From fdf0d9a1ee712f2d46eaeaaf6614eb15846441d7 Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 17:18:22 +0100
Subject: [PATCH 01/45] add zen4 / AMD Genoa

---
 init/arch_specs/eessi_arch_x86.spec           |  7 ++---
 .../x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo | 27 +++++++++++++++++++
 .../x86_64/amd/zen4/Azure-Alma8-9V33X.output  |  1 +
 .../x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo  | 27 +++++++++++++++++++
 .../x86_64/amd/zen4/Shinx-RHEL8-9654.output   |  1 +
 5 files changed, 60 insertions(+), 3 deletions(-)
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output

diff --git a/init/arch_specs/eessi_arch_x86.spec b/init/arch_specs/eessi_arch_x86.spec
index 8d01cb0c03..bfbc5b4be1 100755
--- a/init/arch_specs/eessi_arch_x86.spec
+++ b/init/arch_specs/eessi_arch_x86.spec
@@ -1,6 +1,7 @@
 # x86_64 CPU architecture specifications
 # Software path in EESSI 	| Vendor ID 	| List of defining CPU features
-"x86_64/intel/haswell"		"GenuineIntel"	"avx2 fma" 		# Intel Haswell, Broadwell
+"x86_64/intel/haswell"		"GenuineIntel"	"avx2 fma" 						# Intel Haswell, Broadwell
 "x86_64/intel/skylake_avx512"	"GenuineIntel"	"avx2 fma avx512f avx512bw avx512cd avx512dq avx512vl"	# Intel Skylake, Cascade Lake
-"x86_64/amd/zen2"		"AuthenticAMD"	"avx2 fma"		# AMD Rome
-"x86_64/amd/zen3"		"AuthenticAMD"	"avx2 fma vaes"		# AMD Milan, Milan-X
+"x86_64/amd/zen2"		"AuthenticAMD"	"avx2 fma"						# AMD Rome
+"x86_64/amd/zen3"		"AuthenticAMD"	"avx2 fma vaes"						# AMD Milan, Milan-X
+"x86_64/amd/zen4"		"AuthenticAMD"	"avx2 fma vaes avx512f avx512ifma"			# AMD Genoa, Genoa-X
diff --git a/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo
new file mode 100644
index 0000000000..4a97da862c
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo
@@ -0,0 +1,27 @@
+processor       : 0
+vendor_id       : AuthenticAMD
+cpu family      : 25
+model           : 17
+model name      : AMD EPYC 9V33X 96-Core Processor
+stepping        : 1
+microcode       : 0xffffffff
+cpu MHz         : 3705.853
+cache size      : 1024 KB
+physical id     : 0
+siblings        : 88
+core id         : 0
+cpu cores       : 88
+apicid          : 0
+initial apicid  : 0
+fpu             : yes
+fpu_exception   : yes
+cpuid level     : 13
+wp              : yes
+flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext perfctr_core invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves avx512_bf16 clzero xsaveerptr arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload avx512vbmi umip avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq rdpid fsrm
+bugs            : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass
+bogomips        : 5100.08
+TLB size        : 3584 4K pages
+clflush size    : 64
+cache_alignment : 64
+address sizes   : 48 bits physical, 48 bits virtual
+power management:
diff --git a/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output
new file mode 100644
index 0000000000..950740a78c
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output
@@ -0,0 +1 @@
+x86_64/amd/zen4
diff --git a/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo
new file mode 100644
index 0000000000..f28381d7a2
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo
@@ -0,0 +1,27 @@
+processor	: 0
+vendor_id	: AuthenticAMD
+cpu family	: 25
+model		: 17
+model name	: AMD EPYC 9654 96-Core Processor
+stepping	: 1
+microcode	: 0xa10113e
+cpu MHz		: 3699.993
+cache size	: 1024 KB
+physical id	: 0
+siblings	: 96
+core id		: 0
+cpu cores	: 96
+apicid		: 0
+initial apicid	: 0
+fpu		: yes
+fpu_exception	: yes
+cpuid level	: 16
+wp		: yes
+flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 invpcid_single hw_pstate ssbd mba perfmon_v2 ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid cqm rdt_a avx512f avx512dq rdseed adx avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local avx512_bf16 clzero irperf xsaveerptr wbnoinvd amd_ppin cppc arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif v_spec_ctrl avx512vbmi umip pku ospke avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq la57 rdpid overflow_recov succor smca fsrm flush_l1d
+bugs		: sysret_ss_attrs spectre_v1 spectre_v2 spec_store_bypass
+bogomips	: 4799.99
+TLB size	: 3584 4K pages
+clflush size	: 64
+cache_alignment	: 64
+address sizes	: 52 bits physical, 57 bits virtual
+power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]
diff --git a/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output
new file mode 100644
index 0000000000..950740a78c
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output
@@ -0,0 +1 @@
+x86_64/amd/zen4

From 1ee221bdbfe0ae6015ca3765a8e23b0760a2323f Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 17:24:21 +0100
Subject: [PATCH 02/45] add all.output tests

---
 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output | 1 +
 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output  | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output

diff --git a/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output
new file mode 100644
index 0000000000..e1bbd79e4a
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output
@@ -0,0 +1 @@
+x86_64/amd/zen4:x86_64/amd/zen3:x86_64/amd/zen2:x86_64/generic
diff --git a/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output
new file mode 100644
index 0000000000..e1bbd79e4a
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output
@@ -0,0 +1 @@
+x86_64/amd/zen4:x86_64/amd/zen3:x86_64/amd/zen2:x86_64/generic

From 680e7b91836c33caeb1c2c493f0589d4b5a73219 Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 17:28:59 +0100
Subject: [PATCH 03/45] adding zen4 checks

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

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 37338693c5..d1407637e0 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -13,6 +13,8 @@ jobs:
           - x86_64/intel/skylake_avx512/archspec-linux-6132
           - x86_64/amd/zen2/Azure-CentOS7-7V12
           - x86_64/amd/zen3/Azure-CentOS7-7V73X
+          - x86_64/amd/zen4/Azure-Alma8-9V33X
+          - x86_64/amd/zen4/Shinx-RHEL8-9654
           - ppc64le/power9le/unknown-power9le
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2

From 7070c047ebf57918dd0ae19c11ade011e99cefff Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 18:00:17 +0100
Subject: [PATCH 04/45] commenting out power to prevent conflict

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

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index d1407637e0..45e8dd2e60 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -15,10 +15,10 @@ jobs:
           - x86_64/amd/zen3/Azure-CentOS7-7V73X
           - x86_64/amd/zen4/Azure-Alma8-9V33X
           - x86_64/amd/zen4/Shinx-RHEL8-9654
-          - ppc64le/power9le/unknown-power9le
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2
           - aarch64/neoverse_v1/AWS-awslinux-graviton3
+          # - ppc64le/power9le/unknown-power9le
       fail-fast: false
     steps:
     - name: checkout

From ad70b6b0857f6e3508a73c4675795de30f6b40eb Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 19:27:14 +0100
Subject: [PATCH 05/45] commenting out power9 to prevent conflict

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

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 45e8dd2e60..68d25250ca 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -18,6 +18,8 @@ jobs:
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2
           - aarch64/neoverse_v1/AWS-awslinux-graviton3
+          # commented out since these targets are currently not supported in software.eessi.io repo
+          # (and some tests assume that the corresponding subdirectory in software layer is there)
           # - ppc64le/power9le/unknown-power9le
       fail-fast: false
     steps:

From fd3103e1f75157edffcf16023ef4fb6431c6b5eb Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 20:15:18 +0100
Subject: [PATCH 06/45] move to software.eessi.io

---
 .github/workflows/test_eessi.yml                  | 14 +++++++-------
 .github/workflows/test_eessi_container_script.yml | 12 ++++++------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index 04195dd619..7c96b091d2 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         EESSI_VERSION:
-        - 2021.12
+        - 2023.06
         EESSI_SOFTWARE_SUBDIR:
         - aarch64/generic
         - aarch64/graviton2
@@ -24,19 +24,19 @@ jobs:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
 
-        - name: Mount EESSI CernVM-FS pilot repository
+        - name: Mount EESSI CernVM-FS software repository
           uses: cvmfs-contrib/github-action-cvmfs@d4641d0d591c9a5c3be23835ced2fb648b44c04b # v3.1
           with:
               cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb
               cvmfs_http_proxy: DIRECT
-              cvmfs_repositories: pilot.eessi-hpc.org
+              cvmfs_repositories: software.eessi.io
 
         - name: Test check_missing_installations.sh script
           run: |
-              source /cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}/init/bash
+              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               eb --version
-              export EESSI_PREFIX=/cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
               export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
@@ -45,10 +45,10 @@ jobs:
 
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
           run: |
-              source /cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}/init/bash
+              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               eb --version
-              export EESSI_PREFIX=/cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
               export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index 929fb22cec..590aa4225b 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -90,15 +90,15 @@ jobs:
               elif [[ ${{matrix.SCRIPT_TEST}} == 'readwrite' ]]; then
                 outfile=out_readwrite.txt
                 fn="test_${RANDOM}.txt"
-                echo "touch /cvmfs/pilot.eessi-hpc.org/${fn}" > test_script.sh
+                echo "touch /cvmfs/software.eessi.io/${fn}" > test_script.sh
                 chmod u+x test_script.sh
                 export SINGULARITY_BIND="$PWD:/test"
                 ./eessi_container.sh --verbose --access rw --mode run /test/test_script.sh > ${outfile}
 
                 tmpdir=$(grep "\-\-resume" ${outfile} | sed "s/.*--resume \([^']*\).*/\1/g")
                 # note: must use '--access rw' again here, since touched file is in overlay upper dir
-                ./eessi_container.sh --verbose --resume ${tmpdir} --access rw --mode shell <<< "ls -l /cvmfs/pilot.eessi-hpc.org/${fn}" > ${outfile}
-                grep "/cvmfs/pilot.eessi-hpc.org/${fn}$" $outfile
+                ./eessi_container.sh --verbose --resume ${tmpdir} --access rw --mode shell <<< "ls -l /cvmfs/software.eessi.io/${fn}" > ${outfile}
+                grep "/cvmfs/software.eessi.io/${fn}$" $outfile
 
               # test use of --resume
               elif [[ ${{matrix.SCRIPT_TEST}} == 'resume' ]]; then
@@ -120,12 +120,12 @@ jobs:
               elif [[ ${{matrix.SCRIPT_TEST}} == 'save' ]]; then
                 outfile=out_save.txt
                 fn="test_${RANDOM}.txt"
-                test_cmd="touch /cvmfs/pilot.eessi-hpc.org/${fn}"
+                test_cmd="touch /cvmfs/software.eessi.io/${fn}"
                 ./eessi_container.sh --verbose --mode shell --access rw --save test-save.tar <<< "${test_cmd}" 2>&1 | tee ${outfile}
                 rm -f ${outfile}
 
-                ./eessi_container.sh --verbose --mode shell --access rw --resume test-save.tar <<< "ls -l /cvmfs/pilot.eessi-hpc.org/${fn}" > ${outfile}
-                grep "/cvmfs/pilot.eessi-hpc.org/${fn}$" $outfile
+                ./eessi_container.sh --verbose --mode shell --access rw --resume test-save.tar <<< "ls -l /cvmfs/software.eessi.io/${fn}" > ${outfile}
+                grep "/cvmfs/software.eessi.io/${fn}$" $outfile
 
                 tar tfv test-save.tar | grep "overlay-upper/${fn}"
 

From a13bce84ca477c9d866ad722993252aad924d5fd Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 20:20:48 +0100
Subject: [PATCH 07/45] move from pilot to software

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

diff --git a/.github/workflows/tests_readme.yml b/.github/workflows/tests_readme.yml
index 5c6d0318d4..034dae3780 100644
--- a/.github/workflows/tests_readme.yml
+++ b/.github/workflows/tests_readme.yml
@@ -24,7 +24,7 @@ jobs:
         - name: verify if README.md is consistent with EESSI_PILOT_VERSION from init/eessi_defaults
           run: |
             source init/eessi_defaults
-            grep "${EESSI_PILOT_VERSION}" README.md
+            grep "${EESSI_VERSION}" README.md
 
         - name: verify if README.md is consistent with EESSI_CVMFS_REPO from init/eessi_defaults
           run: |

From 473a5b52b960881f2b4371978279976b9a8bccae Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Thu, 11 Jan 2024 03:51:20 +0100
Subject: [PATCH 08/45] move EESSI action to v3

---
 .github/workflows/tests_archdetect.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 68d25250ca..f09567d125 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -26,7 +26,8 @@ jobs:
     - name: checkout
       uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
     - name: Enable EESSI
-      uses: eessi/github-action-eessi@58b50fd2eead2162c2b9ac258d4fb60cc9f30503 # v2.0.13
+      #uses: eessi/github-action-eessi@58b50fd2eead2162c2b9ac258d4fb60cc9f30503 # v2.0.13
+      uses: eessi/github-action-eessi@v3
     - name: test eessi_archdetect.sh
       run: |
           export EESSI_MACHINE_TYPE=${{matrix.proc_cpuinfo}}

From 807d78471ad4104d0ff3f590dbc697d6cd2a3968 Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Mon, 15 Jan 2024 11:27:42 +0100
Subject: [PATCH 09/45] fix upstream merge

---
 .github/workflows/test_eessi.yml | 72 --------------------------------
 1 file changed, 72 deletions(-)
 delete mode 100644 .github/workflows/test_eessi.yml

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
deleted file mode 100644
index 7c96b091d2..0000000000
--- a/.github/workflows/test_eessi.yml
+++ /dev/null
@@ -1,72 +0,0 @@
-# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
-name: Tests relying on having EESSI pilot repo mounted
-on: [push, pull_request, workflow_dispatch]
-permissions:
-  contents: read # to fetch code (actions/checkout)
-jobs:
-  eessi_pilot_repo:
-    runs-on: ubuntu-20.04
-    strategy:
-      fail-fast: false
-      matrix:
-        EESSI_VERSION:
-        - 2023.06
-        EESSI_SOFTWARE_SUBDIR:
-        - aarch64/generic
-        - aarch64/graviton2
-        - aarch64/graviton3
-        - x86_64/amd/zen2
-        - x86_64/amd/zen3
-        - x86_64/intel/haswell
-        - x86_64/intel/skylake_avx512
-        - x86_64/generic
-    steps:
-        - name: Check out software-layer repository
-          uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
-
-        - name: Mount EESSI CernVM-FS software repository
-          uses: cvmfs-contrib/github-action-cvmfs@d4641d0d591c9a5c3be23835ced2fb648b44c04b # v3.1
-          with:
-              cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb
-              cvmfs_http_proxy: DIRECT
-              cvmfs_repositories: software.eessi.io
-
-        - name: Test check_missing_installations.sh script
-          run: |
-              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
-              module load EasyBuild
-              eb --version
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
-              export EESSI_OS_TYPE=linux
-              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
-              env | grep ^EESSI | sort
-              echo "just run check_missing_installations.sh (should use eessi-${{matrix.EESSI_VERSION}}.yml)"
-              ./check_missing_installations.sh
-
-        - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
-          run: |
-              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
-              module load EasyBuild
-              eb --version
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
-              export EESSI_OS_TYPE=linux
-              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
-              env | grep ^EESSI | sort
-              echo "modify eessi-${{matrix.EESSI_VERSION}}.yml by adding a missing package (GCC/8.3.0)"
-              echo "  GCC:" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              echo "    toolchains:" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              echo "      SYSTEM:" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              echo "        versions: '8.3.0'" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              tail -n 4 eessi-${{matrix.EESSI_VERSION}}.yml
-              # note, check_missing_installations.sh exits 1 if a package was
-              # missing, which is intepreted as false (exit code based, not
-              # boolean logic), hence when the script exits 0 if no package was
-              # missing it is interpreted as true, thus the test did not capture
-              # the missing package
-              if ./check_missing_installations.sh; then
-                echo "did NOT capture missing package; test FAILED"
-                exit 1
-              else
-                echo "captured missing package; test PASSED"
-                exit 0
-              fi

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 10/45] {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 70d94a1361eaa02a8dea4c64495480f0a4cc6910 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 30 Mar 2024 22:58:48 +0100
Subject: [PATCH 11/45] add R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 3962f63bda..8a3e82d760 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -11,3 +11,4 @@ easyconfigs:
   - R-4.2.2-foss-2022b.eb:
       options:
         from-pr: 20238
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

From 3ccecf97e9008ddf98640d3a0ab970607c5b5779 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 12:58:22 +0200
Subject: [PATCH 12/45] Add possibility to ignore certain hooks on local
 modules. E.g. we don't want to be prevented from loading local CUDA modules
 because of the EESSI hook. See
 https://github.com/EESSI/software-layer/issues/523

---
 create_lmodsitepackage.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 29b2d39bd7..ffbe7a1531 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -19,6 +19,18 @@
     return content
 end
 
+local function from_eessi_prefix(t)
+    local eessi_prefix = os.getenv("EESSI_PREFIX")
+    -- If EESSI_PREFIX wasn't defined, we cannot check if this module was from the EESSI environment
+    -- In that case, we assume it isn't, otherwise EESSI_PREFIX would (probably) have been set
+    if eessi_prefix == nil then
+        return False
+    else
+        -- Check if the full modulepath starts with the eessi_prefix
+        return t.fn:find( "^" .. eessi_prefix) ~= nil
+    end
+end
+
 local function load_site_specific_hooks()
     -- This function will be run after the EESSI hooks are registered
     -- It will load a local SitePackage.lua that is architecture independent (if it exists) from e.g.
@@ -152,10 +164,13 @@
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)
-    eessi_cuda_enabled_load_hook(t)
+    -- Only apply CUDA hooks if the loaded module is in the EESSI prefix
+    -- This avoids getting an Lmod Error when trying to load a CUDA module from a local software stack
+    if from_eessi_prefix(t) then
+        eessi_cuda_enabled_load_hook(t)
+    end
 end
 
-
 hook.register("load", eessi_load_hook)
 
 -- Note that this needs to happen at the end, so that any EESSI specific hooks can be overwritten by the site

From bb20ab2078b25041011f242673a848b199aedb74 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 16:36:39 +0200
Subject: [PATCH 13/45] Also use hooks for site extensions in host_injections
 AND for user extensions in /home/casparl/eessi/...

---
 create_lmodsitepackage.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ffbe7a1531..f7d4d06bb9 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -20,14 +20,24 @@
 end
 
 local function from_eessi_prefix(t)
+    -- eessi_prefix is the prefix with official EESSI modules
+    -- e.g. /cvmfs/software.eessi.io/versions/2023.06
     local eessi_prefix = os.getenv("EESSI_PREFIX")
+    -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
+    -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
+    local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
+    -- eessi_prefix_user_home is the prefix with user-extensions (i.e. additional modules)
+    -- to the offocial EESSI modules, e.g. $HOME/eessi/versions/2023.06
+    local eessi_prefix_user_home = string.gsub(eessi_prefix, os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
     -- If EESSI_PREFIX wasn't defined, we cannot check if this module was from the EESSI environment
     -- In that case, we assume it isn't, otherwise EESSI_PREFIX would (probably) have been set
     if eessi_prefix == nil then
         return False
     else
-        -- Check if the full modulepath starts with the eessi_prefix
-        return t.fn:find( "^" .. eessi_prefix) ~= nil
+        -- Check if the full modulepath starts with the eessi_prefix_*
+        return string.find(t.fn, "^" .. eessi_prefix) ~= nil or
+        string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil or
+        string.find(t.fn, "^" .. eessi_prefix_user_home) ~= nil
     end
 end
 

From 838920bd332819b1e50706873ee53f2469cf3794 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 16:38:24 +0200
Subject: [PATCH 14/45] Leave breadcrumb to notify that paths may need to be
 changed in the future

---
 create_lmodsitepackage.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index f7d4d06bb9..ce94a7e311 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -23,6 +23,10 @@
     -- eessi_prefix is the prefix with official EESSI modules
     -- e.g. /cvmfs/software.eessi.io/versions/2023.06
     local eessi_prefix = os.getenv("EESSI_PREFIX")
+
+    -- NOTE: exact paths for site and user extensions aren't final, so may need to be updated later.
+    -- See https://github.com/EESSI/software-layer/pull/371
+
     -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
     -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
     local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')

From 145706e751ea7a73202676894cd58be65bea97d1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Apr 2024 11:53:36 +0200
Subject: [PATCH 15/45] add R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index ad3cfddfb6..2dadc5ab28 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -57,3 +57,4 @@ easyconfigs:
   - Highway-1.0.4-GCCcore-12.3.0.eb
   - ELPA-2023.05.001-foss-2023a.eb
   - libxc-6.2.2-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb

From cef7a277ac4092f8ff1256290ad6bb8b244c2443 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Apr 2024 13:03:35 +0200
Subject: [PATCH 16/45] add from-pr to bioconductor

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index facd4230ab..60b9600589 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -67,4 +67,6 @@ easyconfigs:
   - MODFLOW-6.4.4-foss-2023a.eb:
       options:
         from-pr: 20142
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 19949

From 3745adee2c09aa73d44c7b693baca3ac4c96e70c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 8 Apr 2024 13:52:36 +0200
Subject: [PATCH 17/45] use pr 20316 for Bioconductor

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index d3ac5f1c5b..bfc408e045 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -73,4 +73,4 @@ easyconfigs:
         from-pr: 20238
   - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
       options:
-        from-pr: 19949
+        from-pr: 20316

From 03b708fe7af1fc1aa330bf17bdf3f25a601f093e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 8 Apr 2024 13:54:13 +0200
Subject: [PATCH 18/45] use PR  20316 for Bioconductor

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2022b.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 8a3e82d760..da89e01a51 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -11,4 +11,6 @@ easyconfigs:
   - R-4.2.2-foss-2022b.eb:
       options:
         from-pr: 20238
-  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
+      options:
+        from-pr: 20316

From 8331e4485a5734730b0929be69c3cd3c6beaa4b6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 16 Apr 2024 09:30:02 +0200
Subject: [PATCH 19/45] remove build_container.sh, as we now use
 eessi_container.sh

---
 build_container.sh | 69 ----------------------------------------------
 1 file changed, 69 deletions(-)
 delete mode 100755 build_container.sh

diff --git a/build_container.sh b/build_container.sh
deleted file mode 100755
index 23a9e665c9..0000000000
--- a/build_container.sh
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/bin/bash
-
-base_dir=$(dirname $(realpath $0))
-
-BUILD_CONTAINER="docker://ghcr.io/eessi/build-node:debian11"
-
-if [ $# -lt 2 ]; then
-    echo "Usage: $0 <shell|run> <path for temporary directories>" >&2
-    exit 1
-fi
-SHELL_OR_RUN=$1
-EESSI_TMPDIR=$2
-shift 2
-
-if [ "$SHELL_OR_RUN" == "run" ] && [ $# -eq 0 ]; then
-    echo "ERROR: No command specified to run?!" >&2
-    exit 1
-fi
-
-# make sure specified temporary directory exists
-mkdir -p $EESSI_TMPDIR
-
-echo "Using $EESSI_TMPDIR as parent for temporary directories..."
-
-# create temporary directories
-mkdir -p $EESSI_TMPDIR/{home,overlay-upper,overlay-work}
-mkdir -p $EESSI_TMPDIR/{var-lib-cvmfs,var-run-cvmfs}
-# configure Singularity
-export SINGULARITY_CACHEDIR=$EESSI_TMPDIR/singularity_cache
-
-# take into account that $SINGULARITY_BIND may be defined already, to bind additional paths into the build container
-BIND_PATHS="$EESSI_TMPDIR/var-run-cvmfs:/var/run/cvmfs,$EESSI_TMPDIR/var-lib-cvmfs:/var/lib/cvmfs,$EESSI_TMPDIR"
-if [ -z $SINGULARITY_BIND ]; then
-    export SINGULARITY_BIND="$BIND_PATHS"
-else
-    export SINGULARITY_BIND="$SINGULARITY_BIND,$BIND_PATHS"
-fi
-
-# allow that SINGULARITY_HOME is defined before script is run
-if [ -z $SINGULARITY_HOME ]; then
-    export SINGULARITY_HOME="$EESSI_TMPDIR/home:/home/$USER"
-fi
-
-source ${base_dir}/init/eessi_defaults
-# strip "/cvmfs/" from default setting
-repo_name=${EESSI_CVMFS_REPO/\/cvmfs\//}
-
-# set environment variables for fuse mounts in Singularity container
-export EESSI_PILOT_READONLY="container:cvmfs2 ${repo_name} /cvmfs_ro/${repo_name}"
-export EESSI_PILOT_WRITABLE_OVERLAY="container:fuse-overlayfs -o lowerdir=/cvmfs_ro/${repo_name} -o upperdir=$EESSI_TMPDIR/overlay-upper -o workdir=$EESSI_TMPDIR/overlay-work ${EESSI_CVMFS_REPO}"
-
-# pass $EESSI_SOFTWARE_SUBDIR_OVERRIDE into build container (if set)
-if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
-    export SINGULARITYENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
-    # also specify via $APPTAINERENV_* (future proof, cfr. https://apptainer.org/docs/user/latest/singularity_compatibility.html#singularity-environment-variable-compatibility)
-    export APPTAINERENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
-fi
-
-if [ "$SHELL_OR_RUN" == "shell" ]; then
-    # start shell in Singularity container, with EESSI repository mounted with writable overlay
-    echo "Starting Singularity build container..."
-    singularity shell --fusemount "$EESSI_PILOT_READONLY" --fusemount "$EESSI_PILOT_WRITABLE_OVERLAY" $BUILD_CONTAINER
-elif [ "$SHELL_OR_RUN" == "run" ]; then
-    echo "Running '$@' in Singularity build container..."
-    singularity exec --fusemount "$EESSI_PILOT_READONLY" --fusemount "$EESSI_PILOT_WRITABLE_OVERLAY" $BUILD_CONTAINER "$@"
-else
-    echo "ERROR: Unknown action specified: $SHELL_OR_RUN (should be either 'shell' or 'run')" >&2
-    exit 1
-fi

From a7305456f10ca0289d1cbea8b212aa7cb4fb114a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 16 Apr 2024 09:32:23 +0200
Subject: [PATCH 20/45] replace build_container.sh by eessi_container.sh

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

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 4944d9beaa..76d19d29fe 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -3,9 +3,9 @@ name: Tests for scripts
 on:
   push:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh
@@ -15,9 +15,9 @@ on:
 
   pull_request:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh

From dee801bbf1dc31c61a51a6e4b6dde702bf6337f8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:25:51 +0200
Subject: [PATCH 21/45] move bioconductor to 4.9.1 easystack

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 8a3e82d760..3962f63bda 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -11,4 +11,3 @@ easyconfigs:
   - R-4.2.2-foss-2022b.eb:
       options:
         from-pr: 20238
-  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

From cbad690f01b417a9a185685d20f7e160808242ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:26:05 +0200
Subject: [PATCH 22/45] add bioconductor

---
 .../2023.06/eessi-2023.06-eb-4.9.1-2022b.yml                 | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
new file mode 100644
index 0000000000..f80b99f187
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -0,0 +1,5 @@
+easyconfigs:
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
+      options:
+        from-pr: 20379
+

From b6a222639341313caca5bebb621590f8d0862373 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:30:08 +0200
Subject: [PATCH 23/45] move biocondutor to 4.9.1 stack, use pr 20379

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 ---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index bfc408e045..44952e2765 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,6 +71,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
-      options:
-        from-pr: 20316
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3b51db3b11..57cfc00297 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,5 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 20379

From 786e1e8189d75682c37150d2d7d58e465ec7e9ca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:31:08 +0200
Subject: [PATCH 24/45] remove blank line

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index f80b99f187..e547e45f2b 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -2,4 +2,3 @@ easyconfigs:
   - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
       options:
         from-pr: 20379
-

From d6336e181efb320a74b895e0baf73373e49875f9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 11:50:15 +0200
Subject: [PATCH 25/45] move bioconductor back to 4.9.0 file

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 +++
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 ---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 44952e2765..23d64036f1 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,3 +71,6 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 20379
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 57cfc00297..3b51db3b11 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,5 +1,2 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
-      options:
-        from-pr: 20379

From 339f358e46dd338649939c31042a0faf15f9e532 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 13:59:23 +0200
Subject: [PATCH 26/45] add rebuild easystack for setuptools_scm fix

---
 ...move-setuptools_scm-from-hatchling-to-Python.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
new file mode 100644
index 0000000000..56ea7a46a1
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -0,0 +1,13 @@
+# 2024-04-19
+# Move setuptools_scm extension from hatchling to Python by rebuilding
+# all affected modules with EasyBuild 4.9.1.
+# This solves an issue with pyarrow, which is part of the Arrow installation.
+# https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
+# https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
+easyconfigs:
+  - hatchling-1.18.0-GCCcore-12.3.0.eb
+  - hatchling-1.18.0-GCCcore-13.2.0.eb
+  - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
+  - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+  - Python-3.11.3-GCCcore-12.3.0.eb
+  - Python-3.11.5-GCCcore-13.2.0.eb

From 4d465e9996b61bfb2f2643710bf944ee88bdd355 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Sun, 21 Apr 2024 17:47:40 +0200
Subject: [PATCH 27/45] Add SAMtools-1.18-GCC-12.3.0

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3b51db3b11..ec5fd3c638 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
+  - SAMtools-1.18-GCC-12.3.0.eb

From 8cd5d844e872fe58efcdbb49e38689e656f3f9a1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 22 Apr 2024 16:39:45 +0200
Subject: [PATCH 28/45] attempt to fix the hatchling reinstallation issue

---
 EESSI-remove-software.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 446a156cb8..d8a6dae63e 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -114,6 +114,11 @@ if [ $EUID -eq 0 ]; then
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     rm -rf ${app_dir}
                     rm -rf ${app_module}
+                    # if the parent dir of this application is now empty, remove it too to work around a weird issue with the overlay
+                    # see https://github.com/EESSI/software-layer/pull/546#issuecomment-2067018216
+                    if [ ! -n "$(dirname ${app_dir})" ]; then
+                        rmdir "$(dirname ${app_dir})"
+                    fi
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From 76ecccf629f6b4dda1b65e4ee1f3f2d9d9b9457c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 22 Apr 2024 17:13:37 +0200
Subject: [PATCH 29/45] use right if condition for checking if dir is empty

---
 EESSI-remove-software.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index d8a6dae63e..f3c4f9e618 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -116,8 +116,9 @@ if [ $EUID -eq 0 ]; then
                     rm -rf ${app_module}
                     # if the parent dir of this application is now empty, remove it too to work around a weird issue with the overlay
                     # see https://github.com/EESSI/software-layer/pull/546#issuecomment-2067018216
-                    if [ ! -n "$(dirname ${app_dir})" ]; then
-                        rmdir "$(dirname ${app_dir})"
+                    app_dir_parent=$(dirname "${app_dir}")
+                    if [ ! -n "$(ls -A ${app_dir_parent})" ]; then
+                        rmdir "${app_dir_parent}"
                     fi
                 done
             else

From 1642621d1b47b804f689280d7c797824d1662a2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 14:24:46 +0200
Subject: [PATCH 30/45] undo parent dir removal, workaround didn't work

---
 EESSI-remove-software.sh | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index f3c4f9e618..446a156cb8 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -114,12 +114,6 @@ if [ $EUID -eq 0 ]; then
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     rm -rf ${app_dir}
                     rm -rf ${app_module}
-                    # if the parent dir of this application is now empty, remove it too to work around a weird issue with the overlay
-                    # see https://github.com/EESSI/software-layer/pull/546#issuecomment-2067018216
-                    app_dir_parent=$(dirname "${app_dir}")
-                    if [ ! -n "$(ls -A ${app_dir_parent})" ]; then
-                        rmdir "${app_dir_parent}"
-                    fi
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From a5bf9d3da294fad127aef0dc972af323a0488077 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 14:26:25 +0200
Subject: [PATCH 31/45] only rebuild 2023a easyconfigs

---
 ...eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
index 56ea7a46a1..76dd37e870 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -1,13 +1,10 @@
 # 2024-04-19
 # Move setuptools_scm extension from hatchling to Python by rebuilding
-# all affected modules with EasyBuild 4.9.1.
+# the affected modules in the 2023a toolchain with EasyBuild 4.9.1.
 # This solves an issue with pyarrow, which is part of the Arrow installation.
 # https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
 # https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
 easyconfigs:
   - hatchling-1.18.0-GCCcore-12.3.0.eb
-  - hatchling-1.18.0-GCCcore-13.2.0.eb
   - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
-  - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
   - Python-3.11.3-GCCcore-12.3.0.eb
-  - Python-3.11.5-GCCcore-13.2.0.eb

From c4af218d2c7dd604f10cea7454d1f672b00498ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 15:04:02 +0200
Subject: [PATCH 32/45] only try 2023b versions

---
 ...4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
index 76dd37e870..f3484a3486 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -1,10 +1,10 @@
 # 2024-04-19
 # Move setuptools_scm extension from hatchling to Python by rebuilding
-# the affected modules in the 2023a toolchain with EasyBuild 4.9.1.
+# the affected modules in the 2023b toolchain with EasyBuild 4.9.1.
 # This solves an issue with pyarrow, which is part of the Arrow installation.
 # https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
 # https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
 easyconfigs:
-  - hatchling-1.18.0-GCCcore-12.3.0.eb
-  - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
-  - Python-3.11.3-GCCcore-12.3.0.eb
+  - hatchling-1.18.0-GCCcore-13.2.0.eb
+  - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+  - Python-3.11.5-GCCcore-13.2.0.eb

From 33cb74f5e2f4f63cd286e0d1b71818ccb1eca1a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 15:33:15 +0200
Subject: [PATCH 33/45] try adding write permissions instead of removing

---
 EESSI-remove-software.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 446a156cb8..1a488dcb67 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -112,8 +112,9 @@ if [ $EUID -eq 0 ]; then
                     app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
-                    rm -rf ${app_dir}
-                    rm -rf ${app_module}
+                    #rm -rf ${app_dir}
+                    #rm -rf ${app_module}
+                    chmod -R u+w ${app_dir} ${app_module}
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From 1e92daf31bca8a879b2888cefc5156c76774f7ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 16:12:21 +0200
Subject: [PATCH 34/45] do remove the module to make sure it gets rebuilt

---
 EESSI-remove-software.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 1a488dcb67..9d82dd8aa6 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -113,8 +113,8 @@ if [ $EUID -eq 0 ]; then
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     #rm -rf ${app_dir}
-                    #rm -rf ${app_module}
-                    chmod -R u+w ${app_dir} ${app_module}
+                    rm -rf ${app_module}
+                    chmod -R u+w ${app_dir}
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From d0229ccb3adb03eac5cdddde76858b00d20832bf Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Mon, 29 Apr 2024 14:40:50 +0200
Subject: [PATCH 35/45] Update create_lmodsitepackage.py

---
 create_lmodsitepackage.py | 22 +++++++++-------------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ce94a7e311..862902d80e 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -24,24 +24,20 @@
     -- e.g. /cvmfs/software.eessi.io/versions/2023.06
     local eessi_prefix = os.getenv("EESSI_PREFIX")
 
-    -- NOTE: exact paths for site and user extensions aren't final, so may need to be updated later.
-    -- See https://github.com/EESSI/software-layer/pull/371
-
-    -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
-    -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
-    local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
-    -- eessi_prefix_user_home is the prefix with user-extensions (i.e. additional modules)
-    -- to the offocial EESSI modules, e.g. $HOME/eessi/versions/2023.06
-    local eessi_prefix_user_home = string.gsub(eessi_prefix, os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
     -- If EESSI_PREFIX wasn't defined, we cannot check if this module was from the EESSI environment
     -- In that case, we assume it isn't, otherwise EESSI_PREFIX would (probably) have been set
     if eessi_prefix == nil then
         return False
     else
-        -- Check if the full modulepath starts with the eessi_prefix_*
-        return string.find(t.fn, "^" .. eessi_prefix) ~= nil or
-        string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil or
-        string.find(t.fn, "^" .. eessi_prefix_user_home) ~= nil
+        -- NOTE: exact paths for site so may need to be updated later.
+        -- See https://github.com/EESSI/software-layer/pull/371
+
+        -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
+        -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
+        local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
+        
+       -- Check if the full modulepath starts with the eessi_prefix_*
+        return string.find(t.fn, "^" .. eessi_prefix) ~= nil or string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil
     end
 end
 

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 36/45] 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 b94fa6262a2845a03d58a9095b5da4fb84b8e710 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 30 Apr 2024 15:13:53 +0200
Subject: [PATCH 37/45] restore easystack, rebuild all required versions

---
 ...eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
index f3484a3486..56ea7a46a1 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -1,10 +1,13 @@
 # 2024-04-19
 # Move setuptools_scm extension from hatchling to Python by rebuilding
-# the affected modules in the 2023b toolchain with EasyBuild 4.9.1.
+# all affected modules with EasyBuild 4.9.1.
 # This solves an issue with pyarrow, which is part of the Arrow installation.
 # https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
 # https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
 easyconfigs:
+  - hatchling-1.18.0-GCCcore-12.3.0.eb
   - hatchling-1.18.0-GCCcore-13.2.0.eb
+  - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
   - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+  - Python-3.11.3-GCCcore-12.3.0.eb
   - Python-3.11.5-GCCcore-13.2.0.eb

From 66724f282e405579021811813721aaf79dc35a75 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 30 Apr 2024 15:14:50 +0200
Subject: [PATCH 38/45] undo changes

---
 EESSI-remove-software.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 9d82dd8aa6..446a156cb8 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -112,9 +112,8 @@ if [ $EUID -eq 0 ]; then
                     app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
-                    #rm -rf ${app_dir}
+                    rm -rf ${app_dir}
                     rm -rf ${app_module}
-                    chmod -R u+w ${app_dir}
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

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 39/45] 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 ac82cc840bfbdae0638438fb85f9a5004e020f2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 30 Apr 2024 21:21:32 +0200
Subject: [PATCH 40/45] move bioconductor to eb 4.9.1 file

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 ---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 23d64036f1..44952e2765 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,6 +71,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
-      options:
-        from-pr: 20379
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index ec5fd3c638..e65747e4a5 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,3 +1,6 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
   - SAMtools-1.18-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 20379

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 41/45] 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"

From a9e8ae8192e916b3b6bcbfa6c47206a748d362b8 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 6 May 2024 16:06:22 +0200
Subject: [PATCH 42/45] Match name stub of files to CUDA allow list to ship

---
 .../2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml | 8 ++++++++
 eb_hooks.py                                               | 4 ++--
 2 files changed, 10 insertions(+), 2 deletions(-)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
new file mode 100644
index 0000000000..2a9daf7ba6
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
@@ -0,0 +1,8 @@
+# 2024.05.06
+# Original matching of files we could ship was not done correctly. We were
+# matching the basename for files (e.g., libcudart.so from libcudart.so.12)
+# rather than the name stub (libcudart)
+easyconfigs:
+  - CUDA-12.1.1.eb:
+      options:
+        accept-eula-for: CUDA
diff --git a/eb_hooks.py b/eb_hooks.py
index f02c8db48c..8b0a11b0ed 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -612,8 +612,8 @@ def post_sanitycheck_cuda(self, *args, **kwargs):
                 full_path = os.path.join(dir_path, filename)
                 # we only really care about real files, i.e. not symlinks
                 if not os.path.islink(full_path):
-                    # check if the current file is part of the allowlist
-                    basename = os.path.splitext(filename)[0]
+                    # check if the current file name stub is part of the allowlist
+                    basename = filename.split('.')[0]
                     if basename in allowlist:
                         self.log.debug("%s is found in allowlist, so keeping it: %s", basename, full_path)
                     else:

From 28e5e9c52005cb46855e7fe965cd41997e9c48d6 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Mon, 6 May 2024 18:49:34 +0200
Subject: [PATCH 43/45] Update
 2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml

---
 .../2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml        | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
index 2a9daf7ba6..058ab75e80 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
@@ -2,6 +2,7 @@
 # Original matching of files we could ship was not done correctly. We were
 # matching the basename for files (e.g., libcudart.so from libcudart.so.12)
 # rather than the name stub (libcudart)
+# See https://github.com/EESSI/software-layer/pull/559
 easyconfigs:
   - CUDA-12.1.1.eb:
       options:

From 6682c7d36d54641aeb6a5cd9eeaf2cd981ef89d7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 7 May 2024 13:32:25 +0200
Subject: [PATCH 44/45] move OSU-Micro-Benchmarks 2023b to 2023b easystack

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 -
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml   | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 44952e2765..8f5608d881 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -35,7 +35,6 @@ easyconfigs:
         from-pr: 19996
   - dask-2023.9.2-foss-2023a.eb
   - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb
-  - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
   - JupyterNotebook-7.0.2-GCCcore-12.3.0.eb
   - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb:
       options:
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 86c5106c85..15c02951d7 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
@@ -57,3 +57,4 @@ easyconfigs:
   - Qt5-5.15.13-GCCcore-13.2.0.eb:
       options:
         from-pr: 20201
+  - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb

From 298159e516db7c696b12ca57bf51a5328588ebf9 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 7 May 2024 14:27:24 +0200
Subject: [PATCH 45/45] bumping scorecard-action version to 2.3.1

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

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
index dc18fd584a..7eff557094 100644
--- a/.github/workflows/scorecards.yml
+++ b/.github/workflows/scorecards.yml
@@ -40,7 +40,7 @@ jobs:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@99c53751e09b9529366343771cc321ec74e9bd3d # v2.0.6
+        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
         with:
           results_file: results.sarif
           results_format: sarif