Update TPLs and versions for GPUs

.gitlab/jobs-prod.yml

@@ -8,12 +8,6 @@ cray_update_tpls:
   extends: [.cray_resource2, .update_tpls]
   needs: [toss_update_tpls]
 
-# ------------------------------------------------------------------------------
-# UPDATE PERM JOBS
-
-shared_tpls_update_permissions:
-  extends: [.toss_resource_general, .toss_update_permissions]
-
 # ------------------------------------------------------------------------------
 # PROD BUILD JOBS
 

.gitlab/scripts.yml

@@ -35,27 +35,29 @@
       - ci-dir.txt
       - job-name.txt
 
+.build_job:
+  script:
+    - CI_BUILD_DIR=$(cat ci-dir.txt)
+    - cd $CI_BUILD_DIR && cat job-name.txt
+    - ./$SCRIPT_DIR/devtools/host-config-build.py --no-clean --build --ctest --nprocs $NPROC --host-config gitlab.cmake -DSPHERAL_ENABLE_TIMERS=ON $EXTRA_CMAKE_ARGS
+
 .build:
   extends: [.retry_rule]
   stage: build_and_install
   variables:
     GIT_STRATEGY: none
   script:
-    - CI_BUILD_DIR=$(cat ci-dir.txt)
-    - cd $CI_BUILD_DIR && cat job-name.txt
-    - ./$SCRIPT_DIR/devtools/host-config-build.py --no-clean --build --ctest --nprocs $NPROC --host-config gitlab.cmake -DSPHERAL_ENABLE_TIMERS=ON $EXTRA_CMAKE_ARGS
+    - !reference [.build_job, script]
   artifacts:
     paths:
       - ci-dir.txt
       - job-name.txt
 
 .build_and_test:
   extends: [.build]
-  after_script:
-    - CI_BUILD_DIR=$(cat ci-dir.txt)
-    - cd $CI_BUILD_DIR && cat job-name.txt
-
-    - ./build_gitlab/install/bin/spheral -c "import $SPHERAL_MODULE"
+  script:
+    - !reference [.build_job, script]
+    - $RUN_CMD -n 1 ./build_gitlab/install/bin/spheral -c "import $SPHERAL_MODULE"
   artifacts:
     paths:
       - ci-dir.txt
@@ -134,20 +136,9 @@
     - !reference [.merge_pr_rule, rules]
     - if: '$CI_COMMIT_MESSAGE =~ /update-tpls/'
   script:
+    - umask 027
     - ./$SCRIPT_DIR/devtools/tpl-manager.py --update-upstream
 
-.toss_update_permissions:
-  stage: update_permissions
-  variables:
-    GIT_STRATEGY: none
-  rules:
-    - !reference [.merge_pr_rule, rules]
-    - if: '$CI_COMMIT_MESSAGE =~ /update-tpls/'
-  script:
-    - ml load mpifileutils
-    - $RUN_CMD -n $NPROC dchmod --mode go+rx $UPSTREAM_DIR
-  dependencies: []
-
 # ------------------------------------------------------------------------------
 # Production Installation scripts
 # ------------------------------------------------------------------------------

RELEASE_NOTES.md

@@ -20,20 +20,31 @@ Notable changes include:
       so there is no user interface impact.
     * Added update-tpls commit message trigger.
     * Spheral mpi python interface ensures proper allocation calls are used on Flux machines to avoid strange hangs that can occur if running outside of allocations.
+    * tpl-manager.py updates:
+      * Added --no-upstream option for when on LC machines but cannot access upstream.
+      * Added --dry-run option for testing purposes.
     * Performance testing and CI improvements:
       * Structure for performance tests is different, with the tests themselves set in a perf_tests.py file and run_perf.py runs the perf tests using ATS.
       * The cleanup old directories job is now a scheduled pipelines that runs weekly.
       * The performance tests and deploy jobs are now scheduled pipelines that run on a schedule.
       * Gitlab pages now uses Plotly for interactive visualizations.
       * Gathering of performance data for the deploy stage is now parallelized over ranks and threads.
       * Merges to develop will create installs to a shared directory for use by the performance testing scripts.
+      * Added umask command for updating upstreams and removed separate job to update permissions.
+      * Build and test job now fails if import of Spheral module fails.
     * Builds and installs are cleaner:
       * Rpaths are no longer overwritten, allowing things set in the Spack host config file to be used.
       * Spheral libraries are only installed once now and a Spheral.pth with a relative path to the install lib is used in the virtual python environment.
     * Updated build system support spack v1.
       * Updated TPL Manager to support spack v1.1.0.
       * Updated CI to support python v3.12 and Ubuntu 24.04.
       * Added actual Spheral release versions and TPL conditions to Spheral package.
+      * Added more system libraries to make building on LC faster.
+    * TPL updates:
+      * LEOS updated from 8.4.2 to 8.5.2.
+      * ROCM version updated from 6.2.0 to 6.4.3.
+      * Boost updated from 1.85 to 1.87 to prepare for using Clang 20 eventually.
+      * CHAI, Umpire, and RAJA updated to 2025.12.0.
 
 Version v2025.12.0 -- Release date 2025-12-19
 ==============================================

scripts/devtools/tpl-manager.py

@@ -57,10 +57,14 @@ def parse_args(self):
                             help="Skip downloading Spack repo.")
         parser.add_argument("--ci-run", action="store_true",
                             help="For use by the CI only. Must set a --spec.")
+        parser.add_argument("--no-upstream", action="store_true",
+                            help="Use if on LC machines but cannot access the upstream.")
         parser.add_argument("--dry-run", action="store_true",
                             help="Use to do everything but actually install. For testing purposes.")
         parser.add_argument("--id", type=str, default=None,
                             help="ID string to postfix an initconfig file.")
+        parser.add_argument("--debug-build", action="store_true",
+                            help="Adds the --keep-stage flag to spack for doing debug builds of TPLs")
         parser.add_argument("--dev-pkg", action="store_true",
                             help="Tells tpl-manager to use the dev_pkg environment. "+\
                             "Assumes TPLs are for buildcache creation if no --spec is provided. "+\
@@ -288,6 +292,8 @@ def activate_spack_env(self):
             from spack import environment
             self.spack_env = environment.Environment(self.env_dir)
             environment.activate(self.spack_env)
+            repo_cmd = SpackCommand("repo")
+            repo_cmd(*["update"])
         else:
             # Otherwise, check if environment has been created
             arch_cmd = SpackCommand("arch")
@@ -309,9 +315,7 @@ def concretize_spec(self, check_spec):
         else:
             print("Concretizing environment")
 
-        with self.spack_env.write_transaction():
-            conc_spec = self.spack_env.concretize(force=force_conc)
-            self.spack_env.write()
+        conc_spec = self.do_concretize(force_conc)
 
         if conc_spec:
             print("Concretized specs")
@@ -330,6 +334,15 @@ def concretize_spec(self, check_spec):
             specs = self.spack_env.concrete_roots()
             self.print_specs(specs)
 
+    def do_concretize(self, force_conc):
+        if (self.args.no_upstream):
+            spack.config.set("upstreams", {"spheral_shared": {"install_tree": {}}})
+            print("WARNING: Modifying local Spack files, do not commit these changes.")
+        with self.spack_env.write_transaction():
+            conc_spec = self.spack_env.concretize(force=force_conc)
+            self.spack_env.write()
+        return conc_spec
+
     def install_and_config(self):
         "Install TPLs and create host config file for given spec"
         spec = self.args.spec
@@ -356,6 +369,10 @@ def install_and_config(self):
                                          unsigned=True,
                                          **default_install_args)
         else:
+            if (self.args.debug_build):
+                default_install_args.update(dict(keep_stage=True))
+            if (self.args.dry_run):
+                default_install_args.update(dict(fake=True))
             self.spack_env.install_specs([self.spack_spec], **default_install_args)
         if (self.args.ci_run):
             shutil.copyfile(host_config_file, "gitlab.cmake")
@@ -406,15 +423,14 @@ def __init__(self):
             if self.args.update_upstream:
                 upstream_dir = spack.config.get("upstreams:spheral_shared:install_tree")
                 spack.config.set("config", {"install_tree": {"root": str(upstream_dir), "padded_length": 0}})
-                print("WARNING: Modifying local Spack files, do not commit these changes")
+                print("WARNING: Modifying local Spack files, do not commit these changes.")
                 with self.spack_env.manifest.use_config():
                     print(spack.config.get("config:install_tree"))
                     print(f"Installing to {upstream_dir}")
                     # Pass None so it installs TPLs for all specs
                     self.spack_env.install_all(install_deps=True, install_package=False, fail_fast=True)
                     # Equivalent of running spack reindex
                     spack.store.STORE.reindex()
-                print("WARNING: Be sure to update permissions and groups on upstream.")
             else:
                 self.spack_env.install_specs(None, **default_install_args)
 

scripts/spack/configs/config.yaml

@@ -14,4 +14,4 @@ repos:
   builtin:
     destination: $spack/../packages
     git: "https://github.com/spack/spack-packages.git"
-    commit: 0f833a16999a012153c040c26c98256c14a1a4fd
+    commit: a251c075e32d54b77c283538b45e9327e88f02d2

scripts/spack/configs/toss_4_x86_64_ib/packages.yaml

@@ -11,10 +11,6 @@ packages:
       pil: [py-pillow]
       jpeg: [libjpeg]
       zlib-api: [zlib]
-    permissions:
-      read: group
-      write: group
-      group: sduser
   gcc:
     externals:
     - spec: gcc@10.3.1 languages:='c,c++,fortran'
@@ -75,8 +71,8 @@ packages:
 # ------ SYSTEM LIBS -------
   ncurses:
     externals:
-    - spec: ncurses@5.9
-      prefix: /usr
+    - spec: ncurses@6.1.20180224+termlib abi=6
+      prefix: /usr/lib64
     buildable: false
   autoconf:
     externals:
@@ -168,15 +164,39 @@ packages:
     - spec: fontconfig@2.13.1
       prefix: /usr
     buildable: false
-
-
-#---- Extension Dependencies
-
+  libxml2:
+    externals:
+    - spec: libxml2@3.4.2
+      prefix: /usr/lib64
+    buildable: false
+  libpciaccess:
+    externals:
+    - spec: libpciaccess@0.14
+      prefix: /usr/lib64
+    buildable: false
+  libbsd:
+    externals:
+    - spec: libbsd@0.12.2
+      prefix: /usr/lib64
+    buildable: false
+  libmd:
+    externals:
+    - spec: libmd@1.1.0
+      prefix: /usr/lib64
+    buildable: false
+  libxcrypt:
+    externals:
+    - spec: libxcrypt@4.1.1
+      prefix: /lib64
+    buildable: false
   hwloc:
     externals:
-    - spec: hwloc@5.7.5
-      prefix: /usr
+    - spec: hwloc@2.12.2
+      prefix: /usr/lib64/hwloc
     buildable: false
+
+#---- Extension Dependencies
+
   netlib-lapack:
     buildable: false
     externals: