From 743860fc06d5be09e9b15d62514f91ac2fb4aebc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 Mar 2024 11:29:07 +0100
Subject: [PATCH 1/4] {2023.06}[foss/2023b] GROMACS 2024.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index e2d35276df..f906811a73 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -49,3 +49,6 @@ easyconfigs:
   - libspatialindex-1.9.3-GCCcore-13.2.0.eb:
       options:
         from-pr: 19922
+  - GROMACS-2024.1-foss-2023b.eb:
+      options:
+        from-pr: 20102

From b6371d0e2766720a8fbccdb2ed322b5858dc834f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 30 Apr 2024 11:06:30 +0200
Subject: [PATCH 2/4] use easyconfig PR for GROMACS 2024.1 that uses backported
 patch to fix problems with tests

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 3 ---
 .../2023.06/eessi-2023.06-eb-4.9.1-2023b.yml                  | 4 ++++
 2 files changed, 4 insertions(+), 3 deletions(-)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index d45ebfb9ba..86c5106c85 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -57,6 +57,3 @@ easyconfigs:
   - Qt5-5.15.13-GCCcore-13.2.0.eb:
       options:
         from-pr: 20201
-  - GROMACS-2024.1-foss-2023b.eb:
-      options:
-        from-pr: 20102
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
new file mode 100644
index 0000000000..1392fa2f5a
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -0,0 +1,4 @@
+easyconfigs:
+  - GROMACS-2024.1-foss-2023b.eb:
+      options:
+        from-pr: 20439

From 01c49de45a802aafdc5d0bcf7cd577c0213cfac0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 30 Apr 2024 20:54:28 +0200
Subject: [PATCH 3/4] avoid building GROMACS 2024.1 with SVE on Neoverse V1,
 stick to Neon for now (cfr. https://gitlab.com/gromacs/gromacs/-/issues/5057)

---
 eb_hooks.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index 20b5f76cfc..f02c8db48c 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -335,6 +335,21 @@ def pre_configure_hook(self, *args, **kwargs):
         PRE_CONFIGURE_HOOKS[self.name](self, *args, **kwargs)
 
 
+def pre_configure_hook_gromacs(self, *args, **kwargs):
+    """
+    Pre-configure hook for GROMACS:
+    - avoid building with SVE instructions on Neoverse V1 as workaround for failing tests,
+      see https://gitlab.com/gromacs/gromacs/-/issues/5057 + https://gitlab.com/eessi/support/-/issues/47
+    """
+    if self.name == 'GROMACS':
+        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        if LooseVersion(self.version) <= LooseVersion('2024.1') and cpu_target == CPU_TARGET_NEOVERSE_V1:
+            self.cfg.update('configopts', '-DGMX_SIMD=ARM_NEON_ASIMD')
+            print_msg("Avoiding use of SVE instructions for GROMACS %s by using ARM_NEON_ASIMD as GMX_SIMD value", self.version)
+    else:
+        raise EasyBuildError("GROMACS-specific hook triggered for non-GROMACS easyconfig?!")
+
+
 def pre_configure_hook_openblas_optarch_generic(self, *args, **kwargs):
     """
     Pre-configure hook for OpenBLAS: add DYNAMIC_ARCH=1 to build/test/install options when using --optarch=GENERIC
@@ -665,6 +680,7 @@ def inject_gpu_property(ec):
 }
 
 PRE_CONFIGURE_HOOKS = {
+    'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,

From 3eee364b47b4cae85aa675d020a7bd7a362b47f0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 May 2024 11:11:41 +0200
Subject: [PATCH 4/4] register known issue for GROMACS 2024.1 on neoverse_v1

---
 eessi-2023.06-known-issues.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/eessi-2023.06-known-issues.yml b/eessi-2023.06-known-issues.yml
index 011cb2dc08..2d1256354f 100644
--- a/eessi-2023.06-known-issues.yml
+++ b/eessi-2023.06-known-issues.yml
@@ -19,6 +19,9 @@
   - FFTW.MPI-3.3.10-gompi-2023b:
       - issue: https://github.com/EESSI/software-layer/issues/325
       - info: "Flaky FFTW tests, random failures"
+  - GROMACS-2024.1-foss-2023b:
+      - issue: https://github.com/EESSI/software-layer/issues/557
+      - info: "SVE disabled due to known bug which causes test failures"
   - Highway-1.0.3-GCCcore-12.2.0.eb:
     - issue: https://github.com/EESSI/software-layer/issues/469
     - info: "failing SVE test due to wrong expected value"