release/1.5.1: Update site configs for Derecho, Narwhal, Gaea C5, Dis…

…cover, AWS ParallelCluster, S4 (#853) * Update site config for Derecho * Update documentation for spack-stack-1.5.1 install on AWS ParallelCluster * Turn of ssl variant for Python for Derecho, Gaea C5, Narwhal * Add explicit variant external-xdr for hdf in configs/common/packages.yaml * Update doc/source/PreConfiguredSites.rst for Discover * Update documentation for spack-stack-1.5.1 on S4
JCSDA · Nov 1, 2023 · d1e55f7 · d1e55f7
1 parent 03675e3
commit d1e55f7
Show file tree

Hide file tree

Showing 7 changed files with 86 additions and 78 deletions.
diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml
@@ -112,7 +112,7 @@
       version: ['0.37.0']
     hdf:
       version: ['4.2.15']
-      variants: ~fortran ~netcdf
+      variants: +external-xdr ~fortran ~netcdf
     hdf5:
       version: ['1.14.0']
       variants: +hl +fortran +mpi ~threadsafe +szip
@@ -207,6 +207,8 @@
     proj:
       version: ['8.1.0']
       variants: ~tiff
+    # Check site configs for the following systems when making changes here:
+    # Derecho, Narwhal, Gaea-C5
     python:
       version: ['3.10.8']
     py-attrs:

diff --git a/configs/sites/derecho/compilers.yaml b/configs/sites/derecho/compilers.yaml
@@ -10,15 +10,13 @@ compilers::
       operating_system: sles15
       target: x86_64
       modules:
-      - ncarenv/23.06
-      - intel/2023.2.1
+      - ncarenv/23.09
+      - intel-classic/2023.2.1
       environment:
         prepend_path:
           PATH: '/opt/cray/pe/gcc/12.2.0/bin'
           CPATH: '/opt/cray/pe/gcc/12.2.0/snos/include'
-          LD_LIBRARY_PATH: '/glade/u/apps/common/23.08/spack/opt/spack/intel-oneapi-compilers/2023.2.1/compiler/2023.2.1/linux/compiler/lib/intel64_lin:/opt/cray/pe/gcc/default/snos/lib:/opt/cray/pe/gcc/default/snos/lib64'
-        set:
-          CRAYPE_LINK_TYPE: 'dynamic'
+          LD_LIBRARY_PATH: '/glade/u/apps/common/23.08/spack/opt/spack/intel-oneapi-compilers/2023.2.1/compiler/2023.2.1/linux/compiler/lib/intel64_lin:/opt/cray/pe/gcc/12.2.0/snos/lib:/opt/cray/pe/gcc/12.2.0/lib64'
       extra_rpaths: []
   - compiler:
       spec: gcc@12.2.0
@@ -31,7 +29,7 @@ compilers::
       operating_system: sles15
       target: x86_64
       modules:
-      - ncarenv/23.06
+      - ncarenv/23.09
       - gcc/12.2.0
       environment:
         set:

diff --git a/configs/sites/derecho/packages.yaml b/configs/sites/derecho/packages.yaml
@@ -2,29 +2,29 @@ packages:
   all:
     compiler:: [intel@2021.10.0, gcc@12.2.0]
     providers:
-      mpi:: [cray-mpich@8.1.25] # intel-oneapi-mpi@2021.8.0, 
+      mpi:: [cray-mpich@8.1.25] # intel-oneapi-mpi@2021.10.0,
     target: [core2]
 
 ### MPI, Python, MKL
   mpi:
     buildable: False
   #intel-oneapi-mpi:
   #  externals:
-  #  - spec: intel-oneapi-mpi@2021.8.0%intel@2021.8.0
-  #    prefix: /glade/u/apps/derecho/23.06/spack/opt/spack/intel-oneapi-mpi/2021.8.0/oneapi/2023.0.0/mhf4
+  #  - spec: intel-oneapi-mpi@2021.10.0%intel@2021.10.0
+  #    prefix: /glade/u/apps/derecho/23.09/spack/opt/spack/intel-oneapi-mpi/2021.10.0/oneapi/2023.2.1/ve6v
   #    modules:
-  #    - intel-mpi/2021.8.0
+  #    - intel-mpi/2021.10.0
   cray-mpich:
     externals:
     - spec: cray-mpich@8.1.25%intel@2021.10.0 +wrappers
-      prefix: /opt/cray/pe/mpich/8.1.25/ofi/intel/19.0
+      #prefix: /opt/cray/pe/mpich/8.1.25/ofi/intel/19.0
       modules:
       - craype/2.7.20
       - cray-mpich/8.1.25
       - libfabric/1.15.2.0
       - cray-pals/1.2.11
     - spec: cray-mpich@8.1.25%gcc@12.2.0 +wrappers
-      prefix: /opt/cray/pe/mpich/8.1.25/ofi/gnu/9.1
+      #prefix: /opt/cray/pe/mpich/8.1.25/ofi/gnu/9.1
       modules:
       - craype/2.7.20
       - cray-mpich/8.1.25
@@ -34,18 +34,22 @@ packages:
 ### Modification of common packages
   esmf:
     variants: ~xerces ~pnetcdf snapshot=none ~shared +external-parallelio esmf_os=Linux esmf_comm=mpich
+  # Until problems with OS openssh and spack openssl are resolved,
+  # also use openssl from OS and turn off ssl variant for python
+  python:
+    variants: ~ssl
 
 ### All other external packages listed alphabetically
   autoconf:
     externals:
     - spec: autoconf@2.71
-      prefix: /glade/u/apps/derecho/23.06/opt
+      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: autoconf@2.69
       prefix: /usr
   automake:
     externals:
     - spec: automake@1.16.5
-      prefix: /glade/u/apps/derecho/23.06/opt
+      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: automake@1.15.1
       prefix: /usr
   binutils:
@@ -62,8 +66,8 @@ packages:
       prefix: /usr
   curl:
     externals:
-    - spec: curl@8.0.1+nghttp2
-      prefix: /glade/u/apps/derecho/23.06/opt
+    - spec: curl@8.1.2+nghttp2
+      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: curl@7.79.1+gssapi+ldap+nghttp2
       prefix: /usr
   cvs:
@@ -88,21 +92,21 @@ packages:
   flex:
     externals:
     - spec: flex@2.6.4+lex
-      prefix: /glade/u/apps/derecho/23.06/opt
+      prefix: /glade/u/apps/derecho/23.09/opt/view
   gawk:
     externals:
     - spec: gawk@4.2.1
       prefix: /usr
   git:
     externals:
-    - spec: git@2.40.0~tcltk
-      prefix: /glade/u/apps/derecho/23.06/opt
+    - spec: git@2.41.0+tcltk
+      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: git@2.35.3+tcltk
       prefix: /usr
   git-lfs:
     externals:
     - spec: git-lfs@3.3.0
-      prefix: /glade/u/apps/derecho/23.06/opt
+      prefix: /glade/u/apps/derecho/23.09/opt/view
   gmake:
     externals:
     - spec: gmake@4.2.1
@@ -118,7 +122,7 @@ packages:
   libtool:
     externals:
     - spec: libtool@2.4.7
-      prefix: /glade/u/apps/derecho/23.06/opt
+      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: libtool@2.4.6
       prefix: /usr
   m4:
@@ -128,8 +132,8 @@ packages:
   # Automatically detected, but don't use - missing "ninja" dependency
   #meson:
   #  externals:
-  #  - spec: meson@1.1.0
-  #    prefix: /glade/u/apps/derecho/23.06/opt
+  #  - spec: meson@1.2.0
+  #    prefix: /glade/u/apps/derecho/23.09/opt/view
   mysql:
     buildable: False
     externals:
@@ -158,8 +162,8 @@ packages:
       prefix: /usr
   texinfo:
     externals:
-    - spec: texinfo@7.0
-      prefix: /glade/u/apps/derecho/23.06/opt
+    - spec: texinfo@7.0.3
+      prefix: /glade/u/apps/derecho/23.09/opt/view
     - spec: texinfo@6.5
       prefix: /usr
   wget:

diff --git a/configs/sites/gaea-c5/packages.yaml b/configs/sites/gaea-c5/packages.yaml
@@ -13,6 +13,12 @@ packages:
       - craype-network-ofi
       - cray-mpich/8.1.25
 
+### Modification of common packages
+  # Until problems with OS openssh and spack openssl are resolved,
+  # also use openssl from OS and turn off ssl variant for python
+  python:
+    variants: ~ssl
+
 ### All other external packages listed alphabetically
   autoconf:
     externals:

diff --git a/configs/sites/narwhal/packages.yaml b/configs/sites/narwhal/packages.yaml
@@ -28,6 +28,12 @@ packages:
   #    modules:
   #    - intel/2021.3.0
 
+### Modification of common packages
+  # Until problems with OS openssh and spack openssl are resolved,
+  # also use openssl from OS and turn off ssl variant for python
+  python:
+    variants: ~ssl
+
 ### All other external packages listed alphabetically
   autoconf:
     externals:

diff --git a/doc/source/MaintainersSection.rst b/doc/source/MaintainersSection.rst
@@ -540,14 +540,11 @@ openmpi
 NCAR-Wyoming Derecho
 ------------------------------
 
-intel (temporary)
-  Until CISL makes the newest Intel compilers available in the default module tree, create directory ``/lustre/desc1/scratch/epicufsrt/contrib/modulefiles_extra/intel`` and copy ``/glade/work/csgteam/spack-deployments/derecho/23.06/envs/build/modules/23.06/Core/intel/2023.2.1.lua`` to this directory. Edit the file and remove the block of lines starting with ``-- Find custom moduleroots`` and ending with ``append_path("MODULEPATH", "/glade/work/csgteam/spack-deployments/derecho/23.06/envs/build/modules/23.06/oneapi/2023.2.1")``. Further, replace ``icx`` with ``icc`` and ``icpx`` with ``icpc`` and correct the path in environment variables ``CC``, ``CXX``, etc.
-
 libfabric (temporary)
-  Until CISL makes the newest Intel compilers available in the default module tree, it is necessary to create a libfabrics module to be able to use the cray-mpich MPI library without Cray compiler wrappers. Create directory ``/lustre/desc1/scratch/epicufsrt/contrib/modulefiles_extra/libfabric`` and create a module file based on the template ``doc/modulefile_templates/libfabric``. This module is currently listed in the dependency modules for the ``cray-mpich`` MPI provider in the Derecho site config. It is also necessary to "include" (a confusing term, it used to be "whitelist") the ``cray-mpich`` module in Derecho's ``modules.yaml`` file, because the CISL ``cray-mpich`` module cannot be loaded without loading their compiler modules (yes, they tend to make things difficult).
+  Until CISL fixes its unusual way of setting up Cray module environments, it is necessary to create a libfabrics module to be able to use the cray-mpich MPI library without Cray compiler wrappers. Create a module file based on the template ``doc/modulefile_templates/libfabric`` in directory ``/glade/work/epicufsrt/contrib/spack-stack/derecho/libfabric``. This module is currently listed in the dependency modules for the ``cray-mpich`` MPI provider in the Derecho site config. It is also necessary to "include" (a confusing term, it used to be "whitelist") the ``cray-mpich`` module in Derecho's ``modules.yaml`` file, because the CISL ``cray-mpich`` module cannot be loaded without loading their compiler modules.
 
 cray-pals (temporary)
-  Until CISL fixes its unusual way of setting up Cray module environments, it is necessary to create a cray-pals (parallel application launcher) module to be able to find ``mpirun`` etc. Create directory ``/lustre/desc1/scratch/epicufsrt/contrib/modulefiles_extra/cray-pals`` and copy file ``/opt/cray/pe/lmod/modulefiles/core/cray-pals/1.2.11.lua`` into this directory.
+  Until CISL fixes its unusual way of setting up Cray module environments, it is necessary to create a cray-pals (parallel application launcher) module to be able to find ``mpirun`` etc. Create directory ``/glade/work/epicufsrt/contrib/spack-stack/derecho/cray-pals`` and copy file ``/opt/cray/pe/lmod/modulefiles/core/cray-pals/1.2.11.lua`` into this directory.
 
 ecflow
   ``ecFlow`` must be built manually using the GNU compilers and linked against a static ``boost`` library. After loading the following modules, follow the instructions in :numref:`Section %s <MaintainersSection_ecFlow>` to install ``ecflow``. Be sure to follow the extra instructions for Derecho in that section.