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Merge branch 'release/1.5.1' of https://github.com/jcsda/spack-stack
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…into feature/merge_rel151_into_dev
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climbfuji committed Nov 8, 2023
2 parents 4ec255f + 883ebcb commit 2e67dac
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18 changes: 18 additions & 0 deletions .github/workflows/macos-ci-aarch64.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -104,13 +104,27 @@ jobs:
# base-env
echo "base-env ..."
<<<<<<< HEAD
spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.apple-clang-14.0.3.base-env
spack buildcache create -a -u /Users/ec2-user/spack-stack/build-cache/

# the rest
echo "${{ inputs.template || 'unified-dev' }} ..."
spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.apple-clang-14.0.3.${{ inputs.template || 'unified-dev' }}
spack buildcache create -a -u /Users/ec2-user/spack-stack/build-cache/
=======
# DH* 20230721 - todo remove --no-checksum
spack install --fail-fast --source --no-check-signature --no-checksum base-env 2>&1 | tee log.install.apple-clang-14.0.3.base-env
# DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
spack buildcache create -a -u /Users/ec2-user/spack-stack/build-cache/ || true

# the rest
echo "${{ inputs.template || 'unified-dev' }} ..."
# DH* 20230721 - todo remove --no-checksum
spack install --fail-fast --source --no-check-signature --no-checksum 2>&1 | tee log.install.apple-clang-14.0.3.${{ inputs.template || 'unified-dev' }}
# DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
spack buildcache create -a -u /Users/ec2-user/spack-stack/build-cache/ || true
>>>>>>> 883ebcb2509df68702a7207bdd410926f20e3e9c

# Next steps: synchronize source and build cache to a central/combined mirror?
echo "Next steps ..."
Expand All @@ -136,7 +150,11 @@ jobs:
module use ${ENVDIR}/install/modulefiles/Core
module load stack-apple-clang/14.0.3
<<<<<<< HEAD
module load stack-openmpi/4.1.6
=======
module load stack-openmpi/4.1.5
>>>>>>> 883ebcb2509df68702a7207bdd410926f20e3e9c
module load stack-python/3.10.8
module available

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11 changes: 7 additions & 4 deletions configs/common/packages.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
variants: +pic
# Newer versions of CDO require the C++-17 standard, which doesn't
# work with all compilers that are currently in use in spack-stack
# When making changes here, also check Hercules/Casper site configs
cdo:
version: ['2.0.5']
variants: ~openmp
Expand Down Expand Up @@ -61,7 +62,7 @@
# config and update the projections for lmod/tcl.
# Also, check the acorn and derecho site configs which have esmf modifications.
esmf:
version: ['8.4.2']
version: ['8.5.0']
variants: ~xerces ~pnetcdf snapshot=none ~shared +external-parallelio
require:
- any_of: ['fflags="-fp-model precise" cxxflags="-fp-model precise"']
Expand Down Expand Up @@ -95,7 +96,7 @@
gfsio:
version: ['1.4.1']
gftl-shared:
version: ['1.5.0']
version: ['1.6.1']
#git-lfs:
# Assume git-lfs is provided, hard to install
# because of dependencies on go/go-bootstrap.
Expand All @@ -112,7 +113,7 @@
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
Expand Down Expand Up @@ -141,7 +142,7 @@
# errors with [email protected]+, see
# https://github.com/JCSDA/spack-stack/issues/769
# also: ... extdata2g segfault UFS?
version: ['2.35.2']
version: ['2.40.3']
variants: ~shared ~extdata2g ~pflogger
# If making changes here, also check the Discover site config and the CI workflows
met:
Expand Down Expand Up @@ -207,6 +208,8 @@
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:
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14 changes: 7 additions & 7 deletions configs/containers/specs/jedi-ci.yaml
Original file line number Diff line number Diff line change
@@ -1,20 +1,20 @@
### spack-stack-1.5.0 / skylab-6.0.0 containers for fv3-jedi and mpas-jedi (but not for ufs-jedi)
### spack-stack-1.5.1 / skylab-6.1.0 containers for fv3-jedi and mpas-jedi (but not for ufs-jedi)
specs: [[email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected], [email protected], [email protected], [email protected], ecflow@5,
[email protected], [email protected] +fckit +ectrans +tesselation +fftw, [email protected], [email protected] +fftw,
[email protected], [email protected], fms@release-jcsda, [email protected], [email protected], gftl-shared@1.5.0,
[email protected], [email protected], fms@release-jcsda, [email protected], [email protected], gftl-shared@1.6.1,
[email protected], [email protected], [email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected],
[email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected],
[email protected], py-pip, [email protected], [email protected], [email protected], [email protected],
[email protected], [email protected], [email protected], [email protected], [email protected], esmf@8.4.2, mapl@2.35.2,
[email protected], [email protected], [email protected], [email protected], shumlib@macos_clang_linux_intel_port,
[email protected], [email protected], [email protected], [email protected], [email protected], esmf@8.5.0, mapl@2.40.3,
[email protected], [email protected], [email protected], shumlib@macos_clang_linux_intel_port,
[email protected], [email protected]]
# Notes:
# 1. Remove [email protected] from clang/mpich container, because mapl doesn't work with mpich@4
# 2. Don't build CRTM by default so that it gets built in the JEDI bundles
# 3. Comment out for now until build problems are solved
# 1. Don't build CRTM by default so that it gets built in the JEDI bundles
# 2. Comment out for now until build problems are solved
# https://github.com/jcsda/spack-stack/issues/522
# [email protected]
# 3. Need to update [email protected] to 12.0.1!
25 changes: 8 additions & 17 deletions configs/sites/casper/compilers.yaml
Original file line number Diff line number Diff line change
@@ -1,24 +1,15 @@
compilers::
- compiler:
spec: [email protected]
spec: [email protected]
paths:
cc: /glade/u/apps/opt/intel/2022.1/compiler/2022.0.2/linux/bin/intel64/icc
cxx: /glade/u/apps/opt/intel/2022.1/compiler/2022.0.2/linux/bin/intel64/icpc
f77: /glade/u/apps/opt/intel/2022.1/compiler/2022.0.2/linux/bin/intel64/ifort
fc: /glade/u/apps/opt/intel/2022.1/compiler/2022.0.2/linux/bin/intel64/ifort
cc: /glade/u/apps/casper/23.10/spack/opt/spack/gcc/12.2.0/pucl/bin/gcc
cxx: /glade/u/apps/casper/23.10/spack/opt/spack/gcc/12.2.0/pucl/bin/g++
f77: /glade/u/apps/casper/23.10/spack/opt/spack/gcc/12.2.0/pucl/bin/gfortran
fc: /glade/u/apps/casper/23.10/spack/opt/spack/gcc/12.2.0/pucl/bin/gfortran
flags: {}
operating_system: centos7
operating_system: opensuse15
target: x86_64
modules:
- intel/2022.1
environment:
prepend_path:
PATH: '/glade/work/epicufsrt/contrib/spack-stack/casper/gcc-10.1.0/bin'
CPATH: '/glade/work/epicufsrt/contrib/spack-stack/casper/gcc-10.1.0/include'
LD_LIBRARY_PATH: '/glade/u/apps/opt/intel/2022.1/compiler/latest/linux/compiler/lib/intel64_lin:/glade/u/apps/opt/intel/2022.1/mpi/2021.5.1/libfabric/lib:/glade/work/epicufsrt/contrib/spack-stack/casper/gcc-10.1.0/lib64'
set:
INTEL_LICENSE_FILE: '[email protected]'
LM_LICENSE_FILE: '[email protected]'
I_MPI_ROOT: '/glade/u/apps/opt/intel/2022.1/mpi/2021.5.1'

- gcc/12.2.0
environment: {}
extra_rpaths: []
113 changes: 56 additions & 57 deletions configs/sites/casper/packages.yaml
Original file line number Diff line number Diff line change
@@ -1,45 +1,53 @@
packages:
all:
compiler:: [[email protected]]
compiler:: [[email protected]]
providers:
mpi:: [[email protected]]
mpi:: [[email protected]]

### MPI, Python, MKL
mpi:
buildable: False
intel-oneapi-mpi:
openmpi:
externals:
- spec: [email protected]%[email protected]
prefix: /glade/u/apps/opt/intel/2022.1
- spec: [email protected]%[email protected]+cuda~cxx~cxx_exceptions~java+lustre~memchecker+pmi+static~wrapper-rpath fabrics=ucx schedulers=tm
prefix: /glade/u/apps/casper/23.10/spack/opt/spack/openmpi/4.1.6/gcc/12.2.0/yia4
modules:
- intel-oneapi-mpi/2021.5.1.lua
- openmpi/4.1.6
- ucx/1.14.1
- cuda/12.2.1

### Modification of common packages
# Default gdal (3.7.0) doesn't build on Casper with [email protected]
gdal:
version:: ['3.6.3']
### Modifications of common packages
# Version 2.0.5 doesn't compile on Hercules with gcc
cdo
version:: ['2.2.0']

### All other external packages listed alphabetically
autoconf:
externals:
- spec: autoconf@2.69
prefix: /usr
- spec: autoconf@2.71
prefix: /glade/u/apps/casper/23.10/opt/view
automake:
externals:
- spec: [email protected]
- spec: [email protected]
prefix: /glade/u/apps/casper/23.10/opt/view
- spec: [email protected]
prefix: /usr
berkeley-db:
externals:
- spec: [email protected]
prefix: /usr
binutils:
externals:
- spec: binutils@2.27.43
- spec: binutils@2.41.0
prefix: /usr
bzip2:
externals:
- spec: [email protected]
prefix: /usr
coreutils:
externals:
- spec: [email protected]
prefix: /usr
cmake:
externals:
- spec: [email protected]
Expand All @@ -53,19 +61,21 @@ packages:
prefix: /usr
cvs:
externals:
- spec: cvs@1.11.23
- spec: cvs@1.12.13
prefix: /usr
curl:
externals:
- spec: [email protected]+gssapi+ldap+nghttp2
- spec: [email protected]+nghttp2
prefix: /glade/u/apps/casper/23.10/opt/view
- spec: [email protected]+gssapi+ldap+nghttp2
prefix: /usr
diffutils:
externals:
- spec: [email protected]
prefix: /usr
doxygen:
externals:
- spec: [email protected]+graphviz~mscgen
- spec: [email protected]
prefix: /usr
ecflow:
buildable: False
Expand All @@ -74,23 +84,19 @@ packages:
prefix: /glade/work/epicufsrt/contrib/spack-stack/casper/ecflow-5.8.4
modules:
- ecflow/5.8.4
file:
externals:
- spec: [email protected]
prefix: /usr
findutils:
externals:
- spec: findutils@4.5.11
- spec: findutils@4.8.0
prefix: /usr
flex:
# Must set buildable: false to avoid duplicate packages
buildable: false
#buildable: false
externals:
- spec: flex@2.5.37+lex
prefix: /usr
- spec: flex@2.6.4+lex
prefix: /glade/u/apps/casper/23.10/opt/view
gawk:
externals:
- spec: gawk@4.0.2
- spec: gawk@4.2.1
prefix: /usr
gettext:
externals:
Expand All @@ -102,21 +108,21 @@ packages:
prefix: /usr
git:
externals:
- spec: [email protected]
modules:
- git/2.33.1
- spec: [email protected]~tcltk
prefix: /glade/u/apps/casper/23.10/opt/view
- spec: [email protected]+tcltk
prefix: /usr
git-lfs:
externals:
- spec: [email protected]
modules:
- git/2.33.1
- spec: [email protected]
prefix: /glade/u/apps/casper/23.10/opt/view
gmake:
externals:
- spec: gmake@3.82
- spec: gmake@4.2.1
prefix: /usr
groff:
externals:
- spec: [email protected].2
- spec: [email protected].4
prefix: /usr
krb5:
buildable: False
Expand All @@ -131,15 +137,13 @@ packages:
variants: ~gssapi
libtool:
externals:
- spec: [email protected]
prefix: /usr
libxpm:
externals:
- spec: [email protected]
- spec: [email protected]
prefix: /glade/u/apps/casper/23.10/opt/view
- spec: [email protected]
prefix: /usr
m4:
externals:
- spec: [email protected].16
- spec: [email protected].18
prefix: /usr
mysql:
buildable: False
Expand All @@ -150,34 +154,31 @@ packages:
- mysql/8.0.31
ncurses:
externals:
- spec: ncurses@5.9.20130511+termlib abi=5
prefix: /usr
- spec: ncurses@6.4.20221231+termlib abi=6
prefix: /glade/u/apps/casper/23.10/opt/view
# Old re2c on Casper unable to build newer versions of ninja
ninja:
version:: ['1.10.2']
openssh:
externals:
- spec: openssh@7.4p1
- spec: openssh@8.4p1
prefix: /usr
openssl:
externals:
- spec: openssl@1.0.2k-fips
- spec: openssl@1.1.1l
prefix: /usr
# Pin patchelf to 0.15.0 for Intel compiler (no C++-17 features)
#patchelf:
# version:: ['0.15.0']
perl:
externals:
- spec: [email protected]~cpanm+shared+threads
prefix: /usr
pkg-config:
externals:
- spec: pkg-config@0.27.1
- spec: pkg-config@0.29.2
prefix: /usr
qt:
externals:
- spec: qt@5.15.2
prefix: /glade/work/epicufsrt/contrib/spack-stack/casper/qt-5.15.2
- spec: qt@5.14.2
prefix: /glade/u/apps/casper/23.10/opt/view
rsync:
externals:
- spec: [email protected]
Expand All @@ -192,19 +193,17 @@ packages:
prefix: /usr
subversion:
externals:
- spec: [email protected]
prefix: /usr
swig:
externals:
- spec: [email protected]
- spec: [email protected]
prefix: /usr
tar:
externals:
- spec: tar@1.26
- spec: tar@1.34
prefix: /usr
texinfo:
externals:
- spec: [email protected]
- spec: [email protected]
prefix: /glade/u/apps/casper/23.10/opt/view
- spec: [email protected]
prefix: /usr
texlive:
externals:
Expand Down
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