Merge remote-tracking branch 'origin/main' into nix

Author: krystophny

README.md

@@ -16,8 +16,9 @@ CODE is based around our standard Debian bookworm system at ITPcp and provides
 
 ## Getting Started
 
-If you haven't done so earlier, set up your SSH keys in `~/.ssh` via `ssh-keygen` and
-add the content of `id_rsa.pub` to Gitlab and GitHub for authentication.
+If you haven't done so earlier, set up your SSH keys in `~/.ssh` via `ssh-keygen`
+with a **blank passphrase** and add the content of `id_rsa.pub` to Gitlab and GitHub 
+for authentication.
 
 ### Perparing your machine
 
@@ -47,14 +48,20 @@ Run the setup script manually with
 
     scripts/setup.sh
 
-The setup will install external dependencies and create and activate
+The setup will install external dependencies and create
 a Python virtual environment in the hidden `.venv` directory.
 
-If you work outside a container, also manually run
+Finally, activate the environment with
+    
+    source activate.sh
 
-    source /path/to/code/activate.sh
+To use this environment as a standard, edit your bashrc with
 
-and put this line in your bashrc.
+    code ~/.bashrc
+
+and put as a last line
+
+    source <path to your code copy>/activate.sh
 
 
 ## Testing

modules/mars/2022

@@ -2,7 +2,7 @@
 
 module-whatis "MARS (2022)"
 
-prereq nvhpc/24.5
+prereq nvhpc/24.1
 
 setenv       MARSHOME        $env(CODE)/external/MARS/MarsQ_2022
 prepend-path PATH            $env(MARSHOME)

scripts/setup/debian.sh

@@ -1,16 +1,14 @@
 #!/bin/bash
+set -e
 
-# Enable non-free packages
-sudo sed -i -e's/ main$/ main contrib non-free non-free-firmware/g' \
-    /etc/apt/sources.list.d/debian.sources
-sudo sed -i -e's/ main$/ main contrib non-free non-free-firmware/g' \
-    /etc/apt/sources.list
+# src: https://stackoverflow.com/a/246128/16527499
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
 
-sudo apt-get update -y && apt-get upgrade -y -q --no-install-recommends
+sudo apt-get update -y && sudo apt-get upgrade -y -q --no-install-recommends
 
-sudo $CODE/scripts/setup/debian/base.sh
-sudo $CODE/scripts/setup/debian/interactive.sh
-sudo $CODE/scripts/setup/debian/libs.sh
-sudo $CODE/scripts/setup/debian/octave.sh
-sudo $CODE/scripts/setup/debian/texlive.sh
-sudo $CODE/scripts/setup/debian/fonts.sh
+sudo $SCRIPT_DIR/debian/base.sh
+sudo $SCRIPT_DIR/debian/interactive.sh
+sudo $SCRIPT_DIR/debian/libs.sh
+sudo $SCRIPT_DIR/debian/octave.sh
+sudo $SCRIPT_DIR/debian/texlive.sh
+sudo $SCRIPT_DIR/debian/fonts.sh

scripts/setup/debian/base.sh

@@ -25,4 +25,6 @@ apt-get install -y -q --no-install-recommends \
     python3-dev \
     python3-pip \
     python3-venv \
-    nix-bin
+    nix-bin \
+    bash \
+    csh

scripts/setup/debian/libs.sh

@@ -23,7 +23,8 @@ apt-get install -y -q --no-install-recommends \
     libparmetis-dev \
     libscotch-dev \
     libzstd-dev \
-    cppzmq-dev \
+    libgmp-dev \
+    libmpfr-dev \
     uuid-dev \
     petsc-dev \
     slepc-dev \

scripts/setup/kamel.sh

@@ -6,17 +6,7 @@ cd slatec
 mkdir lib
 curl -L https://www.netlib.org/slatec/slatec_src.tgz -o - | tar xz
 
-# Check the operating system
-if [[ "$(uname)" == "Darwin" ]]; then
-    # macOS specific compiler flags
-    CFLAGS="-O2"
-elif [[ "$(uname)" == "Linux" ]]; then
-    # Linux specific compiler flags
-    CFLAGS="-msse2 -mfpmath=sse"
-else
-    # Default compiler flags for other operating systems
-    CFLAGS=""
-fi
+CFLAGS="-O2"
 gfortran -c -Wall -Wtabs -mtune=generic $CFLAGS src/*.f
 ar rcs libslatec.a *.o
 rm *.o
@@ -27,7 +17,7 @@ echo ""
 echo "Building Sundials..."
 cd ..
 git clone [email protected]:LLNL/sundials.git
-cd sundials 
+cd sundials
 git checkout v5.7.0
 mkdir build
 cd build

scripts/setup/lazygit.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+install_lazygit() {
+    if ! command -v lazygit &>/dev/null; then
+        echo installing Lazygit...
+        LAZYGIT_VERSION=$(curl -s "https://api.github.com/repos/jesseduffield/lazygit/releases/latest" | grep -Po '"tag_name": "v\K[^"]*')
+        curl -Lo lazygit.tar.gz --output-dir /tmp "https://github.com/jesseduffield/lazygit/releases/latest/download/lazygit_${LAZYGIT_VERSION}_Linux_x86_64.tar.gz"
+        tar -xf /tmp/lazygit.tar.gz -C /tmp lazygit
+	mkdir -p $HOME/.local/bin
+        install /tmp/lazygit $HOME/.local/bin
+        rm /tmp/lazygit*
+        echo Lazygit installed
+    else
+        echo Lazygit already installed
+    fi
+}
+
+install_lazygit

scripts/setup/mars.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 set -e
-module load nvhpc/24.5
+module load nvhpc/24.1
 git clone [email protected]:plasma/codes/mars.git MARS
 cd MARS/MarsQ_2022
 make