From d7c69cd673e0d53b4d2750de229337cd128f6624 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 6 Apr 2026 15:56:49 -0600
Subject: [PATCH 01/13] Add gcc@14.2.1 on Bounty

---
 .../sites/tier2/bounty/README_gcc-14.2.1.yaml | 21 +++++++++++++++++++
 .../tier2/bounty/packages_gcc-14.2.1.yaml     | 18 ++++++++++++++++
 util/nrl/batch_install.sh                     |  2 +-
 3 files changed, 40 insertions(+), 1 deletion(-)
 create mode 100644 configs/sites/tier2/bounty/README_gcc-14.2.1.yaml
 create mode 100644 configs/sites/tier2/bounty/packages_gcc-14.2.1.yaml

diff --git a/configs/sites/tier2/bounty/README_gcc-14.2.1.yaml b/configs/sites/tier2/bounty/README_gcc-14.2.1.yaml
new file mode 100644
index 000000000..1c8ce329a
--- /dev/null
+++ b/configs/sites/tier2/bounty/README_gcc-14.2.1.yaml
@@ -0,0 +1,21 @@
+WSL 2 Alma Linux 9 installation notes for GCC 14 compiler
+
+yum install \
+gdb \
+gcc-toolset-14-runtime \
+gcc-toolset-14-dwz \
+gcc-toolset-14 \
+gcc-toolset-14-gcc \
+gcc-toolset-14-libquadmath-devel \
+gcc-toolset-14-libstdc++-devel \
+gcc-toolset-14-annobin-docs \
+gcc-toolset-14-annobin-plugin-gcc \
+gcc-toolset-14-gcc-c++ \
+gcc-toolset-14-gcc-gfortran \
+gcc-toolset-14-libtsan-devel \
+gcc-toolset-14-libasan-devel \
+gcc-toolset-14-libubsan-devel \
+gcc-toolset-14-liblsan-devel \
+gcc-toolset-14-binutils-gold \
+gcc-toolset-14-binutils \
+gcc-toolset-14-gcc-plugin-devel
diff --git a/configs/sites/tier2/bounty/packages_gcc-14.2.1.yaml b/configs/sites/tier2/bounty/packages_gcc-14.2.1.yaml
new file mode 100644
index 000000000..a6655fd9b
--- /dev/null
+++ b/configs/sites/tier2/bounty/packages_gcc-14.2.1.yaml
@@ -0,0 +1,18 @@
+packages:
+  all:
+    require:
+    - any_of: ['%gcc@=14.2.1']
+      when: '%gcc'
+  mpi:
+    require:
+    - "openmpi@=5.0.8"
+  gcc:
+    buildable: False
+    externals:
+    - spec: gcc@14.2.1 languages:='c,c++,fortran'
+      prefix: /opt/rh/gcc-toolset-14/root/usr
+      extra_attributes:
+        compilers:
+          c: /opt/rh/gcc-toolset-14/root/usr/bin/gcc
+          cxx: /opt/rh/gcc-toolset-14/root/usr/bin/g++
+          fortran: /opt/rh/gcc-toolset-14/root/usr/bin/gfortran
diff --git a/util/nrl/batch_install.sh b/util/nrl/batch_install.sh
index d47b85d26..d04c3333d 100755
--- a/util/nrl/batch_install.sh
+++ b/util/nrl/batch_install.sh
@@ -176,7 +176,7 @@ case ${SPACK_STACK_BATCH_HOST} in
     SPACK_STACK_CARGO_MIRROR="/home/dom/prod/spack-cargo-mirror"
     ;;
   bounty)
-    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2025.3.0" "gcc@=13.3.1" "clang@=22.1.0")
+    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2025.3.0" "gcc@=14.2.1" "gcc@=13.3.1" "clang@=22.1.0")
     SPACK_STACK_BATCH_TEMPLATES=("neptune-dev" "neptune-dev-llvm" "unified-dev" "cylc-dev")
     SPACK_STACK_MODULE_CHOICE="tcl"
     SPACK_STACK_BOOTSTRAP_MIRROR="/home/dom/prod/spack-bootstrap-mirror"

From 7608096d8956caed296991a71f80f9745f59c445 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Fri, 10 Apr 2026 09:10:37 -0600
Subject: [PATCH 02/13] Update submodule pointer for repos/builtin

---
 repos/builtin | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/repos/builtin b/repos/builtin
index e2e4f2d6e..c91028b6f 160000
--- a/repos/builtin
+++ b/repos/builtin
@@ -1 +1 @@
-Subproject commit e2e4f2d6ea11685a3aec5dc725c28b6d188dc8b1
+Subproject commit c91028b6f955f1676718c293168beb9b4c727333

From c864f9f5eb6f62ee44857664b1149fee8d702fdc Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 14 Apr 2026 20:41:33 -0600
Subject: [PATCH 03/13] Update .gitmodules and submodule pointer for
 repos/builtin for code review and testing

---
 .gitmodules   | 4 +++-
 repos/builtin | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 2f6cb0566..bfb5a571d 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -4,5 +4,7 @@
   branch = spack-stack-dev
 [submodule "repos/builtin"]
   path = repos/builtin
+  #url = https://github.com/jcsda/spack-packages
+  #branch = spack-stack-dev
   url = https://github.com/jcsda/spack-packages
-  branch = spack-stack-dev
+  branch = bugfix/py_protobuf_gcc14
\ No newline at end of file
diff --git a/repos/builtin b/repos/builtin
index c91028b6f..440f44599 160000
--- a/repos/builtin
+++ b/repos/builtin
@@ -1 +1 @@
-Subproject commit c91028b6f955f1676718c293168beb9b4c727333
+Subproject commit 440f44599676b467a586e4e856b38bd8fd7032b2

From b5681ad7cd4f00cbdd0f335872d63b25c74e9aa7 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Thu, 16 Apr 2026 08:54:04 -0600
Subject: [PATCH 04/13] Revert .gitmodules and update submodule pointer for
 repos/builtin

---
 .gitmodules   | 4 +---
 repos/builtin | 2 +-
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index bfb5a571d..2f6cb0566 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -4,7 +4,5 @@
   branch = spack-stack-dev
 [submodule "repos/builtin"]
   path = repos/builtin
-  #url = https://github.com/jcsda/spack-packages
-  #branch = spack-stack-dev
   url = https://github.com/jcsda/spack-packages
-  branch = bugfix/py_protobuf_gcc14
\ No newline at end of file
+  branch = spack-stack-dev
diff --git a/repos/builtin b/repos/builtin
index 440f44599..d04c20752 160000
--- a/repos/builtin
+++ b/repos/builtin
@@ -1 +1 @@
-Subproject commit 440f44599676b467a586e4e856b38bd8fd7032b2
+Subproject commit d04c2075209f4080864183c60d753bc1b2b96391

From fa26ecc830981de299080619ce2fae88cc628750 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Fri, 17 Apr 2026 11:13:13 +0000
Subject: [PATCH 05/13] Add
 configs/sites/tier1/blueback/packages_gcc-14.3.0.yaml

---
 .../tier1/blueback/packages_gcc-14.3.0.yaml   | 39 +++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 configs/sites/tier1/blueback/packages_gcc-14.3.0.yaml

diff --git a/configs/sites/tier1/blueback/packages_gcc-14.3.0.yaml b/configs/sites/tier1/blueback/packages_gcc-14.3.0.yaml
new file mode 100644
index 000000000..76c642d1f
--- /dev/null
+++ b/configs/sites/tier1/blueback/packages_gcc-14.3.0.yaml
@@ -0,0 +1,39 @@
+packages:
+  all:
+    require:
+    - any_of: ['%gcc@=14.3.0']
+      when: '%gcc'
+  mpi:
+    buildable: false
+    require:
+    - cray-mpich@8.1.32
+  gcc:
+    buildable: false
+    externals:
+    - spec: gcc@14.3.0 languages:='c,c++,fortran'
+      prefix: /usr
+      modules:
+      - PrgEnv-gnu/8.6.0
+      - gcc-native/14.2
+      extra_attributes:
+        compilers:
+          c: /opt/cray/pe/gcc-native/14/bin/gcc
+          cxx: /opt/cray/pe/gcc-native/14/bin/g++
+          fortran: /opt/cray/pe/gcc-native/14/bin/gfortran
+        environment:
+          set:
+            CONFIG_SITE: ''
+            PE_GCC_EXTERNAL: native
+  cray-mpich:
+    buildable: false
+    externals:
+    - spec: cray-mpich@8.1.32
+      prefix: /opt/cray/pe/mpich/8.1.32/ofi/GNU/12.3
+      modules:
+      - libfabric/1.22.0
+      - craype-network-ofi
+      - cray-mpich/8.1.32
+      extra_attributes:
+        environment:
+          prepend_path:
+            CMAKE_PREFIX_PATH: /p/app/projects/NEPTUNE/spack-stack/cmake-findmpi

From 3a4edc08b2c4044b154f01e52607882bcd111974 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 27 Apr 2026 13:53:34 +0000
Subject: [PATCH 06/13] Fix bug in gcc@14 config for Blueback in
 util/nrl/batch_install.sh; reduce number of concurrent package builds from 10
 to 4

---
 util/nrl/batch_install.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/util/nrl/batch_install.sh b/util/nrl/batch_install.sh
index d04c3333d..73990dfaf 100755
--- a/util/nrl/batch_install.sh
+++ b/util/nrl/batch_install.sh
@@ -141,7 +141,7 @@ case ${SPACK_STACK_BATCH_HOST} in
     SPACK_STACK_CARGO_MIRROR="/neptune_diagnostics/spack-stack/cargo-mirror"
     ;;
   blueback)
-    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2025.0.4" "gcc@=13.3.0") # oneapi@=2025.2.1
+    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2025.0.4" "gcc@=13.3.0" "gcc@=14.3.0") # oneapi@=2025.2.1
     SPACK_STACK_BATCH_TEMPLATES=("neptune-dev" "unified-dev" "cylc-dev")
     SPACK_STACK_MODULE_CHOICE="tcl"
     SPACK_STACK_BOOTSTRAP_MIRROR="/p/app/projects/NEPTUNE/spack-stack/bootstrap-mirror"
@@ -671,7 +671,7 @@ for compiler in "${SPACK_STACK_BATCH_COMPILERS[@]}"; do
     case ${submit_to_scheduler} in
       "true")
         jobs=$(tasks_per_node ${host})
-        parallel_install_flags="--concurrent-packages=10 --jobs=${jobs}"
+        parallel_install_flags="--concurrent-packages=4 --jobs=${jobs}"
         ;;
       "false")
         parallel_install_flags=""

From 762c0744fc6f0bf0f34bfd828a8c7b0413dd55b2 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 27 Apr 2026 07:55:59 -0600
Subject: [PATCH 07/13] Update .gitmodules and submodule pointer for
 repos/builtin

---
 .gitmodules   | 3 ++-
 repos/builtin | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 2f6cb0566..216702200 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -5,4 +5,5 @@
 [submodule "repos/builtin"]
   path = repos/builtin
   url = https://github.com/jcsda/spack-packages
-  branch = spack-stack-dev
+  #branch = spack-stack-dev
+  branch = feature/fix_rt_linkage_jcsda
diff --git a/repos/builtin b/repos/builtin
index 89af8e824..d25e0bd49 160000
--- a/repos/builtin
+++ b/repos/builtin
@@ -1 +1 @@
-Subproject commit 89af8e82400c8b5b8ae62c2915e7707cb4b8445f
+Subproject commit d25e0bd49bb551a91f0cebe79d1334c8c225cfba

From ee212885878c1fec889298d84df926a7a050f6a5 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 27 Apr 2026 07:57:15 -0600
Subject: [PATCH 08/13] 
 configs/sites/tier1/blueback/packages_oneapi-2025.0.4.yaml: add variant
 fix_rt_linkage to external intel-oneapi-compilers

---
 configs/sites/tier1/blueback/packages_oneapi-2025.0.4.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configs/sites/tier1/blueback/packages_oneapi-2025.0.4.yaml b/configs/sites/tier1/blueback/packages_oneapi-2025.0.4.yaml
index 13fe28a26..73694faaf 100644
--- a/configs/sites/tier1/blueback/packages_oneapi-2025.0.4.yaml
+++ b/configs/sites/tier1/blueback/packages_oneapi-2025.0.4.yaml
@@ -12,7 +12,7 @@ packages:
   intel-oneapi-compilers:
     buildable: false
     externals:
-    - spec: intel-oneapi-compilers@2025.0.4
+    - spec: intel-oneapi-compilers@2025.0.4 +fix_rt_linkage
       prefix: /p/app/intel/oneapi-combined
       modules:
       - PrgEnv-intel/8.6.0

From 56faa1355ce0641bd66b486474f476952ac09f2b Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 27 Apr 2026 14:18:52 -0600
Subject: [PATCH 09/13] Revert .gitmodules and update submodule pointer for
 repos/builtin

---
 .gitmodules   | 3 +--
 repos/builtin | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.gitmodules b/.gitmodules
index 216702200..2f6cb0566 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -5,5 +5,4 @@
 [submodule "repos/builtin"]
   path = repos/builtin
   url = https://github.com/jcsda/spack-packages
-  #branch = spack-stack-dev
-  branch = feature/fix_rt_linkage_jcsda
+  branch = spack-stack-dev
diff --git a/repos/builtin b/repos/builtin
index d25e0bd49..8a4eb5d32 160000
--- a/repos/builtin
+++ b/repos/builtin
@@ -1 +1 @@
-Subproject commit d25e0bd49bb551a91f0cebe79d1334c8c225cfba
+Subproject commit 8a4eb5d32aa6981f630dd4f8aefb8069bc8e2cae

From 346b897d936b552b069ca13cb90ca02d78c93d91 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Mon, 27 Apr 2026 14:19:59 -0600
Subject: [PATCH 10/13] Add +fix_rt_linkage variant to external Intel oneAPI
 compiler specs in .github/workflows/ubuntu-ci-x86_64-oneapi.cfg and
 .github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg

---
 .github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg | 2 +-
 .github/workflows/ubuntu-ci-x86_64-oneapi.cfg     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg b/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg
index 714e30d1f..36af6d2ca 100644
--- a/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg
+++ b/.github/workflows/ubuntu-ci-x86_64-oneapi-ifx.cfg
@@ -1,6 +1,6 @@
   intel-oneapi-compilers:
     externals:
-    - spec: intel-oneapi-compilers@2024.2.0
+    - spec: intel-oneapi-compilers@2024.2.0 +fix_rt_linkage
       prefix: /opt/intel/oneapi
       extra_attributes:
         compilers:
diff --git a/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg b/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg
index 26eb5420f..dad047776 100644
--- a/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg
+++ b/.github/workflows/ubuntu-ci-x86_64-oneapi.cfg
@@ -1,6 +1,6 @@
   intel-oneapi-compilers:
     externals:
-    - spec: intel-oneapi-compilers@2024.2.0
+    - spec: intel-oneapi-compilers@2024.2.0 +fix_rt_linkage
       prefix: /opt/intel/oneapi
       extra_attributes:
         compilers:

From f064929e379dd86d9c8d50d5eb9db248bf703497 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 28 Apr 2026 05:59:13 -0600
Subject: [PATCH 11/13] Bug fix in
 spack-ext/lib/jcsda-emc/spack-stack/stack/compiler_utils.py: handle package
 that doesn't have an explicit package config but isn't built with the
 default=preferred compiler

---
 .../lib/jcsda-emc/spack-stack/stack/compiler_utils.py    | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/spack-ext/lib/jcsda-emc/spack-stack/stack/compiler_utils.py b/spack-ext/lib/jcsda-emc/spack-stack/stack/compiler_utils.py
index 013ba0f6d..fcb54871c 100644
--- a/spack-ext/lib/jcsda-emc/spack-stack/stack/compiler_utils.py
+++ b/spack-ext/lib/jcsda-emc/spack-stack/stack/compiler_utils.py
@@ -101,6 +101,12 @@ def check_preferred_compiler():
         # different) compiler for the environment instead.
         if preferred_compiler_name == compiler_name and preferred_compiler_version  == compiler_version:
             logging.info(f"  ... {spec.name}@{spec.version}/{spec.dag_hash(length=7)} uses preferred compiler")
+        # If the package config doesn't have an entry for the package, then it should be
+        # built with the preferred compiler. However, because it failed the "if" test
+        # above, we know it is not.
+        elif not spec.name in package_config.keys():
+            errors += 1
+            logging.error(f"  ... {RED}error: {spec.name}@{spec.version}/{spec.dag_hash(length=7)} does not use intended compiler{RESET}")
         else:
             spec_required_compiler_name = None
             spec_required_compiler_version = None
@@ -147,8 +153,7 @@ def check_preferred_compiler():
                 logging.info(f"  ... {spec.name}@{spec.version}/{spec.dag_hash(length=7)} uses explicitly preferred compiler")
             else:
                 errors += 1
-                logging.error(f"  ... {RED}error: {spec.name}@{spec.version}/{spec.dag_hash(length=7)} does not use intended compiler\n" + \
-                    f"      check also that any explicit preferred/required compiler dependencies are using Spack v1 syntax{RESET}")
+                logging.error(f"  ... {RED}error: {spec.name}@{spec.version}/{spec.dag_hash(length=7)} does not use intended compiler{RESET}")
     if errors==1:
         raise Exception(f"{RED}Detected {errors} compiler mismatch!{RESET}")
     elif errors:

From 6177af9227c6833c9aa28a65c3a69423e53dde10 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 28 Apr 2026 06:04:04 -0600
Subject: [PATCH 12/13] Add variant +fix_rt_linkage to bounty tier2 site config
 for oneapi@2025.3.0

---
 configs/sites/tier2/bounty/packages_oneapi-2025.3.0.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configs/sites/tier2/bounty/packages_oneapi-2025.3.0.yaml b/configs/sites/tier2/bounty/packages_oneapi-2025.3.0.yaml
index 86fd28a86..a81903d45 100644
--- a/configs/sites/tier2/bounty/packages_oneapi-2025.3.0.yaml
+++ b/configs/sites/tier2/bounty/packages_oneapi-2025.3.0.yaml
@@ -12,7 +12,7 @@ packages:
   intel-oneapi-compilers:
     buildable: false
     externals:
-    - spec: intel-oneapi-compilers@2025.3.0
+    - spec: intel-oneapi-compilers@2025.3.0 +fix_rt_linkage
       prefix: /opt/intel/oneapi
       extra_attributes:
         compilers:

From 89b0f0560efa3deef59f4a5f5c61c52843579393 Mon Sep 17 00:00:00 2001
From: Dom Heinzeller <dom.heinzeller@icloud.com>
Date: Tue, 28 Apr 2026 06:04:33 -0600
Subject: [PATCH 13/13] configs/common/packages_oneapi.yaml: build patchelf
 with gcc

---
 configs/common/packages.yaml        | 1 +
 configs/common/packages_oneapi.yaml | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml
index 069c8c28f..a85df12f3 100644
--- a/configs/common/packages.yaml
+++ b/configs/common/packages.yaml
@@ -86,6 +86,7 @@ packages:
       - +ownlibs
     codee:
       require:
+      # TODO UPDATE TO 2026.1.2 once https://github.com/JCSDA/spack-packages/pull/56 is merged
       - '@2026.1'
     crtm_fix:
       require:
diff --git a/configs/common/packages_oneapi.yaml b/configs/common/packages_oneapi.yaml
index 05f2e7e35..e6516bcab 100644
--- a/configs/common/packages_oneapi.yaml
+++ b/configs/common/packages_oneapi.yaml
@@ -62,6 +62,9 @@ packages:
     parallel-netcdf:
       require:
       - +shared-intel
+    patchelf:
+      require:
+      - '%c=gcc'
     py-maturin:
       require:
       - '%c=gcc'