From 9585270e9107f37edcc6963bec6f2a44552336af Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 7 Jan 2026 21:23:14 +0100
Subject: [PATCH 01/61] GitHub CI: mpiexec -n 4 --oversubscribe

---
 .github/actions/alf_test/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index ef675919..01471be7 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -42,7 +42,7 @@ runs:
         if echo "$MODE" | grep -iq -e "serial" -e "noMPI"; then
           "$ALF_DIR/Prog/ALF.out"
         else
-          mpiexec -n 2 "$ALF_DIR/Prog/ALF.out" # only 2 cores available in githubs runners
+          mpiexec -n 4 --oversubscribe "$ALF_DIR/Prog/ALF.out"
         fi
         if echo "$MODE" | grep -iq -e "TEMPERING" -e "PARALLEL_PARAMS"; then cd Temp_0; fi
         if echo "$CONFIG_ARGS" | grep -iq "HDF5"; then

From e0aa5b3e47da5440eabb9d11e2e9b17c1522a3c0 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 7 Jan 2026 21:25:08 +0100
Subject: [PATCH 02/61] test

---
 .github/actions/alf_test/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index 01471be7..d63f8e77 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -42,7 +42,7 @@ runs:
         if echo "$MODE" | grep -iq -e "serial" -e "noMPI"; then
           "$ALF_DIR/Prog/ALF.out"
         else
-          mpiexec -n 4 --oversubscribe "$ALF_DIR/Prog/ALF.out"
+          mpiexec -n 4 --oversubscribe "$ALF_DIR/Prog/ALF.out"  # test
         fi
         if echo "$MODE" | grep -iq -e "TEMPERING" -e "PARALLEL_PARAMS"; then cd Temp_0; fi
         if echo "$CONFIG_ARGS" | grep -iq "HDF5"; then

From 02ea0cb2c4e392d17681b1dd76b12d274d60e1d7 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 7 Jan 2026 21:35:12 +0100
Subject: [PATCH 03/61] Enable mpi oversubscribe via environment variable.

---
 .github/actions/alf_test/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index d63f8e77..4dc68ad2 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -42,7 +42,7 @@ runs:
         if echo "$MODE" | grep -iq -e "serial" -e "noMPI"; then
           "$ALF_DIR/Prog/ALF.out"
         else
-          mpiexec -n 4 --oversubscribe "$ALF_DIR/Prog/ALF.out"  # test
+          OMPI_MCA_rmaps_base_oversubscribe=true mpiexec -n 4 "$ALF_DIR/Prog/ALF.out"
         fi
         if echo "$MODE" | grep -iq -e "TEMPERING" -e "PARALLEL_PARAMS"; then cd Temp_0; fi
         if echo "$CONFIG_ARGS" | grep -iq "HDF5"; then

From fe298331d935bffa5cae1413906688a14c115b04 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 14:08:44 +0100
Subject: [PATCH 04/61] test

---
 .github/actions/alf_test/action.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index 4dc68ad2..f6e39683 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -29,6 +29,7 @@ runs:
         OMPI_ALLOW_RUN_AS_ROOT: 1 # needed for mpi runnig as root, needed by github runner
         OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
       run: |
+        nproc
         . ./configure.sh $ARGS
         echo $ALF_FC
         $ALF_FC --version

From 89db50fcb13a6468001a54f81f500f8d963bf57d Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 14:13:15 +0100
Subject: [PATCH 05/61] Do not run containers as root

---
 .github/actions/alf_test/action.yml | 2 --
 .github/workflows/ci.yml            | 6 ------
 2 files changed, 8 deletions(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index f6e39683..973352e4 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -26,8 +26,6 @@ runs:
       shell: bash
       env:
         ARGS: ${{ inputs.args }}
-        OMPI_ALLOW_RUN_AS_ROOT: 1 # needed for mpi runnig as root, needed by github runner
-        OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
       run: |
         nproc
         . ./configure.sh $ARGS
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 62c5cd93..7f565ce2 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -128,7 +128,6 @@ jobs:
         config: ["", "HDF5"]
     container:
       image: ghcr.io/alf-qmc/alf-container/alf-requirements/${{ matrix.image_minor }}
-      options: --user 0
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/alf_test
@@ -145,7 +144,6 @@ jobs:
         config: ["", "HDF5"]
     container:
       image: ghcr.io/alf-qmc/alf-container/alf-requirements/bullseye-openblas
-      options: --user 0
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/alf_test
@@ -163,7 +161,6 @@ jobs:
         config: ["", "HDF5"]
     container:
       image: ghcr.io/alf-qmc/alf-container/alf-requirements/bullseye-pgi-21-03
-      options: --user 0
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/alf_test
@@ -183,7 +180,6 @@ jobs:
         config: ["", "HDF5"]
     container:
       image: ghcr.io/alf-qmc/alf-container/alf-requirements/${{ matrix.image_minor }}
-      options: --user 0
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/alf_test
@@ -201,7 +197,6 @@ jobs:
         config: ["", "HDF5"]
     container:
       image: ghcr.io/alf-qmc/alf-container/alf-requirements/bookworm-intel
-      options: --user 0
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/alf_test
@@ -230,7 +225,6 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ghcr.io/alf-qmc/alf-container/alf-requirements/bullseye
-      options: --user 0
     steps:
       - uses: actions/checkout@v4
       - name: Run Valgrind

From 347033e81c9e73b90ba81e7bb52d0cb3d48bdc6a Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 14:18:06 +0100
Subject: [PATCH 06/61] test

---
 .github/actions/alf_test/action.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index 973352e4..1720d51b 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -27,7 +27,12 @@ runs:
       env:
         ARGS: ${{ inputs.args }}
       run: |
-        nproc
+        if [[ $(uname) == "Darwin" ]]; then
+          export NPROC=$(sysctl -n hw.ncpu)
+        else
+          export NPROC=$(nproc)
+        fi
+        echo "There are $NPROC processors available."
         . ./configure.sh $ARGS
         echo $ALF_FC
         $ALF_FC --version

From 09b06243773c62d49d93827813ea307674613f70 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 16:48:11 +0100
Subject: [PATCH 07/61] test

---
 .github/actions/alf_test/action.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index 1720d51b..d72a3055 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -9,7 +9,6 @@ runs:
   using: "composite"
   steps:
     - name: macOS Toolchain install
-
       if: runner.os == 'macOS'
       shell: bash
       run: |
@@ -22,7 +21,6 @@ runs:
         ln -fs ${bindir}/g++-${gcc_version} /usr/local/bin/g++
 
     - name: Build & Test
-
       shell: bash
       env:
         ARGS: ${{ inputs.args }}
@@ -54,6 +52,10 @@ runs:
         else
           "$ALF_DIR/Analysis/ana.out" *
         fi
+
+    - name: Run unit tests
+      shell: bash
+      run: |
         mkdir -p "$ALF_DIR/testsuite/tests"
         cd "$ALF_DIR/testsuite/tests"
         if echo "$ALF_FC" | grep -q "mpiifort -fc=ifx"; then exit 0; fi

From 925f4e480e9951f023d06b07f9a9dc700c550bd4 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 17:05:42 +0100
Subject: [PATCH 08/61] test

---
 .github/actions/alf_test/action.yml | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index d72a3055..713ae079 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -20,17 +20,21 @@ runs:
         ln -fs ${bindir}/gcc-${gcc_version} /usr/local/bin/gcc
         ln -fs ${bindir}/g++-${gcc_version} /usr/local/bin/g++
 
-    - name: Build & Test
+    - name: Get number of processors
       shell: bash
-      env:
-        ARGS: ${{ inputs.args }}
       run: |
         if [[ $(uname) == "Darwin" ]]; then
-          export NPROC=$(sysctl -n hw.ncpu)
+          NPROC=$(sysctl -n hw.ncpu)
         else
-          export NPROC=$(nproc)
+          NPROC=$(nproc)
         fi
         echo "There are $NPROC processors available."
+
+    - name: Build & Test
+      shell: bash
+      env:
+        ARGS: ${{ inputs.args }}
+      run: |
         . ./configure.sh $ARGS
         echo $ALF_FC
         $ALF_FC --version
@@ -55,7 +59,10 @@ runs:
 
     - name: Run unit tests
       shell: bash
+      env:
+        ARGS: ${{ inputs.args }}
       run: |
+        . ./configure.sh $ARGS
         mkdir -p "$ALF_DIR/testsuite/tests"
         cd "$ALF_DIR/testsuite/tests"
         if echo "$ALF_FC" | grep -q "mpiifort -fc=ifx"; then exit 0; fi

From a7680484930457dc08bcdb0e8a5fa69ba83084e3 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 21:10:27 +0100
Subject: [PATCH 09/61] Mac runner: Use MPICH instead of Open-MPI

---
 .github/actions/alf_test/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index 713ae079..834b92e1 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -13,7 +13,7 @@ runs:
       shell: bash
       run: |
         brew update
-        brew install gcc cmake open-mpi
+        brew install gcc cmake mpich
         gcc_version=$(brew list --versions gcc | grep -o '[0-9]\+' | head -1)
         bindir=$(brew --prefix)/bin
         ln -fs ${bindir}/gfortran-${gcc_version} /usr/local/bin/gfortran

From 666d8580de3d21dc081d506a938fa07732c64680 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 21:19:55 +0100
Subject: [PATCH 10/61] CI: OpenMPI: --use-hwthread-cpus

---
 .github/actions/alf_test/action.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index 834b92e1..eba47aa2 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -48,7 +48,9 @@ runs:
         if echo "$MODE" | grep -iq -e "serial" -e "noMPI"; then
           "$ALF_DIR/Prog/ALF.out"
         else
-          OMPI_MCA_rmaps_base_oversubscribe=true mpiexec -n 4 "$ALF_DIR/Prog/ALF.out"
+          MPI_OPTS="-n 4"
+          if mpiexec --version | grep -iq 'Open MPI'; then MPI_OPTS="$MPI_OPTS --use-hwthread-cpus"; fi
+          mpiexec $MPI_OPTS "$ALF_DIR/Prog/ALF.out"
         fi
         if echo "$MODE" | grep -iq -e "TEMPERING" -e "PARALLEL_PARAMS"; then cd Temp_0; fi
         if echo "$CONFIG_ARGS" | grep -iq "HDF5"; then

From e6f0752210f13419569eab75e9019b9bb9de905b Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 21:43:38 +0100
Subject: [PATCH 11/61] Simpify CI config

---
 .github/workflows/ci.yml | 91 ++++++++--------------------------------
 1 file changed, 18 insertions(+), 73 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 7f565ce2..9d8ed50c 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -116,92 +116,36 @@ jobs:
   # Linux tests
   # ======================
 
-  test_linux_gnu:
+  test_linux:
     name: ${{ matrix.image_minor }} · ${{ matrix.mode }} · ${{ matrix.devel }} · ${{ matrix.config }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        image_minor: [bullseye, bookworm, trixie]
+        image_minor: 
+          - [bullseye, GNU]
+          - [bookworm, GNU]
+          - [trixie, GNU]
+          - [tumbleweed, GNU]
+          - [bullseye-pgi-21-03, PGI]
+          - [bullseye-intel, INTEL]
+          - [bookworm-intel-2024.2, INTEL]
+          - [bookworm-intel, INTELLLVM]
         mode: [noMPI, MPI, TEMPERING, PARALLEL_PARAMS]
         devel: ["", "Devel"]
         config: ["", "HDF5"]
+        include:
+          - image_minor: [bullseye-openblas, GNU]
+            mode: [noMPI]
+            devel: ["", "Devel"]
+            config: ["", "HDF5"]
     container:
-      image: ghcr.io/alf-qmc/alf-container/alf-requirements/${{ matrix.image_minor }}
+      image: ghcr.io/alf-qmc/alf-container/alf-requirements/${{ matrix.image_minor[0] }}
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/alf_test
         with:
-          args: GNU ${{ matrix.mode }} ${{ matrix.devel }} ${{ matrix.config }}
-
-  test_linux_gnu_openblas:
-    name: bullseye-openblas · ${{ matrix.devel }} · ${{ matrix.config }}
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        devel: ["", "Devel"]
-        config: ["", "HDF5"]
-    container:
-      image: ghcr.io/alf-qmc/alf-container/alf-requirements/bullseye-openblas
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/alf_test
-        with:
-          args: GNU ${{ matrix.mode }} ${{ matrix.devel }} ${{ matrix.config }}
-
-  test_linux_pgi:
-    name: bullseye-pgi-21-03 · ${{ matrix.mode }} · ${{ matrix.devel }} · ${{ matrix.config }}
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        mode: [noMPI, MPI, TEMPERING, PARALLEL_PARAMS]
-        devel: ["", "Devel"]
-        config: ["", "HDF5"]
-    container:
-      image: ghcr.io/alf-qmc/alf-container/alf-requirements/bullseye-pgi-21-03
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/alf_test
-        with:
-          with:
-          args: PGI ${{ matrix.mode }} ${{ matrix.devel }} ${{ matrix.config }}
-
-  test_linux_intel:
-    name: ${{ matrix.image_minor }} · ${{ matrix.mode }} · ${{ matrix.devel }} · ${{ matrix.config }}
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        image_minor: [bullseye-intel, bookworm-intel-2024.2]
-        mode: [noMPI, MPI, TEMPERING, PARALLEL_PARAMS]
-        devel: ["", "Devel"]
-        config: ["", "HDF5"]
-    container:
-      image: ghcr.io/alf-qmc/alf-container/alf-requirements/${{ matrix.image_minor }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/alf_test
-        with:
-          args: INTEL ${{ matrix.mode }} ${{ matrix.devel }} ${{ matrix.config }}
-
-  test_linux_intelllvm:
-    name: bookworm-intel · ${{ matrix.mode }} · ${{ matrix.devel }} · ${{ matrix.config }}
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        mode: [noMPI, MPI, TEMPERING, PARALLEL_PARAMS]
-        devel: ["", "Devel"]
-        config: ["", "HDF5"]
-    container:
-      image: ghcr.io/alf-qmc/alf-container/alf-requirements/bookworm-intel
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/alf_test
-        with:
-          args: INTELLLVM ${{ matrix.mode }} ${{ matrix.devel }} ${{ matrix.config }}
+          args: ${{ matrix.image_minor[1] }} ${{ matrix.mode }} ${{ matrix.devel }} ${{ matrix.config }}
 
   test_macos:
     name: macOS · ${{ matrix.mode }} · ${{ matrix.devel }}
@@ -211,6 +155,7 @@ jobs:
       matrix:
         mode: [noMPI, MPI, TEMPERING, PARALLEL_PARAMS]
         devel: ["", "Devel"]
+        config: [""]  # TODO: Enable fast access to HDF5 on macOS runners
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/alf_test

From c9850835b778693e366c4c6d164d9e5d598e5d1f Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 21:58:07 +0100
Subject: [PATCH 12/61] CI: No tumbleweed for now

---
 .github/workflows/ci.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9d8ed50c..76e08d02 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -117,7 +117,7 @@ jobs:
   # ======================
 
   test_linux:
-    name: ${{ matrix.image_minor }} · ${{ matrix.mode }} · ${{ matrix.devel }} · ${{ matrix.config }}
+    name: ${{ matrix.image_minor[0] }} · ${{ matrix.mode }} · ${{ matrix.devel }} · ${{ matrix.config }}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -126,7 +126,7 @@ jobs:
           - [bullseye, GNU]
           - [bookworm, GNU]
           - [trixie, GNU]
-          - [tumbleweed, GNU]
+          # - [tumbleweed, GNU]
           - [bullseye-pgi-21-03, PGI]
           - [bullseye-intel, INTEL]
           - [bookworm-intel-2024.2, INTEL]

From 32b4ee169b2af175007b4916ab494f95faf695de Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 22:15:43 +0100
Subject: [PATCH 13/61] CI: OpenMPI: --use-hwthread-cpus, catch more

---
 .github/actions/alf_test/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index eba47aa2..f3fca40c 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -49,7 +49,7 @@ runs:
           "$ALF_DIR/Prog/ALF.out"
         else
           MPI_OPTS="-n 4"
-          if mpiexec --version | grep -iq 'Open MPI'; then MPI_OPTS="$MPI_OPTS --use-hwthread-cpus"; fi
+          if mpiexec --version | grep -iq -e 'Open MPI' -e 'OpenRTE'; then MPI_OPTS="$MPI_OPTS --use-hwthread-cpus"; fi
           mpiexec $MPI_OPTS "$ALF_DIR/Prog/ALF.out"
         fi
         if echo "$MODE" | grep -iq -e "TEMPERING" -e "PARALLEL_PARAMS"; then cd Temp_0; fi

From 6c374741688eaa697f53af7c733e3a0e0f4c2243 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 8 Jan 2026 22:26:41 +0100
Subject: [PATCH 14/61] CI: Handle MacOS warnings

---
 .github/actions/alf_test/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index f3fca40c..b685f592 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -13,7 +13,7 @@ runs:
       shell: bash
       run: |
         brew update
-        brew install gcc cmake mpich
+        brew install mpich
         gcc_version=$(brew list --versions gcc | grep -o '[0-9]\+' | head -1)
         bindir=$(brew --prefix)/bin
         ln -fs ${bindir}/gfortran-${gcc_version} /usr/local/bin/gfortran

From 60814f60673c52f036b7f707bdf6e38190a73cd6 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 9 Jan 2026 00:45:02 +0100
Subject: [PATCH 15/61] CI: Add tumbleweed and PGI images

---
 .github/workflows/ci.yml | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 76e08d02..d7bf83a5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -126,19 +126,16 @@ jobs:
           - [bullseye, GNU]
           - [bookworm, GNU]
           - [trixie, GNU]
+          - [bullseye-openblas, GNU]
           # - [tumbleweed, GNU]
           - [bullseye-pgi-21-03, PGI]
+          - [bookworm-pgi-24-09, PGI]
           - [bullseye-intel, INTEL]
           - [bookworm-intel-2024.2, INTEL]
           - [bookworm-intel, INTELLLVM]
         mode: [noMPI, MPI, TEMPERING, PARALLEL_PARAMS]
         devel: ["", "Devel"]
         config: ["", "HDF5"]
-        include:
-          - image_minor: [bullseye-openblas, GNU]
-            mode: [noMPI]
-            devel: ["", "Devel"]
-            config: ["", "HDF5"]
     container:
       image: ghcr.io/alf-qmc/alf-container/alf-requirements/${{ matrix.image_minor[0] }}
     steps:
@@ -175,7 +172,6 @@ jobs:
       - name: Run Valgrind
         shell: bash
         run: |
-          apt-get update && apt-get install -y valgrind
           . ./configure.sh GNU devel serial
           gfortran -v
           make lib

From 57ed632690db352704365f99cd4cee901af8ee79 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 9 Jan 2026 00:45:46 +0100
Subject: [PATCH 16/61] CI: Add tumbleweed

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d7bf83a5..1fa808d9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -127,7 +127,7 @@ jobs:
           - [bookworm, GNU]
           - [trixie, GNU]
           - [bullseye-openblas, GNU]
-          # - [tumbleweed, GNU]
+          - [tumbleweed, GNU]
           - [bullseye-pgi-21-03, PGI]
           - [bookworm-pgi-24-09, PGI]
           - [bullseye-intel, INTEL]

From 9ab3ec7aeedad2f37d8abf74fc327663b2a9a465 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 9 Jan 2026 01:31:02 +0100
Subject: [PATCH 17/61] CI: No Tumbleweed

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1fa808d9..d7bf83a5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -127,7 +127,7 @@ jobs:
           - [bookworm, GNU]
           - [trixie, GNU]
           - [bullseye-openblas, GNU]
-          - [tumbleweed, GNU]
+          # - [tumbleweed, GNU]
           - [bullseye-pgi-21-03, PGI]
           - [bookworm-pgi-24-09, PGI]
           - [bullseye-intel, INTEL]

From bdb4890175ffdd406a01ab4e4d3279be6d59e9d8 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Mon, 12 Jan 2026 15:37:06 +0100
Subject: [PATCH 18/61] CI: Try ubuntu-slim

---
 .github/workflows/ci.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d7bf83a5..bbcc3dc0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -20,7 +20,7 @@ concurrency:
 jobs:
   lint_stopcommands:
     name: Lint Fortran STOP statements
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     steps:
       - uses: actions/checkout@v4
       - name: Check for forbidden STOP/ERROR STOP
@@ -34,7 +34,7 @@ jobs:
 
   create_doc:
     name: Build LaTeX documentation (doc.pdf)
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     needs: [lint_stopcommands]
     container:
       image: aergus/latex
@@ -62,7 +62,7 @@ jobs:
 
   create_doxygen:
     name: Generate Doxygen HTML
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     needs: [lint_stopcommands]
     steps:
       - uses: actions/checkout@v4
@@ -82,7 +82,7 @@ jobs:
 
   deploy_pages:
     name: Deploy GitHub Pages (master only)
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     needs: [create_doc, create_doxygen]
     if: github.ref == 'refs/heads/master'
     environment:

From c2a262eae589101953f17cbbac062b3dd7171635 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 10:37:47 +0100
Subject: [PATCH 19/61] CI: ubuntu-slim only without custom container image

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bbcc3dc0..2834481d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -34,7 +34,7 @@ jobs:
 
   create_doc:
     name: Build LaTeX documentation (doc.pdf)
-    runs-on: ubuntu-slim
+    runs-on: ubuntu-latest
     needs: [lint_stopcommands]
     container:
       image: aergus/latex

From dfbd03c2cb231b966f81b262e4b8dd13302bebbe Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 14:09:32 +0100
Subject: [PATCH 20/61] Documentation/: add Makefile create-hash.sh doc.hash

---
 Documentation/Makefile       | 5 +++++
 Documentation/create-hash.sh | 5 +++++
 Documentation/doc.hash       | 1 +
 3 files changed, 11 insertions(+)
 create mode 100644 Documentation/Makefile
 create mode 100755 Documentation/create-hash.sh
 create mode 100644 Documentation/doc.hash

diff --git a/Documentation/Makefile b/Documentation/Makefile
new file mode 100644
index 00000000..0db8a54e
--- /dev/null
+++ b/Documentation/Makefile
@@ -0,0 +1,5 @@
+.PHONY: doc.pdf
+
+doc.pdf:
+	latexmk -pdf doc.tex
+	./create-hash.sh
diff --git a/Documentation/create-hash.sh b/Documentation/create-hash.sh
new file mode 100755
index 00000000..233e1d29
--- /dev/null
+++ b/Documentation/create-hash.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+# Create a SHA256 hash of all relevant documentation files.
+# Useful for checking if the document has changed.
+
+cat ./*.tex $(find Figures -name "*.pdf" | sort) $(find Figures -name "*.png" | sort) doc.bib fassaad.bib  | sha256sum | cut -f1 -d' ' > doc.hash
diff --git a/Documentation/doc.hash b/Documentation/doc.hash
new file mode 100644
index 00000000..77fabb67
--- /dev/null
+++ b/Documentation/doc.hash
@@ -0,0 +1 @@
+823813a7a17a2ad994f11df8036bfad765930fea36c15967c2babdf79ca0229e

From 161681bbbb359029fe613dc9a478d2c8f80cb0fe Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 15:29:34 +0100
Subject: [PATCH 21/61] First steps towards adapting test-branch to GitHub CI

---
 .github/workflows/test-branch.yaml | 38 ++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 .github/workflows/test-branch.yaml

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
new file mode 100644
index 00000000..d4b2293c
--- /dev/null
+++ b/.github/workflows/test-branch.yaml
@@ -0,0 +1,38 @@
+name: Test vs main branch
+
+on: workflow_dispatch
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set.outputs.matrix }}
+    steps:
+        - id: set
+          run: |
+            echo "matrix={'image_minor': ['bookworm-buildd'], 'mode': ['test_vs_main'], 'devel': ['devel', 'stable'], 'config': ['default']}" >> $GITHUB_OUTPUT
+    #   - uses: actions/checkout@v4
+    #   - name: Prepare test branch
+    #     run: |
+    #       python3 ./testsuite/test_branch_generate_config.py
+    #       cat generated-config.yml >> $GITHUB_OUTPUT
+    #   - name: Upload generated config artifact
+    #     uses: actions/upload-artifact@v4
+    #     with:
+    #       name: generated-config
+
+  compile:
+    runs-on: ubuntu-latest
+    needs: prepare
+    strategy:
+      matrix: ${{ fromJson(needs.prepare.outputs.matrix) }}
+    steps:
+    #   - uses: actions/checkout@v4
+    #   - name: Download generated config artifact
+    #     uses: actions/download-artifact@v4
+    #     with:
+    #       name: generated-config
+    #   - name: Compile test branch
+    #     run: |
+    #       cat generated-config/generated-config.yml
+      - run: echo "Running test with ${{ matrix.image_minor[0] }} - ${{ matrix.mode }} - ${{ matrix.devel }} - ${{ matrix.config }}"

From 7b0262ac27c11b2c064fa70125230c2f9ccfb129 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 18:33:13 +0100
Subject: [PATCH 22/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 60 ++++++++++++++++++++----------
 1 file changed, 40 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index d4b2293c..312a2636 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -3,30 +3,51 @@ name: Test vs main branch
 on: workflow_dispatch
 
 jobs:
-  prepare:
-    runs-on: ubuntu-latest
-    outputs:
-      matrix: ${{ steps.set.outputs.matrix }}
-    steps:
-        - id: set
-          run: |
-            echo "matrix={'image_minor': ['bookworm-buildd'], 'mode': ['test_vs_main'], 'devel': ['devel', 'stable'], 'config': ['default']}" >> $GITHUB_OUTPUT
-    #   - uses: actions/checkout@v4
-    #   - name: Prepare test branch
-    #     run: |
-    #       python3 ./testsuite/test_branch_generate_config.py
-    #       cat generated-config.yml >> $GITHUB_OUTPUT
-    #   - name: Upload generated config artifact
-    #     uses: actions/upload-artifact@v4
-    #     with:
-    #       name: generated-config
+#   prepare:
+#     runs-on: ubuntu-latest
+#     outputs:
+#       env_names: ${{ steps.set.outputs.env_names }}
+#       test_names: ${{ steps.set.outputs.test_names }}
+#     steps:
+#       - id: set
+#         run: |
+#           echo "env_names=['Bullseye', 'Bookworm']" >> $GITHUB_OUTPUT
+#           echo "test_names=['Hubbard_N_Leg_Ladder_temper', 'Langevin', 'Langevin_1']" >> $GITHUB_OUTPUT
+#     #   - name: Prepare test branch
+#     #     run: |
+#     #       python3 ./testsuite/test_branch_generate_config.py
+#     #       cat generated-config.yml >> $GITHUB_OUTPUT
+#     #   - name: Upload generated config artifact
+#     #     uses: actions/upload-artifact@v4
+#     #     with:
+#     #       name: generated-config
 
   compile:
+    # needs: prepare
     runs-on: ubuntu-latest
-    needs: prepare
+    container:
+      image: git.physik.uni-wuerzburg.de:25812/z03/pdi/debian:bookworm-buildd
     strategy:
-      matrix: ${{ fromJson(needs.prepare.outputs.matrix) }}
+      matrix:
+        env_name: ${{ fromJson(needs.prepare.outputs.env_names) }}
     steps:
+      - name: Install pyALF
+        run: pip install --no-deps pyALF
+      - uses: actions/checkout@v6
+        with:
+          ref: master
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event.inputs.test_branch || github.ref_name }}
+      - run: alf_test_branch
+            --sim_pars $PWD/testsuite/test_branch_parameters.json
+            --machine $MACHINE
+            --mpi
+            --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
+            --branch_R master
+            --devel
+            --no_sim
+            --no_analyze
     #   - uses: actions/checkout@v4
     #   - name: Download generated config artifact
     #     uses: actions/download-artifact@v4
@@ -35,4 +56,3 @@ jobs:
     #   - name: Compile test branch
     #     run: |
     #       cat generated-config/generated-config.yml
-      - run: echo "Running test with ${{ matrix.image_minor[0] }} - ${{ matrix.mode }} - ${{ matrix.devel }} - ${{ matrix.config }}"

From d3f1be8f2da29d5c9fc6f3f42957ee948d3cd504 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 18:34:23 +0100
Subject: [PATCH 23/61] testsuite/test_branch_generate_config.py: use argparse

---
 testsuite/test_branch_generate_config.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/testsuite/test_branch_generate_config.py b/testsuite/test_branch_generate_config.py
index e0a6e8d3..69f0f233 100755
--- a/testsuite/test_branch_generate_config.py
+++ b/testsuite/test_branch_generate_config.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-import sys
+import argparse
 import json
 import copy
 import yaml
@@ -155,12 +155,15 @@ def prep_runs(test_specs, env_name, env_spec):
     }
 
 if __name__ == "__main__":
-    try:
-        specs_file = sys.argv[1]
-    except IndexError:
-        specs_file = "testsuite/test_branch_parameters.json"
+    parser = argparse.ArgumentParser()
+    parser.add_argument('specs_file', nargs='?', default="testsuite/test_branch_parameters.json")
+    parser.add_argument('--github', action='store_true',
+                        help="Generate matrix for GitHub Actions workflow instead of GitLab CI config")
+    args = parser.parse_args()
+    if args.github:
+        raise NotImplementedError("GitHub Actions config generation not implemented yet.")
 
-    with open(specs_file, 'r', encoding='UTF-8') as f:
+    with open(args.specs_file, 'r', encoding='UTF-8') as f:
         test_specs = json.load(f)
 
     for env_name, env_spec in ENVIRONMENTS.items():

From 01e405b280b30d667851cc8f2b3b3007aa7dcc3b Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 18:36:07 +0100
Subject: [PATCH 24/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 312a2636..04762d7c 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -29,7 +29,17 @@ jobs:
       image: git.physik.uni-wuerzburg.de:25812/z03/pdi/debian:bookworm-buildd
     strategy:
       matrix:
-        env_name: ${{ fromJson(needs.prepare.outputs.env_names) }}
+        image_minor: 
+          - [bullseye, GNU]
+          - [bookworm, GNU]
+          - [trixie, GNU]
+          - [bullseye-openblas, GNU]
+          # - [tumbleweed, GNU]
+          - [bullseye-pgi-21-03, PGI]
+          - [bookworm-pgi-24-09, PGI]
+          - [bullseye-intel, INTEL]
+          - [bookworm-intel-2024.2, INTEL]
+          - [bookworm-intel, INTELLLVM]
     steps:
       - name: Install pyALF
         run: pip install --no-deps pyALF

From 74b892c30513bb07aac3d3c393de4f74ab7d2849 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 18:37:47 +0100
Subject: [PATCH 25/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 04762d7c..6dc9d26c 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -26,7 +26,7 @@ jobs:
     # needs: prepare
     runs-on: ubuntu-latest
     container:
-      image: git.physik.uni-wuerzburg.de:25812/z03/pdi/debian:bookworm-buildd
+      image: ghcr.io/alf-qmc/alf-container/alf-requirements/${{ matrix.image_minor[0] }}
     strategy:
       matrix:
         image_minor: 
@@ -51,7 +51,7 @@ jobs:
           ref: ${{ github.event.inputs.test_branch || github.ref_name }}
       - run: alf_test_branch
             --sim_pars $PWD/testsuite/test_branch_parameters.json
-            --machine $MACHINE
+            --machine ${{ matrix.image_minor[1] }}
             --mpi
             --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
             --branch_R master

From dbf593ff52b61646f3dd2b49f4698894da528ae4 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 18:40:08 +0100
Subject: [PATCH 26/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 6dc9d26c..ff444773 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -26,7 +26,7 @@ jobs:
     # needs: prepare
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/alf-qmc/alf-container/alf-requirements/${{ matrix.image_minor[0] }}
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/${{ matrix.image_minor[0] }}
     strategy:
       matrix:
         image_minor: 

From 1e3a06b97273ce971d52309c2ea4951c2e55aa8f Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 18:41:41 +0100
Subject: [PATCH 27/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index ff444773..60fd2ede 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -33,13 +33,13 @@ jobs:
           - [bullseye, GNU]
           - [bookworm, GNU]
           - [trixie, GNU]
-          - [bullseye-openblas, GNU]
+        #   - [bullseye-openblas, GNU]
           # - [tumbleweed, GNU]
           - [bullseye-pgi-21-03, PGI]
-          - [bookworm-pgi-24-09, PGI]
-          - [bullseye-intel, INTEL]
-          - [bookworm-intel-2024.2, INTEL]
-          - [bookworm-intel, INTELLLVM]
+        #   - [bookworm-pgi-24-09, PGI]
+        #   - [bullseye-intel, INTEL]
+        #   - [bookworm-intel-2024.2, INTEL]
+        #   - [bookworm-intel, INTELLLVM]
     steps:
       - name: Install pyALF
         run: pip install --no-deps pyALF

From be55c76abae96cd92a8568a9442dc90e6e6a6610 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 18:44:45 +0100
Subject: [PATCH 28/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 60fd2ede..bc37478e 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -50,6 +50,7 @@ jobs:
         with:
           ref: ${{ github.event.inputs.test_branch || github.ref_name }}
       - run: alf_test_branch
+            --alfdir $PWD
             --sim_pars $PWD/testsuite/test_branch_parameters.json
             --machine ${{ matrix.image_minor[1] }}
             --mpi

From a69694cddeefccad16b541f5d4db7e0c7d2b5213 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 22:51:23 +0100
Subject: [PATCH 29/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index bc37478e..847904ab 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -34,12 +34,12 @@ jobs:
           - [bookworm, GNU]
           - [trixie, GNU]
         #   - [bullseye-openblas, GNU]
-          # - [tumbleweed, GNU]
+          - [tumbleweed, GNU]
           - [bullseye-pgi-21-03, PGI]
-        #   - [bookworm-pgi-24-09, PGI]
-        #   - [bullseye-intel, INTEL]
-        #   - [bookworm-intel-2024.2, INTEL]
-        #   - [bookworm-intel, INTELLLVM]
+          - [bookworm-pgi-24-09, PGI]
+          - [bullseye-intel, INTEL]
+          - [bookworm-intel-2024.2, INTEL]
+          - [bookworm-intel, INTELLLVM]
     steps:
       - name: Install pyALF
         run: pip install --no-deps pyALF
@@ -59,11 +59,3 @@ jobs:
             --devel
             --no_sim
             --no_analyze
-    #   - uses: actions/checkout@v4
-    #   - name: Download generated config artifact
-    #     uses: actions/download-artifact@v4
-    #     with:
-    #       name: generated-config
-    #   - name: Compile test branch
-    #     run: |
-    #       cat generated-config/generated-config.yml

From b61976546c5ec5a7f4efd879076a71018d2f9fa5 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Tue, 13 Jan 2026 22:59:33 +0100
Subject: [PATCH 30/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 847904ab..0b2e398e 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -57,5 +57,5 @@ jobs:
             --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
             --branch_R master
             --devel
-            --no_sim
-            --no_analyze
+            # --no_sim
+            # --no_analyze

From b1b6ebccee919b997f4ea0102e0cd39e9c3c13e0 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 11:18:56 +0100
Subject: [PATCH 31/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 0b2e398e..b99ea226 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -33,8 +33,8 @@ jobs:
           - [bullseye, GNU]
           - [bookworm, GNU]
           - [trixie, GNU]
-        #   - [bullseye-openblas, GNU]
-          - [tumbleweed, GNU]
+          # - [bullseye-openblas, GNU]
+          # - [tumbleweed, GNU]
           - [bullseye-pgi-21-03, PGI]
           - [bookworm-pgi-24-09, PGI]
           - [bullseye-intel, INTEL]

From 4ea2063645d2dc8b8043f79730acf329bd38918f Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 12:32:34 +0100
Subject: [PATCH 32/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index b99ea226..f9fe49ce 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -57,5 +57,6 @@ jobs:
             --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
             --branch_R master
             --devel
+            --mpiexec_args "--use-hwthread-cpus"
             # --no_sim
             # --no_analyze

From a2823c340eea354aad73b9b50f32ec05b68ce5f3 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 14:03:17 +0100
Subject: [PATCH 33/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index f9fe49ce..b52da6e9 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -57,6 +57,6 @@ jobs:
             --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
             --branch_R master
             --devel
-            --mpiexec_args "--use-hwthread-cpus"
+            --mpiexec_args="--use-hwthread-cpus"
             # --no_sim
             # --no_analyze

From 5aa81ea32b30b375d7e026e264fe55aea77e08c3 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 14:22:55 +0100
Subject: [PATCH 34/61] CI: Work on test-branch

---
 .github/actions/alf_test/action.yml |  2 +-
 .github/workflows/test-branch.yaml  | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index b685f592..1ed3f13c 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -49,7 +49,7 @@ runs:
           "$ALF_DIR/Prog/ALF.out"
         else
           MPI_OPTS="-n 4"
-          if mpiexec --version | grep -iq -e 'Open MPI' -e 'OpenRTE'; then MPI_OPTS="$MPI_OPTS --use-hwthread-cpus"; fi
+          mpiexec --version | grep -iq -e 'Open MPI' -e 'OpenRTE' && MPI_OPTS="$MPI_OPTS --use-hwthread-cpus"
           mpiexec $MPI_OPTS "$ALF_DIR/Prog/ALF.out"
         fi
         if echo "$MODE" | grep -iq -e "TEMPERING" -e "PARALLEL_PARAMS"; then cd Temp_0; fi
diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index b52da6e9..8a61de21 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -49,7 +49,13 @@ jobs:
       - uses: actions/checkout@v6
         with:
           ref: ${{ github.event.inputs.test_branch || github.ref_name }}
-      - run: alf_test_branch
+      - name: Check if mpiexec supports --use-hwthread-cpus
+        id: mpi_flag_check
+        run: mpiexec --version | grep -iq -e 'Open MPI' -e 'OpenRTE' &&
+             echo "value='--use-hwthread-cpus'" >> $GITHUB_OUTPUT ||
+             echo "value=''" >> $GITHUB_OUTPUT
+      - name: Run ALF test vs main branch
+        run: alf_test_branch
             --alfdir $PWD
             --sim_pars $PWD/testsuite/test_branch_parameters.json
             --machine ${{ matrix.image_minor[1] }}
@@ -57,6 +63,6 @@ jobs:
             --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
             --branch_R master
             --devel
-            --mpiexec_args="--use-hwthread-cpus"
+            --mpiexec_args="${{ steps.mpi_flag_check.outputs.value }}"
             # --no_sim
             # --no_analyze

From 12aea33c3b04ac662407e06408f14b9e766419ab Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 14:41:17 +0100
Subject: [PATCH 35/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 8a61de21..25ec167c 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -22,14 +22,14 @@ jobs:
 #     #     with:
 #     #       name: generated-config
 
-  compile:
+  test_branch:
     # needs: prepare
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/${{ matrix.image_minor[0] }}
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/${{ matrix.image[0] }}
     strategy:
       matrix:
-        image_minor: 
+        image: 
           - [bullseye, GNU]
           - [bookworm, GNU]
           - [trixie, GNU]
@@ -52,17 +52,22 @@ jobs:
       - name: Check if mpiexec supports --use-hwthread-cpus
         id: mpi_flag_check
         run: mpiexec --version | grep -iq -e 'Open MPI' -e 'OpenRTE' &&
-             echo "value='--use-hwthread-cpus'" >> $GITHUB_OUTPUT ||
+             echo "value='--mpiexec_args=--use-hwthread-cpus'" >> $GITHUB_OUTPUT ||
              echo "value=''" >> $GITHUB_OUTPUT
       - name: Run ALF test vs main branch
         run: alf_test_branch
             --alfdir $PWD
             --sim_pars $PWD/testsuite/test_branch_parameters.json
-            --machine ${{ matrix.image_minor[1] }}
+            --machine ${{ matrix.image[1] }}
             --mpi
             --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
             --branch_R master
             --devel
-            --mpiexec_args="${{ steps.mpi_flag_check.outputs.value }}"
-            # --no_sim
-            # --no_analyze
+            ${{ steps.mpi_flag_check.outputs.value }}
+      - name: Upload test branch results
+        if: always()
+        uses: actions/upload-artifact@v6
+        with:
+          name: test-branch-results-${{ matrix.image }}
+          path: 
+            test.txt
\ No newline at end of file

From 3349011b9a9a069d37958ed75dc88f110c20ee7c Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 15:04:58 +0100
Subject: [PATCH 36/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 25ec167c..2f070f93 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -28,6 +28,7 @@ jobs:
     container:
       image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/${{ matrix.image[0] }}
     strategy:
+      fail-fast: false
       matrix:
         image: 
           - [bullseye, GNU]
@@ -52,8 +53,7 @@ jobs:
       - name: Check if mpiexec supports --use-hwthread-cpus
         id: mpi_flag_check
         run: mpiexec --version | grep -iq -e 'Open MPI' -e 'OpenRTE' &&
-             echo "value='--mpiexec_args=--use-hwthread-cpus'" >> $GITHUB_OUTPUT ||
-             echo "value=''" >> $GITHUB_OUTPUT
+             echo "value='--mpiexec_args=--use-hwthread-cpus'" >> $GITHUB_OUTPUT
       - name: Run ALF test vs main branch
         run: alf_test_branch
             --alfdir $PWD

From 0cecf7ab5d850ab8f0c031496ce826ffa2830b41 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 15:29:15 +0100
Subject: [PATCH 37/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 2f070f93..188c8dc8 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -53,7 +53,8 @@ jobs:
       - name: Check if mpiexec supports --use-hwthread-cpus
         id: mpi_flag_check
         run: mpiexec --version | grep -iq -e 'Open MPI' -e 'OpenRTE' &&
-             echo "value='--mpiexec_args=--use-hwthread-cpus'" >> $GITHUB_OUTPUT
+             echo "value='--mpiexec_args=--use-hwthread-cpus'" >> $GITHUB_OUTPUT ||
+             echo "No Open MPI, so --use-hwthread-cpus not needed"
       - name: Run ALF test vs main branch
         run: alf_test_branch
             --alfdir $PWD

From 099f3eba85dfe4beec2d4f39de49dbe725dee282 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 15:44:04 +0100
Subject: [PATCH 38/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 188c8dc8..8da2dff5 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -61,6 +61,7 @@ jobs:
             --sim_pars $PWD/testsuite/test_branch_parameters.json
             --machine ${{ matrix.image[1] }}
             --mpi
+            --n_mpi 4
             --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
             --branch_R master
             --devel
@@ -69,6 +70,6 @@ jobs:
         if: always()
         uses: actions/upload-artifact@v6
         with:
-          name: test-branch-results-${{ matrix.image }}
+          name: test-branch-results-${{ matrix.image[0] }}-${{ matrix.image[1] }}
           path: 
             test.txt
\ No newline at end of file

From cffec1be2a319a0f5c6fe4b42493b2b902166295 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 16:04:09 +0100
Subject: [PATCH 39/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 42 ++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 8da2dff5..a5ef1bc4 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -71,5 +71,47 @@ jobs:
         uses: actions/upload-artifact@v6
         with:
           name: test-branch-results-${{ matrix.image[0] }}-${{ matrix.image[1] }}
+          path: 
+            test.txt
+  
+  test_branch_macos:
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        compiler: [GNU]
+    steps:
+      - name: Install pyALF
+        run: pip install --no-deps pyALF
+      - name: macOS Toolchain install
+        run: |
+          brew update
+          brew install mpich
+          gcc_version=$(brew list --versions gcc | grep -o '[0-9]\+' | head -1)
+          bindir=$(brew --prefix)/bin
+          ln -fs ${bindir}/gfortran-${gcc_version} /usr/local/bin/gfortran
+          ln -fs ${bindir}/gcc-${gcc_version} /usr/local/bin/gcc
+          ln -fs ${bindir}/g++-${gcc_version} /usr/local/bin/g++
+      - uses: actions/checkout@v6
+        with:
+          ref: master
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event.inputs.test_branch || github.ref_name }}
+      - name: Run ALF test vs main branch on macOS
+        run: alf_test_branch
+            --alfdir $PWD
+            --sim_pars $PWD/testsuite/test_branch_parameters.json
+            --machine ${{ matrix.compiler }}
+            --mpi
+            --n_mpi 4
+            --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
+            --branch_R master
+            --devel
+      - name: Upload test branch results macOS
+        if: always()
+        uses: actions/upload-artifact@v6
+        with:
+          name: test-branch-results-macos-${{ matrix.compiler }}
           path: 
             test.txt
\ No newline at end of file

From fce700161c5d092e24d3d20e4effc8100a38eb57 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 16:20:42 +0100
Subject: [PATCH 40/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index a5ef1bc4..571c9d45 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -82,7 +82,7 @@ jobs:
         compiler: [GNU]
     steps:
       - name: Install pyALF
-        run: pip install --no-deps pyALF
+        run: pipx install pyALF
       - name: macOS Toolchain install
         run: |
           brew update

From 9796b3e23786c6aac0fe9e977f57093405db9c06 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 16:55:02 +0100
Subject: [PATCH 41/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 571c9d45..43603120 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -80,6 +80,10 @@ jobs:
       fail-fast: false
       matrix:
         compiler: [GNU]
+    cache:
+      key: macos-HDF5
+      paths:
+        - HDF5/
     steps:
       - name: Install pyALF
         run: pipx install pyALF
@@ -99,7 +103,7 @@ jobs:
         with:
           ref: ${{ github.event.inputs.test_branch || github.ref_name }}
       - name: Run ALF test vs main branch on macOS
-        run: alf_test_branch
+        run: OMP_NUM_THREADS=1 alf_test_branch
             --alfdir $PWD
             --sim_pars $PWD/testsuite/test_branch_parameters.json
             --machine ${{ matrix.compiler }}

From bd509dd82173fb69f02362345853b13f58c60af8 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 17:19:41 +0100
Subject: [PATCH 42/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 43603120..8bf6071f 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -80,14 +80,12 @@ jobs:
       fail-fast: false
       matrix:
         compiler: [GNU]
-    cache:
-      key: macos-HDF5
-      paths:
-        - HDF5/
     steps:
       - name: Install pyALF
         run: pipx install pyALF
+
       - name: macOS Toolchain install
+        id: mac_toolchain
         run: |
           brew update
           brew install mpich
@@ -96,12 +94,21 @@ jobs:
           ln -fs ${bindir}/gfortran-${gcc_version} /usr/local/bin/gfortran
           ln -fs ${bindir}/gcc-${gcc_version} /usr/local/bin/gcc
           ln -fs ${bindir}/g++-${gcc_version} /usr/local/bin/g++
+          echo "gcc_version=$gcc_version" >> $GITHUB_OUTPUT
+
       - uses: actions/checkout@v6
         with:
           ref: master
       - uses: actions/checkout@v6
         with:
           ref: ${{ github.event.inputs.test_branch || github.ref_name }}
+
+      - name: Restore HDF5 cache
+        uses: actions/cache@v5
+        with:
+          key: macos-HDF5-${{ steps.mac_toolchain.outputs.gcc_version }}
+          path: HDF5/*/
+
       - name: Run ALF test vs main branch on macOS
         run: OMP_NUM_THREADS=1 alf_test_branch
             --alfdir $PWD
@@ -112,6 +119,13 @@ jobs:
             --branch_T ${{ github.event.inputs.test_branch || github.ref_name }}
             --branch_R master
             --devel
+
+      - name: Save HDF5 cache
+        uses: actions/cache@v5
+        with:
+          key: macos-HDF5-${{ steps.mac_toolchain.outputs.gcc_version }}
+          path: HDF5/*/
+
       - name: Upload test branch results macOS
         if: always()
         uses: actions/upload-artifact@v6

From 0f62d13d26f3ff8d087dd60d01f6754ba3fe011f Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 17:43:54 +0100
Subject: [PATCH 43/61] CI: cache HDF5 for MacOS

---
 .github/actions/alf_test/action.yml | 11 ++++++++++-
 .github/workflows/test-branch.yaml  |  6 ------
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/.github/actions/alf_test/action.yml b/.github/actions/alf_test/action.yml
index 1ed3f13c..b4c970cf 100644
--- a/.github/actions/alf_test/action.yml
+++ b/.github/actions/alf_test/action.yml
@@ -10,6 +10,7 @@ runs:
   steps:
     - name: macOS Toolchain install
       if: runner.os == 'macOS'
+      id: mac_toolchain
       shell: bash
       run: |
         brew update
@@ -19,6 +20,7 @@ runs:
         ln -fs ${bindir}/gfortran-${gcc_version} /usr/local/bin/gfortran
         ln -fs ${bindir}/gcc-${gcc_version} /usr/local/bin/gcc
         ln -fs ${bindir}/g++-${gcc_version} /usr/local/bin/g++
+        echo "gcc_version=$gcc_version" >> $GITHUB_OUTPUT
 
     - name: Get number of processors
       shell: bash
@@ -30,6 +32,13 @@ runs:
         fi
         echo "There are $NPROC processors available."
 
+    - name: Restore HDF5 cache
+      if: runner.os == 'macOS'
+      uses: actions/cache@v5
+      with:
+        key: macos-HDF5-${{ steps.mac_toolchain.outputs.gcc_version }}
+        path: HDF5/*/
+
     - name: Build & Test
       shell: bash
       env:
@@ -71,4 +80,4 @@ runs:
         cmake ..
         cmake --build . --target all --config Release
         ctest -VV -O log.txt
-        grep "tests passed" log.txt | cut -d " " -f 1
\ No newline at end of file
+        grep "tests passed" log.txt | cut -d " " -f 1
diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index 8bf6071f..e6a4acbb 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -120,12 +120,6 @@ jobs:
             --branch_R master
             --devel
 
-      - name: Save HDF5 cache
-        uses: actions/cache@v5
-        with:
-          key: macos-HDF5-${{ steps.mac_toolchain.outputs.gcc_version }}
-          path: HDF5/*/
-
       - name: Upload test branch results macOS
         if: always()
         uses: actions/upload-artifact@v6

From 82cac4e6ad027215ce6ddb422a115b76487d01d5 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 17:48:00 +0100
Subject: [PATCH 44/61] CI: use HDF5 for MacOS

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2834481d..d67388b6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -152,7 +152,7 @@ jobs:
       matrix:
         mode: [noMPI, MPI, TEMPERING, PARALLEL_PARAMS]
         devel: ["", "Devel"]
-        config: [""]  # TODO: Enable fast access to HDF5 on macOS runners
+        config: ["", "HDF5"]
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/alf_test

From 9701163cd2e34161528880f3206b7fe738c63bf3 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Wed, 14 Jan 2026 21:40:23 +0100
Subject: [PATCH 45/61] CI: Work on test-branch

---
 .github/workflows/test-branch.yaml | 21 +--------------------
 1 file changed, 1 insertion(+), 20 deletions(-)

diff --git a/.github/workflows/test-branch.yaml b/.github/workflows/test-branch.yaml
index e6a4acbb..aa6786bc 100644
--- a/.github/workflows/test-branch.yaml
+++ b/.github/workflows/test-branch.yaml
@@ -3,25 +3,6 @@ name: Test vs main branch
 on: workflow_dispatch
 
 jobs:
-#   prepare:
-#     runs-on: ubuntu-latest
-#     outputs:
-#       env_names: ${{ steps.set.outputs.env_names }}
-#       test_names: ${{ steps.set.outputs.test_names }}
-#     steps:
-#       - id: set
-#         run: |
-#           echo "env_names=['Bullseye', 'Bookworm']" >> $GITHUB_OUTPUT
-#           echo "test_names=['Hubbard_N_Leg_Ladder_temper', 'Langevin', 'Langevin_1']" >> $GITHUB_OUTPUT
-#     #   - name: Prepare test branch
-#     #     run: |
-#     #       python3 ./testsuite/test_branch_generate_config.py
-#     #       cat generated-config.yml >> $GITHUB_OUTPUT
-#     #   - name: Upload generated config artifact
-#     #     uses: actions/upload-artifact@v4
-#     #     with:
-#     #       name: generated-config
-
   test_branch:
     # needs: prepare
     runs-on: ubuntu-latest
@@ -110,7 +91,7 @@ jobs:
           path: HDF5/*/
 
       - name: Run ALF test vs main branch on macOS
-        run: OMP_NUM_THREADS=1 alf_test_branch
+        run: alf_test_branch
             --alfdir $PWD
             --sim_pars $PWD/testsuite/test_branch_parameters.json
             --machine ${{ matrix.compiler }}

From 387c0c76d53b296a71ad0c88fd64e5c54440ce28 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Thu, 15 Jan 2026 15:20:25 +0100
Subject: [PATCH 46/61] add .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml | 80 +++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100644 .github/workflows/test-vs-ed.yaml

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
new file mode 100644
index 00000000..ed738f0e
--- /dev/null
+++ b/.github/workflows/test-vs-ed.yaml
@@ -0,0 +1,80 @@
+name: Test vs given ED reference results
+on: workflow_dispatch
+
+jobs:
+  prepare_matrix:
+    runs-on: ubuntu-latest
+    outputs:
+      test_specs: ${{ steps.set-matrix.outputs.test_specs }}
+    steps:
+      - id: set-matrix
+        run: |
+          echo "test_specs={'hubbard_finT_chain':, 'hubbard_T0_chain'}" >> $GITHUB_OUTPUT
+          echo "env_names=['bullseye', 'bookworm', 'trixie']" >> $GITHUB_OUTPUT
+  compile:
+    needs: prepare_matrix
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/${{ matrix.image[0] }}
+    strategy:
+      fail-fast: false
+      matrix:
+        image: 
+          - [bullseye, GNU]
+          - [bookworm, GNU]
+          - [trixie, GNU]
+    steps:
+      - name: Install pyALF
+        run: pip install --no-deps pyALF
+      - uses: actions/checkout@v6
+      - name: Compile ALF
+        run: cd ${{ matrix.test_dir }} && ../compile.py ${{ matrix.image[1] }}
+      - name: Upload compiled ALF binary and test directory
+        uses: actions/upload-artifact@v6
+        with:
+          name: simdir-${{ matrix.test_dir }}-${{ matrix.image[0] }}-${{ matrix.image[1] }}
+          path: ${{ matrix.test_dir }}
+
+  simulate:
+    needs: compile
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/${{ matrix.image[0] }}
+    strategy:
+      fail-fast: false
+      matrix:
+        test_name: ${{ fromJson(needs.prepare_matrix.outputs.test_names) }}
+        image: 
+          - [bullseye, GNU]
+          - [bookworm, GNU]
+          - [trixie, GNU]
+    steps:
+      - name: Download compiled ALF binary
+        uses: actions/download-artifact@v6
+        with:
+          name: simdir-${{ matrix.test_dir }}-${{ matrix.image[0] }}-${{ matrix.image[1] }}
+      - name: Run ALF test vs main branch
+        run: cd ${{ matrix.test_dir }}/$CI_NODE_INDEX && ../ALF.out
+
+      - name: Upload simulation results
+        uses: actions/upload-artifact@v6
+        with:
+          name: simulation-results-${{ matrix.test_name }}-${{ matrix.image[1] }}-${{ matrix.env_name }}
+          path: ${{ matrix.test_dir }}/$CI_NODE_INDEX
+
+  analyze:
+    needs: simulate
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install pyALF
+        run: pip install --no-deps pyALF
+      - name: Analyze simulation results
+        run: cd ${{ matrix.test_dir }} && ../analysis.py
+      - name: Upload compiled ALF binary and test directory
+        uses: actions/upload-artifact@v6
+        with:
+          name: simdir-${{ matrix.test_dir }}-${{ matrix.image[0] }}-${{ matrix.image[1] }}
+          path: |
+            ${{ matrix.test_dir }}/results.json
+            ${{ matrix.test_dir }}/test.png
+            ${{ matrix.test_dir }}/spec.yaml

From 9ba6522e489119e66a1e2ef47346e999ee7fb594 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 17:00:58 +0100
Subject: [PATCH 47/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml    | 69 +++++++++++++++++-----------
 testsuite/test_vs_ed/compile.py      |  2 +-
 testsuite/test_vs_ed/prep_test.py    | 28 +++++++++--
 testsuite/test_vs_ed/test_specs.yaml |  6 +--
 4 files changed, 69 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index ed738f0e..914af8d9 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -5,76 +5,89 @@ jobs:
   prepare_matrix:
     runs-on: ubuntu-latest
     outputs:
-      test_specs: ${{ steps.set-matrix.outputs.test_specs }}
+      compile_matrix: ${{ steps.set-matrix.outputs.compile_matrix }}
+      simulation_matrix: ${{ steps.set-matrix.outputs.simulation_matrix }}
     steps:
       - id: set-matrix
         run: |
+          ./testsuite/test_vs_ed/prep_test.py
           echo "test_specs={'hubbard_finT_chain':, 'hubbard_T0_chain'}" >> $GITHUB_OUTPUT
           echo "env_names=['bullseye', 'bookworm', 'trixie']" >> $GITHUB_OUTPUT
+
+      - name: Upload prepared test directories
+        uses: actions/upload-artifact@v6
+        with:
+          name: prepared-test-directories
+          path: testsuite/test_vs_ed/*/
   compile:
     needs: prepare_matrix
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/${{ matrix.image[0] }}
+      image: ${{ matrix.image }}
     strategy:
       fail-fast: false
       matrix:
-        image: 
-          - [bullseye, GNU]
-          - [bookworm, GNU]
-          - [trixie, GNU]
+        include: ${{ fromJson(needs.prepare_matrix.outputs.compile_matrix) }}
     steps:
       - name: Install pyALF
         run: pip install --no-deps pyALF
       - uses: actions/checkout@v6
+      - name: Download prepared test directories
+        uses: actions/download-artifact@v7
+        with:
+          name: prepared-test-directories
       - name: Compile ALF
-        run: cd ${{ matrix.test_dir }} && ../compile.py ${{ matrix.image[1] }}
+        run: cd ${{ matrix.test_dir }} && ../compile.py ${{ matrix.machine }}
       - name: Upload compiled ALF binary and test directory
         uses: actions/upload-artifact@v6
         with:
-          name: simdir-${{ matrix.test_dir }}-${{ matrix.image[0] }}-${{ matrix.image[1] }}
+          name: simdir-${{ matrix.test_dir }}-${{ matrix.image }}-${{ matrix.machine }}
           path: ${{ matrix.test_dir }}
 
   simulate:
-    needs: compile
+    needs: [prepare_matrix, compile]
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/${{ matrix.image[0] }}
+      image: ${{ matrix.image }}
     strategy:
       fail-fast: false
       matrix:
-        test_name: ${{ fromJson(needs.prepare_matrix.outputs.test_names) }}
-        image: 
-          - [bullseye, GNU]
-          - [bookworm, GNU]
-          - [trixie, GNU]
+        include: ${{ fromJson(needs.prepare_matrix.outputs.simulation_matrix) }}
     steps:
       - name: Download compiled ALF binary
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v7
         with:
-          name: simdir-${{ matrix.test_dir }}-${{ matrix.image[0] }}-${{ matrix.image[1] }}
+          name: simdir-${{ matrix.test_dir }}-${{ matrix.image }}-${{ matrix.machine }}
       - name: Run ALF test vs main branch
         run: cd ${{ matrix.test_dir }}/$CI_NODE_INDEX && ../ALF.out
 
       - name: Upload simulation results
         uses: actions/upload-artifact@v6
         with:
-          name: simulation-results-${{ matrix.test_name }}-${{ matrix.image[1] }}-${{ matrix.env_name }}
-          path: ${{ matrix.test_dir }}/$CI_NODE_INDEX
+          name: simulation-results-${{ matrix.test_name }}-${{ matrix.image }}-${{ matrix.machine }}
+          path: ${{ matrix.test_dir }}/${{ matrix.CI_NODE_INDEX }}
 
   analyze:
     needs: simulate
     runs-on: ubuntu-latest
     steps:
+      - uses: actions/checkout@v6
       - name: Install pyALF
         run: pip install --no-deps pyALF
+      - name: Download simulation results
+        uses: actions/download-artifact@v7
       - name: Analyze simulation results
-        run: cd ${{ matrix.test_dir }} && ../analysis.py
-      - name: Upload compiled ALF binary and test directory
-        uses: actions/upload-artifact@v6
-        with:
-          name: simdir-${{ matrix.test_dir }}-${{ matrix.image[0] }}-${{ matrix.image[1] }}
-          path: |
-            ${{ matrix.test_dir }}/results.json
-            ${{ matrix.test_dir }}/test.png
-            ${{ matrix.test_dir }}/spec.yaml
+        run: |
+          cd testsuite/test_vs_ed
+          for dir in */; do
+            cd "$dir" && ../analysis.py
+            cd ..
+          done
+      # - name: Upload compiled ALF binary and test directory
+      #   uses: actions/upload-artifact@v6
+      #   with:
+      #     name: simdir-${{ matrix.test_dir }}-${{ matrix.image[0] }}-${{ matrix.image[1] }}
+      #     path: |
+      #       ${{ matrix.test_dir }}/results.json
+      #       ${{ matrix.test_dir }}/test.png
+      #       ${{ matrix.test_dir }}/spec.yaml
diff --git a/testsuite/test_vs_ed/compile.py b/testsuite/test_vs_ed/compile.py
index 0b40c18d..c168df9f 100755
--- a/testsuite/test_vs_ed/compile.py
+++ b/testsuite/test_vs_ed/compile.py
@@ -10,7 +10,7 @@
 if __name__ == "__main__":
     machine = sys.argv[1]
     with open("spec.yaml", 'r', encoding='UTF-8') as f:
-        spec = yaml.load(f, yaml.Loader)
+        spec = yaml.safe_load(f)
 
     alf_src = ALF_source(alf_dir='../../..')
     sims = []
diff --git a/testsuite/test_vs_ed/prep_test.py b/testsuite/test_vs_ed/prep_test.py
index 8cf1b96d..f279d259 100755
--- a/testsuite/test_vs_ed/prep_test.py
+++ b/testsuite/test_vs_ed/prep_test.py
@@ -1,10 +1,11 @@
 #!/usr/bin/env python3
+import json
 import os
 import sys
 import yaml
 import copy
 
-pipeline_config = yaml.load("""
+pipeline_config = yaml.safe_load("""
 default:
   tags:
     - k8s
@@ -72,7 +73,7 @@
       - $TEST_DIR/test.png
       - $TEST_DIR/spec.yaml
     when: always
-""", yaml.Loader)
+""")
 
 
 def prep_runs(test_name, test_spec, env_name, env_spec):
@@ -115,11 +116,30 @@ def prep_runs(test_name, test_spec, env_name, env_spec):
     except IndexError:
         specs_file = "testsuite/test_vs_ed/test_specs.yaml"
     with open(specs_file, 'r', encoding='UTF-8') as f:
-        test_specs = yaml.load(f, yaml.Loader)
+        test_specs = yaml.safe_load(f)
+    
+    compile_matrix = []
+    simulation_matrix = []
+    analysis_matrix = []
 
     for test_name, test_spec in test_specs.items():
         for env_name, env_spec in test_spec['environments'].items():
-            prep_runs(test_name, test_spec, env_name, env_spec)
+            # prep_runs(test_name, test_spec, env_name, env_spec)
+            print(env_spec)
+            compile_matrix.append({
+                'test_dir': f'testsuite/test_vs_ed/{test_name}_{env_name}',
+                'machine': env_spec['variables']['MACHINE'],
+                'image': env_spec['image'],
+            })
+            for i, _ in enumerate(test_spec["sim_dicts"]):
+                simulation_matrix.append({
+                    'test_dir': f'testsuite/test_vs_ed/{test_name}_{env_name}',
+                    'machine': env_spec['variables']['MACHINE'],
+                    'image': env_spec['image'],
+                    'CI_NODE_INDEX': i+1,
+                })
+    print(f'compile_matrix={json.dumps(compile_matrix)}')
+    print(f'simulation_matrix={json.dumps(simulation_matrix)}')
 
     with open('generated-config.yml', 'w', encoding='UTF-8') as f:
         f.write(yaml.dump(pipeline_config))
diff --git a/testsuite/test_vs_ed/test_specs.yaml b/testsuite/test_vs_ed/test_specs.yaml
index f94982d4..f95a1902 100644
--- a/testsuite/test_vs_ed/test_specs.yaml
+++ b/testsuite/test_vs_ed/test_specs.yaml
@@ -18,9 +18,9 @@ hubbard_finT_chain:
     PGI-21-03:
       image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/bullseye-pgi-21-03
       variables: {MACHINE: PGI}
-    macGNU:
-      tags: ['macos']
-      variables: {MACHINE: GNU}
+    # macGNU:
+    #   tags: ['macos']
+    #   variables: {MACHINE: GNU}
   ham_name: "Hubbard"
   ed_energy: -1.47261997
   max_sigma: 3

From 67a9bb52fea21d161de2e1f15d800b16fd412baa Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 17:04:53 +0100
Subject: [PATCH 48/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index 914af8d9..7b19c804 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -8,11 +8,10 @@ jobs:
       compile_matrix: ${{ steps.set-matrix.outputs.compile_matrix }}
       simulation_matrix: ${{ steps.set-matrix.outputs.simulation_matrix }}
     steps:
+      - uses: actions/checkout@v6
+
       - id: set-matrix
-        run: |
-          ./testsuite/test_vs_ed/prep_test.py
-          echo "test_specs={'hubbard_finT_chain':, 'hubbard_T0_chain'}" >> $GITHUB_OUTPUT
-          echo "env_names=['bullseye', 'bookworm', 'trixie']" >> $GITHUB_OUTPUT
+        run: ./testsuite/test_vs_ed/prep_test.py
 
       - name: Upload prepared test directories
         uses: actions/upload-artifact@v6

From a8b1236e5e4c386a065b5e4dd0e5eac45f5a54c1 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 17:09:02 +0100
Subject: [PATCH 49/61] Work on .github/workflows/test-vs-ed.yaml

---
 testsuite/test_vs_ed/prep_test.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/testsuite/test_vs_ed/prep_test.py b/testsuite/test_vs_ed/prep_test.py
index f279d259..637618d5 100755
--- a/testsuite/test_vs_ed/prep_test.py
+++ b/testsuite/test_vs_ed/prep_test.py
@@ -138,8 +138,10 @@ def prep_runs(test_name, test_spec, env_name, env_spec):
                     'image': env_spec['image'],
                     'CI_NODE_INDEX': i+1,
                 })
-    print(f'compile_matrix={json.dumps(compile_matrix)}')
-    print(f'simulation_matrix={json.dumps(simulation_matrix)}')
+    
+    with open(sys.getenv('GITHUB_OUTPUT'), 'w+', encoding='UTF-8') as f:
+      f.write(f'compile_matrix={json.dumps(compile_matrix)}\n')
+      f.write(f'simulation_matrix={json.dumps(simulation_matrix)}')
 
     with open('generated-config.yml', 'w', encoding='UTF-8') as f:
         f.write(yaml.dump(pipeline_config))

From 02aaac849fa39e9397b9a24f7cbbdf807c9dd1c5 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 17:10:55 +0100
Subject: [PATCH 50/61] Work on .github/workflows/test-vs-ed.yaml

---
 testsuite/test_vs_ed/prep_test.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/testsuite/test_vs_ed/prep_test.py b/testsuite/test_vs_ed/prep_test.py
index 637618d5..52b6b595 100755
--- a/testsuite/test_vs_ed/prep_test.py
+++ b/testsuite/test_vs_ed/prep_test.py
@@ -125,7 +125,6 @@ def prep_runs(test_name, test_spec, env_name, env_spec):
     for test_name, test_spec in test_specs.items():
         for env_name, env_spec in test_spec['environments'].items():
             # prep_runs(test_name, test_spec, env_name, env_spec)
-            print(env_spec)
             compile_matrix.append({
                 'test_dir': f'testsuite/test_vs_ed/{test_name}_{env_name}',
                 'machine': env_spec['variables']['MACHINE'],
@@ -139,7 +138,7 @@ def prep_runs(test_name, test_spec, env_name, env_spec):
                     'CI_NODE_INDEX': i+1,
                 })
     
-    with open(sys.getenv('GITHUB_OUTPUT'), 'w+', encoding='UTF-8') as f:
+    with open(os.getenv('GITHUB_OUTPUT', 'test.json'), 'w+', encoding='UTF-8') as f:
       f.write(f'compile_matrix={json.dumps(compile_matrix)}\n')
       f.write(f'simulation_matrix={json.dumps(simulation_matrix)}')
 

From 08dd4f49e6173a3a67347aee2ad72c09e524a56f Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 17:12:03 +0100
Subject: [PATCH 51/61] Work on .github/workflows/test-vs-ed.yaml

---
 testsuite/test_vs_ed/prep_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/testsuite/test_vs_ed/prep_test.py b/testsuite/test_vs_ed/prep_test.py
index 52b6b595..260fcf2c 100755
--- a/testsuite/test_vs_ed/prep_test.py
+++ b/testsuite/test_vs_ed/prep_test.py
@@ -124,7 +124,7 @@ def prep_runs(test_name, test_spec, env_name, env_spec):
 
     for test_name, test_spec in test_specs.items():
         for env_name, env_spec in test_spec['environments'].items():
-            # prep_runs(test_name, test_spec, env_name, env_spec)
+            prep_runs(test_name, test_spec, env_name, env_spec)
             compile_matrix.append({
                 'test_dir': f'testsuite/test_vs_ed/{test_name}_{env_name}',
                 'machine': env_spec['variables']['MACHINE'],

From eda47d7c0e58e81e98352c12d6ea1e4af513c1d4 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 20:25:30 +0100
Subject: [PATCH 52/61] Work on .github/workflows/test-vs-ed.yaml

---
 testsuite/test_vs_ed/test_specs.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/testsuite/test_vs_ed/test_specs.yaml b/testsuite/test_vs_ed/test_specs.yaml
index f95a1902..fcd439da 100644
--- a/testsuite/test_vs_ed/test_specs.yaml
+++ b/testsuite/test_vs_ed/test_specs.yaml
@@ -1,22 +1,22 @@
 hubbard_finT_chain:
   environments: &environments
     Bullseye:
-      image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/bullseye
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/bullseye
       variables: {MACHINE: GNU}
     Bookworm:
-      image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/bookworm
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/bookworm
       variables: {MACHINE: GNU}
     Intel21:
-      image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/bullseye-intel
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/bullseye-intel
       variables: {MACHINE: INTEL}
     Intel-2024.2:
-      image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/bookworm-intel-2024.2
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/bookworm-intel-2024.2
       variables: {MACHINE: INTEL}
     IntelLLVM-Latest:
-      image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/bookworm-intel
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/bookworm-intel
       variables: {MACHINE: IntelLLVM}
     PGI-21-03:
-      image: git.physik.uni-wuerzburg.de:25812/alf/alf_docker/pyalf-requirements/bullseye-pgi-21-03
+      image: ghcr.io/alf-qmc/alf-container/pyalf-requirements/bullseye-pgi-21-03
       variables: {MACHINE: PGI}
     # macGNU:
     #   tags: ['macos']

From 0ddeb93d10cbb064057beb3af040b2054b50f7d4 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 20:33:44 +0100
Subject: [PATCH 53/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index 7b19c804..d1c23899 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -35,6 +35,9 @@ jobs:
         uses: actions/download-artifact@v7
         with:
           name: prepared-test-directories
+      - run: ls -la
+      - run: ls -la testsuite/test_vs_ed/
+      - run: ls -la ${{ matrix.test_dir }}
       - name: Compile ALF
         run: cd ${{ matrix.test_dir }} && ../compile.py ${{ matrix.machine }}
       - name: Upload compiled ALF binary and test directory

From 28851fb651b9d0a417d8f317d504a1db5a30bc16 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 20:37:40 +0100
Subject: [PATCH 54/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/ci.yml          | 9 +++++----
 .github/workflows/test-vs-ed.yaml | 7 +++++--
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d67388b6..50e77b86 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,10 +1,11 @@
 name: CI
 
 on:
-  push:
-    branches: ["**"]
-  pull_request:
-    branches: ["**"]
+  workflow_dispatch:
+#   push:
+#     branches: ["**"]
+#   pull_request:
+#     branches: ["**"]
 
 permissions:
   contents: read
diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index d1c23899..50871689 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -1,5 +1,8 @@
 name: Test vs given ED reference results
-on: workflow_dispatch
+on: 
+  workflow_dispatch:
+  push:
+    branches: ["adapt-test-branch"]
 
 jobs:
   prepare_matrix:
@@ -35,7 +38,7 @@ jobs:
         uses: actions/download-artifact@v7
         with:
           name: prepared-test-directories
-      - run: ls -la
+      - run: ls -la $PWD
       - run: ls -la testsuite/test_vs_ed/
       - run: ls -la ${{ matrix.test_dir }}
       - name: Compile ALF

From 611fda3908bb8ba3fdeaa8a3e0cc474593584e5f Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 20:48:17 +0100
Subject: [PATCH 55/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index 50871689..04e8fa2d 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -38,6 +38,7 @@ jobs:
         uses: actions/download-artifact@v7
         with:
           name: prepared-test-directories
+          path: testsuite/test_vs_ed/
       - run: ls -la $PWD
       - run: ls -la testsuite/test_vs_ed/
       - run: ls -la ${{ matrix.test_dir }}
@@ -63,6 +64,10 @@ jobs:
         uses: actions/download-artifact@v7
         with:
           name: simdir-${{ matrix.test_dir }}-${{ matrix.image }}-${{ matrix.machine }}
+          path: testsuite/test_vs_ed/
+      - run: ls -la $PWD
+      - run: ls -la testsuite/test_vs_ed/
+      - run: ls -la ${{ matrix.test_dir }}
       - name: Run ALF test vs main branch
         run: cd ${{ matrix.test_dir }}/$CI_NODE_INDEX && ../ALF.out
 
@@ -81,6 +86,8 @@ jobs:
         run: pip install --no-deps pyALF
       - name: Download simulation results
         uses: actions/download-artifact@v7
+        with:
+          path: testsuite/test_vs_ed/
       - name: Analyze simulation results
         run: |
           cd testsuite/test_vs_ed

From ae1cce04ccb8df149f1a386feb0f1b8a262c1952 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 20:59:35 +0100
Subject: [PATCH 56/61] Work on .github/workflows/test-vs-ed.yaml

---
 testsuite/test_vs_ed/prep_test.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/testsuite/test_vs_ed/prep_test.py b/testsuite/test_vs_ed/prep_test.py
index 260fcf2c..619a8b97 100755
--- a/testsuite/test_vs_ed/prep_test.py
+++ b/testsuite/test_vs_ed/prep_test.py
@@ -126,13 +126,15 @@ def prep_runs(test_name, test_spec, env_name, env_spec):
         for env_name, env_spec in test_spec['environments'].items():
             prep_runs(test_name, test_spec, env_name, env_spec)
             compile_matrix.append({
-                'test_dir': f'testsuite/test_vs_ed/{test_name}_{env_name}',
+                'test_name': test_name,
+                'env_name': env_name,
                 'machine': env_spec['variables']['MACHINE'],
                 'image': env_spec['image'],
             })
             for i, _ in enumerate(test_spec["sim_dicts"]):
                 simulation_matrix.append({
-                    'test_dir': f'testsuite/test_vs_ed/{test_name}_{env_name}',
+                    'test_name': test_name,
+                    'env_name': env_name,
                     'machine': env_spec['variables']['MACHINE'],
                     'image': env_spec['image'],
                     'CI_NODE_INDEX': i+1,

From b799a223baf91b6f3a9b628d612739951de6578a Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Fri, 16 Jan 2026 21:06:55 +0100
Subject: [PATCH 57/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index 04e8fa2d..4b7c69af 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -41,14 +41,14 @@ jobs:
           path: testsuite/test_vs_ed/
       - run: ls -la $PWD
       - run: ls -la testsuite/test_vs_ed/
-      - run: ls -la ${{ matrix.test_dir }}
+      - run: ls -la testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}
       - name: Compile ALF
-        run: cd ${{ matrix.test_dir }} && ../compile.py ${{ matrix.machine }}
+        run: cd testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }} && ../compile.py ${{ matrix.machine }}
       - name: Upload compiled ALF binary and test directory
         uses: actions/upload-artifact@v6
         with:
-          name: simdir-${{ matrix.test_dir }}-${{ matrix.image }}-${{ matrix.machine }}
-          path: ${{ matrix.test_dir }}
+          name: simdir-${{ matrix.test_name }}-${{ matrix.env_name }}-${{ matrix.machine }}
+          path: testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}
 
   simulate:
     needs: [prepare_matrix, compile]
@@ -63,19 +63,19 @@ jobs:
       - name: Download compiled ALF binary
         uses: actions/download-artifact@v7
         with:
-          name: simdir-${{ matrix.test_dir }}-${{ matrix.image }}-${{ matrix.machine }}
+          name: simdir-${{ matrix.test_name }}-${{ matrix.env_name }}-${{ matrix.machine }}
           path: testsuite/test_vs_ed/
       - run: ls -la $PWD
       - run: ls -la testsuite/test_vs_ed/
-      - run: ls -la ${{ matrix.test_dir }}
+      - run: ls -la testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}
       - name: Run ALF test vs main branch
-        run: cd ${{ matrix.test_dir }}/$CI_NODE_INDEX && ../ALF.out
+        run: cd testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}/${{ matrix.CI_NODE_INDEX }} && ../ALF.out
 
       - name: Upload simulation results
         uses: actions/upload-artifact@v6
         with:
-          name: simulation-results-${{ matrix.test_name }}-${{ matrix.image }}-${{ matrix.machine }}
-          path: ${{ matrix.test_dir }}/${{ matrix.CI_NODE_INDEX }}
+          name: simulation-results-${{ matrix.test_name }}-${{ matrix.env_name }}-${{ matrix.machine }}
+          path: testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}/${{ matrix.CI_NODE_INDEX }}
 
   analyze:
     needs: simulate

From 96caea797a0c3e49f664c00d8b22bebf3c343df5 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Sat, 17 Jan 2026 00:09:46 +0100
Subject: [PATCH 58/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index 4b7c69af..0f0608bf 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -64,7 +64,7 @@ jobs:
         uses: actions/download-artifact@v7
         with:
           name: simdir-${{ matrix.test_name }}-${{ matrix.env_name }}-${{ matrix.machine }}
-          path: testsuite/test_vs_ed/
+          path: testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}
       - run: ls -la $PWD
       - run: ls -la testsuite/test_vs_ed/
       - run: ls -la testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}
@@ -75,7 +75,7 @@ jobs:
         uses: actions/upload-artifact@v6
         with:
           name: simulation-results-${{ matrix.test_name }}-${{ matrix.env_name }}-${{ matrix.machine }}
-          path: testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}/${{ matrix.CI_NODE_INDEX }}
+          path: testsuite/test_vs_ed/
 
   analyze:
     needs: simulate

From 5be1f49dc307581bef2106ffed82f137ced7be93 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Sat, 17 Jan 2026 00:18:24 +0100
Subject: [PATCH 59/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index 0f0608bf..cbfb8302 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -68,6 +68,7 @@ jobs:
       - run: ls -la $PWD
       - run: ls -la testsuite/test_vs_ed/
       - run: ls -la testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}
+      - run: chmod +x testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}/ALF.out
       - name: Run ALF test vs main branch
         run: cd testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}/${{ matrix.CI_NODE_INDEX }} && ../ALF.out
 

From a0f98eed6c79c71d6056d088f95a435a5e51e1c2 Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Sat, 17 Jan 2026 00:25:51 +0100
Subject: [PATCH 60/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index cbfb8302..70122e6c 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -70,7 +70,7 @@ jobs:
       - run: ls -la testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}
       - run: chmod +x testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}/ALF.out
       - name: Run ALF test vs main branch
-        run: cd testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}/${{ matrix.CI_NODE_INDEX }} && ../ALF.out
+        run: cd testsuite/test_vs_ed/${{ matrix.test_name }}_${{ matrix.env_name }}/${{ matrix.CI_NODE_INDEX }} && mpiexec -n 2 ../ALF.out
 
       - name: Upload simulation results
         uses: actions/upload-artifact@v6

From b177ac96f4ec0b37e35db9de88e00c6ae45d4fbb Mon Sep 17 00:00:00 2001
From: Jonas Schwab <jonas.schwab@uni-wuerzburg.de>
Date: Sat, 17 Jan 2026 08:47:57 +0100
Subject: [PATCH 61/61] Work on .github/workflows/test-vs-ed.yaml

---
 .github/workflows/test-vs-ed.yaml | 2 +-
 testsuite/test_vs_ed/compile.py   | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-vs-ed.yaml b/.github/workflows/test-vs-ed.yaml
index 70122e6c..988e9979 100644
--- a/.github/workflows/test-vs-ed.yaml
+++ b/.github/workflows/test-vs-ed.yaml
@@ -75,7 +75,7 @@ jobs:
       - name: Upload simulation results
         uses: actions/upload-artifact@v6
         with:
-          name: simulation-results-${{ matrix.test_name }}-${{ matrix.env_name }}-${{ matrix.machine }}
+          name: simulation-results-${{ matrix.test_name }}-${{ matrix.env_name }}-${{ matrix.machine }}-${{ matrix.CI_NODE_INDEX }}
           path: testsuite/test_vs_ed/
 
   analyze:
diff --git a/testsuite/test_vs_ed/compile.py b/testsuite/test_vs_ed/compile.py
index c168df9f..eae589a5 100755
--- a/testsuite/test_vs_ed/compile.py
+++ b/testsuite/test_vs_ed/compile.py
@@ -22,6 +22,7 @@
             sim_root='.',
             sim_dir=f'{i+1}',
             machine=machine,
+            mpi=True,
         )
         sims.append(sim)