From 31801af11bd0b00d51d6ab6e16f93268ec4c8f1c Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Wed, 13 May 2026 14:29:48 +0100
Subject: [PATCH 01/14] #106 Use cmake for HDF5 2+

---
 scripts/custom/install_hdf5.sh | 40 ++++++++++++++++++++++++----------
 1 file changed, 28 insertions(+), 12 deletions(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 847ae83..427871f 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -100,18 +100,34 @@ mkdir -p ${install_dir}
 
 cd ${src_dir}
 
-./configure \
-    --prefix=${install_dir} \
-    --enable-parallel \
-    --enable-shared \
-    CFLAGS=-fPIC \
-    LDFLAGS=-fPIC \
-    CPPFLAGS=-fPIC \
-    CXXFLAGS=-fPIC \
-    CC=mpicc \
-    CXX=mpic++ &&
-    make -j $parallel all &&
-    make install
+if version_lt "${version}" '2.0.0'; then # HDF5 < 2.0.0
+    ./configure \
+        --prefix=${install_dir} \
+        --enable-parallel \
+        --enable-shared \
+        CFLAGS=-fPIC \
+        LDFLAGS=-fPIC \
+        CPPFLAGS=-fPIC \
+        CXXFLAGS=-fPIC \
+        CC=mpicc \
+        CXX=mpic++ &&
+        make -j $parallel all &&
+        make install
+
+else # HDF5 >= 2.0.0
+    CC=mpicc CXX=mpic++ cmake \
+        -DCMAKE_BUILD_SHARED_LIBS=ON \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_INSTALL_PREFIX=${install_dir} \
+        -DHDF5_BUILD_HL_LIB=ON \
+        -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
+fi
 
 # Add modulefile
 mkdir -p ${base_dir}/modulefiles/hdf5

From 983d0d6d55548a989fbbfaef8856e9f5ed9ba981 Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Wed, 13 May 2026 14:41:25 +0100
Subject: [PATCH 02/14] #106 Update hdf5 2.x links

---
 scripts/custom/install_hdf5.sh | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 427871f..6eec0e3 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -85,13 +85,17 @@ elif (version_ge "${version}" '1.12.2' && version_lt "${version}" '1.12.4') ||
     wget -nc https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5-${ver_si_on}.tar.gz
     tar -xzf hdf5-${ver_si_on}.tar.gz -C ${src_dir} --strip-components=1
 
-else
-    # HDF5 >=1.10.12, <1.11
-    # HDF5 >=1.12.4, <1.13
-    # HDF5 >=1.14.4, <1.15
-    # + catch-all
+elif (version_ge "${version}" '1.10.12' && version_lt "${version}" '1.11') ||   # HDF5 >=1.10.12, <1.11
+    (version_ge "${version}" '1.12.4' && version_lt "${version}" '1.13') || # HDF5 >=1.12.4, <1.13
+    (version_ge "${version}" '1.14.4' && version_lt "${version}" '1.15'); then # HDF5 >=1.14.4, <1.15
     wget -nc https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz
     tar -xzf hdf5_${version}.tar.gz -C ${src_dir} --strip-components=1
+
+else
+    # HDF5 >=2.0.0
+    # + catch-all
+    wget -nc https://github.com/HDFGroup/hdf5/archive/refs/tags/${version}.tar.gz
+    tar -xzf ${version}.tar.gz -C ${src_dir} --strip-components=1
 fi
 
 # Build and install

From dba6081be3abfa18f798ebb699201c1ccf01022f Mon Sep 17 00:00:00 2001
From: Kwabena N Amponsah <kwabenantim@yahoo.com>
Date: Tue, 19 May 2026 09:01:25 +0000
Subject: [PATCH 03/14] #106 Fix HDF5 build path

---
 scripts/custom/install_hdf5.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 6eec0e3..f83508b 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -119,6 +119,7 @@ if version_lt "${version}" '2.0.0'; then # HDF5 < 2.0.0
         make install
 
 else # HDF5 >= 2.0.0
+    mkdir -p build && cd build
     CC=mpicc CXX=mpic++ cmake \
         -DCMAKE_BUILD_SHARED_LIBS=ON \
         -DCMAKE_BUILD_TYPE=Release \

From 4a8a3fa9618257f4fa786f69eefcf3dadf928fb8 Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Tue, 19 May 2026 12:42:33 +0100
Subject: [PATCH 04/14] Update HDF5 DBUILD_SHARED_LIBS flag

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 scripts/custom/install_hdf5.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index f83508b..efafc65 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -121,7 +121,7 @@ if version_lt "${version}" '2.0.0'; then # HDF5 < 2.0.0
 else # HDF5 >= 2.0.0
     mkdir -p build && cd build
     CC=mpicc CXX=mpic++ cmake \
-        -DCMAKE_BUILD_SHARED_LIBS=ON \
+        -DBUILD_SHARED_LIBS=ON \
         -DCMAKE_BUILD_TYPE=Release \
         -DCMAKE_INSTALL_PREFIX=${install_dir} \
         -DHDF5_BUILD_HL_LIB=ON \

From 0635dbbc7bdae744f88579c7a247738a75d74d1f Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Tue, 19 May 2026 12:55:30 +0100
Subject: [PATCH 05/14] #106 Improve catch-all urls for unknown hdf5 1.x

---
 scripts/custom/install_hdf5.sh | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index efafc65..5c8d165 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -91,9 +91,13 @@ elif (version_ge "${version}" '1.10.12' && version_lt "${version}" '1.11') ||
     wget -nc https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz
     tar -xzf hdf5_${version}.tar.gz -C ${src_dir} --strip-components=1
 
+elif version_lt "${version}" '2.0.0'; then
+    # + catch-all for remaining HDF5 1.x versions
+    wget -nc https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz
+    tar -xzf hdf5_${version}.tar.gz -C ${src_dir} --strip-components=1
+
 else
     # HDF5 >=2.0.0
-    # + catch-all
     wget -nc https://github.com/HDFGroup/hdf5/archive/refs/tags/${version}.tar.gz
     tar -xzf ${version}.tar.gz -C ${src_dir} --strip-components=1
 fi
@@ -115,7 +119,7 @@ if version_lt "${version}" '2.0.0'; then # HDF5 < 2.0.0
         CXXFLAGS=-fPIC \
         CC=mpicc \
         CXX=mpic++ &&
-        make -j $parallel all &&
+        make -j ${parallel} all &&
         make install
 
 else # HDF5 >= 2.0.0

From 8bbab3af67a753d07776e75c1651b3d0b05e2ae1 Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Tue, 19 May 2026 13:03:21 +0100
Subject: [PATCH 06/14] #106 Don't enforce HDF5 szip support

---
 scripts/custom/install_hdf5.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 5c8d165..5fd37a4 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -132,7 +132,6 @@ else # HDF5 >= 2.0.0
         -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

From cf038765c2f5d158bd7b88a10b49a4eb568e1623 Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Tue, 19 May 2026 13:09:07 +0100
Subject: [PATCH 07/14] DHDF5_BUILD_TOOLS=ON

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 scripts/custom/install_hdf5.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 5fd37a4..29f90b4 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -129,7 +129,7 @@ else # HDF5 >= 2.0.0
         -DCMAKE_BUILD_TYPE=Release \
         -DCMAKE_INSTALL_PREFIX=${install_dir} \
         -DHDF5_BUILD_HL_LIB=ON \
-        -DHDF5_BUILD_TOOLS=OFF \
+        -DHDF5_BUILD_TOOLS=ON \
         -DHDF5_ENABLE_PARALLEL=ON \
         -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
         -DHDF5_ENABLE_UNSUPPORTED=OFF .. &&

From cfc10c7e0187ce2dfcc9674776376298769f638b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 19 May 2026 12:21:19 +0000
Subject: [PATCH 08/14] Handle HDF5 2.x CMake compatibility issues

Agent-Logs-Url: https://github.com/Chaste/dependency-modules/sessions/2163e0ad-04cc-4735-8e96-776f28a15324

Co-authored-by: kwabenantim <1944963+kwabenantim@users.noreply.github.com>
---
 scripts/custom/install_hdf5.sh | 15 +++++++++++++++
 scripts/custom/setup_custom.sh |  5 +++++
 2 files changed, 20 insertions(+)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 29f90b4..0b8f95e 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -135,6 +135,21 @@ else # HDF5 >= 2.0.0
         -DHDF5_ENABLE_UNSUPPORTED=OFF .. &&
         make -j ${parallel} &&
         make install
+
+    for cmake_config in \
+        "${install_dir}/cmake/hdf5-config.cmake" \
+        "${install_dir}/lib/cmake/hdf5/hdf5-config.cmake"; do
+        if [ -f "${cmake_config}" ] && ! grep -q "HDF5_PROVIDES_PARALLEL AND NOT DEFINED HDF5_IS_PARALLEL" "${cmake_config}"; then
+            cat <<'EOF' >> "${cmake_config}"
+
+# Backward compatibility for consumers expecting HDF5_IS_PARALLEL.
+if(DEFINED HDF5_PROVIDES_PARALLEL AND NOT DEFINED HDF5_IS_PARALLEL)
+  set(HDF5_IS_PARALLEL "${HDF5_PROVIDES_PARALLEL}")
+endif()
+EOF
+            break
+        fi
+    done
 fi
 
 # Add modulefile
diff --git a/scripts/custom/setup_custom.sh b/scripts/custom/setup_custom.sh
index 4ed27fb..5155a11 100755
--- a/scripts/custom/setup_custom.sh
+++ b/scripts/custom/setup_custom.sh
@@ -32,6 +32,11 @@ apt-get install -y --no-install-recommends \
   python3-venv \
   valgrind
 
+cmake_ver=$(cmake --version | awk '/version/{print $3; exit}')
+if dpkg --compare-versions "${cmake_ver}" lt 3.26.0; then
+  python3 -m pip install --no-cache-dir "cmake>=3.26,<4"
+fi
+
 # Chaste dependencies
 apt-get install -y --no-install-recommends \
   libfftw3-3 \

From 2af0b892a6864e8d5a1876ff9ba2e4e9a3935878 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 19 May 2026 12:22:14 +0000
Subject: [PATCH 09/14] Harden CMake and HDF5 parallel compatibility checks

Agent-Logs-Url: https://github.com/Chaste/dependency-modules/sessions/2163e0ad-04cc-4735-8e96-776f28a15324

Co-authored-by: kwabenantim <1944963+kwabenantim@users.noreply.github.com>
---
 scripts/custom/install_hdf5.sh | 3 ++-
 scripts/custom/setup_custom.sh | 7 +++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 0b8f95e..45f1406 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -139,9 +139,10 @@ else # HDF5 >= 2.0.0
     for cmake_config in \
         "${install_dir}/cmake/hdf5-config.cmake" \
         "${install_dir}/lib/cmake/hdf5/hdf5-config.cmake"; do
-        if [ -f "${cmake_config}" ] && ! grep -q "HDF5_PROVIDES_PARALLEL AND NOT DEFINED HDF5_IS_PARALLEL" "${cmake_config}"; then
+        if [ -f "${cmake_config}" ] && ! grep -q "HDF5_IS_PARALLEL_COMPAT_SHIM" "${cmake_config}"; then
             cat <<'EOF' >> "${cmake_config}"
 
+# HDF5_IS_PARALLEL_COMPAT_SHIM
 # Backward compatibility for consumers expecting HDF5_IS_PARALLEL.
 if(DEFINED HDF5_PROVIDES_PARALLEL AND NOT DEFINED HDF5_IS_PARALLEL)
   set(HDF5_IS_PARALLEL "${HDF5_PROVIDES_PARALLEL}")
diff --git a/scripts/custom/setup_custom.sh b/scripts/custom/setup_custom.sh
index 5155a11..635e049 100755
--- a/scripts/custom/setup_custom.sh
+++ b/scripts/custom/setup_custom.sh
@@ -32,8 +32,11 @@ apt-get install -y --no-install-recommends \
   python3-venv \
   valgrind
 
-cmake_ver=$(cmake --version | awk '/version/{print $3; exit}')
-if dpkg --compare-versions "${cmake_ver}" lt 3.26.0; then
+cmake_ver=
+if command -v cmake >/dev/null 2>&1; then
+  cmake_ver=$(cmake --version | awk '/version/{print $3; exit}')
+fi
+if [ -z "${cmake_ver}" ] || dpkg --compare-versions "${cmake_ver}" lt 3.26.0; then
   python3 -m pip install --no-cache-dir "cmake>=3.26,<4"
 fi
 

From 7edfe27fe8db8030618da07d5b751c90980aa1b9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 19 May 2026 12:23:00 +0000
Subject: [PATCH 10/14] Refine CMake version parsing and HDF5 shim handling

Agent-Logs-Url: https://github.com/Chaste/dependency-modules/sessions/2163e0ad-04cc-4735-8e96-776f28a15324

Co-authored-by: kwabenantim <1944963+kwabenantim@users.noreply.github.com>
---
 scripts/custom/install_hdf5.sh | 2 ++
 scripts/custom/setup_custom.sh | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 45f1406..1a7315c 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -136,6 +136,7 @@ else # HDF5 >= 2.0.0
         make -j ${parallel} &&
         make install
 
+    shim_applied=false
     for cmake_config in \
         "${install_dir}/cmake/hdf5-config.cmake" \
         "${install_dir}/lib/cmake/hdf5/hdf5-config.cmake"; do
@@ -148,6 +149,7 @@ if(DEFINED HDF5_PROVIDES_PARALLEL AND NOT DEFINED HDF5_IS_PARALLEL)
   set(HDF5_IS_PARALLEL "${HDF5_PROVIDES_PARALLEL}")
 endif()
 EOF
+            shim_applied=true
             break
         fi
     done
diff --git a/scripts/custom/setup_custom.sh b/scripts/custom/setup_custom.sh
index 635e049..094ee5c 100755
--- a/scripts/custom/setup_custom.sh
+++ b/scripts/custom/setup_custom.sh
@@ -34,7 +34,7 @@ apt-get install -y --no-install-recommends \
 
 cmake_ver=
 if command -v cmake >/dev/null 2>&1; then
-  cmake_ver=$(cmake --version | awk '/version/{print $3; exit}')
+  cmake_ver=$(cmake --version | awk 'NR==1{print $3; exit}')
 fi
 if [ -z "${cmake_ver}" ] || dpkg --compare-versions "${cmake_ver}" lt 3.26.0; then
   python3 -m pip install --no-cache-dir "cmake>=3.26,<4"

From 996bef49d13da22f04922c7aef2cd98b1a0c4531 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 19 May 2026 12:23:40 +0000
Subject: [PATCH 11/14] Tighten CMake version validation and cleanup shim logic

Agent-Logs-Url: https://github.com/Chaste/dependency-modules/sessions/2163e0ad-04cc-4735-8e96-776f28a15324

Co-authored-by: kwabenantim <1944963+kwabenantim@users.noreply.github.com>
---
 scripts/custom/install_hdf5.sh | 2 --
 scripts/custom/setup_custom.sh | 3 +++
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 1a7315c..45f1406 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -136,7 +136,6 @@ else # HDF5 >= 2.0.0
         make -j ${parallel} &&
         make install
 
-    shim_applied=false
     for cmake_config in \
         "${install_dir}/cmake/hdf5-config.cmake" \
         "${install_dir}/lib/cmake/hdf5/hdf5-config.cmake"; do
@@ -149,7 +148,6 @@ if(DEFINED HDF5_PROVIDES_PARALLEL AND NOT DEFINED HDF5_IS_PARALLEL)
   set(HDF5_IS_PARALLEL "${HDF5_PROVIDES_PARALLEL}")
 endif()
 EOF
-            shim_applied=true
             break
         fi
     done
diff --git a/scripts/custom/setup_custom.sh b/scripts/custom/setup_custom.sh
index 094ee5c..6b14d1d 100755
--- a/scripts/custom/setup_custom.sh
+++ b/scripts/custom/setup_custom.sh
@@ -36,6 +36,9 @@ cmake_ver=
 if command -v cmake >/dev/null 2>&1; then
   cmake_ver=$(cmake --version | awk 'NR==1{print $3; exit}')
 fi
+if ! echo "${cmake_ver}" | grep -Eq '^[0-9]+\.[0-9]+\.[0-9]+$'; then
+  cmake_ver=
+fi
 if [ -z "${cmake_ver}" ] || dpkg --compare-versions "${cmake_ver}" lt 3.26.0; then
   python3 -m pip install --no-cache-dir "cmake>=3.26,<4"
 fi

From 8e9bb15d817fa3bc191f82ad09b9bd6f58ab9ffd Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Tue, 19 May 2026 13:41:52 +0100
Subject: [PATCH 12/14] #106 Remove hdf5 compatibility shim to be handled
 downstream

---
 scripts/custom/install_hdf5.sh | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 45f1406..29f90b4 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -135,22 +135,6 @@ else # HDF5 >= 2.0.0
         -DHDF5_ENABLE_UNSUPPORTED=OFF .. &&
         make -j ${parallel} &&
         make install
-
-    for cmake_config in \
-        "${install_dir}/cmake/hdf5-config.cmake" \
-        "${install_dir}/lib/cmake/hdf5/hdf5-config.cmake"; do
-        if [ -f "${cmake_config}" ] && ! grep -q "HDF5_IS_PARALLEL_COMPAT_SHIM" "${cmake_config}"; then
-            cat <<'EOF' >> "${cmake_config}"
-
-# HDF5_IS_PARALLEL_COMPAT_SHIM
-# Backward compatibility for consumers expecting HDF5_IS_PARALLEL.
-if(DEFINED HDF5_PROVIDES_PARALLEL AND NOT DEFINED HDF5_IS_PARALLEL)
-  set(HDF5_IS_PARALLEL "${HDF5_PROVIDES_PARALLEL}")
-endif()
-EOF
-            break
-        fi
-    done
 fi
 
 # Add modulefile

From 25d1cc4f0c45114b4f808da0afd32b6dfd033463 Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Tue, 19 May 2026 13:55:22 +0100
Subject: [PATCH 13/14] #106 Simplify hdf5 cmake

---
 scripts/custom/install_hdf5.sh |  7 ++++---
 scripts/custom/setup_custom.sh | 14 ++------------
 2 files changed, 6 insertions(+), 15 deletions(-)

diff --git a/scripts/custom/install_hdf5.sh b/scripts/custom/install_hdf5.sh
index 29f90b4..6be6658 100755
--- a/scripts/custom/install_hdf5.sh
+++ b/scripts/custom/install_hdf5.sh
@@ -123,6 +123,9 @@ if version_lt "${version}" '2.0.0'; then # HDF5 < 2.0.0
         make install
 
 else # HDF5 >= 2.0.0
+    # Check cmake version (HDF5 2.0+ requires cmake >= 3.26)
+    cmake --version
+
     mkdir -p build && cd build
     CC=mpicc CXX=mpic++ cmake \
         -DBUILD_SHARED_LIBS=ON \
@@ -130,9 +133,7 @@ else # HDF5 >= 2.0.0
         -DCMAKE_INSTALL_PREFIX=${install_dir} \
         -DHDF5_BUILD_HL_LIB=ON \
         -DHDF5_BUILD_TOOLS=ON \
-        -DHDF5_ENABLE_PARALLEL=ON \
-        -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
-        -DHDF5_ENABLE_UNSUPPORTED=OFF .. &&
+        -DHDF5_ENABLE_PARALLEL=ON .. &&
         make -j ${parallel} &&
         make install
 fi
diff --git a/scripts/custom/setup_custom.sh b/scripts/custom/setup_custom.sh
index 6b14d1d..18c3e00 100755
--- a/scripts/custom/setup_custom.sh
+++ b/scripts/custom/setup_custom.sh
@@ -21,8 +21,6 @@ apt-get install -y --no-install-recommends \
 # Build/dev dependencies
 apt-get install -y --no-install-recommends \
   build-essential \
-  cmake \
-  cmake-curses-gui \
   doxygen \
   git \
   lcov \
@@ -32,16 +30,8 @@ apt-get install -y --no-install-recommends \
   python3-venv \
   valgrind
 
-cmake_ver=
-if command -v cmake >/dev/null 2>&1; then
-  cmake_ver=$(cmake --version | awk 'NR==1{print $3; exit}')
-fi
-if ! echo "${cmake_ver}" | grep -Eq '^[0-9]+\.[0-9]+\.[0-9]+$'; then
-  cmake_ver=
-fi
-if [ -z "${cmake_ver}" ] || dpkg --compare-versions "${cmake_ver}" lt 3.26.0; then
-  python3 -m pip install --no-cache-dir "cmake>=3.26,<4"
-fi
+# Install cmake 3.26+ for HDF5 2.0+ (Ubuntu 22.04 has cmake 3.22)
+python3 -m pip install --no-cache-dir "cmake>=3.26,<4"
 
 # Chaste dependencies
 apt-get install -y --no-install-recommends \

From d8636f89be5ea4780a369adc529852583aa9bb9a Mon Sep 17 00:00:00 2001
From: Kwabena Amponsah <kwabenantim@yahoo.com>
Date: Tue, 19 May 2026 14:43:58 +0100
Subject: [PATCH 14/14] #106 Allow CMake 4 installation

---
 scripts/custom/setup_custom.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/custom/setup_custom.sh b/scripts/custom/setup_custom.sh
index 18c3e00..3d745de 100755
--- a/scripts/custom/setup_custom.sh
+++ b/scripts/custom/setup_custom.sh
@@ -31,7 +31,7 @@ apt-get install -y --no-install-recommends \
   valgrind
 
 # Install cmake 3.26+ for HDF5 2.0+ (Ubuntu 22.04 has cmake 3.22)
-python3 -m pip install --no-cache-dir "cmake>=3.26,<4"
+python3 -m pip install --no-cache-dir "cmake>=3.26,<5"
 
 # Chaste dependencies
 apt-get install -y --no-install-recommends \