Add python basic packages as externals

.gitignore

@@ -0,0 +1,2 @@
+environments/*/.spack-env/
+repos/*/packages/*/__pycache__/

config-hlrs/packages.yaml

@@ -5,8 +5,9 @@ packages:
       blas: [cray-libsci]
       lapack: [cray-libsci]
       scalapack: [cray-libsci]
-      pkgconf: [pkg-config]
+      fftw-api: [cray-fftw]
-      zlib-ng: [zlib]
+      pkgconfig: [pkg-config]
+      zlib-api: [zlib-ng+compat]
   cray-mpich:
     externals:
     - spec: cray-mpich@8.1.30%gcc
@@ -34,6 +35,68 @@ packages:
       modules:
       - cray-libsci/24.03.0
     buildable: false
+  fftw:
+    externals:
+    - spec: fftw@3.3.10.7
+      prefix: /opt/cray/pe/fftw/3.3.10.7/x86_64
+      modules:
+      - cray-fftw/3.3.10.7
+    buildable: false
+  hdf5:
+    externals:
+    - spec: hdf5@1.14.3.1%cce
+      prefix: /opt/cray/pe/hdf5/1.14.3.1/cray/18.0
+      modules:
+      - cray-hdf5/1.14.3.1
+    - spec: hdf5@1.14.3.1%gcc
+      prefix: /opt/cray/pe/hdf5/1.14.3.1/gnu/12.3
+      modules:
+      - cray-hdf5/1.14.3.1      
+    buildable: false
+  netcdf-c:
+    externals:
+    - spec: netcdf-c@4.9.0.13%cce
+      prefix: /opt/cray/pe/netcdf/4.9.0.13/crayclang/18.0
+      modules:
+      - cray-netcdf/4.9.0.13
+    - spec: netcdf-c@4.9.0.13%gcc
+      prefix: /opt/cray/pe/netcdf/4.9.0.13/gnu/12.3
+      modules:
+      - cray-netcdf/4.9.0.13
+    buildable: false
+  netcdf-cxx4:
+    externals:
+    - spec: netcdf-cxx4@4.9.0.13%cce
+      prefix: /opt/cray/pe/netcdf/4.9.0.13/crayclang/18.0
+      modules:
+      - cray-netcdf/4.9.0.13
+    - spec: netcdf-cxx4@4.9.0.13%gcc
+      prefix: /opt/cray/pe/netcdf/4.9.0.13/gnu/12.3
+      modules:
+      - cray-netcdf/4.9.0.13  
+    buildable: false
+  netcdf-fortran:
+    externals:
+    - spec: netcdf-fortran@4.9.0.13%cce
+      prefix: /opt/cray/pe/netcdf/4.9.0.13/crayclang/18.0
+      modules:
+      - cray-netcdf/4.9.0.13
+    - spec: netcdf-fortran@4.9.0.13%gcc
+      prefix: /opt/cray/pe/netcdf/4.9.0.13/gnu/12.3
+      modules:
+      - cray-netcdf/4.9.0.13
+    buildable: false
+  parallel-netcdf:
+    externals:
+    - spec: parallel-netcdf@1.12.3.13%cce
+      prefix: /opt/cray/pe/parallel-netcdf/1.12.3.13/crayclang/18.0
+      modules:
+      - cray-parallel-netcdf/1.12.3.13
+    - spec: parallel-netcdf@1.12.3.13%gcc
+      prefix: /opt/cray/pe/parallel-netcdf/1.12.3.13/gnu/12.3
+      modules:
+      - cray-parallel-netcdf/1.12.3.13
+    buildable: false
 # Packages which have not been discovered by spack external find 
 # and packages which are not in the OS image but low-level.
 # Declare libs as externals only if a -devel OS package is installed
@@ -48,9 +111,7 @@ packages:
       prefix: /usr
     buildable: false
   libxml2:
-    externals:
+    require: '%gcc@7.5'
-    - spec: libxml2@2.9.14
-    buildable: false
   libdwarf:
     require: '%gcc@7.5'
   zstd:
@@ -59,6 +120,23 @@ packages:
     require: '%gcc@7.5'
   zlib-ng:
     require: '%gcc@7.5'
+  xz:
+    require: '%gcc@7.5'
+  binutils:
+    require:
+      - '%gcc@7.5'
+      - '+libiberty' 
+# Some basic python packages which are part of the OS python
+  py-pip:
+    externals:
+    - spec: py-pip@20.0.2
+      prefix: /usr
+    buildable: false
+  py-setuptools:
+    externals:
+    - spec: py-setuptools@44.1.1
+      prefix: /usr
+    buildable: false
 # packages which have been discovered by spack external find --all
   python:
     externals:
@@ -100,11 +178,6 @@ packages:
     - spec: openjdk@11.0.19_0-suse-150000.3.96.1-x8664
       prefix: /usr
     buildable: false
-  binutils:
-    externals:
-    - spec: binutils@2.39.0
-      prefix: /usr
-    buildable: false
   zip:
     externals:
     - spec: zip@3.0
@@ -120,11 +193,6 @@ packages:
     - spec: subversion@1.14.1
       prefix: /usr
     buildable: false
-  xz:
-    externals:
-    - spec: xz@5.2.3
-      prefix: /usr
-    buildable: false
   lustre:
     externals:
     - spec: lustre@2.15.0.7_rc2_cray_25_ga33b7d9
@@ -276,10 +344,11 @@ packages:
       prefix: /usr
     buildable: false
   sqlite:
-    externals:
+    require: '%gcc@7.5'
-    - spec: sqlite@3.39.3+fts~functions+rtree
+#    externals:
-      prefix: /usr
+#    - spec: sqlite@3.39.3+fts~functions+rtree  # does not provide include files
-    buildable: false
+#      prefix: /usr
+#    buildable: false
   findutils:
     externals:
     - spec: findutils@4.8.0

environments/hlrs/spack.yaml

@@ -1,8 +1,9 @@
 # This is a Spack Environment file fot he main HLRS software stack
 spack:
-#  definitions:
+  definitions:
-#    core_compiler: [gcc@7.5]
+    - core_compiler: [gcc@7.5]
-#    compilers: [gcc@13.2, cce@18.0]    
+    - compilers: [gcc@13.2, cce@18.0]
+    - mpis: [cray-mpich@8.1.30]
 #  packages:
 #    all:
 #      compiler: [gcc@13.2, cce@18.0]
@@ -10,13 +11,12 @@ spack:
   specs:
     - matrix:    # modules for low-level tools
       - [libunwind, papi]
-      - ['%gcc@7.5']
+      - [$%core_compiler]
-#      - [$%core_compiler]
     - matrix:
       - [mpip, extrae]
-      - ['cflags="-Wno-error=implicit-function-declaration -Wno-error=implicit-int"']
+      - ['cflags="-Wno-error=implicit-function-declaration -Wno-error=implicit-int -Wno-error=int-conversion"']
-      - [^mpi]
+      - [$^mpis]
-      - ['%gcc@13.2', '%cce@18.0'] 
+      - [$%compilers]
   view: false
   concretizer:
     unify: when_possible