/${{ env.XSD_VER }}
 
-      - name: Build PETSc + HDF5
+      - name: Build HDF5
         run: |
           module use ${{ env.MODULES_DIR }}/modulefiles
           module load boost/${{ env.BOOST_VER }}
           module load xercesc/${{ env.XERCESC_VER }}
           module load xsd/${{ env.XSD_VER }}
 
-          ./install_petsc_hdf5.sh \
-            --petsc-version=${{ env.PETSC_VER }} \
-            --petsc-arch=${{ env.PETSC_ARCH }} \
-            --hdf5-version=${{ env.HDF5_VER }} \
+          ./install_hdf5.sh \
+            --version=${{ env.HDF5_VER }} \
             --modules-dir=${{ env.MODULES_DIR }}
 
-          module test petsc_hdf5/${{ env.PETSC_VER }}_${{ env.HDF5_VER }}/${{ env.PETSC_ARCH }}
+          module test hdf5/${{ env.HDF5_VER }}
+
+      - name: Build PETSc
+        run: |
+          module use ${{ env.MODULES_DIR }}/modulefiles
+          module load boost/${{ env.BOOST_VER }}
+          module load xercesc/${{ env.XERCESC_VER }}
+          module load xsd/${{ env.XSD_VER }}
+          module load hdf5/${{ env.HDF5_VER }}
+
+          ./install_petsc.sh \
+            --version=${{ env.PETSC_VER }} \
+            --arch=${{ env.PETSC_ARCH }} \
+            --modules-dir=${{ env.MODULES_DIR }}
+
+          module test petsc/${{ env.PETSC_VER }}/${{ env.PETSC_ARCH }}
 
       - name: Build SUNDIALS
         run: |
@@ -149,7 +162,8 @@ jobs:
           module load boost/${{ env.BOOST_VER }}
           module load xercesc/${{ env.XERCESC_VER }}
           module load xsd/${{ env.XSD_VER }}
-          module load petsc_hdf5/${{ env.PETSC_VER }}_${{ env.HDF5_VER }}/${{ env.PETSC_ARCH }}
+          module load hdf5/${{ env.HDF5_VER }}
+          module load petsc/${{ env.PETSC_VER }}/${{ env.PETSC_ARCH }}
 
           ./install_sundials.sh \
             --version=${{ env.SUNDIALS_VER }} \
@@ -163,7 +177,8 @@ jobs:
           module load boost/${{ env.BOOST_VER }}
           module load xercesc/${{ env.XERCESC_VER }}
           module load xsd/${{ env.XSD_VER }}
-          module load petsc_hdf5/${{ env.PETSC_VER }}_${{ env.HDF5_VER }}/${{ env.PETSC_ARCH }}
+          module load hdf5/${{ env.HDF5_VER }}
+          module load petsc/${{ env.PETSC_VER }}/${{ env.PETSC_ARCH }}
           module load sundials/${{ env.SUNDIALS_VER }}
 
           ./install_vtk.sh \
@@ -183,7 +198,8 @@ jobs:
           module load boost/${{ env.BOOST_VER }}
           module load xercesc/${{ env.XERCESC_VER }}
           module load xsd/${{ env.XSD_VER }}
-          module load petsc_hdf5/${{ env.PETSC_VER }}_${{ env.HDF5_VER }}/${{ env.PETSC_ARCH }}
+          module load hdf5/${{ env.HDF5_VER }}
+          module load petsc/${{ env.PETSC_VER }}/${{ env.PETSC_ARCH }}
           module load sundials/${{ env.SUNDIALS_VER }}
           module load vtk/${{ env.VTK_VER }}
 
diff --git a/.github/workflows/build-hdf5.yml b/.github/workflows/build-hdf5.yml
new file mode 100644
index 0000000..751dd49
--- /dev/null
+++ b/.github/workflows/build-hdf5.yml
@@ -0,0 +1,51 @@
+name: Build HDF5
+
+on:
+  workflow_dispatch:
+    inputs:
+      hdf5_ver:
+        description: "HDF5 version"
+        required: true
+        type: string
+        default: "1.10.10"
+
+defaults:
+  run:
+    shell: bash --login -e -o pipefail {0} # login for environment modules
+    working-directory: ./scripts/custom
+
+jobs:
+  setup:
+    name: Build HDF5 ${{github.event.inputs.hdf5_ver }}
+
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set env
+        run: |
+          echo "MODULES_DIR=$HOME/modules" >> $GITHUB_ENV
+          echo "HDF5_VER=${{ github.event.inputs.hdf5_ver }}" >> $GITHUB_ENV
+
+      - name: Setup OS
+        run: |
+          sudo ./setup_custom.sh
+
+      - name: List environment modules
+        run: |
+          module avail
+
+      - name: Run build script
+        run: |
+          ./install_hdf5.sh \
+            --version=${{ env.HDF5_VER }} \
+            --modules-dir=${{ env.MODULES_DIR }}
+
+      - name: Test
+        run: |
+          module use ${{ env.MODULES_DIR }}/modulefiles
+          module avail
+          module load hdf5/${{ env.HDF5_VER }}
+          module test hdf5/${{ env.HDF5_VER }}
diff --git a/.github/workflows/build-petsc_hdf5.yml b/.github/workflows/build-petsc.yml
similarity index 63%
rename from .github/workflows/build-petsc_hdf5.yml
rename to .github/workflows/build-petsc.yml
index ed741ec..4e4da78 100644
--- a/.github/workflows/build-petsc_hdf5.yml
+++ b/.github/workflows/build-petsc.yml
@@ -1,4 +1,4 @@
-name: Build PETSc + HDF5
+name: Build PETSc
 
 on:
   workflow_dispatch:
@@ -18,12 +18,6 @@ on:
           - "linux-gnu-opt"
         default: "linux-gnu"
 
-      hdf5_ver:
-        description: "HDF5 version"
-        required: true
-        type: string
-        default: "1.10.10"
-
 defaults:
   run:
     shell: bash --login -e -o pipefail {0} # login for environment modules
@@ -31,7 +25,7 @@ defaults:
 
 jobs:
   setup:
-    name: Build PETSc ${{ github.event.inputs.petsc_ver }} + HDF5 ${{github.event.inputs.hdf5_ver }}
+    name: Build PETSc ${{ github.event.inputs.petsc_ver }}/${{github.event.inputs.petsc_arch }}
 
     runs-on: ubuntu-22.04
 
@@ -44,7 +38,6 @@ jobs:
           echo "MODULES_DIR=$HOME/modules" >> $GITHUB_ENV
           echo "PETSC_VER=${{ github.event.inputs.petsc_ver }}" >> $GITHUB_ENV
           echo "PETSC_ARCH=${{ github.event.inputs.petsc_arch }}" >> $GITHUB_ENV
-          echo "HDF5_VER=${{ github.event.inputs.hdf5_ver }}" >> $GITHUB_ENV
 
       - name: Setup OS
         run: |
@@ -56,15 +49,14 @@ jobs:
 
       - name: Run build script
         run: |
-          ./install_petsc_hdf5.sh \
-            --petsc-version=${{ env.PETSC_VER }} \
-            --petsc-arch=${{ env.PETSC_ARCH }} \
-            --hdf5-version=${{ env.HDF5_VER }} \
+          ./install_petsc.sh \
+            --version=${{ env.PETSC_VER }} \
+            --arch=${{ env.PETSC_ARCH }} \
             --modules-dir=${{ env.MODULES_DIR }}
 
       - name: Test
         run: |
           module use ${{ env.MODULES_DIR }}/modulefiles
           module avail
-          module load petsc_hdf5/${{ env.PETSC_VER }}_${{ env.HDF5_VER }}/${{ env.PETSC_ARCH }}
-          module test petsc_hdf5/${{ env.PETSC_VER }}_${{ env.HDF5_VER }}/${{ env.PETSC_ARCH }}
+          module load petsc/${{ env.PETSC_VER }}/${{ env.PETSC_ARCH }}
+          module test petsc/${{ env.PETSC_VER }}/${{ env.PETSC_ARCH }}
diff --git a/.github/workflows/portability-tests.yml b/.github/workflows/portability-tests.yml
index c7c5086..8654438 100644
--- a/.github/workflows/portability-tests.yml
+++ b/.github/workflows/portability-tests.yml
@@ -43,7 +43,7 @@ jobs:
           source /etc/profile.d/modules.sh
           module use /home/runner/modules/modulefiles
           module avail
-          module load boost petsc_hdf5 sundials vtk xercesc xsd
+          module load boost hdf5 petsc sundials vtk xercesc xsd
           module list
           EOF
         working-directory: build
diff --git a/Dockerfile.custom b/Dockerfile.custom
index 1d8d6d1..b69f812 100755
--- a/Dockerfile.custom
+++ b/Dockerfile.custom
@@ -28,7 +28,7 @@ ENV DEFAULT_USER="runner" \
     MODULES_DIR="/home/runner/modules"
 
 # Copy scripts
-COPY scripts/*.sh scripts/custom/ /usr/local/bin/
+COPY scripts/custom/ scripts/*.sh /usr/local/bin/
 
 # Setup base dependencies and install actions runner
 RUN useradd -r -m -d ${DEFAULT_HOME} -s /bin/bash ${DEFAULT_USER} && \
@@ -84,11 +84,37 @@ RUN source /etc/profile.d/modules.sh && \
     module load boost && \
     module load xercesc && \
     module load xsd && \
+    install_hdf5.sh \
+        --version=${HDF5} \
+        --parallel=$(nproc) \
+        --modules-dir=${MODULES_DIR} && \
+    module test hdf5 && \
+    rm -rf ${MODULES_DIR}/src/* && \
+    rm -rf /tmp/*
+
+RUN source /etc/profile.d/modules.sh && \
+    module use ${MODULES_DIR}/modulefiles && \
+    module load boost && \
+    module load xercesc && \
+    module load xsd && \
+    module load hdf5 && \
+    install_petsc.sh \
+        --version=${PETSC} \
+        --arch=linux-gnu \
+        --parallel=$(nproc) \
+        --modules-dir=${MODULES_DIR} && \
+    module test petsc && \
+    rm -rf ${MODULES_DIR}/src/* && \
+    rm -rf /tmp/*
+
+# TODO: This RUN section is a temporary workaround for backwards compatibility.
+# Remove once the combined PETSc/HDF5 module is no longer needed.
+RUN source /etc/profile.d/modules.sh && \
+    module use ${MODULES_DIR}/modulefiles && \
     install_petsc_hdf5.sh \
         --petsc-version=${PETSC} \
         --petsc-arch=linux-gnu \
         --hdf5-version=${HDF5} \
-        --parallel=$(nproc) \
         --modules-dir=${MODULES_DIR} && \
     module test petsc_hdf5 && \
     rm -rf ${MODULES_DIR}/src/* && \
@@ -99,7 +125,8 @@ RUN source /etc/profile.d/modules.sh && \
     module load boost && \
     module load xercesc && \
     module load xsd && \
-    module load petsc_hdf5 && \
+    module load hdf5 && \
+    module load petsc && \
     install_sundials.sh \
         --version=${SUNDIALS} \
         --parallel=$(nproc) \
@@ -113,7 +140,8 @@ RUN source /etc/profile.d/modules.sh && \
     module load boost && \
     module load xercesc && \
     module load xsd && \
-    module load petsc_hdf5 && \
+    module load hdf5 && \
+    module load petsc && \
     module load sundials && \
     install_vtk.sh \
         --version=${VTK} \
diff --git a/Dockerfile.system b/Dockerfile.system
index f19cd55..0f4582d 100755
--- a/Dockerfile.system
+++ b/Dockerfile.system
@@ -22,7 +22,7 @@ ENV DEFAULT_USER="runner" \
     MODULES_DIR="/home/runner/modules"
 
 # Copy scripts
-COPY scripts/*.sh scripts/system/ /usr/local/bin/
+COPY scripts/system/ scripts/*.sh /usr/local/bin/
 
 # Setup Chaste dependencies and install actions runner
 RUN useradd -r -m -d ${DEFAULT_HOME} -s /bin/bash ${DEFAULT_USER} && \
@@ -47,7 +47,8 @@ RUN source /etc/profile.d/modules.sh && \
     module test boost && \
     module test xsd && \
     module test xercesc && \
-    module test petsc_hdf5 && \
+    module test hdf5 && \
+    module test petsc && \
     module test sundials && \
     module test vtk
 
diff --git a/README.md b/README.md
index 9433f63..747eb13 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
 ![boost](https://github.com/Chaste/dependency-modules/actions/workflows/build-boost.yml/badge.svg)
-![petsc_hdf5](https://github.com/Chaste/dependency-modules/actions/workflows/build-petsc_hdf5.yml/badge.svg)
+![hdf5](https://github.com/Chaste/dependency-modules/actions/workflows/build-hdf5.yml/badge.svg)
+![petsc](https://github.com/Chaste/dependency-modules/actions/workflows/build-petsc.yml/badge.svg)
 ![sundials](https://github.com/Chaste/dependency-modules/actions/workflows/build-sundials.yml/badge.svg)
 ![vtk](https://github.com/Chaste/dependency-modules/actions/workflows/build-vtk.yml/badge.svg)
 ![xercesc](https://github.com/Chaste/dependency-modules/actions/workflows/build-xercesc.yml/badge.svg)
@@ -75,27 +76,32 @@ Install XSD
 
 Install Xerces-C
 ```sh
-./install_xercesc.sh --version=3.2.4 --modules-dir=${MODULES_DIR}
+./install_xercesc.sh --version=3.2.4 --modules-dir=${MODULES_DIR} --parallel=4
 ```
 
 Install SUNDIALS
 ```sh
-./install_sundials.sh --version=6.4.0 --modules-dir=${MODULES_DIR}
+./install_sundials.sh --version=6.4.0 --modules-dir=${MODULES_DIR} --parallel=4
 ```
 
 Install Boost
 ```sh
-./install_boost.sh --version=1.83.0 --modules-dir=${MODULES_DIR}
+./install_boost.sh --version=1.83.0 --modules-dir=${MODULES_DIR} --parallel=4
 ```
 
-Install VTK
+Install HDF5
 ```sh
-./install_vtk.sh --version=9.3.1 --modules-dir=${MODULES_DIR}
+./install_hdf5.sh --version=1.10.10 --modules-dir=${MODULES_DIR} --parallel=4
 ```
 
-Install PETSc + HDF5
+Install PETSc
+```sh
+./install_petsc.sh --version=3.19.6 --arch=linux-gnu-opt --modules-dir=${MODULES_DIR} --parallel=4
+```
+
+Install VTK
 ```sh
-./install_petsc_hdf5.sh --petsc-version=3.19.6 --hdf5-version=1.10.10 --petsc-arch=linux-gnu-opt --modules-dir=${MODULES_DIR}
+./install_vtk.sh --version=9.3.1 --modules-dir=${MODULES_DIR} --parallel=4
 ```
 
 > [!TIP]
@@ -110,8 +116,9 @@ Use `module avail` to show available software modules
 ```
 ---------------- /home/<user>/modules/modulefiles ----------------
 boost/1.83.0                                    vtk/9.3.1
-petsc_hdf5/3.19.6_1.10.810/linux-gnu-opt        xercesc/3.2.4
-sundials/6.4.0                                  xsd/4.0.0
+hdf5/1.10.10                                    xercesc/3.2.4
+petsc/3.19.6/linux-gnu-opt                      xsd/4.0.0
+sundials/6.4.0
 ```
 
 Use `module load` to activate software modules
@@ -120,8 +127,9 @@ module load xsd/4.0.0
 module load xercesc/3.2.4
 module load sundials/6.4.0
 module load boost/1.83.0
+module load hdf5/1.10.10
+module load petsc/3.19.6/linux-gnu-opt
 module load vtk/9.3.1
-module load petsc_hdf5/3.19.6_1.10.10/linux-gnu-opt
 ```
 
 ### 5. Build Chaste
diff --git a/scripts/custom/common.sh b/scripts/custom/common.sh
new file mode 120000
index 0000000..f918132
--- /dev/null
+++ b/scripts/custom/common.sh
@@ -0,0 +1 @@
+../common.sh
\ No newline at end of file
diff --git a/scripts/custom/example.sh b/scripts/custom/example.sh
index 55aa1a9..fc22a38 100755
--- a/scripts/custom/example.sh
+++ b/scripts/custom/example.sh
@@ -18,41 +18,35 @@ module use ${modules_dir}/modulefiles
 # Add modulefiles directory to bash user profile configuration
 echo "module use ${modules_dir}/modulefiles" >> ${HOME}/.bashrc
 
-# Set number of parallel processes
-parallel=$(( $(nproc) < 8 ? $(nproc) : 8 ))
-
 # Get install scripts
 git clone https://github.com/Chaste/dependency-modules.git /tmp/dependency-modules
 cd /tmp/dependency-modules/scripts
 
 # Install specific dependency versions
-./install_cmake.sh --version=3.28.6 --modules-dir=${modules_dir} --parallel=${parallel}
+./install_cmake.sh --version=3.28.6 --modules-dir=${modules_dir} --parallel=4
 module test cmake/3.28.6
 module load cmake/3.28.6
 
 ./install_xsd.sh --version=4.0.0 --modules-dir=${modules_dir}
 module test xsd/4.0.0
 
-./install_xercesc.sh --version=3.2.4 --modules-dir=${modules_dir} --parallel=${parallel}
+./install_xercesc.sh --version=3.2.4 --modules-dir=${modules_dir} --parallel=4
 module test xercesc/3.2.4
 
-./install_sundials.sh --version=6.4.0 --modules-dir=${modules_dir} --parallel=${parallel}
+./install_sundials.sh --version=6.4.0 --modules-dir=${modules_dir} --parallel=4
 module test sundials/6.4.0
 
-./install_boost.sh --version=1.83.0 --modules-dir=${modules_dir} --parallel=${parallel}
+./install_boost.sh --version=1.83.0 --modules-dir=${modules_dir} --parallel=4
 module test boost/1.83.0
 
-./install_vtk.sh --version=9.3.1 --modules-dir=${modules_dir} --parallel=${parallel}
-module test vtk/9.3.1
+./install_hdf5.sh --version=1.10.10 --modules-dir=${modules_dir} --parallel=4
+module test hdf5/1.10.10
 
-./install_petsc_hdf5.sh \
-    --petsc-version=3.19.6 \
-    --hdf5-version=1.10.10 \
-    --petsc-arch=linux-gnu \
-    --modules-dir=${modules_dir} \
-    --parallel=${parallel}
+./install_petsc.sh --version=3.19.6 --arch=linux-gnu --modules-dir=${modules_dir} --parallel=4
+module test petsc/3.19.6/linux-gnu
 
-module test petsc_hdf5/3.19.6_1.10.10/linux-gnu
+./install_vtk.sh --version=9.3.1 --modules-dir=${modules_dir} --parallel=4
+module test vtk/9.3.1
 
 # Cleanup
 cd -
diff --git a/scripts/custom/install_boost.sh b/scripts/custom/install_boost.sh
index 19a1bc2..5d5a62b 100755
--- a/scripts/custom/install_boost.sh
+++ b/scripts/custom/install_boost.sh
@@ -1,5 +1,14 @@
 #!/bin/bash -eu
 
+# Installs Boost from source and creates a modulefile for it.
+# Arguments:
+#   --version=version: The Boost version to install (e.g., 1.74.0).
+#   --modules-dir=path: The base directory for the installation and modulefile.
+#   --parallel=value: The number of parallel jobs to use for building (default: number of CPU cores).
+# Example usage:
+#   ./install_boost.sh --version=1.74.0 --modules-dir=/path/to/modules --parallel=4
+#   module load boost/1.74.0
+
 usage()
 {
     echo 'Usage: '"$(basename $0)"' --version=version --modules-dir=path [--parallel=value]'
@@ -7,7 +16,7 @@ usage()
 }
 
 script_dir="$(cd "$(dirname "$0")"; pwd)"
-. ${script_dir}/../common.sh
+. ${script_dir}/common.sh
 
 # Parse arguments
 version=
diff --git a/scripts/custom/install_cmake.sh b/scripts/custom/install_cmake.sh
index 26e955f..de74474 100755
--- a/scripts/custom/install_cmake.sh
+++ b/scripts/custom/install_cmake.sh
@@ -1,5 +1,14 @@
 #!/bin/bash -eu
 
+# Installs CMake from source and creates a modulefile for it.
+# Arguments:
+#   --version=version: The CMake version to install (e.g., 3.21.2).
+#   --modules-dir=path: The base directory for the installation and modulefile.
+#   --parallel=value: The number of parallel jobs to use for building (default: number of CPU cores).
+# Example usage:
+#   ./install_cmake.sh --version=3.21.2 --modules-dir=/path/to/modules --parallel=4
+#   module load cmake/3.21.2
+
 usage()
 {
     echo 'Usage: '"$(basename $0)"' --version=version --modules-dir=path [--parallel=value]'
@@ -7,7 +16,7 @@ usage()
 }
 
 script_dir="$(cd "$(dirname "$0")"; pwd)"
-. ${script_dir}/../common.sh
+. ${script_dir}/common.sh
 
 # Parse arguments
 version=
diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
new file mode 100755
index 0000000..6def052
--- /dev/null
+++ b/scripts/custom/install_hdf5.sh
@@ -0,0 +1,161 @@
+#!/bin/bash -eu
+
+# Installs HDF5 from source and creates a modulefile for it.
+# Arguments:
+#   --version=version: The HDF5 version to install (e.g., 1.12.0).
+#   --modules-dir=path: The base directory for the installation and modulefile.
+#   --parallel=value: The number of parallel jobs to use for building (default: number of CPU cores).
+# Example usage:
+#   ./install_hdf5.sh --version=1.12.0 --modules-dir=/path/to/modules --parallel=4
+#   module load hdf5/1.12.0
+
+usage()
+{
+    echo 'Usage: '"$(basename $0)"' --version=version --modules-dir=path [--parallel=value]'
+    exit 1
+}
+
+script_dir="$(cd "$(dirname "$0")"; pwd)"
+. ${script_dir}/common.sh
+
+# Parse arguments
+version=
+base_dir=
+parallel=
+
+for option; do
+    case $option in
+        --version=*)
+            version=$(expr "x$option" : "x--version=\(.*\)")
+            ;;
+        --modules-dir=*)
+            base_dir=$(expr "x$option" : "x--modules-dir=\(.*\)")
+            ;;
+        --parallel=*)
+            parallel=$(expr "x$option" : "x--parallel=\(.*\)")
+            ;;
+        *)
+            echo "Unknown option: $option" 1>&2
+            exit 1
+            ;;
+    esac
+done
+
+if [ -z "${version}" ]; then usage; fi
+if [ -z "${base_dir}" ]; then usage; fi
+
+parallel="${parallel:-$(nproc)}"
+
+read -r version major minor _ < <(split_version ${version})
+ver_si_on=${version//\./_}  # Converts 1.14.0 to 1_14_0
+
+# Unsupported versions: https://chaste.github.io/docs/installguides/dependency-versions/
+if version_lt "${version}" '1.10.4'; then  # HDF5 < 1.10.4
+    echo "$(basename $0): HDF5 versions < 1.10.4 not supported"
+    exit 1
+fi
+
+if version_eq "${major}.${minor}" '1.11'; then  # HDF5 == 1.11.x
+    echo "$(basename $0): HDF5 1.11.x not supported"
+    exit 1
+fi
+
+if version_eq "${major}.${minor}" '1.13'; then  # HDF5 == 1.13.x
+    echo "$(basename $0): HDF5 1.13.x not supported"
+    exit 1
+fi
+
+# Download and extract source
+mkdir -p ${base_dir}/src/hdf5
+cd ${base_dir}/src/hdf5
+
+URL_HDF5=
+if (version_ge "${version}" '1.10.0' && version_lt "${version}" '1.10.12') ||  # HDF5 >=1.10.0, <1.10.12
+   (version_ge "${version}" '1.12.0' && version_lt "${version}" '1.12.2')      # HDF5 >=1.12.0, <1.12.2
+then
+    URL_HDF5=https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${major}.${minor}/hdf5-${version}/src/hdf5-${version}.tar.gz
+
+elif (version_ge "${version}" '1.12.2' && version_lt "${version}" '1.12.4') ||  # HDF5 >=1.12.2, <1.12.4
+     (version_ge "${version}" '1.14.0' && version_lt "${version}" '1.14.4')     # HDF5 >=1.14.0, <1.14.4
+then
+    URL_HDF5=https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-${ver_si_on}.tar.gz
+
+else
+    # HDF5 >=1.10.12, <1.11
+    # HDF5 >=1.12.4, <1.13
+    # HDF5 >=1.14.4, <1.15
+    # + catch-all
+    URL_HDF5=https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-${version}.tar.gz
+fi
+
+src_dir=$(pwd)/hdf5-${version}
+mkdir -p ${src_dir}
+
+wget -nc ${URL_HDF5}
+tar -xzf $(basename ${URL_HDF5}) -C ${src_dir} --strip-components=1
+
+# Build and install
+install_dir=${base_dir}/opt/hdf5/${version}
+mkdir -p ${install_dir}
+
+cd ${src_dir}
+mkdir -p build
+cd build
+
+CC=mpicc cmake \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=${install_dir} \
+    -DHDF5_BUILD_TOOLS=OFF \
+    -DHDF5_ENABLE_PARALLEL=ON \
+    -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
+    -DHDF5_ENABLE_SZIP_SUPPORT=ON \
+    -DHDF5_ENABLE_UNSUPPORTED=OFF .. && \
+make -j ${parallel} && \
+make install
+
+# Add modulefile
+mkdir -p ${base_dir}/modulefiles/hdf5
+cd  ${base_dir}/modulefiles/hdf5
+cat <<EOF > ${version}
+#%Module1.0#####################################################################
+###
+## hdf5 ${version} modulefile
+##
+proc ModulesTest { } {
+    set paths "[getenv HDF5_ROOT]
+               [getenv HDF5_ROOT]/bin/h5pcc
+               [getenv HDF5_ROOT]/include
+               [getenv HDF5_ROOT]/lib
+               [getenv HDF5_ROOT]/lib/libhdf5.so"
+
+    foreach path \$paths {
+        if { ![file exists \$path] } {
+            puts stderr "ERROR: Does not exist: \$path"
+            return 0
+        }
+    }
+    return 1
+}
+
+proc ModulesHelp { } {
+    puts stderr "\tThis adds the environment variables for hdf5 ${version}\n"
+}
+
+module-whatis "This adds the environment variables for hdf5 ${version}"
+
+setenv          HDF5_ROOT            ${install_dir}
+
+prepend-path    PATH                 ${install_dir}/bin
+
+prepend-path    LIBRARY_PATH         ${install_dir}/lib
+prepend-path    LD_LIBRARY_PATH      ${install_dir}/lib
+prepend-path    LD_RUN_PATH          ${install_dir}/lib
+
+prepend-path    INCLUDE              ${install_dir}/include
+prepend-path    C_INCLUDE_PATH       ${install_dir}/include
+prepend-path    CPLUS_INCLUDE_PATH   ${install_dir}/include
+
+prepend-path    CMAKE_PREFIX_PATH    ${install_dir}
+
+conflict hdf5
+EOF
diff --git a/scripts/custom/install_petsc.sh b/scripts/custom/install_petsc.sh
new file mode 100755
index 0000000..9c88c79
--- /dev/null
+++ b/scripts/custom/install_petsc.sh
@@ -0,0 +1,190 @@
+#!/bin/bash -eu
+
+# Installs PETSc from source and adds a modulefile for it.
+# Arguments:
+#   --version=version: The PETSc version to install (e.g., 3.15.0).
+#   --arch=[{linux-gnu|linux-gnu-opt}]: The build type (default: linux-gnu).
+#   --modules-dir=path: The base directory for the installation and modulefile.
+#   --parallel=value: The number of parallel jobs to use for building (default: number of CPU cores).
+# Example usage:
+#   ./install_petsc.sh --version=3.15.0 --arch=linux-gnu --modules-dir=/path/to/modules --parallel=4
+#   module load petsc/3.15.0/linux-gnu
+
+usage()
+{
+    echo 'Usage: '"$(basename $0)"' --version=version --arch=[{linux-gnu|linux-gnu-opt}]'
+    echo '        --modules-dir=path [--parallel=value]'
+    exit 1
+}
+
+script_dir="$(cd "$(dirname "$0")"; pwd)"
+. ${script_dir}/common.sh
+
+# Parse arguments
+version=
+arch=
+base_dir=
+parallel=
+
+for option; do
+    case $option in
+        --version=*)
+            version=$(expr "x$option" : "x--version=\(.*\)")
+            ;;
+        --arch=*)
+            arch=$(expr "x$option" : "x--arch=\(.*\)")
+            ;;
+        --modules-dir=*)
+            base_dir=$(expr "x$option" : "x--modules-dir=\(.*\)")
+            ;;
+        --parallel=*)
+            parallel=$(expr "x$option" : "x--parallel=\(.*\)")
+            ;;
+        *)
+            echo "Unknown option: $option" 1>&2
+            exit 1
+            ;;
+    esac
+done
+
+if [ -z "${version}" ]; then usage; fi
+if [ -z "${base_dir}" ]; then usage; fi
+
+if [ -z "${arch}" ]; then
+   arch=linux-gnu
+fi
+
+if [[ ! (${arch} = 'linux-gnu' || ${arch} = 'linux-gnu-opt') ]]; then
+    usage
+fi
+
+parallel="${parallel:-$(nproc)}"
+
+read -r version major minor _ < <(split_version ${version})
+
+# Unsupported versions: https://chaste.github.io/docs/installguides/dependency-versions/
+if version_lt "${version}" '3.12'; then  # PETSc < 3.12.x
+    echo "$(basename $0): PETSc versions < 3.12 not supported"
+    exit 1
+fi
+
+# Get tarballs to prevent download errors
+mkdir -p ${base_dir}/src/petsc
+cd ${base_dir}/src/petsc
+
+download_f2cblaslapack=1
+if (version_eq "${major}.${minor}" '3.17'); then # PETSc == 3.17.x
+    wget -nc https://www.mcs.anl.gov/petsc/mirror/externalpackages/f2cblaslapack-3.4.2.q4.tar.gz
+    download_f2cblaslapack=$(pwd)/f2cblaslapack-3.4.2.q4.tar.gz
+fi
+
+# Download and extract PETSc
+URL_PETSC=https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-lite-${version}.tar.gz
+wget -nc ${URL_PETSC}
+
+install_dir=${base_dir}/opt/petsc/${version}
+mkdir -p ${install_dir}
+
+tar -xzf $(basename ${URL_PETSC}) -C ${install_dir} --strip-components=1
+
+# Fix for isAlive() removal from Python 3.9+
+# https://bugs.python.org/issue37804
+if [[ (${major} -eq 3) && ((${minor} -eq 12) || (${minor} -eq 13)) ]]; then  # PETSc 3.12.x & 3.13.x
+    cd ${install_dir}
+    sed -i.bak 's/thread.isAlive()/thread.is_alive()/g' config/BuildSystem/script.py
+fi
+
+# Build and install
+cd ${install_dir}
+export PETSC_DIR=$(pwd)
+
+case ${arch} in
+
+    linux-gnu)
+        export PETSC_ARCH=linux-gnu
+        python3 ./configure \
+            --COPTFLAGS=-Og \
+            --CXXOPTFLAGS=-Og \
+            --download-f2cblaslapack=${download_f2cblaslapack} \
+            --download-hypre=1 \
+            --download-metis=1 \
+            --download-parmetis=1 \
+            --with-cc=mpicc \
+            --with-cxx=mpicxx \
+            --with-debugging=1 \
+            --with-fc=0 \
+            --with-shared-libraries \
+            --with-ssl=false \
+            --with-x=false && \
+        make -j ${parallel} all
+        ;;
+
+    linux-gnu-opt)
+        export PETSC_ARCH=linux-gnu-opt
+        python3 ./configure \
+            --download-f2cblaslapack=${download_f2cblaslapack} \
+            --download-hypre=1 \
+            --download-metis=1 \
+            --download-parmetis=1 \
+            --with-cc=mpicc \
+            --with-cxx=mpicxx \
+            --with-fc=0 \
+            --with-shared-libraries \
+            --with-ssl=false \
+            --with-x=false && \
+        make -j ${parallel} all
+        ;;
+    *)
+        ;;
+esac
+
+# Add modulefile
+mkdir -p ${base_dir}/modulefiles/petsc/${version}
+cd  ${base_dir}/modulefiles/petsc/${version}
+cat <<EOF > ${arch}
+#%Module1.0#####################################################################
+###
+## petsc ${version}/${arch} modulefile
+##
+proc ModulesTest { } {
+    set paths "[getenv PETSC_DIR]
+               [getenv PETSC_DIR]/[getenv PETSC_ARCH]
+               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/bin
+               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/include
+               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/lib
+               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/lib/libpetsc.so"
+
+    foreach path \$paths {
+        if { ![file exists \$path] } {
+            puts stderr "ERROR: Does not exist: \$path"
+            return 0
+        }
+    }
+    return 1
+}
+
+proc ModulesHelp { } {
+    puts stderr "\tThis adds the environment variables for petsc ${version}, with PETSC_ARCH=${arch}\n"
+}
+
+module-whatis "This adds the environment variables for petsc ${version}, with PETSC_ARCH=${arch}"
+
+setenv          PETSC_DIR            ${install_dir}
+setenv          PETSC_ARCH           ${arch}
+
+prepend-path    PATH                 ${install_dir}/${arch}/bin
+
+prepend-path    LIBRARY_PATH         ${install_dir}/${arch}/lib
+prepend-path    LD_LIBRARY_PATH      ${install_dir}/${arch}/lib
+prepend-path    LD_RUN_PATH          ${install_dir}/${arch}/lib
+
+prepend-path    INCLUDE              ${install_dir}/${arch}/include
+prepend-path    C_INCLUDE_PATH       ${install_dir}/${arch}/include
+prepend-path    CPLUS_INCLUDE_PATH   ${install_dir}/${arch}/include
+
+prepend-path    CMAKE_PREFIX_PATH    ${install_dir}/${arch}
+
+setenv          PARMETIS_ROOT        ${install_dir}/${arch}
+
+conflict petsc
+EOF
diff --git a/scripts/custom/install_petsc_hdf5.sh b/scripts/custom/install_petsc_hdf5.sh
index 768c607..de88580 100755
--- a/scripts/custom/install_petsc_hdf5.sh
+++ b/scripts/custom/install_petsc_hdf5.sh
@@ -1,21 +1,23 @@
 #!/bin/bash -eu
 
+# TODO: This script adds a PETSc/HDF5 modulefile as a temporary workaround for backwards compatibility.
+# Remove once the combined PETSc/HDF5 module is no longer needed.
+
 usage()
 {
     echo 'Usage: '"$(basename $0)"' --petsc-version=version --petsc-arch=[{linux-gnu|linux-gnu-opt}]'
-    echo '        --hdf5-version=version --modules-dir=path [--parallel=value]'
+    echo '        --hdf5-version=version --modules-dir=path'
     exit 1
 }
 
 script_dir="$(cd "$(dirname "$0")"; pwd)"
-. ${script_dir}/../common.sh
+. ${script_dir}/common.sh
 
 # Parse arguments
 petsc_version=
 petsc_arch=
 hdf5_version=
 base_dir=
-parallel=
 
 for option; do
     case $option in
@@ -31,9 +33,6 @@ for option; do
         --modules-dir=*)
             base_dir=$(expr "x$option" : "x--modules-dir=\(.*\)")
             ;;
-        --parallel=*)
-            parallel=$(expr "x$option" : "x--parallel=\(.*\)")
-            ;;
         *)
             echo "Unknown option: $option" 1>&2
             exit 1
@@ -53,124 +52,9 @@ if [[ ! (${petsc_arch} = 'linux-gnu' || ${petsc_arch} = 'linux-gnu-opt') ]]; the
     usage
 fi
 
-parallel="${parallel:-$(nproc)}"
-
-read -r petsc_version petsc_major petsc_minor _ < <(split_version ${petsc_version})
-
-read -r hdf5_version hdf5_major hdf5_minor _ < <(split_version ${hdf5_version})
-hdf5_ver_si_on=${hdf5_version//\./_}  # Converts 1.14.0 to 1_14_0
+read -r petsc_version _ < <(split_version ${petsc_version})
 
-# Unsupported versions: https://chaste.github.io/docs/installguides/dependency-versions/
-if version_lt "${petsc_version}" '3.12'; then  # PETSc < 3.12.x
-    echo "$(basename $0): PETSc versions < 3.12 not supported"
-    exit 1
-fi
-
-if version_lt "${hdf5_version}" '1.10.4'; then  # HDF5 < 1.10.4
-    echo "$(basename $0): HDF5 versions < 1.10.4 not supported"
-    exit 1
-fi
-
-if version_eq "${hdf5_major}.${hdf5_minor}" '1.11'; then  # HDF5 == 1.11.x
-    echo "$(basename $0): HDF5 1.11.x not supported"
-    exit 1
-fi
-
-if version_eq "${hdf5_major}.${hdf5_minor}" '1.13'; then  # HDF5 == 1.13.x
-    echo "$(basename $0): HDF5 1.13.x not supported"
-    exit 1
-fi
-
-# Retrieve packages to fix "url is not a tarball" errors
-mkdir -p ${base_dir}/src/petsc_hdf5
-cd ${base_dir}/src/petsc_hdf5
-
-download_hdf5=1
-URL_HDF5=
-if (version_ge "${hdf5_version}" '1.10.0' && version_lt "${hdf5_version}" '1.10.12') ||  # HDF5 >=1.10.0, <1.10.12
-   (version_ge "${hdf5_version}" '1.12.0' && version_lt "${hdf5_version}" '1.12.2')      # HDF5 >=1.12.0, <1.12.2
-then
-    URL_HDF5=https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${hdf5_major}.${hdf5_minor}/hdf5-${hdf5_version}/src/hdf5-${hdf5_version}.tar.gz
-
-elif (version_ge "${hdf5_version}" '1.12.2' && version_lt "${hdf5_version}" '1.12.4') ||  # HDF5 >=1.12.2, <1.12.4
-     (version_ge "${hdf5_version}" '1.14.0' && version_lt "${hdf5_version}" '1.14.4')     # HDF5 >=1.14.0, <1.14.4
-then
-    URL_HDF5=https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-${hdf5_ver_si_on}.tar.gz
-
-else
-    # HDF5 >=1.10.12, <1.11
-    # HDF5 >=1.12.4, <1.13
-    # HDF5 >=1.14.4, <1.15
-    # + catch-all
-    URL_HDF5=https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-${hdf5_version}.tar.gz
-fi
-
-wget -nc ${URL_HDF5}
-download_hdf5=$(pwd)/$(basename ${URL_HDF5})
-
-# Download and extract PETSc
-URL_PETSC=https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-lite-${petsc_version}.tar.gz
-wget -nc ${URL_PETSC}
-
-install_dir=${base_dir}/opt/petsc_hdf5/${petsc_version}_${hdf5_version}
-mkdir -p ${install_dir}
-
-tar -xzf $(basename ${URL_PETSC}) -C ${install_dir} --strip-components=1
-
-# Fix for isAlive() removal from Python 3.9+
-# https://bugs.python.org/issue37804
-if [[ (${petsc_major} -eq 3) && ((${petsc_minor} -eq 12) || (${petsc_minor} -eq 13)) ]]; then  # PETSc 3.12.x & 3.13.x
-    cd ${install_dir}
-    sed -i.bak 's/thread.isAlive()/thread.is_alive()/g' config/BuildSystem/script.py
-fi
-
-# Build and install
-cd ${install_dir}
-export PETSC_DIR=$(pwd)
-
-case ${petsc_arch} in
-
-    linux-gnu)
-        export PETSC_ARCH=linux-gnu
-        python3 ./configure \
-            --COPTFLAGS=-Og \
-            --CXXOPTFLAGS=-Og \
-            --download-f2cblaslapack=1 \
-            --download-hdf5=${download_hdf5} \
-            --download-hypre=1 \
-            --download-metis=1 \
-            --download-mpich=1 \
-            --download-parmetis=1 \
-            --with-cc=gcc \
-            --with-cxx=g++ \
-            --with-debugging=1 \
-            --with-fc=0 \
-            --with-shared-libraries \
-            --with-ssl=false \
-            --with-x=false && \
-        make -j ${parallel} all
-        ;;
-
-    linux-gnu-opt)
-        export PETSC_ARCH=linux-gnu-opt
-        python3 ./configure \
-            --download-f2cblaslapack=1 \
-            --download-hdf5=${download_hdf5} \
-            --download-hypre=1 \
-            --download-metis=1 \
-            --download-mpich=1 \
-            --download-parmetis=1 \
-            --with-cc=gcc \
-            --with-cxx=g++ \
-            --with-fc=0 \
-            --with-shared-libraries \
-            --with-ssl=false \
-            --with-x=false && \
-        make -j ${parallel} all
-        ;;
-    *)
-        ;;
-esac
+read -r hdf5_version _ < <(split_version ${hdf5_version})
 
 # Add modulefile
 mkdir -p ${base_dir}/modulefiles/petsc_hdf5/${petsc_version}_${hdf5_version}
@@ -181,14 +65,8 @@ cat <<EOF > ${petsc_arch}
 ## petsc_hdf5 ${petsc_version}_${hdf5_version}/${petsc_arch} modulefile
 ##
 proc ModulesTest { } {
-    set paths "[getenv PETSC_DIR]
-               [getenv PETSC_DIR]/[getenv PETSC_ARCH]
-               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/bin
-               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/bin/h5pcc
-               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/include
-               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/lib
-               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/lib/libhdf5.so
-               [getenv PETSC_DIR]/[getenv PETSC_ARCH]/lib/libpetsc.so"
+    set paths "[getenv HDF5_ROOT]
+               [getenv PETSC_DIR]/[getenv PETSC_ARCH]"
 
     foreach path \$paths {
         if { ![file exists \$path] } {
@@ -205,25 +83,8 @@ proc ModulesHelp { } {
 
 module-whatis "This adds the environment variables for petsc ${petsc_version} and hdf5 ${hdf5_version}, with PETSC_ARCH=${petsc_arch}"
 
-setenv          PETSC_DIR            ${install_dir}
-setenv          PETSC_ARCH           ${petsc_arch}
-
-prepend-path    PATH                 ${install_dir}/${petsc_arch}/bin
-
-prepend-path    LIBRARY_PATH         ${install_dir}/${petsc_arch}/lib
-prepend-path    LD_LIBRARY_PATH      ${install_dir}/${petsc_arch}/lib
-prepend-path    LD_RUN_PATH          ${install_dir}/${petsc_arch}/lib
-
-prepend-path    INCLUDE              ${install_dir}/${petsc_arch}/include
-prepend-path    C_INCLUDE_PATH       ${install_dir}/${petsc_arch}/include
-prepend-path    CPLUS_INCLUDE_PATH   ${install_dir}/${petsc_arch}/include
-
-prepend-path    CMAKE_PREFIX_PATH    ${install_dir}/${petsc_arch}
-
-setenv          HDF5_ROOT            ${install_dir}/${petsc_arch}
-setenv          PARMETIS_ROOT        ${install_dir}/${petsc_arch}
+module load hdf5/${hdf5_version}
+module load petsc/${petsc_version}/${petsc_arch}
 
-conflict petsc
-conflict hdf5
 conflict petsc_hdf5
 EOF
diff --git a/scripts/custom/install_python.sh b/scripts/custom/install_python.sh
index c0a6f0c..a0e108e 100755
--- a/scripts/custom/install_python.sh
+++ b/scripts/custom/install_python.sh
@@ -7,7 +7,7 @@ usage()
 }
 
 script_dir="$(cd "$(dirname "$0")"; pwd)"
-. ${script_dir}/../common.sh
+. ${script_dir}/common.sh
 
 # Parse arguments
 version=
diff --git a/scripts/custom/install_sundials.sh b/scripts/custom/install_sundials.sh
index 0e0b21d..8d421fd 100755
--- a/scripts/custom/install_sundials.sh
+++ b/scripts/custom/install_sundials.sh
@@ -1,5 +1,14 @@
 #!/bin/bash -eu
 
+# Installs Sundials from source and creates a modulefile for it.
+# Arguments:
+#   --version=version: The Sundials version to install (e.g., 5.7.0).
+#   --modules-dir=path: The base directory for the installation and modulefile.
+#   --parallel=value: The number of parallel jobs to use for building (default: number of CPU cores).
+# Example usage:
+#   ./install_sundials.sh --version=5.7.0 --modules-dir=/path/to/modules --parallel=4
+#   module load sundials/5.7.0
+
 usage()
 {
     echo 'Usage: '"$(basename $0)"' --version=version --modules-dir=path [--parallel=value]'
@@ -7,7 +16,7 @@ usage()
 }
 
 script_dir="$(cd "$(dirname "$0")"; pwd)"
-. ${script_dir}/../common.sh
+. ${script_dir}/common.sh
 
 # Parse arguments
 version=
diff --git a/scripts/custom/install_vtk.sh b/scripts/custom/install_vtk.sh
index cc19ba0..d7894b9 100755
--- a/scripts/custom/install_vtk.sh
+++ b/scripts/custom/install_vtk.sh
@@ -1,5 +1,14 @@
 #!/bin/bash -eu
 
+# Installs VTK from source and creates a modulefile for it.
+# Arguments:
+#   --version=version: The VTK version to install (e.g., 9.3.0).
+#   --modules-dir=path: The base directory for the installation and modulefile.
+#   --parallel=value: The number of parallel jobs to use for building (default: number of CPU cores).
+# Example usage:
+#   ./install_vtk.sh --version=9.3.0 --modules-dir=/path/to/modules --parallel=4
+#   module load vtk/9.3.0
+
 usage()
 {
     echo 'Usage: '"$(basename $0)"' --version=version --modules-dir=path [--parallel=value]'
@@ -7,7 +16,7 @@ usage()
 }
 
 script_dir="$(cd "$(dirname "$0")"; pwd)"
-. ${script_dir}/../common.sh
+. ${script_dir}/common.sh
 
 # Parse arguments
 version=
diff --git a/scripts/custom/install_xercesc.sh b/scripts/custom/install_xercesc.sh
index 341e2ba..fa2fad9 100755
--- a/scripts/custom/install_xercesc.sh
+++ b/scripts/custom/install_xercesc.sh
@@ -1,5 +1,14 @@
 #!/bin/bash -eu
 
+# Installs Xerces-C++ from source and creates a modulefile for it.
+# Arguments:
+#   --version=version: Version of Xerces-C++ to install (e.g., 3.2.3)
+#   --modules-dir=path: The base directory for the installation and modulefile.
+#   --parallel=value: Number of parallel jobs for building (default: number of CPU cores)
+# Example usage:
+#   ./install_xercesc.sh --version=3.2.3 --modules-dir=/path/to/modules --parallel=4
+#   module load xercesc/3.2.3
+
 usage()
 {
     echo 'Usage: '"$(basename $0)"' --version=version --modules-dir=path [--parallel=value]'
@@ -7,7 +16,7 @@ usage()
 }
 
 script_dir="$(cd "$(dirname "$0")"; pwd)"
-. ${script_dir}/../common.sh
+. ${script_dir}/common.sh
 
 # Parse arguments
 version=
diff --git a/scripts/custom/install_xsd.sh b/scripts/custom/install_xsd.sh
index 7285310..8ff9c0b 100755
--- a/scripts/custom/install_xsd.sh
+++ b/scripts/custom/install_xsd.sh
@@ -1,5 +1,13 @@
 #!/bin/bash -eu
 
+# Installs XSD from source and creates a modulefile for it.
+# Arguments:
+#   --version=version: Version of XSD to install (e.g., 4.0.0)
+#   --modules-dir=path: The base directory for the installation and modulefile.
+# Example usage:
+#   ./install_xsd.sh --version=4.0.0 --modules-dir=/path/to/modules
+#   module load xsd/4.0.0
+
 usage()
 {
     echo 'Usage: '"$(basename $0)"' --version=version --modules-dir=path'
@@ -7,7 +15,7 @@ usage()
 }
 
 script_dir="$(cd "$(dirname "$0")"; pwd)"
-. ${script_dir}/../common.sh
+. ${script_dir}/common.sh
 
 # Parse arguments
 version=
diff --git a/scripts/custom/setup_custom.sh b/scripts/custom/setup_custom.sh
index b793417..c8206c1 100755
--- a/scripts/custom/setup_custom.sh
+++ b/scripts/custom/setup_custom.sh
@@ -1,10 +1,11 @@
 #!/bin/sh
+
 # Setup required libraries for building Chaste dependencies on Ubuntu 22.04 Jammy
 
 export DEBIAN_FRONTEND=noninteractive
 
 # Base dependencies
-apt-get update && \
+apt-get update
 apt-get install -y --no-install-recommends \
   apt-transport-https \
   apt-utils \
@@ -34,7 +35,9 @@ apt-get install -y --no-install-recommends \
 apt-get install -y --no-install-recommends \
   libfftw3-3 \
   libfftw3-bin \
-  libfftw3-dev
+  libfftw3-dev \
+  mpi-default-bin \
+  mpi-default-dev
 
 # VTK dependencies
 apt-get install -y --no-install-recommends \
@@ -116,9 +119,6 @@ apt-get install -y --no-install-recommends \
   zlib1g \
   zlib1g-dev
 
-# mpi-default-bin mpi-default-dev:
-# To be supplied by custom PETSc build for better compatibility.
-
 # libexpat1-dev libexpat1:
 # To be supplied by custom VTK build due to version conflicts.
 
diff --git a/scripts/system/common.sh b/scripts/system/common.sh
new file mode 120000
index 0000000..f918132
--- /dev/null
+++ b/scripts/system/common.sh
@@ -0,0 +1 @@
+../common.sh
\ No newline at end of file
diff --git a/scripts/system/install_modulefiles.sh b/scripts/system/install_modulefiles.sh
index b9a81fa..c44d0b5 100755
--- a/scripts/system/install_modulefiles.sh
+++ b/scripts/system/install_modulefiles.sh
@@ -59,12 +59,77 @@ module-whatis "This adds the environment variables for boost ${version}"
 conflict boost
 EOF
 
+# HDF5 modulefile stub
+hdf5_version=$(dpkg -s libhdf5-openmpi-dev | grep 'Version:' | cut -d' ' -f2 | cut -d. -f1,2,3 | cut -d+ -f1)
+
+mkdir -p ${base_dir}/modulefiles/hdf5/${hdf5_version}
+cd  ${base_dir}/modulefiles/hdf5/${hdf5_version}
+
+cat <<EOF > linux-gnu
+#%Module1.0#####################################################################
+###
+## hdf5 ${hdf5_version} modulefile
+##
+proc ModulesTest { } {
+    set paths "/usr/bin/h5pcc
+               /usr/include/hdf5
+               /usr/lib/x86_64-linux-gnu/hdf5"
+
+    foreach path \$paths {
+        if { ![file exists \$path] } {
+            puts stderr "ERROR: Does not exist: \$path"
+            return 0
+        }
+    }
+    return 1
+}
+
+proc ModulesHelp { } {
+    puts stderr "\tThis adds the environment variables for hdf5 ${hdf5_version}\n"
+}
+
+module-whatis "This adds the environment variables for hdf5 ${hdf5_version}"
 
-# PETSc and HDF5 modulefile stub
+conflict hdf5
+EOF
+
+# PETSc modulefile stub
 petsc_arch=linux-gnu
 petsc_version=$(dpkg -s libpetsc-real-dev | grep 'Version:' | cut -d' ' -f2 | cut -d. -f1,2,3 | cut -d+ -f1)
-hdf5_version=$(dpkg -s libhdf5-openmpi-dev | grep 'Version:' | cut -d' ' -f2 | cut -d. -f1,2,3 | cut -d+ -f1)
 
+mkdir -p ${base_dir}/modulefiles/petsc/${petsc_version}
+cd  ${base_dir}/modulefiles/petsc/${petsc_version}
+
+cat <<EOF > linux-gnu
+#%Module1.0#####################################################################
+###
+## petsc ${petsc_version}/${petsc_arch} modulefile
+##
+proc ModulesTest { } {
+    set paths "/usr/include/petsc
+               /usr/lib/x86_64-linux-gnu/libpetsc.so
+               /usr/lib/libparmetis.so"
+
+    foreach path \$paths {
+        if { ![file exists \$path] } {
+            puts stderr "ERROR: Does not exist: \$path"
+            return 0
+        }
+    }
+    return 1
+}
+
+proc ModulesHelp { } {
+    puts stderr "\tThis adds the environment variables for petsc ${petsc_version} with PETSC_ARCH=${petsc_arch}\n"
+}
+
+module-whatis "This adds the environment variables for petsc ${petsc_version} with PETSC_ARCH=${petsc_arch}"
+
+conflict petsc
+EOF
+
+# TODO: This adds PETSc/HDF5 modulefile stub as a temporary workaround for backwards compatibility.
+# Remove once the combined PETSc/HDF5 module is no longer needed.
 mkdir -p ${base_dir}/modulefiles/petsc_hdf5/${petsc_version}_${hdf5_version}
 cd  ${base_dir}/modulefiles/petsc_hdf5/${petsc_version}_${hdf5_version}
 
@@ -74,12 +139,8 @@ cat <<EOF > linux-gnu
 ## petsc_hdf5 ${petsc_version}_${hdf5_version}/${petsc_arch} modulefile
 ##
 proc ModulesTest { } {
-    set paths "/usr/bin/h5pcc
-               /usr/include/hdf5
-               /usr/lib/x86_64-linux-gnu/hdf5
-               /usr/include/petsc
-               /usr/lib/x86_64-linux-gnu/libpetsc.so
-               /usr/lib/libparmetis.so"
+    set paths "/usr/include/hdf5
+               /usr/include/petsc"
 
     foreach path \$paths {
         if { ![file exists \$path] } {
@@ -96,12 +157,9 @@ proc ModulesHelp { } {
 
 module-whatis "This adds the environment variables for petsc ${petsc_version} and hdf5 ${hdf5_version}, with PETSC_ARCH=${petsc_arch}"
 
-conflict petsc
-conflict hdf5
 conflict petsc_hdf5
 EOF
 
-
 # Sundials modulefile stub
 version=$(dpkg -s libsundials-dev | grep 'Version:' | cut -d' ' -f2 | cut -d. -f1,2,3 | cut -d+ -f1)
 
diff --git a/scripts/system/setup_system.sh b/scripts/system/setup_system.sh
index 9f4def9..e70f491 100755
--- a/scripts/system/setup_system.sh
+++ b/scripts/system/setup_system.sh
@@ -1,4 +1,5 @@
 #!/bin/sh
+
 # Setup Chaste system dependency versions on Ubuntu
 
 export DEBIAN_FRONTEND=noninteractive