From a6aa83507b12e775ad11dfb2c328c8de2609562f Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Tue, 4 Jun 2024 16:18:19 +0200
Subject: [PATCH 1/3] Update MPCDF instructions

---
 bin/bout-build-deps.sh                       | 12 ++++++------
 manual/sphinx/user_docs/advanced_install.rst | 15 +++++++--------
 2 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/bin/bout-build-deps.sh b/bin/bout-build-deps.sh
index 19e3b2a0d3..25b50e0948 100755
--- a/bin/bout-build-deps.sh
+++ b/bin/bout-build-deps.sh
@@ -286,17 +286,17 @@ set -x
 ## Setup folders and links
 setup
 ## Build and install hdf5
-hdf5
+test $NO_HDF5 || hdf5
 ## Build and install netcdf
-netcdf
+test $NO_NETCDF || netcdf
 ## Build and install C++ interface for netcdf
-nccxx
+test $NO_NCXX || nccxx
 ## Build and install FFTW
-fftw
+test $NO_FFTW || fftw
 ## Build and install Sundials
-sundials
+test $NO_SUNDIALS || sundials
 ## Build and install PETSc
-petsc
+test $NO_PETSC || petsc
 ## Download BOUT++ submodules
 submod
 # Install python packages
diff --git a/manual/sphinx/user_docs/advanced_install.rst b/manual/sphinx/user_docs/advanced_install.rst
index 57ac5f8e3f..048a26a6e3 100644
--- a/manual/sphinx/user_docs/advanced_install.rst
+++ b/manual/sphinx/user_docs/advanced_install.rst
@@ -145,13 +145,12 @@ where ``<build-directory>`` is the path to the build directory
 
 MPCDF HPC Systems
 ~~~~~~~~~~~~~~~~~
+After cloning BOUT-dev and checking out the branch you want (e.g. db-outer), run:
 .. code-block:: bash
 
-    module purge # or at least onload intel and impi and mkl
-    module load gcc/10 cmake/3.18 openmpi/4
-    # ensure python3 is >= python3.6 - skip if you have a newer python3 loaded
-    mkdir -p $HOME/bin ; test -e $HOME/bin/python3 || ln -s $(which python3.6) $HOME/bin/python3
-    BUILD=/ptmp/$USER/bout-deps bin/bout-build-deps.sh
+    module purge # or at least onload intel
+    module load gcc/13 anaconda/3/2021.11 impi/2021.9 hdf5-serial/1.12.2 mkl/2022.0 netcdf-serial/4.8.1 fftw-mpi/3.3.10
+    BUILD=/ptmp/$USER/bout-deps NO_HDF5=1 NO_NETCDF=1 NO_FFTW=1 bin/bout-build-deps.sh
 
 and follow the instructions for configuring BOUT++. To enable openMP
 for a production run use:
@@ -159,11 +158,11 @@ for a production run use:
 .. code-block:: bash
 
     module load bout-dep
-    cmake .. -DBOUT_USE_NETCDF=ON -DnetCDF_ROOT=$BOUT_DEP -DnetCDFCxx_ROOT=$BOUT_DEP \
+    cmake .. -DBOUT_USE_NETCDF=ON -DnetCDFCxx_ROOT=$BOUT_DEP \
       -DBOUT_USE_PETSC=ON -DPETSC_DIR=$BOUT_DEP \
-      -DBOUT_USE_FFTW=ON -DFFTW_ROOT=$BOUT_DEP \
+      -DBOUT_USE_FFTW=ON \
       -DBOUT_USE_SUNDIALS=ON -DSUNDIALS_ROOT=$BOUT_DEP \
-      -DBOUT_ENABLE_OPENMP=ON \
+      -DBOUT_ENABLE_OPENMP=OFF \
       -DCMAKE_BUILD_TYPE=Release
 
 

From 77103c2463af2031b24ee2555586a6c89ede4190 Mon Sep 17 00:00:00 2001
From: David Bold <dave@ipp.mpg.de>
Date: Wed, 5 Jun 2024 12:00:52 +0200
Subject: [PATCH 2/3] Fix netcdf-cxx4 url

---
 bin/bout-build-deps.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/bout-build-deps.sh b/bin/bout-build-deps.sh
index 25b50e0948..6acd3d82bf 100755
--- a/bin/bout-build-deps.sh
+++ b/bin/bout-build-deps.sh
@@ -98,7 +98,7 @@ netcdf() {
 
 nccxx() {
     cd $BUILD
-    wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-cxx4-$NCCXXVER.tar.gz || :
+    wget -c https://downloads.unidata.ucar.edu/netcdf-cxx/4.3.1/netcdf-cxx4-$NCCXXVER.tar.gz || :
     tar -xf netcdf-cxx4-$NCCXXVER.tar.gz
     cd netcdf-cxx4-$NCCXXVER
     CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib/" ./configure --prefix=$PREFIX $NCCXXFLAGS

From d67016ad5f43e0ea15f4fc002c87dcac74cc56b3 Mon Sep 17 00:00:00 2001
From: David Bold <dschwoerer@users.noreply.github.com>
Date: Mon, 10 Jun 2024 10:12:31 +0200
Subject: [PATCH 3/3] Fix URL

thanks @ZedThree for noticing
---
 bin/bout-build-deps.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/bout-build-deps.sh b/bin/bout-build-deps.sh
index 6acd3d82bf..d96d500dc9 100755
--- a/bin/bout-build-deps.sh
+++ b/bin/bout-build-deps.sh
@@ -98,7 +98,7 @@ netcdf() {
 
 nccxx() {
     cd $BUILD
-    wget -c https://downloads.unidata.ucar.edu/netcdf-cxx/4.3.1/netcdf-cxx4-$NCCXXVER.tar.gz || :
+    wget -c https://downloads.unidata.ucar.edu/netcdf-cxx/$NCCXXVER/netcdf-cxx4-$NCCXXVER.tar.gz || :
     tar -xf netcdf-cxx4-$NCCXXVER.tar.gz
     cd netcdf-cxx4-$NCCXXVER
     CPPFLAGS="-I$PREFIX/include" LDFLAGS="-L$PREFIX/lib/" ./configure --prefix=$PREFIX $NCCXXFLAGS