release/1.6.0: update site configs and documentation for Hercules/Nautilus/Narwhal-Intel/S4/Discover

configs/sites/discover/packages.yaml

@@ -121,10 +121,6 @@ packages:
     externals:
     - spec: libfuse@2.9.3
       prefix: /usr
-  libtool:
-    externals:
-    - spec: libtool@2.4.2
-      prefix: /usr
   libxpm:
     externals:
     - spec: libxpm@4.11.0

configs/sites/hercules/compilers.yaml

@@ -11,7 +11,10 @@ compilers:
     target: x86_64
     modules:
     - intel-oneapi-compilers/2023.1.0
-    environment: {}
+    environment:
+      set:
+        # https://github.com/ufs-community/ufs-weather-model/issues/2015#issuecomment-1864438186
+        I_MPI_EXTRA_FILESYSTEM: 'ON'
     extra_rpaths: []
 - compiler:
     spec: gcc@12.2.0

configs/sites/hercules/packages.yaml

@@ -22,9 +22,6 @@ packages:
       - mvapich2/2.3.7
 
 ### Modifications of common packages
-  # DH* TRY IF THIS IS STILL TRUE # Version 2.0.8 doesn't compile on Hercules
-  # DH* TRY IF THIS IS STILL TRUE wgrib2:
-  # DH* TRY IF THIS IS STILL TRUE   version:: ['3.1.1']
 
 ### All other external packages listed alphabetically
   autoconf:
@@ -84,10 +81,6 @@ packages:
     externals:
     - spec: groff@1.22.4
       prefix: /usr
-  libtool:
-    externals:
-    - spec: libtool@2.4.6
-      prefix: /usr
   m4:
     externals:
     - spec: m4@1.4.19
@@ -109,6 +102,10 @@ packages:
       prefix: /apps/spack-managed/gcc-11.3.1/qt-5.15.8-d47tsna6f5dylcpblkfgw4gpn2cucihd
       modules:
       - qt/5.15.8
+  sed:
+    externals:
+    - spec: sed@4.8
+      prefix: /usr
   subversion:
     externals:
     - spec: subversion@1.14.1

configs/sites/narwhal/compilers.yaml

@@ -11,6 +11,7 @@ compilers::
       modules:
       - PrgEnv-intel/8.3.2
       - intel-classic/2021.4.0
+      - node.js/20.10.0
       environment:
         prepend_path:
           PATH: '/opt/cray/pe/gcc/10.3.0/snos/bin'
@@ -31,6 +32,7 @@ compilers::
       modules:
       - PrgEnv-gnu/8.3.2
       - gcc/10.3.0
+      - node.js/20.10.0
       environment:
         prepend_path:
           LD_LIBRARY_PATH: '/opt/cray/pe/libsci/22.08.1.1/GNU/9.1/x86_64/lib'

configs/sites/narwhal/packages.yaml

@@ -115,6 +115,10 @@ packages:
       prefix: /p/app/projects/NEPTUNE/spack-stack/qt-5.15.2/5.15.2/gcc_64
       modules:
       - qt/5.15.2
+  sed:
+    externals:
+    - spec: sed@4.4
+      prefix: /usr
   subversion:
     externals:
     - spec: subversion@1.10.6

configs/sites/nautilus/packages.yaml

@@ -103,10 +103,6 @@ packages:
     externals:
     - spec: groff@1.22.3
       prefix: /usr
-  libtool:
-    externals:
-    - spec: libtool@2.4.6
-      prefix: /usr
   m4:
     externals:
     - spec: m4@1.4.18
@@ -125,6 +121,10 @@ packages:
     externals:
     - spec: pkgconf@1.4.2
       prefix: /usr
+  sed:
+    externals:
+    - spec: sed@4.5
+      prefix: /usr
   tar:
     externals:
     - spec: tar@1.30

doc/modulefile_templates/node.js

@@ -0,0 +1,23 @@
+#%Module1.0
+
+module-whatis "Provides an node.js-20.10.0 installation for use with spack."
+
+# Only allow one instance of compiler to load
+conflict ecflow
+
+proc ModulesHelp { } {
+puts stderr "Provides an node.js-20.10.0 installation for use with spack."
+}
+
+if { [ module-info mode load ] && ![ is-loaded gcc/10.3.0 ] } {
+    module load gcc/10.3.0
+}
+
+# Set this value
+set NODEJS_PATH "/p/app/projects/NEPTUNE/spack-stack/node-js-20.10.0/gcc-10.3.0"
+
+prepend-path PATH "${NODEJS_PATH}/bin"
+prepend-path LD_LIBRARY_PATH "${NODEJS_PATH}/lib"
+prepend-path LIBRARY_PATH "${NODEJS_PATH}/lib"
+prepend-path CPATH "${NODEJS_PATH}/include"
+prepend-path CMAKE_PREFIX_PATH "${NODEJS_PATH}"

doc/source/MaintainersSection.rst

@@ -346,7 +346,7 @@ mysql
 NAVY HPCMP Narwhal
 ------------------------------
 
-On Narwhal, ``git-lfs``, ``qt``, ``ecflow``, and ``mysql`` need to be installed as a one-off before spack can be used.
+On Narwhal, ``git-lfs``, ``qt``, ``ecflow``, and ``mysql`` need to be installed as a one-off before spack can be used. Also, temporarily it is necessary to install ``node.js`` as an external package to work around build errors for ``py-jupyter-server`` (see https://github.com/JCSDA/spack-stack/issues/928 and https://github.com/spack/spack/issues/41899).
 
 git-lfs
    The following instructions install ``git-lfs`` in ``/p/app/projects/NEPTUNE/spack-stack/git-lfs-2.10.0``. Version 2.10.0 is the default version for Narwhal. First, download the ``git-lfs`` RPM on a system with full internet access (e.g., Derecho) using ``wget https://download.opensuse.org/repositories/openSUSE:/Leap:/15.2/standard/x86_64/git-lfs-2.10.0-lp152.1.2.x86_64.rpm`` and copy this file to ``/p/app/projects/NEPTUNE/spack-stack/git-lfs-2.10.0/src``. Then switch to Narwhal and run the following commands. 
@@ -397,6 +397,26 @@ ecflow
 mysql
   ``mysql`` must be installed separately from ``spack`` using a binary tarball provided by the MySQL community. Follow the instructions in :numref:`Section %s <MaintainersSection_MySQL>` to install ``mysql`` in ``/p/app/projects/NEPTUNE/spack-stack/mysql-8.0.31``.
 
+node.js
+  ``node.js`` is difficult to install via ``spack``, but is needed to install certain Python packages. The complication is that when using a newer ``gcc`` compiler (either directly or as backend for ``icc`` etc.), the OS ``node.js`` errors out with unresolved symbols in the ``libstdc++`` library. Therefore, we need to install ``node.js`` with ``gcc@10.3.0`` loaded, and create modulefile ``node.js/20.10.0`` from template ``modulefiles/node.js``.
+
+.. code-block:: console
+
+   module unload PrgEnv-cray
+   module load PrgEnv-gnu/8.3.2
+   module unload gcc
+   module load gcc/10.3.0
+
+   mkdir -p node-js-20.10.0/src && cd node-js-20.10.0/src
+   wget https://nodejs.org/dist/v20.10.0/node-v20.10.0.tar.gz
+   tar -xvzf node-v20.10.0.tar.gz
+   cd node-v20.10.0/
+   ./configure --partly-static \
+       --prefix=/p/app/projects/NEPTUNE/spack-stack/node-js-20.10.0/gcc-10.3.0 \
+       2>&1 | tee log.config
+   make 2>&1 | tee log.make
+   make install 2>&1 | tee log.install
+
 .. _MaintainersSection_Nautilus:
 
 ------------------------------