hercules site config for release/1.9.0 (#1506)

Update / add required config files for tier1 site hercules
JCSDA · Feb 13, 2025 · 2887da0 · 2887da0
1 parent a468143
commit 2887da0
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Showing 5 changed files with 132 additions and 27 deletions.
diff --git a/configs/sites/tier1/hercules/compilers.yaml b/configs/sites/tier1/hercules/compilers.yaml
@@ -1,4 +1,29 @@
 compilers:
+- compiler:
+    spec: oneapi@=2024.2.1
+    paths:
+      cc: /apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-compilers-2024.2.1-podbez65l57ms4uba527kg7pomxk5y3m/compiler/2024.2/bin/icx
+      cxx: /apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-compilers-2024.2.1-podbez65l57ms4uba527kg7pomxk5y3m/compiler/2024.2/bin/icpx
+      f77: /apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-compilers-2024.2.1-podbez65l57ms4uba527kg7pomxk5y3m/compiler/2024.2/bin/ifort
+      fc: /apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-compilers-2024.2.1-podbez65l57ms4uba527kg7pomxk5y3m/compiler/2024.2/bin/ifort
+    flags: {}
+    operating_system: rocky9
+    target: x86_64
+    modules:
+    - spack-managed-x86-64_v3
+    - intel-oneapi-compilers/2024.2.1
+    environment:
+      set:
+        # https://github.com/ufs-community/ufs-weather-model/issues/2015#issuecomment-1864438186
+        I_MPI_EXTRA_FILESYSTEM: 'ON'
+        # Override system module settings for FC and F77 (they're set to ifx)
+        F77: '/apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-compilers-2024.2.1-podbez65l57ms4uba527kg7pomxk5y3m/compiler/2024.2/bin/ifort'
+        FC: '/apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-compilers-2024.2.1-podbez65l57ms4uba527kg7pomxk5y3m/compiler/2024.2/bin/ifort'
+      prepend_path:
+        PATH: /usr/bin
+        LD_LIBRARY_PATH: /usr/lib:/usr/lib64
+        CPATH: '/usr/include/c++/11:/usr/include/c++/11/x86_64-redhat-linux'
+    extra_rpaths: []
 - compiler:
     spec: [email protected]
     paths:

diff --git a/configs/sites/tier1/hercules/packages.yaml b/configs/sites/tier1/hercules/packages.yaml
@@ -1,4 +1,17 @@
 packages:
+  # For addressing https://github.com/JCSDA/spack-stack/issues/1355
+  #   Use system zlib instead of spack-built zlib-ng
+  all:
+    providers:
+      zlib-api:: [zlib]
+  zlib-api:
+    buildable: False
+  zlib:
+    buildable: False
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+
   autoconf:
     externals:
     - spec: [email protected]
@@ -15,10 +28,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  curl:
-    externals:
-    - spec: [email protected]+gssapi+ldap+nghttp2
-      prefix: /usr
   diffutils:
     externals:
     - spec: [email protected]
@@ -35,6 +44,10 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+  gettext:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
   git:
     externals:
     - spec: [email protected]~tcltk
@@ -57,35 +70,24 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+  # Don't use, incomplete installation!
+  #libtool:
+  #  externals:
+  #  - spec: [email protected]
+  #    prefix: /usr
   m4:
     externals:
     - spec: [email protected]
       prefix: /usr
-  mysql:
-    buildable: False
-    externals:
-    - spec: [email protected]
-      prefix: /work/noaa/epic/role-epic/spack-stack/hercules/mysql-8.0.31
-      modules:
-      - mysql/8.0.31
-  openssh:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-  openssl:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
+  # Don't use, issues with py-cryptography
+  #openssl:
+  #  externals:
+  #  - spec: [email protected]
+  #    prefix: /usr
   pkgconf:
     externals:
     - spec: [email protected]
       prefix: /usr
-  qt:
-    externals:
-    - spec: [email protected]
-      prefix: /apps/contrib/spack-stack-1.1/gcc-11.3.1/qt-5.15.14-mfeuvcidmyqoi2m5i2tfrk6yd7xtk6pt
-      modules:
-      - qt/5.15.14
   sed:
     externals:
     - spec: [email protected]
@@ -94,6 +96,10 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+  tar:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
   texinfo:
     externals:
     - spec: [email protected]
@@ -102,3 +108,7 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+  which:
+    externals:
+      - spec: [email protected]
+        prefix: /usr
diff --git a/configs/sites/tier1/hercules/packages_gcc.yaml b/configs/sites/tier1/hercules/packages_gcc.yaml
@@ -7,8 +7,22 @@ packages:
     buildable: False
   openmpi:
     externals:
-    - spec: [email protected]%[email protected]~cuda~cxx~cxx_exceptions~java~memchecker+pmi+static~wrapper-rpath
-        schedulers=slurm
+    - spec: [email protected]%[email protected] ~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~internal-libevent~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix+pmi+romio+rsh~singularity+static+vt+wrapper-rpath fabrics=none romio-filesystem=none schedulers=slurm  
+      prefix: /apps/spack-managed/gcc-12.2.0/openmpi-4.1.4-hf3dkf6r56x3klzcgs3u7esgt3fhnk63
       modules:
       - gcc/12.2.0
       - openmpi/4.1.4
+
+  ectrans:
+    require::
+    - '~mkl +fftw'
+  gsibec:
+    require::
+    - '~mkl'
+  py-numpy:
+    require::
+    - '@1.26'
+    - '^openblas'
+  zlib-ng:
+    require:
+    - '~shared'
diff --git a/configs/sites/tier1/hercules/packages_intel.yaml b/configs/sites/tier1/hercules/packages_intel.yaml
@@ -30,4 +30,5 @@ packages:
     - '@1.2.1 ~mkl'
   py-numpy:
     require::
+    - '@1.26'
     - '^openblas'
diff --git a/configs/sites/tier1/hercules/packages_oneapi.yaml b/configs/sites/tier1/hercules/packages_oneapi.yaml
@@ -0,0 +1,55 @@
+packages:
+  all:
+    compiler:: [[email protected]]
+    providers:
+      mpi:: [[email protected]]
+      # If using intel-oneapi-mkl, make appropriate changes below
+      blas:: [openblas]
+      fftw-api:: [fftw]
+      lapack:: [openblas]
+  mpi:
+    buildable: False
+  intel-oneapi-mpi:
+    buildable: False
+    externals:
+    - spec: [email protected]%[email protected]
+      prefix: /apps/spack-managed-x86_64_v3-v1.0/oneapi-2024.2.1/intel-oneapi-mpi-2021.13.1-3pv63eugwmse2xpeglxib4dr2oeb42g2
+      modules:
+      - spack-managed-x86-64_v3
+      - intel-oneapi-compilers/2024.2.1
+      - [email protected]
+
+  intel-oneapi-mkl:
+    buildable: False
+    externals:
+    - spec: [email protected]
+      prefix: /apps/spack-managed-x86_64_v3-v1.0/gcc-11.3.1/intel-oneapi-mkl-2024.2.1-aeiool3i5jj4newwifvkhow5almp67rt
+      modules:
+      - spack-managed-x86-64_v3
+      - intel-oneapi-mkl/2024.2.1
+
+  intel-oneapi-runtime:
+    externals:
+    - spec: [email protected]%[email protected]
+      prefix: /apps/spack-managed-x86_64_v3-v1.0/oneapi-2024.2.1/intel-oneapi-runtime-2024.2.1-hl5zgdjaldynq35dq3yotclfy2vblybx
+      modules:
+      - spack-managed-x86-64_v3
+      - intel-oneapi-compilers/2024.2.1
+      - intel-oneapi-runtime/2024.2.1
+
+  ectrans:
+    require::
+    - '@1.5.0 ~mkl +fftw'
+  gsibec:
+    require::
+    - '@1.2.1 ~mkl'
+  py-numpy:
+    require::
+    - '@1.26'
+    - '^openblas'
+  py-scipy:
+    require:
+      '%gcc'
+  zlib-ng:
+    require:
+    - '~shared'