Merge pull request #927 from climbfuji/bugfix/rel160_hercules

Update site configs and documentation for spack-stack-1.6.0 for:

Hercules
Nautilus
Narwhal (Intel only so far)
S4
Discover
Also: submodule pointer update for spack for a PR required to build on these platforms (spack PR JCSDA/spack#386 already merged).

Note the workaround for Narwhal that uses an external node.js that is supplied via the compiler config while the correct solution (for after release 1.6.0) is being worked on.

configs/sites/discover/packages.yaml

@@ -121,10 +121,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   libxpm:
     externals:
     - spec: [email protected]

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: [email protected]

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: [email protected]
       prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   m4:
     externals:
     - spec: [email protected]
@@ -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: [email protected]
+      prefix: /usr
   subversion:
     externals:
     - spec: [email protected]

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: [email protected]
+      prefix: /usr
   subversion:
     externals:
     - spec: [email protected]

configs/sites/nautilus/packages.yaml

@@ -103,10 +103,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  libtool:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   m4:
     externals:
     - spec: [email protected]
@@ -125,6 +121,10 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+  sed:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
   tar:
     externals:
     - spec: [email protected]

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 ``[email protected]`` 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:
 
 ------------------------------