diff --git a/.github/workflows/macos-ci-aarch64.yaml b/.github/workflows/macos-ci-aarch64.yaml index 74177f928..b93935ed9 100644 --- a/.github/workflows/macos-ci-aarch64.yaml +++ b/.github/workflows/macos-ci-aarch64.yaml @@ -105,7 +105,7 @@ jobs: # base-env echo "base-env ..." 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/ + spack buildcache create -a -u /Users/ec2-user/spack-stack/build-cache/ base-env # the rest echo "${{ inputs.template || 'unified-dev' }} ..." diff --git a/.github/workflows/macos-ci-x86_64.yaml b/.github/workflows/macos-ci-x86_64.yaml index 9fa39abb3..2c8762154 100644 --- a/.github/workflows/macos-ci-x86_64.yaml +++ b/.github/workflows/macos-ci-x86_64.yaml @@ -98,7 +98,7 @@ jobs: # base-env echo "base-env ..." spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.apple-clang-14.0.0.base-env - spack buildcache create -a -u /Users/ec2-user/spack-stack/build-cache/ + spack buildcache create -a -u /Users/ec2-user/spack-stack/build-cache/ base-env # the rest echo "${{ inputs.template || 'unified-dev' }} ..." diff --git a/.github/workflows/ubuntu-ci-x86_64.yaml b/.github/workflows/ubuntu-ci-x86_64.yaml index 88b1b9584..5afece5c1 100644 --- a/.github/workflows/ubuntu-ci-x86_64.yaml +++ b/.github/workflows/ubuntu-ci-x86_64.yaml @@ -136,7 +136,7 @@ jobs: # base-env echo "base-env ..." spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.intel-2022.1.0.base-env - spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ + spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ base-env # the rest echo "${{ inputs.template || 'unified-dev' }} ..." diff --git a/configs/common/packages.yaml b/configs/common/packages.yaml index b5608aeee..7521c5a35 100644 --- a/configs/common/packages.yaml +++ b/configs/common/packages.yaml @@ -10,6 +10,7 @@ jpeg: [libjpeg-turbo] lapack: [openblas] yacc: [bison] + zlib-api: [zlib] # # This version of awscli goes with py-pyyaml@5.4.1 awscli: @@ -52,7 +53,7 @@ variants: linalg=eigen,lapack compression=lz4,bzip2 ecmwf-atlas: version: ['0.35.0'] - variants: +fckit +ectrans +tesselation +fftw + variants: +fckit +trans +tesselation +fftw ectrans: version: ['1.2.0'] variants: ~mkl +fftw @@ -82,7 +83,7 @@ #version: ['2023.01'] #variants: precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release version: ['2023.02.01'] - variants: precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +use_fmsio + variants: precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +deprecated_io fontconfig: variants: +pic freetype: @@ -93,6 +94,8 @@ version: ['1.6.4'] g2tmpl: version: ['1.10.2'] + gettext: + version: ['0.21.1'] gfsio: version: ['1.4.1'] gftl-shared: @@ -119,6 +122,7 @@ variants: +hl +fortran +mpi ~threadsafe +szip ip: version: ['4.3.0'] + variants: precision=4,d,8 ip2: version: ['1.1.2'] jasper: @@ -152,6 +156,8 @@ version: ['5.1.0'] mpich: variants: ~hwloc +two_level_namespace + mysql: + variants: +download_boost nco: version: ['5.0.6'] variants: ~doc @@ -189,7 +195,6 @@ variants: +internal-hwloc +two_level_namespace # Pin openssl to avoid duplicate packages being built openssl: - version: ['1.1.1u'] variants: +shared p4est: version: ['2.8'] @@ -204,7 +209,7 @@ pkgconf: buildable: False prod-util: - version: ['1.2.2'] + version: ['2.1.0'] proj: version: ['8.1.0'] variants: ~tiff @@ -219,9 +224,8 @@ variants: +plotting py-click: version: ['8.0.3'] - # Pin py-cryptography to a version earlier than 3.4 to avoid the rust dependency py-cryptography: - version: ['3.3.2'] + variants: +rust_bootstrap py-eccodes: version: ['1.4.2'] py-h5py: @@ -237,8 +241,7 @@ version: ['1.5.8'] variants: ~mpi py-numpy: - version: ['1.22.3'] - variants: +blas +lapack + require: ['@1.22.3'] py-pandas: variants: +excel # To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer @@ -266,10 +269,9 @@ version: ['1.9.3'] # Pin the py-setuptools version to avoid duplicate Python packages py-setuptools: - version: ['59.4.0'] - # Pin the py-setuptools-scm version to avoid duplicate Python packages - py-setuptools-scm: - version: ['7.0.5'] + require: ['@63.4.3'] + py-setuptools-rust: + variants: +rust_bootstrap py-shapely: version: ['1.8.0'] qt: @@ -284,13 +286,15 @@ sigio: version: ['2.3.2'] sp: - version: ['2.3.3'] + version: ['2.5.0'] + variants: precision=4,d,8 udunits: version: ['2.2.28'] upp: version: ['10.0.10'] w3emc: version: ['2.10.0'] + variants: precision=4,d,8 w3nco: version: ['2.4.1'] wget: diff --git a/configs/containers/specs/jedi-ci.yaml b/configs/containers/specs/jedi-ci.yaml index 3cc655da3..c97f23e5e 100644 --- a/configs/containers/specs/jedi-ci.yaml +++ b/configs/containers/specs/jedi-ci.yaml @@ -1,7 +1,7 @@ ### spack-stack-1.5.1 / skylab-6.1.0 containers for fv3-jedi and mpas-jedi (but not for ufs-jedi) specs: [base-env@1.0.0, jedi-base-env@1.0.0, ewok-env@1.0.0, jedi-fv3-env@1.0.0, jedi-mpas-env@1.0.0, bacio@2.4.1, bison@3.8.2, bufr@12.0.1, ecbuild@3.7.2, eccodes@2.27.0, ecflow@5, - eckit@1.24.4, ecmwf-atlas@0.35.0 +fckit +ectrans +tesselation +fftw, fiat@1.2.0, ectrans@1.2.0 +fftw, + eckit@1.24.4, ecmwf-atlas@0.35.0 +fckit +trans +tesselation +fftw, fiat@1.2.0, ectrans@1.2.0 +fftw, eigen@3.4.0, fckit@0.11.0, fms@release-jcsda, g2@3.4.5, g2tmpl@1.10.2, gftl-shared@1.6.1, gsibec@1.1.3, hdf@4.2.15, hdf5@1.14.0, ip@4.3.0, jasper@2.0.32, jedi-cmake@1.4.0, libpng@1.6.37, nccmp@1.9.0.1, netcdf-c@4.9.2, netcdf-cxx4@4.3.1, @@ -9,7 +9,7 @@ parallelio@2.5.10, parallel-netcdf@1.12.2, py-eccodes@1.4.2, py-f90nml@1.4.3, py-gitpython@3.1.27, py-h5py@3.7.0, py-numpy@1.22.3, py-pandas@1.5.3, py-pip, py-pyyaml@5.4.1, py-scipy@1.9.3, py-shapely@1.8.0, py-xarray@2022.3.0, - sp@2.3.3, udunits@2.2.28, w3nco@2.4.1, w3emc@2.10.0, nco@5.0.6, esmf@8.5.0, mapl@2.40.3, + sp@2.5.0, udunits@2.2.28, w3nco@2.4.1, w3emc@2.10.0, nco@5.0.6, esmf@8.5.0, mapl@2.40.3, zlib@1.2.13, zstd@1.5.2, odc@1.4.6, shumlib@macos_clang_linux_intel_port, awscli-v2@2.13.22, py-globus-cli@3.16.0] # Notes: diff --git a/configs/sites/derecho/packages.yaml b/configs/sites/derecho/packages.yaml index 0b6d107a0..f06ac3933 100644 --- a/configs/sites/derecho/packages.yaml +++ b/configs/sites/derecho/packages.yaml @@ -29,6 +29,9 @@ packages: # Need to force spack to build python with ssl variant when using older openssl from OS python: require: "+ssl" + # Newer versions of patchelf (tested 0.18.0) don't build with Intel on Derecho + patchelf: + version:: ['0.17.2'] ### All other external packages listed alphabetically autoconf: diff --git a/configs/sites/emc-rhel/packages.yaml b/configs/sites/emc-rhel/packages.yaml index 811495c36..d9071c300 100644 --- a/configs/sites/emc-rhel/packages.yaml +++ b/configs/sites/emc-rhel/packages.yaml @@ -21,10 +21,6 @@ packages: externals: - spec: binutils@2.30.117 prefix: /usr - bison: - externals: - - spec: bison@3.0.4 - prefix: /usr bzip2: externals: - spec: bzip2@1.0.6 @@ -128,22 +124,6 @@ packages: externals: - spec: libtool@2.4.6 prefix: /usr - llvm: - externals: - - spec: llvm@14.0.6+clang~lld~lldb - prefix: /usr - extra_attributes: - compilers: - c: /usr/bin/clang - cxx: /usr/bin/clang++ - llvm-doe: - externals: - - spec: llvm-doe@14.0.6+clang~lld~lldb - prefix: /usr - extra_attributes: - compilers: - c: /usr/bin/clang - cxx: /usr/bin/clang++ m4: externals: - spec: m4@1.4.18 @@ -156,10 +136,6 @@ packages: externals: - spec: pkgconf@1.4.2 prefix: /usr - python: - externals: - - spec: python@3.9.13+bz2+crypt+ctypes+dbm+lzma+nis+pyexpat~pythoncmd+readline+sqlite3+ssl+tix+tkinter+uuid+zlib - prefix: /usr rsync: externals: - spec: rsync@3.1.3 diff --git a/configs/sites/nautilus/packages.yaml b/configs/sites/nautilus/packages.yaml index 85f82c909..233e6d993 100644 --- a/configs/sites/nautilus/packages.yaml +++ b/configs/sites/nautilus/packages.yaml @@ -10,7 +10,7 @@ packages: fftw-api:: [intel-oneapi-mkl] lapack:: [intel-oneapi-mkl] ectrans: - variants:: +mkl + variants:: +mkl ~fftw gsibec: variants:: +mkl diff --git a/configs/sites/s4/packages.yaml b/configs/sites/s4/packages.yaml index 606b8cc16..20ad01b68 100644 --- a/configs/sites/s4/packages.yaml +++ b/configs/sites/s4/packages.yaml @@ -144,10 +144,6 @@ packages: prefix: /data/prod/jedi/spack-stack/mysql-8.0.31 modules: - mysql/8.0.31 - perl: - externals: - - spec: perl@5.16.3~cpanm+shared+threads - prefix: /usr pkg-config: externals: - spec: pkg-config@0.27.1 diff --git a/doc/source/KnownIssues.rst b/doc/source/KnownIssues.rst index 3392210dd..b168084b6 100644 --- a/doc/source/KnownIssues.rst +++ b/doc/source/KnownIssues.rst @@ -31,6 +31,10 @@ General When using a role account to install spack-stack, it is sometimes necessary to run graphical applications such as the ``qt`` online installer. The following website describes in detail how this can be done: https://www.thegeekdiary.com/how-to-set-x11-forwarding-export-remote-display-for-users-who-switch-accounts-using-sudo/ +7. ``==> Error: the key "core_compilers" must be set in modules.yaml`` during ``spack module [lmod|tcl] refresh`` + + This error usually indicates that the wrong module type is used in the ``spack module ... refresh`` command. For example, the system is configured for ``lmod``, but the command used is ``spack module tcl refresh``. + ============================== MSU Hercules ============================== @@ -45,6 +49,10 @@ NASA Discover Discover's connection to the outside world can be very slow and spack sometimes aborts with fetch timeouts. Try again until it works, sometimes have to wait for a bit. +2. ``configure: error: cannot guess build type; you must specify one`` when building ``freetype`` or other packages that use configure scripts + + This can happen if a spack install is started in a ``screen`` session, because Discover puts the temporary data in directories like ``/gpfsm/dnb33/tdirs/login/discover13.29716.dheinzel``, which get wiped out after some time. Without ``screen``, this problem doesn't occur. + ============================== NOAA Parallel Works ============================== diff --git a/doc/source/NewSiteConfigs.rst b/doc/source/NewSiteConfigs.rst index 6a722a8c0..2487bd4b8 100644 --- a/doc/source/NewSiteConfigs.rst +++ b/doc/source/NewSiteConfigs.rst @@ -450,7 +450,6 @@ It is recommended to increase the stacksize limit by using ``ulimit -S -s unlimi --exclude bison --exclude cmake \ --exclude curl --exclude openssl \ --exclude openssh - spack external find --scope system perl spack external find --scope system wget spack external find --scope system mysql spack external find --scope system texlive diff --git a/spack b/spack index b1baf5b70..8683cc4f1 160000 --- a/spack +++ b/spack @@ -1 +1 @@ -Subproject commit b1baf5b700e098a45f59da5ab990e1ace6b8442b +Subproject commit 8683cc4f1a42329cab38d2fd607476e202ce50d1