From 1f2e7d4b9af55b03623290b97d14c49fcbd6a46f Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Tue, 29 Oct 2024 16:54:32 +0100
Subject: [PATCH 01/13] update submodules

---
 .gitignore                                             |  1 +
 p4est                                                  |  2 +-
 sc                                                     |  2 +-
 src/t8.h                                               |  2 +-
 .../t8_default/t8_default_hex/t8_default_hex.cxx       |  6 +++---
 .../t8_default/t8_default_line/t8_default_line.cxx     |  6 +++---
 .../t8_default/t8_default_prism/t8_default_prism.cxx   | 10 +++++-----
 .../t8_default_pyramid/t8_default_pyramid.cxx          |  6 +++---
 .../t8_default/t8_default_quad/t8_default_quad.cxx     |  6 +++---
 .../t8_default/t8_default_tri/t8_dtri_bits.c           | 10 +++++-----
 .../t8_default/t8_default_vertex/t8_default_vertex.cxx |  6 +++---
 11 files changed, 29 insertions(+), 28 deletions(-)

diff --git a/.gitignore b/.gitignore
index 122db9868d..d085775b76 100644
--- a/.gitignore
+++ b/.gitignore
@@ -24,6 +24,7 @@ doxygen/
 
 CMakeCache.txt
 CMakeFiles/
+version.txt
 
 src/stamp-h1
 src/t8_config.h
diff --git a/p4est b/p4est
index 8206f0e56d..851774a0c9 160000
--- a/p4est
+++ b/p4est
@@ -1 +1 @@
-Subproject commit 8206f0e56d536d6d7f2e1d106c491b8c9386e28f
+Subproject commit 851774a0c993aaf6f1719da6fd62c2f3acd761ee
diff --git a/sc b/sc
index 2b209eab18..c371874cdd 160000
--- a/sc
+++ b/sc
@@ -1 +1 @@
-Subproject commit 2b209eab184d2feee7bd146ee580ae3c983b85f4
+Subproject commit c371874cdde434e831175d0feef3d869aa340c11
diff --git a/src/t8.h b/src/t8.h
index 705659359c..a39d3311ef 100644
--- a/src/t8.h
+++ b/src/t8.h
@@ -108,7 +108,7 @@ typedef int64_t t8_gloidx_t;
 /** A type for storing SFC indices */
 typedef uint64_t t8_linearidx_t;
 /** The MPI datatype of t8_linearidx_t */
-#define T8_MPI_LINEARIDX sc_MPI_UNSIGNED_LONG_LONG
+#define T8_MPI_LINEARIDX MPI_UNSIGNED_LONG_LONG
 
 #define T8_PADDING_SIZE (sizeof (void *))
 /** Compute the number of bytes that have to be added to a given byte_count
diff --git a/src/t8_schemes/t8_default/t8_default_hex/t8_default_hex.cxx b/src/t8_schemes/t8_default/t8_default_hex/t8_default_hex.cxx
index 5465eda575..6f6b4f2062 100644
--- a/src/t8_schemes/t8_default/t8_default_hex/t8_default_hex.cxx
+++ b/src/t8_schemes/t8_default/t8_default_hex/t8_default_hex.cxx
@@ -671,7 +671,7 @@ t8_default_scheme_hex_c::t8_element_MPI_Pack (t8_element_t **const elements, con
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Pack (&quads[ielem]->z, 1, sc_MPI_INT, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&quads[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&quads[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -690,7 +690,7 @@ t8_default_scheme_hex_c::t8_element_MPI_Pack_size (const unsigned int count, sc_
   singlesize += 3 * datasize;
 
   /* level */
-  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
@@ -712,7 +712,7 @@ t8_default_scheme_hex_c::t8_element_MPI_Unpack (void *recvbuf, const int buffer_
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->z), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->level), 1, sc_MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->level), 1, MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_line/t8_default_line.cxx b/src/t8_schemes/t8_default/t8_default_line/t8_default_line.cxx
index 392ccc735a..94f126cc0b 100644
--- a/src/t8_schemes/t8_default/t8_default_line/t8_default_line.cxx
+++ b/src/t8_schemes/t8_default/t8_default_line/t8_default_line.cxx
@@ -465,7 +465,7 @@ t8_default_scheme_line_c::t8_element_MPI_Pack (t8_element_t **const elements, co
   for (unsigned int ielem = 0; ielem < count; ielem++) {
     mpiret = sc_MPI_Pack (&(lines[ielem]->x), 1, sc_MPI_INT, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&lines[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&lines[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -482,7 +482,7 @@ t8_default_scheme_line_c::t8_element_MPI_Pack_size (const unsigned int count, sc
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
-  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
@@ -500,7 +500,7 @@ t8_default_scheme_line_c::t8_element_MPI_Unpack (void *recvbuf, const int buffer
   for (unsigned int ielem = 0; ielem < count; ielem++) {
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(lines[ielem]->x), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(lines[ielem]->level), 1, sc_MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(lines[ielem]->level), 1, MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_prism/t8_default_prism.cxx b/src/t8_schemes/t8_default/t8_default_prism/t8_default_prism.cxx
index da2b18338d..6d3bc17aa0 100644
--- a/src/t8_schemes/t8_default/t8_default_prism/t8_default_prism.cxx
+++ b/src/t8_schemes/t8_default/t8_default_prism/t8_default_prism.cxx
@@ -488,11 +488,11 @@ t8_default_scheme_prism_c::t8_element_MPI_Pack (t8_element_t **const elements, c
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Pack (&prisms[ielem]->tri.y, 1, sc_MPI_INT, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&prisms[ielem]->tri.type, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&prisms[ielem]->tri.type, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
 
     T8_ASSERT (prisms[ielem]->line.level == prisms[ielem]->tri.level);
-    mpiret = sc_MPI_Pack (&prisms[ielem]->line.level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&prisms[ielem]->line.level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -511,7 +511,7 @@ t8_default_scheme_prism_c::t8_element_MPI_Pack_size (const unsigned int count, s
   singlesize += 3 * datasize;
 
   /*type, level*/
-  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += 2 * datasize;
 
@@ -533,9 +533,9 @@ t8_default_scheme_prism_c::t8_element_MPI_Unpack (void *recvbuf, const int buffe
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.y), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.type), 1, sc_MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.type), 1, MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.level), 1, sc_MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.level), 1, MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
     prisms[ielem]->line.level = prisms[ielem]->tri.level;
   }
diff --git a/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx b/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
index 7a7ee358bf..8996b4c20e 100644
--- a/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
+++ b/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
@@ -452,7 +452,7 @@ t8_default_scheme_pyramid_c::t8_element_MPI_Pack (t8_element_t **const elements,
     t8_dtet_t *p = &pyramids[ielem]->pyramid;
     t8_dtet_element_pack (&p, 1, send_buffer, buffer_size, position, comm);
 
-    SC_CHECK_MPI (sc_MPI_Pack (&pyramids[ielem]->switch_shape_at_level, 1, sc_MPI_INT8_T, send_buffer, buffer_size,
+    SC_CHECK_MPI (sc_MPI_Pack (&pyramids[ielem]->switch_shape_at_level, 1, MPI_INT8_T, send_buffer, buffer_size,
                                position, comm));
   }
 }
@@ -468,7 +468,7 @@ t8_default_scheme_pyramid_c::t8_element_MPI_Pack_size (const unsigned int count,
   singlesize += datasize;
 
   /* switch shape at level */
-  SC_CHECK_MPI (sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize));
+  SC_CHECK_MPI (sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize));
   singlesize += datasize;
 
   *pack_size = count * singlesize;
@@ -487,7 +487,7 @@ t8_default_scheme_pyramid_c::t8_element_MPI_Unpack (void *recvbuf, const int buf
     t8_dtet_element_unpack (recvbuf, buffer_size, position, &p, 1, comm);
 
     mpiret
-      = sc_MPI_Unpack (recvbuf, buffer_size, position, &pyramids[ielem]->switch_shape_at_level, 1, sc_MPI_INT8_T, comm);
+      = sc_MPI_Unpack (recvbuf, buffer_size, position, &pyramids[ielem]->switch_shape_at_level, 1, MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_quad/t8_default_quad.cxx b/src/t8_schemes/t8_default/t8_default_quad/t8_default_quad.cxx
index 7a146353e9..d867c7dd41 100644
--- a/src/t8_schemes/t8_default/t8_default_quad/t8_default_quad.cxx
+++ b/src/t8_schemes/t8_default/t8_default_quad/t8_default_quad.cxx
@@ -799,7 +799,7 @@ t8_default_scheme_quad_c::t8_element_MPI_Pack (t8_element_t **const elements, co
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Pack (&quads[ielem]->y, 1, sc_MPI_INT, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&quads[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&quads[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -818,7 +818,7 @@ t8_default_scheme_quad_c::t8_element_MPI_Pack_size (const unsigned int count, sc
   singlesize += 2 * datasize;
 
   /* level */
-  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
@@ -838,7 +838,7 @@ t8_default_scheme_quad_c::t8_element_MPI_Unpack (void *recvbuf, const int buffer
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->y), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->level), 1, sc_MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->level), 1, MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_tri/t8_dtri_bits.c b/src/t8_schemes/t8_default/t8_default_tri/t8_dtri_bits.c
index fed3b9039e..8fed8fdc48 100644
--- a/src/t8_schemes/t8_default/t8_default_tri/t8_dtri_bits.c
+++ b/src/t8_schemes/t8_default/t8_default_tri/t8_dtri_bits.c
@@ -1718,9 +1718,9 @@ t8_dtri_element_pack (t8_dtri_t **const elements, const unsigned int count, void
     SC_CHECK_MPI (mpiret);
 #endif
 
-    mpiret = sc_MPI_Pack (&elements[ielem]->type, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&elements[ielem]->type, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&elements[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&elements[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -1744,7 +1744,7 @@ t8_dtri_element_pack_size (const unsigned int count, sc_MPI_Comm comm, int *pack
   singlesize += coord_count * datasize;
 
   /* type, level*/
-  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += 2 * datasize;
 
@@ -1766,9 +1766,9 @@ t8_dtri_element_unpack (void *recvbuf, const int buffer_size, int *position, t8_
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->z), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
 #endif
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->type), 1, sc_MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->type), 1, MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->level), 1, sc_MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->level), 1, MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_vertex/t8_default_vertex.cxx b/src/t8_schemes/t8_default/t8_default_vertex/t8_default_vertex.cxx
index cefea160e6..d4b0118804 100644
--- a/src/t8_schemes/t8_default/t8_default_vertex/t8_default_vertex.cxx
+++ b/src/t8_schemes/t8_default/t8_default_vertex/t8_default_vertex.cxx
@@ -352,7 +352,7 @@ t8_default_scheme_vertex_c::t8_element_MPI_Pack (t8_element_t **const elements,
   int mpiret;
   t8_dvertex_t **vertices = (t8_dvertex_t **) elements;
   for (unsigned int ielem = 0; ielem < count; ielem++) {
-    mpiret = sc_MPI_Pack (&vertices[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&vertices[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -365,7 +365,7 @@ t8_default_scheme_vertex_c::t8_element_MPI_Pack_size (const unsigned int count,
   int datasize = 0;
   int mpiret;
 
-  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
@@ -381,7 +381,7 @@ t8_default_scheme_vertex_c::t8_element_MPI_Unpack (void *recvbuf, const int buff
   int mpiret;
   t8_dvertex_t **vertices = (t8_dvertex_t **) elements;
   for (unsigned int ielem = 0; ielem < count; ielem++) {
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(vertices[ielem]->level), 1, sc_MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(vertices[ielem]->level), 1, MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }

From 71f02363d2e14e54d7aea9971d667aa513d310d8 Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Tue, 29 Oct 2024 17:09:16 +0100
Subject: [PATCH 02/13] remove noise from sc and p4est

---
 CMakeLists.txt | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c94ceaca0a..f3d157f9a9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -120,12 +120,16 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH true)
 if ( T8CODE_USE_SYSTEM_SC )
     find_package( SC REQUIRED PATHS /path/to/system/sc )
 else()
+    set( SC_BUILD_EXAMPLES OFF )
+    set( SC_BUILD_TESTING OFF )
     add_subdirectory( ${CMAKE_CURRENT_LIST_DIR}/sc )
 endif()
 
 if ( T8CODE_USE_SYSTEM_P4EST )
     find_package( P4EST REQUIRED PATHS /path/to/system/p4est )
 else()
+    set( P4EST_BUILD_EXAMPLES OFF )
+    set( P4EST_BUILD_TESTING OFF )
     add_subdirectory( ${CMAKE_CURRENT_LIST_DIR}/p4est )
 endif()
 

From 52a93da657ef79f446b287abd59ec0ad9faba15e Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Wed, 30 Oct 2024 16:40:12 +0100
Subject: [PATCH 03/13] replace hardcoded OFFs by dependent options

---
 CMakeLists.txt | 36 +++++++++++++++++++++---------------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f3d157f9a9..a573e8c8ec 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -6,29 +6,35 @@ project( T8CODE
   DESCRIPTION "Parallel algorithms and data structures for tree-based AMR with arbitrary element shapes."
   LANGUAGES C CXX Fortran
   VERSION "${T8CODE_VERSION_MAJOR}.${T8CODE_VERSION_MINOR}.${T8CODE_VERSION_PATCH}" )
+
 include( CTest )
+include(CMakeDependentOption)
+
+option( T8CODE_ENABLE_MPI "Enable t8code's features which rely on MPI" ON )
+option( T8CODE_ENABLE_VTK "Enable t8code's features which rely on VTK" OFF )
+option( T8CODE_ENABLE_OCC "Enable t8code's features which rely on OpenCASCADE" OFF )
+option( T8CODE_ENABLE_NETCDF "Enable t8code's features which rely on netCDF" OFF )
+
+option( T8CODE_USE_SYSTEM_SC "Use system-installed sc library" OFF )
+option( T8CODE_USE_SYSTEM_P4EST "Use system-installed p4est library" OFF )
 
 option( T8CODE_BUILD_AS_SHARED_LIBRARY "Whether t8code should be built as a shared or a static library" ON )
 option( T8CODE_BUILD_PEDANTIC "Compile t8code with `-Wall -pedantic -Werror` as done in the Github CI." OFF )
 option( T8CODE_EXPORT_COMPILE_COMMANDS "Export the compile commands as json. Can be used by IDEs for code completion (e.g. intellisense, clangd)" OFF )
+
 option( T8CODE_BUILD_TESTS "Build t8code's automated tests" ON )
+cmake_dependent_option( T8CODE_BUILD_TPL_TESTS "Build the tests from libsc and p4est" OFF "T8CODE_BUILD_TESTS" OFF )
+cmake_dependent_option( T8CODE_ENABLE_LESS_TESTS "Tests not as thoroughly to speed up the test suite. Tests the same functionality. (WARNING: Use with care.)" OFF "T8CODE_BUILD_TESTS" OFF )
+
 option( T8CODE_BUILD_TUTORIALS "Build t8code's tutorials" ON )
+
 option( T8CODE_BUILD_EXAMPLES "Build t8code's examples" ON )
+cmake_dependent_option( T8CODE_BUILD_TPL_EXAMPLES "Build the examples from libsc and p4est" OFF "T8CODE_BUILD_EXAMPLES" OFF )
+
 option( T8CODE_BUILD_BENCHMARKS "Build t8code's benchmarks" ON )
 option( T8CODE_BUILD_FORTRAN_INTERFACE "Build t8code's Fortran interface" OFF )
-option( T8CODE_ENABLE_LESS_TESTS "Tests not as thoroughly to speed up the test suite. Tests the same functionality. (WARNING: Use with care.)" OFF )
-
-option( T8CODE_ENABLE_MPI "Enable t8code's features which rely on MPI" ON )
-option( T8CODE_ENABLE_VTK "Enable t8code's features which rely on VTK" OFF )
-option( T8CODE_ENABLE_OCC "Enable t8code's features which rely on OpenCASCADE" OFF )
-option( T8CODE_ENABLE_NETCDF "Enable t8code's features which rely on netCDF" OFF )
-
-option( T8CODE_USE_SYSTEM_SC "Use system-installed sc library" OFF )
-option( T8CODE_USE_SYSTEM_P4EST "Use system-installed p4est library" OFF )
 
 option( T8CODE_BUILD_DOCUMENTATION "Build t8code's documentation" OFF )
-
-include(CMakeDependentOption)
 cmake_dependent_option( T8CODE_BUILD_DOCUMENTATION_SPHINX "Build t8code's documentation using sphinx" OFF "T8CODE_BUILD_DOCUMENTATION" OFF )
 
 set(T8CODE_CUSTOM_PARALLEL_TEST_COMMAND "" CACHE STRING "Define a custom command for parallel tests , e.g.: mpirun -np 8 (overwrites standard mpirun -np 4 if build with mpi)")
@@ -120,16 +126,16 @@ set(CMAKE_INSTALL_RPATH_USE_LINK_PATH true)
 if ( T8CODE_USE_SYSTEM_SC )
     find_package( SC REQUIRED PATHS /path/to/system/sc )
 else()
-    set( SC_BUILD_EXAMPLES OFF )
-    set( SC_BUILD_TESTING OFF )
+    set( SC_BUILD_EXAMPLES ${T8CODE_BUILD_TPL_EXAMPLES} )
+    set( SC_BUILD_TESTING ${T8CODE_BUILD_TPL_TESTS} )
     add_subdirectory( ${CMAKE_CURRENT_LIST_DIR}/sc )
 endif()
 
 if ( T8CODE_USE_SYSTEM_P4EST )
     find_package( P4EST REQUIRED PATHS /path/to/system/p4est )
 else()
-    set( P4EST_BUILD_EXAMPLES OFF )
-    set( P4EST_BUILD_TESTING OFF )
+    set( P4EST_BUILD_EXAMPLES ${T8CODE_BUILD_TPL_EXAMPLES} )
+    set( P4EST_BUILD_TESTING ${T8CODE_BUILD_TPL_TESTS} )
     add_subdirectory( ${CMAKE_CURRENT_LIST_DIR}/p4est )
 endif()
 

From 903eeb7ae543b4decf01bfdf336a5b6d106b672f Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Wed, 30 Oct 2024 16:41:42 +0100
Subject: [PATCH 04/13] indent

---
 .../t8_default/t8_default_pyramid/t8_default_pyramid.cxx      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx b/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
index 8996b4c20e..488a010797 100644
--- a/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
+++ b/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
@@ -452,8 +452,8 @@ t8_default_scheme_pyramid_c::t8_element_MPI_Pack (t8_element_t **const elements,
     t8_dtet_t *p = &pyramids[ielem]->pyramid;
     t8_dtet_element_pack (&p, 1, send_buffer, buffer_size, position, comm);
 
-    SC_CHECK_MPI (sc_MPI_Pack (&pyramids[ielem]->switch_shape_at_level, 1, MPI_INT8_T, send_buffer, buffer_size,
-                               position, comm));
+    SC_CHECK_MPI (
+      sc_MPI_Pack (&pyramids[ielem]->switch_shape_at_level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm));
   }
 }
 

From 0e6523ab8e3c669dade899edb22c21a271b46fe2 Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Mon, 4 Nov 2024 10:46:55 +0100
Subject: [PATCH 05/13] Enable sc and p4est tests by default

---
 CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a573e8c8ec..c874789c8a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ option( T8CODE_BUILD_PEDANTIC "Compile t8code with `-Wall -pedantic -Werror` as
 option( T8CODE_EXPORT_COMPILE_COMMANDS "Export the compile commands as json. Can be used by IDEs for code completion (e.g. intellisense, clangd)" OFF )
 
 option( T8CODE_BUILD_TESTS "Build t8code's automated tests" ON )
-cmake_dependent_option( T8CODE_BUILD_TPL_TESTS "Build the tests from libsc and p4est" OFF "T8CODE_BUILD_TESTS" OFF )
+cmake_dependent_option( T8CODE_BUILD_TPL_TESTS "Build the tests from libsc and p4est" ON "T8CODE_BUILD_TESTS" OFF )
 cmake_dependent_option( T8CODE_ENABLE_LESS_TESTS "Tests not as thoroughly to speed up the test suite. Tests the same functionality. (WARNING: Use with care.)" OFF "T8CODE_BUILD_TESTS" OFF )
 
 option( T8CODE_BUILD_TUTORIALS "Build t8code's tutorials" ON )

From d4614d7b1bcc594cbb25e9ca120a0d1d0d869c4e Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Mon, 13 Jan 2025 14:38:25 +0100
Subject: [PATCH 06/13] MPI_INT8_T -> sc_MPI_INT8_T

---
 src/t8.h                                               |  2 +-
 .../t8_default/t8_default_hex/t8_default_hex.cxx       |  6 +++---
 .../t8_default/t8_default_line/t8_default_line.cxx     |  6 +++---
 .../t8_default/t8_default_prism/t8_default_prism.cxx   | 10 +++++-----
 .../t8_default_pyramid/t8_default_pyramid.cxx          |  6 +++---
 .../t8_default/t8_default_quad/t8_default_quad.cxx     |  6 +++---
 .../t8_default/t8_default_tri/t8_dtri_bits.c           | 10 +++++-----
 .../t8_default/t8_default_vertex/t8_default_vertex.cxx |  6 +++---
 8 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/src/t8.h b/src/t8.h
index adc573e2b7..232a597534 100644
--- a/src/t8.h
+++ b/src/t8.h
@@ -115,7 +115,7 @@ typedef int64_t t8_gloidx_t;
 /** A type for storing SFC indices */
 typedef uint64_t t8_linearidx_t;
 /** The MPI datatype of t8_linearidx_t */
-#define T8_MPI_LINEARIDX MPI_UNSIGNED_LONG_LONG
+#define T8_MPI_LINEARIDX sc_MPI_UNSIGNED_LONG_LONG
 
 #define T8_PADDING_SIZE (sizeof (void *))
 /** Compute the number of bytes that have to be added to a given byte_count
diff --git a/src/t8_schemes/t8_default/t8_default_hex/t8_default_hex.cxx b/src/t8_schemes/t8_default/t8_default_hex/t8_default_hex.cxx
index 801bf14e6b..222675e2f9 100644
--- a/src/t8_schemes/t8_default/t8_default_hex/t8_default_hex.cxx
+++ b/src/t8_schemes/t8_default/t8_default_hex/t8_default_hex.cxx
@@ -656,7 +656,7 @@ t8_default_scheme_hex::element_MPI_Pack (t8_element_t **const elements, const un
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Pack (&quads[ielem]->z, 1, sc_MPI_INT, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&quads[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&quads[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -675,7 +675,7 @@ t8_default_scheme_hex::element_MPI_Pack_size (const unsigned int count, sc_MPI_C
   singlesize += 3 * datasize;
 
   /* level */
-  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
@@ -696,7 +696,7 @@ t8_default_scheme_hex::element_MPI_Unpack (void *recvbuf, const int buffer_size,
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->z), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->level), 1, MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->level), 1, sc_MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_line/t8_default_line.cxx b/src/t8_schemes/t8_default/t8_default_line/t8_default_line.cxx
index d996dfb178..89ed58f541 100644
--- a/src/t8_schemes/t8_default/t8_default_line/t8_default_line.cxx
+++ b/src/t8_schemes/t8_default/t8_default_line/t8_default_line.cxx
@@ -449,7 +449,7 @@ t8_default_scheme_line::element_MPI_Pack (t8_element_t **const elements, const u
   for (unsigned int ielem = 0; ielem < count; ielem++) {
     mpiret = sc_MPI_Pack (&(lines[ielem]->x), 1, sc_MPI_INT, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&lines[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&lines[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -466,7 +466,7 @@ t8_default_scheme_line::element_MPI_Pack_size (const unsigned int count, sc_MPI_
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
-  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
@@ -483,7 +483,7 @@ t8_default_scheme_line::element_MPI_Unpack (void *recvbuf, const int buffer_size
   for (unsigned int ielem = 0; ielem < count; ielem++) {
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(lines[ielem]->x), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(lines[ielem]->level), 1, MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(lines[ielem]->level), 1, sc_MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_prism/t8_default_prism.cxx b/src/t8_schemes/t8_default/t8_default_prism/t8_default_prism.cxx
index 7405573d9f..d220d5b899 100644
--- a/src/t8_schemes/t8_default/t8_default_prism/t8_default_prism.cxx
+++ b/src/t8_schemes/t8_default/t8_default_prism/t8_default_prism.cxx
@@ -477,11 +477,11 @@ t8_default_scheme_prism::element_MPI_Pack (t8_element_t **const elements, const
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Pack (&prisms[ielem]->tri.y, 1, sc_MPI_INT, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&prisms[ielem]->tri.type, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&prisms[ielem]->tri.type, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
 
     T8_ASSERT (prisms[ielem]->line.level == prisms[ielem]->tri.level);
-    mpiret = sc_MPI_Pack (&prisms[ielem]->line.level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&prisms[ielem]->line.level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -500,7 +500,7 @@ t8_default_scheme_prism::element_MPI_Pack_size (const unsigned int count, sc_MPI
   singlesize += 3 * datasize;
 
   /*type, level*/
-  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += 2 * datasize;
 
@@ -521,9 +521,9 @@ t8_default_scheme_prism::element_MPI_Unpack (void *recvbuf, const int buffer_siz
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.y), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.type), 1, MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.type), 1, sc_MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.level), 1, MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(prisms[ielem]->tri.level), 1, sc_MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
     prisms[ielem]->line.level = prisms[ielem]->tri.level;
   }
diff --git a/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx b/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
index e0693be973..88bb4b3ca0 100644
--- a/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
+++ b/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
@@ -464,7 +464,7 @@ t8_default_scheme_pyramid::element_MPI_Pack (t8_element_t **const elements, cons
     t8_dtet_element_pack (&p, 1, send_buffer, buffer_size, position, comm);
 
     SC_CHECK_MPI (
-      sc_MPI_Pack (&pyramids[ielem]->switch_shape_at_level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm));
+      sc_MPI_Pack (&pyramids[ielem]->switch_shape_at_level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm));
   }
 }
 
@@ -479,7 +479,7 @@ t8_default_scheme_pyramid::element_MPI_Pack_size (const unsigned int count, sc_M
   singlesize += datasize;
 
   /* switch shape at level */
-  SC_CHECK_MPI (sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize));
+  SC_CHECK_MPI (sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize));
   singlesize += datasize;
 
   *pack_size = count * singlesize;
@@ -498,7 +498,7 @@ t8_default_scheme_pyramid::element_MPI_Unpack (void *recvbuf, const int buffer_s
     t8_dtet_element_unpack (recvbuf, buffer_size, position, &p, 1, comm);
 
     mpiret
-      = sc_MPI_Unpack (recvbuf, buffer_size, position, &pyramids[ielem]->switch_shape_at_level, 1, MPI_INT8_T, comm);
+      = sc_MPI_Unpack (recvbuf, buffer_size, position, &pyramids[ielem]->switch_shape_at_level, 1, sc_MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_quad/t8_default_quad.cxx b/src/t8_schemes/t8_default/t8_default_quad/t8_default_quad.cxx
index c0fa9b55b5..de115bae75 100644
--- a/src/t8_schemes/t8_default/t8_default_quad/t8_default_quad.cxx
+++ b/src/t8_schemes/t8_default/t8_default_quad/t8_default_quad.cxx
@@ -774,7 +774,7 @@ t8_default_scheme_quad::element_MPI_Pack (t8_element_t **const elements, const u
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Pack (&quads[ielem]->y, 1, sc_MPI_INT, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&quads[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&quads[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -793,7 +793,7 @@ t8_default_scheme_quad::element_MPI_Pack_size (const unsigned int count, sc_MPI_
   singlesize += 2 * datasize;
 
   /* level */
-  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
@@ -812,7 +812,7 @@ t8_default_scheme_quad::element_MPI_Unpack (void *recvbuf, const int buffer_size
     SC_CHECK_MPI (mpiret);
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->y), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->level), 1, MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(quads[ielem]->level), 1, sc_MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_tri/t8_dtri_bits.c b/src/t8_schemes/t8_default/t8_default_tri/t8_dtri_bits.c
index 8fed8fdc48..fed3b9039e 100644
--- a/src/t8_schemes/t8_default/t8_default_tri/t8_dtri_bits.c
+++ b/src/t8_schemes/t8_default/t8_default_tri/t8_dtri_bits.c
@@ -1718,9 +1718,9 @@ t8_dtri_element_pack (t8_dtri_t **const elements, const unsigned int count, void
     SC_CHECK_MPI (mpiret);
 #endif
 
-    mpiret = sc_MPI_Pack (&elements[ielem]->type, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&elements[ielem]->type, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Pack (&elements[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&elements[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -1744,7 +1744,7 @@ t8_dtri_element_pack_size (const unsigned int count, sc_MPI_Comm comm, int *pack
   singlesize += coord_count * datasize;
 
   /* type, level*/
-  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += 2 * datasize;
 
@@ -1766,9 +1766,9 @@ t8_dtri_element_unpack (void *recvbuf, const int buffer_size, int *position, t8_
     mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->z), 1, sc_MPI_INT, comm);
     SC_CHECK_MPI (mpiret);
 #endif
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->type), 1, MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->type), 1, sc_MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->level), 1, MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(elements[ielem]->level), 1, sc_MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
diff --git a/src/t8_schemes/t8_default/t8_default_vertex/t8_default_vertex.cxx b/src/t8_schemes/t8_default/t8_default_vertex/t8_default_vertex.cxx
index ab6a27696c..5c7bea179f 100644
--- a/src/t8_schemes/t8_default/t8_default_vertex/t8_default_vertex.cxx
+++ b/src/t8_schemes/t8_default/t8_default_vertex/t8_default_vertex.cxx
@@ -336,7 +336,7 @@ t8_default_scheme_vertex::element_MPI_Pack (t8_element_t **const elements, const
   int mpiret;
   t8_dvertex_t **vertices = (t8_dvertex_t **) elements;
   for (unsigned int ielem = 0; ielem < count; ielem++) {
-    mpiret = sc_MPI_Pack (&vertices[ielem]->level, 1, MPI_INT8_T, send_buffer, buffer_size, position, comm);
+    mpiret = sc_MPI_Pack (&vertices[ielem]->level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm);
     SC_CHECK_MPI (mpiret);
   }
 }
@@ -349,7 +349,7 @@ t8_default_scheme_vertex::element_MPI_Pack_size (const unsigned int count, sc_MP
   int datasize = 0;
   int mpiret;
 
-  mpiret = sc_MPI_Pack_size (1, MPI_INT8_T, comm, &datasize);
+  mpiret = sc_MPI_Pack_size (1, sc_MPI_INT8_T, comm, &datasize);
   SC_CHECK_MPI (mpiret);
   singlesize += datasize;
 
@@ -364,7 +364,7 @@ t8_default_scheme_vertex::element_MPI_Unpack (void *recvbuf, const int buffer_si
   int mpiret;
   t8_dvertex_t **vertices = (t8_dvertex_t **) elements;
   for (unsigned int ielem = 0; ielem < count; ielem++) {
-    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(vertices[ielem]->level), 1, MPI_INT8_T, comm);
+    mpiret = sc_MPI_Unpack (recvbuf, buffer_size, position, &(vertices[ielem]->level), 1, sc_MPI_INT8_T, comm);
     SC_CHECK_MPI (mpiret);
   }
 }

From 97409866ba415a6a23335adaf598f73de0cd4cdc Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Mon, 13 Jan 2025 14:47:38 +0100
Subject: [PATCH 07/13] fix indent

---
 .../t8_default/t8_default_pyramid/t8_default_pyramid.cxx      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx b/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
index 88bb4b3ca0..7ddd238aa3 100644
--- a/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
+++ b/src/t8_schemes/t8_default/t8_default_pyramid/t8_default_pyramid.cxx
@@ -463,8 +463,8 @@ t8_default_scheme_pyramid::element_MPI_Pack (t8_element_t **const elements, cons
     t8_dtet_t *p = &pyramids[ielem]->pyramid;
     t8_dtet_element_pack (&p, 1, send_buffer, buffer_size, position, comm);
 
-    SC_CHECK_MPI (
-      sc_MPI_Pack (&pyramids[ielem]->switch_shape_at_level, 1, sc_MPI_INT8_T, send_buffer, buffer_size, position, comm));
+    SC_CHECK_MPI (sc_MPI_Pack (&pyramids[ielem]->switch_shape_at_level, 1, sc_MPI_INT8_T, send_buffer, buffer_size,
+                               position, comm));
   }
 }
 

From 6709a74c16122919831db476bcd56db870bcb695 Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Mon, 13 Jan 2025 14:50:09 +0100
Subject: [PATCH 08/13] fix CMakeLists.txt

---
 CMakeLists.txt | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 65166ba839..2a129b6488 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,11 +1,15 @@
 cmake_minimum_required( VERSION 3.16 )
 
-include(cmake/GitProjectVersion.cmake)
+project( 
+    T8CODE
+    DESCRIPTION "Parallel algorithms and data structures for tree-based AMR with arbitrary element shapes."
+    LANGUAGES C CXX
+    VERSION "${T8CODE_VERSION_MAJOR}.${T8CODE_VERSION_MINOR}.${T8CODE_VERSION_PATCH}" 
+)
 
-project( T8CODE
-  DESCRIPTION "Parallel algorithms and data structures for tree-based AMR with arbitrary element shapes."
-  LANGUAGES C CXX
-  VERSION "${T8CODE_VERSION_MAJOR}.${T8CODE_VERSION_MINOR}.${T8CODE_VERSION_PATCH}" )
+include(cmake/GitProjectVersion.cmake)
+include( CTest )
+include( CMakeDependentOption )
 
 option( T8CODE_BUILD_AS_SHARED_LIBRARY "Whether t8code should be built as a shared or a static library" ON )
 option( T8CODE_BUILD_PEDANTIC "Compile t8code with `-pedantic` as done in the Github CI." OFF )

From 93f9688410e34e721cc1a9039632141fac68fddc Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Mon, 13 Jan 2025 15:01:17 +0100
Subject: [PATCH 09/13] fix CMakeLists.txt

---
 CMakeLists.txt | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2a129b6488..466657ace8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,7 @@
 cmake_minimum_required( VERSION 3.16 )
+include( cmake/GitProjectVersion.cmake )
+include( CTest )
+include( CMakeDependentOption )
 
 project( 
     T8CODE
@@ -7,10 +10,6 @@ project(
     VERSION "${T8CODE_VERSION_MAJOR}.${T8CODE_VERSION_MINOR}.${T8CODE_VERSION_PATCH}" 
 )
 
-include(cmake/GitProjectVersion.cmake)
-include( CTest )
-include( CMakeDependentOption )
-
 option( T8CODE_BUILD_AS_SHARED_LIBRARY "Whether t8code should be built as a shared or a static library" ON )
 option( T8CODE_BUILD_PEDANTIC "Compile t8code with `-pedantic` as done in the Github CI." OFF )
 option( T8CODE_BUILD_WALL "Compile t8code with `-Wall` as done in the Github CI." OFF )

From 5b880058c0c6d98c23caa53693b2b436c5cc8063 Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Mon, 13 Jan 2025 15:08:16 +0100
Subject: [PATCH 10/13] fix CMakeLists.txt

---
 CMakeLists.txt | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 466657ace8..c767ce4f08 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,7 +1,6 @@
 cmake_minimum_required( VERSION 3.16 )
+
 include( cmake/GitProjectVersion.cmake )
-include( CTest )
-include( CMakeDependentOption )
 
 project( 
     T8CODE
@@ -10,6 +9,9 @@ project(
     VERSION "${T8CODE_VERSION_MAJOR}.${T8CODE_VERSION_MINOR}.${T8CODE_VERSION_PATCH}" 
 )
 
+include( CTest )
+include( CMakeDependentOption )
+
 option( T8CODE_BUILD_AS_SHARED_LIBRARY "Whether t8code should be built as a shared or a static library" ON )
 option( T8CODE_BUILD_PEDANTIC "Compile t8code with `-pedantic` as done in the Github CI." OFF )
 option( T8CODE_BUILD_WALL "Compile t8code with `-Wall` as done in the Github CI." OFF )

From 3fb41f35da6b130b60cd1d76398c596e18173944 Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Mon, 13 Jan 2025 15:31:28 +0100
Subject: [PATCH 11/13] update libsc

---
 sc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sc b/sc
index c371874cdd..1b127f01c5 160000
--- a/sc
+++ b/sc
@@ -1 +1 @@
-Subproject commit c371874cdde434e831175d0feef3d869aa340c11
+Subproject commit 1b127f01c5e472039e938f61201ae0611fb25bad

From 2132126e55dd441ec96356c2a9dcde8a20f240c7 Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Thu, 16 Jan 2025 19:25:23 +0100
Subject: [PATCH 12/13] remove duplicates

---
 CMakeLists.txt | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index c767ce4f08..384be04072 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -33,10 +33,6 @@ option( T8CODE_ENABLE_NETCDF "Enable t8code's features which rely on netCDF" OFF
 option( T8CODE_USE_SYSTEM_SC "Use system-installed sc library" OFF )
 option( T8CODE_USE_SYSTEM_P4EST "Use system-installed p4est library" OFF )
 
-option( T8CODE_BUILD_AS_SHARED_LIBRARY "Whether t8code should be built as a shared or a static library" ON )
-option( T8CODE_BUILD_PEDANTIC "Compile t8code with `-Wall -pedantic -Werror` as done in the Github CI." OFF )
-option( T8CODE_EXPORT_COMPILE_COMMANDS "Export the compile commands as json. Can be used by IDEs for code completion (e.g. intellisense, clangd)" OFF )
-
 option( T8CODE_BUILD_TESTS "Build t8code's automated tests" ON )
 cmake_dependent_option( T8CODE_BUILD_TPL_TESTS "Build the tests from libsc and p4est" ON "T8CODE_BUILD_TESTS" OFF )
 cmake_dependent_option( T8CODE_ENABLE_LESS_TESTS "Tests not as thoroughly to speed up the test suite. Tests the same functionality. (WARNING: Use with care.)" OFF "T8CODE_BUILD_TESTS" OFF )

From a953e47e83597d40470baffcfbb5d7a3d7c367cd Mon Sep 17 00:00:00 2001
From: Alex Dutka <97711898+dutkalex@users.noreply.github.com>
Date: Mon, 20 Jan 2025 17:05:24 +0100
Subject: [PATCH 13/13] remove more duplicated options

---
 CMakeLists.txt | 21 +++++++--------------
 1 file changed, 7 insertions(+), 14 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 384be04072..94c036839a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -18,12 +18,17 @@ option( T8CODE_BUILD_WALL "Compile t8code with `-Wall` as done in the Github CI.
 option( T8CODE_BUILD_WERROR "Compile t8code with `-Werror` as done in the Github CI." OFF )
 option( T8CODE_BUILD_EXTRA_WARNINGS "Compile t8code with extra warnings as done in the Github CI." OFF )
 option( T8CODE_EXPORT_COMPILE_COMMANDS "Export the compile commands as json. Can be used by IDEs for code completion (e.g. intellisense, clangd)" OFF )
+
 option( T8CODE_BUILD_TESTS "Build t8code's automated tests" ON )
-option( T8CODE_BUILD_TUTORIALS "Build t8code's tutorials" ON )
+cmake_dependent_option( T8CODE_BUILD_TPL_TESTS "Build the tests from libsc and p4est" ON "T8CODE_BUILD_TESTS" OFF )
+cmake_dependent_option( T8CODE_ENABLE_LESS_TESTS "Tests not as thoroughly to speed up the test suite. Tests the same functionality. (WARNING: Use with care.)" OFF "T8CODE_BUILD_TESTS" OFF )
+
 option( T8CODE_BUILD_EXAMPLES "Build t8code's examples" ON )
+cmake_dependent_option( T8CODE_BUILD_TPL_EXAMPLES "Build the examples from libsc and p4est" OFF "T8CODE_BUILD_EXAMPLES" OFF )
+
+option( T8CODE_BUILD_TUTORIALS "Build t8code's tutorials" ON )
 option( T8CODE_BUILD_BENCHMARKS "Build t8code's benchmarks" ON )
 option( T8CODE_BUILD_FORTRAN_INTERFACE "Build t8code's Fortran interface" OFF )
-option( T8CODE_ENABLE_LESS_TESTS "Tests not as thoroughly to speed up the test suite. Tests the same functionality. (WARNING: Use with care.)" OFF )
 
 option( T8CODE_ENABLE_MPI "Enable t8code's features which rely on MPI" ON )
 option( T8CODE_ENABLE_VTK "Enable t8code's features which rely on VTK" OFF )
@@ -33,18 +38,6 @@ option( T8CODE_ENABLE_NETCDF "Enable t8code's features which rely on netCDF" OFF
 option( T8CODE_USE_SYSTEM_SC "Use system-installed sc library" OFF )
 option( T8CODE_USE_SYSTEM_P4EST "Use system-installed p4est library" OFF )
 
-option( T8CODE_BUILD_TESTS "Build t8code's automated tests" ON )
-cmake_dependent_option( T8CODE_BUILD_TPL_TESTS "Build the tests from libsc and p4est" ON "T8CODE_BUILD_TESTS" OFF )
-cmake_dependent_option( T8CODE_ENABLE_LESS_TESTS "Tests not as thoroughly to speed up the test suite. Tests the same functionality. (WARNING: Use with care.)" OFF "T8CODE_BUILD_TESTS" OFF )
-
-option( T8CODE_BUILD_TUTORIALS "Build t8code's tutorials" ON )
-
-option( T8CODE_BUILD_EXAMPLES "Build t8code's examples" ON )
-cmake_dependent_option( T8CODE_BUILD_TPL_EXAMPLES "Build the examples from libsc and p4est" OFF "T8CODE_BUILD_EXAMPLES" OFF )
-
-option( T8CODE_BUILD_BENCHMARKS "Build t8code's benchmarks" ON )
-option( T8CODE_BUILD_FORTRAN_INTERFACE "Build t8code's Fortran interface" OFF )
-
 option( T8CODE_BUILD_DOCUMENTATION "Build t8code's documentation" OFF )
 cmake_dependent_option( T8CODE_BUILD_DOCUMENTATION_SPHINX "Build t8code's documentation using sphinx" OFF "T8CODE_BUILD_DOCUMENTATION" OFF )