mch climate analysis (#121)

add the R-based `climana` uenv for MCH research.

config.yaml

@@ -69,6 +69,15 @@ uenvs:
       deploy:
         eiger: [zen2]
         todi: [gh200]
+  climana:
+    "24.7":
+      recipes:
+        zen2: mch/climana/24.7
+        zen3: mch/climana/24.7
+        a100: mch/climana/24.7
+      deploy:
+        balfrin: [zen3, a100]
+      develop: False
   editors:
     "24.7":
       recipes:

recipes/mch/climana/24.7/compilers.yaml

@@ -0,0 +1,5 @@
+bootstrap:
+  spec: [email protected]
+gcc:
+  specs:
+  - [email protected]

recipes/mch/climana/24.7/config.yaml

@@ -0,0 +1,6 @@
+name: mch
+store: /user-environment
+spack:
+  commit: releases/v0.22
+  repo: https://github.com/spack/spack.git
+description: Tools for MCH validation.

recipes/mch/climana/24.7/environments.yaml

@@ -0,0 +1,54 @@
+climana:
+  compiler:
+    - toolchain: gcc
+      spec: gcc@12
+  unify: when_possible
+  mpi:
+    spec: [email protected]
+  packages:
+  - perl
+  - autoconf
+  - m4
+  - automake
+  - texinfo
+  - libtool
+  - gawk
+  - curl
+  specs:
+  # choose fftw instead of the default intel-oneapi-mkl.
+  # this saves ~2GB of space, and reduces image build time.
+  - cdo ^[virtuals=fftw-api] fftw
+  - gdal
+  - geos
+  - gsl
+  - [email protected] +fortran +threadsafe ~mpi
+  - ncview
+  - nco
+  - ncl
+  - [email protected]~mpi ^hdf5~mpi api=v18
+  - proj
+  - [email protected]
+  - sqlite
+  - udunits
+  # R and its packages
+  # +X is required for png, tiff, jpeg, etc support
+  - [email protected] +X
+  # install here so that the openssl built by Spack is used.
+  - r-curl
+  # R needs to find all of the following use pkg-config
+  # so we add them to the view, where they will be picked up.
+  - freetype
+  - fribidi
+  - glib
+  - harfbuzz
+  - libjpeg-turbo
+  - libpng
+  - libtiff
+  # required as a runtime dependency of the ssl R package
+  - openssl
+  views:
+    climana:
+      link: roots
+      uenv:
+        prefix_paths:
+          LD_LIBRARY_PATH: [lib, lib64]

recipes/mch/climana/24.7/modules.yaml

@@ -0,0 +1,36 @@
+modules:
+  # Paths to check when creating modules for all module sets
+  prefix_inspections:
+    bin:
+      - PATH
+    lib:
+      - LD_LIBRARY_PATH
+    lib64:
+      - LD_LIBRARY_PATH
+    lib/pkgconfig:
+      - PKG_CONFIG_PATH
+    lib64/pkgconfig:
+      - PKG_CONFIG_PATH
+
+  default:
+    arch_folder: false
+    # Where to install modules
+    roots:
+      tcl: /user-environment/modules
+    tcl:
+      all:
+        autoload: none
+      netcdf-c:
+        environment:
+          set:
+            NETCDF_C_ROOT: '{prefix}'
+      hash_length: 0
+      exclude_implicits: true
+      include:
+        - hdf5
+        - zlib+shared
+      exclude:
+        - '%[email protected]'
+        - 'gcc %[email protected]'
+      projections:
+        all: '{name}/{version}'

recipes/mch/climana/24.7/post-install

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+# don't generate an error message if a glob does not match any files
+shopt -s nullglob
+
+# where all of the applications built by spack are installed
+# this has to change if
+# - the compiler version used to build software changes
+# - we build for a different micro-architecture
+# - we upgrade to SLES 16
+install_base=/user-environment/linux-sles15-zen3/gcc-12.3.0
+view_base=/user-environment/env/climana
+
+# iterate over all of the locations where pkgconfig files are likely to be installed
+for pkbase in "lib/pkgconfig" "lib64/pkgconfig" "share/pkgconfig" "rlib/pkgconfig"
+do
+    # find all directories that match the pattern
+    pkgpaths=$(find $install_base -type d -path '*/'$pkbase)
+
+    # iterate over each directory, searching for pkg-config .pc files
+    for pkpath in $pkgpaths
+    do
+        pcfiles=($pkpath/*.pc)
+        for pcpath in ${pcfiles[@]}
+        do
+            pcfile=$(basename $pcpath)
+            from=$pkpath/$pcfile
+            to_root=$view_base/$pkbase
+            to=$to_root/$pcfile
+            mkdir -p $to_root
+            if [ ! -e $to ]; then
+                echo '+    ' $pkbase/$pcfile
+                ln -s "$from" "$to"
+            else
+                echo 'skip ' $pkbase/$pcfile
+            fi
+        done
+    done
+done

recipes/mch/climana/24.7/repo/packages/r/change_optflags_tmp.patch

@@ -0,0 +1,67 @@
+diff -ur R-3.6.3.org/configure R-3.6.3/configure
+--- R-3.6.3.org/configure	2020-03-09 11:09:16.060825352 +0900
++++ R-3.6.3/configure	2020-03-09 11:10:47.011280195 +0900
+@@ -6470,13 +6470,13 @@
+   CFLAGS=$ac_save_CFLAGS
+ elif test $ac_cv_prog_cc_g = yes; then
+   if test "$GCC" = yes; then
+-    CFLAGS="-g -O2"
++    CFLAGS="-g -O1"
+   else
+     CFLAGS="-g"
+   fi
+ else
+   if test "$GCC" = yes; then
+-    CFLAGS="-O2"
++    CFLAGS="-O1"
+   else
+     CFLAGS=
+   fi
+@@ -7445,13 +7445,13 @@
+   FCFLAGS=$ac_save_FCFLAGS
+ elif test $ac_cv_prog_fc_g = yes; then
+   if test "x$ac_cv_fc_compiler_gnu" = xyes; then
+-    FCFLAGS="-g -O2"
++    FCFLAGS="-g -O1"
+   else
+     FCFLAGS="-g"
+   fi
+ else
+   if test "x$ac_cv_fc_compiler_gnu" = xyes; then
+-    FCFLAGS="-O2"
++    FCFLAGS="-O1"
+   else
+     FCFLAGS=
+   fi
+@@ -7717,13 +7717,13 @@
+   CXXFLAGS=$ac_save_CXXFLAGS
+ elif test $ac_cv_prog_cxx_g = yes; then
+   if test "$GXX" = yes; then
+-    CXXFLAGS="-g -O2"
++    CXXFLAGS="-g -O1"
+   else
+     CXXFLAGS="-g"
+   fi
+ else
+   if test "$GXX" = yes; then
+-    CXXFLAGS="-O2"
++    CXXFLAGS="-O1"
+   else
+     CXXFLAGS=
+   fi
+@@ -8336,13 +8336,13 @@
+   OBJCFLAGS=$ac_save_OBJCFLAGS
+ elif test $ac_cv_prog_objc_g = yes; then
+   if test "$GOBJC" = yes; then
+-    OBJCFLAGS="-g -O2"
++    OBJCFLAGS="-g -O1"
+   else
+     OBJCFLAGS="-g"
+   fi
+ else
+   if test "$GOBJC" = yes; then
+-    OBJCFLAGS="-O2"
++    OBJCFLAGS="-O1"
+   else
+     OBJCFLAGS=
+   fi