petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0 #32938

balay · 2022-10-01T20:07:05Z

No description provided.

joseeroman

@balay I have changed configure in SLEPc 3.18 so that arguments like --with-arpack-lib now take a quoted string instead of a comma-separated list. Hence the line arpacklib = "-lparpack,-larpack" should be changed to arpacklib = "-lparpack -larpack" when spec.satisfies("@3.18:").

I think this change will be good to avoid problems such as #28593

tldahlgren

Confirmed all 6 new sha256.

balay · 2022-10-05T18:16:09Z

@balay I have changed configure in SLEPc 3.18 so that arguments like --with-arpack-lib now take a quoted string instead of a comma-separated list. Hence the line arpacklib = "-lparpack,-larpack" should be changed to arpacklib = "-lparpack -larpack" when spec.satisfies("@3.18:").

@joseeroman the current code is:

            if spec.satisfies("@3.15:"):
                options.extend(
                    [
	                "--with-arpack-include=%s" % spec["arpack-ng"].prefix.include,
                        "--with-arpack-lib=%s" % spec["arpack-ng"].libs.joined(),
                    ]
                )

And thats using:

 '--with-arpack-include=/home/balay/spack/opt/spack/linux-fedora37-skylake/gcc-12.1.1/arpack-ng-3.8.0-agop4qxhb3qsldv6krh7vgvlzzmh5ti5/include'
 '--with-arpack-lib=/home/balay/spack/opt/spack/linux-fedora37-skylake/gcc-12.1.1/arpack-ng-3.8.0-agop4qxhb3qsldv6krh7vgvlzzmh5ti5/lib64/libparpack.so /home/balay/spack/opt/spack/linux-fedora37-skylake/gcc-12.1.1/arpack-ng-3.8.0-agop4qxhb3qsldv6krh7vgvlzzmh5ti5/lib64/libarpack.so'

And the build is successful - so I guess no change is needed on the spack side?

balay · 2022-10-05T18:17:33Z

@spackbot run pipeline

spackbot-app · 2022-10-05T18:17:37Z

I've started that pipeline for you!

balay · 2022-10-05T18:50:12Z

Ok - I guess the issue is - missing '-rpath'.

petsc configure processes `--with-hypre-lib=/home/balay/spack/opt/spack/linux-fedora37-skylake/gcc-12.1.1/hypre-2.25.0-lflu2k55f52q5aypuzwnt53yl5fq44vj/lib/libHYPRE.so to:

  Libraries:  -Wl,-rpath,/home/balay/spack/opt/spack/linux-fedora37-skylake/gcc-12.1.1/hypre-2.25.0-lflu2k55f52q5aypuzwnt53yl5fq44vj/lib -L/home/balay/spack/opt/spack/linux-fedora37-skylake/gcc-12.1.1/hypre-2.25.0-lflu2k55f52q5aypuzwnt53yl5fq44vj/lib -lHYPRE

However slepc:

ARPACK library flags:
  /home/balay/spack/opt/spack/linux-fedora37-skylake/gcc-12.1.1/arpack-ng-3.8.0-agop4qxhb3qsldv6krh7vgvlzzmh5ti5/lib64/libparpack.so /home/balay/spack/opt/spack/linux-fedora37-skylake/gcc-12.1.1/arpack-ng-3.8.0-agop4qxhb3qsldv6krh7vgvlzzmh5ti5/lib64/libarpack.so

So you would like -rpath option to get passed in via --with-arpack-lib option?

Perhaps there is a simple way to do this via spack. But that can be a different PR.

balay · 2022-10-05T19:07:24Z

I can do:

"--with-arpack-lib=%s" % spec["arpack-ng"].libs.ld_flags

And this gives:

ARPACK library flags:
  -L/home/balay/spack/opt/spack/linux-fedora37-skylake/gcc-12.1.1/arpack-ng-3.8.0-agop4qxhb3qsldv6krh7vgvlzzmh5ti5/lib64 -lparpack -larpack

i.e rpath might need to be setup inside slepc configure?

balay · 2022-10-06T04:17:49Z

I don't really understand the reason for CI failures

@spackbot run pipeline

spackbot-app · 2022-10-06T04:17:52Z

I've started that pipeline for you!

joseeroman · 2022-10-07T13:31:13Z

@balay if the pipeline failures are due to SLEPc, you can leave PETSc only in this MR and update SLEPc later. I will have a look at the rpath stuff during the weekend.

eugeneswalker · 2022-10-07T16:15:04Z

@spackbot run pipeline - hard to tell the reason for the failures because the logs are truncated, but there are jobs failing that shouldn't be failing because this PR doesn't change anything that would affect them... Could be infrastructure/spurious failures for some of them.

spackbot-app · 2022-10-07T16:15:08Z

I've started that pipeline for you!

eugeneswalker · 2022-10-07T16:53:18Z

@spackbot run pipeline - hard to tell the reason for the failures because the logs are truncated, but there are jobs failing that shouldn't be failing because this PR doesn't change anything that would affect them... Could be infrastructure/spurious failures for some of them.

Nevermind, the CI errors seem legit for:

pism@1.1.4
dealii@9.4.0 +cuda
petsc@3.18.0 +rocm

Logs are truncated so can't tell exactly why. Will reproduce locally and post log here.

spackbot-app · 2022-10-07T16:53:22Z

I've started that pipeline for you!

eugeneswalker · 2022-10-07T19:35:55Z

dealii@9.4.0 +cuda CI job is failing because:

Error Log

==> Installing dealii-9.4.0-u6vf5ou66f6dlpngdw4qqaqasmhegpab ==> No binary for dealii-9.4.0-u6vf5ou66f6dlpngdw4qqaqasmhegpab found: installing from source ==> Fetching https://github.com/dealii/dealii/releases/download/v9.4.0/dealii-9.4.0.tar.gz ==> Fetching https://github.com/dealii/dealii/commit/06bb9dc07efb6fea9912ee0d66264af548c552c8.patch?full_index=1 ==> Fetching https://github.com/dealii/dealii/commit/40076ac1a013cd7d221f9dda913b4d0e6452c21e.patch?full_index=1 ==> Applied patch https://github.com/dealii/dealii/commit/06bb9dc07efb6fea9912ee0d66264af548c552c8.patch?full_index=1 ==> Applied patch https://github.com/dealii/dealii/commit/40076ac1a013cd7d221f9dda913b4d0e6452c21e.patch?full_index=1 ==> dealii: Executing phase: 'cmake' ==> Error: ProcessError: Command exited with status 1: '/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/cmake-3.24.2-fzllxrl7cwsyvq7aob7yrxqvj6rj2qr6/bin/cmake' '-G' 'Ninja' '-DCMAKE_INSTALL_PREFIX:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/dealii-9.4.0-u6vf5ou66f6dlpngdw4qqaqasmhegpab' '-DCMAKE_BUILD_TYPE:STRING=DebugRelease' '-DBUILD_TESTING:BOOL=OFF' '-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON' '-DCMAKE_INSTALL_RPATH:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/dealii-9.4.0-u6vf5ou66f6dlpngdw4qqaqasmhegpab/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/dealii-9.4.0-u6vf5ou66f6dlpngdw4qqaqasmhegpab/lib64;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/arborx-1.2-kjf2nxv45q5fahyhigl4pgr54h3mxify/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/arpack-ng-3.8.0-ei2k6xl3lbqy7pv2lpj6thfodcrklxfm/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/assimp-5.2.4-mbai3dhs6wo5tra7gjusmrzyyosoovrw/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/boost-1.79.0-vdbuo2yqndt4coafs6ip4ojmbdmispke/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/cgal-5.4.1-s2tm34krddhsxpk4sdutf6vo2dizzud4/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/ginkgo-1.4.0-nnmnt3hakr7nvn72g4rckweconcvrerp/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/gsl-2.7.1-o6l5d3nimrhnqhkkygdajlfe7ocrtes2/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktzocshodmzhj6zhocqdc5pra/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/intel-tbb-2020.3-4xmnc4rzxvxng5bn4uhivmdyjeg6m2wr/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/metis-5.1.0-v3fsq7kdbz7rzxqrv36lutpvcmaxtbw3/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/muparser-2.2.6.1-eeqwgpr3a72lzlakb3k6dcamcbrujrwh/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/netlib-scalapack-2.2.0-4k3wbeyaaqiuptj5jx2fyuhz4ui2mxmg/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/oce-0.18.3-zechrvnbxhq6sudsnpvumvbu4saealzh/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/openblas-0.3.21-uny2vcq2bo7k6v3ai6dmhfx6rmw4tqxc/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/p4est-2.8-i4c2nk5r4snu7efkius3qu342hdim5hj/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/petsc-3.18.0-bhh4j4aicnl4dqw6tzfwnebqfdlt7e3c/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/slepc-3.18.0-pe35nul6k64usjxcsqibgwo5fxqcmv66/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/suite-sparse-5.10.1-sj5tgusbhex7wq3uaajqftvauozs4mby/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/sundials-6.3.0-cwzbfq7yo4aajiqn26rgj2i624o5bft5/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/symengine-0.9.0-b4lsi6ex2sce6g25i4q7kyekplykjkm5/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/zlib-1.2.12-hdtjtngxfoicw3xoif5xrdopjdngev3h/lib;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/adol-c-2.7.2-nrwbssdgpmiesk5oc7paimvdz7np36a4/lib64;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/cuda-11.7.0-e3sjwsuxybpqrnvntdnjxbvdlloy5xpl/lib64' '-DCMAKE_PREFIX_PATH:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/symengine-0.9.0-b4lsi6ex2sce6g25i4q7kyekplykjkm5;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpc-1.2.1-mvi6qhro3u7q4rpjebdlw6tvcfoxlles;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/cereal-1.3.2-ucx7xvsth26d7g6xluhr3vb3jczgcdhp;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/sundials-6.3.0-cwzbfq7yo4aajiqn26rgj2i624o5bft5;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/suite-sparse-5.10.1-sj5tgusbhex7wq3uaajqftvauozs4mby;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/slepc-3.18.0-pe35nul6k64usjxcsqibgwo5fxqcmv66;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/petsc-3.18.0-bhh4j4aicnl4dqw6tzfwnebqfdlt7e3c;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/superlu-dist-8.1.1-zf6v5we3hdcbwk6uogg5negj25dzwimq;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/parmetis-4.0.3-voh6wdwpjneknyyrpyi2xn64foj4764x;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hypre-2.25.0-fefm2mcox2q7sdv2froqvmicwkg6usmp;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/p4est-2.8-i4c2nk5r4snu7efkius3qu342hdim5hj;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/netlib-scalapack-2.2.0-4k3wbeyaaqiuptj5jx2fyuhz4ui2mxmg;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/muparser-2.2.6.1-eeqwgpr3a72lzlakb3k6dcamcbrujrwh;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/metis-5.1.0-v3fsq7kdbz7rzxqrv36lutpvcmaxtbw3;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/gsl-2.7.1-o6l5d3nimrhnqhkkygdajlfe7ocrtes2;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/gmsh-4.8.4-jbl6zyzfkdj347bnzd7ldhdj3gc2pc6l;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/oce-0.18.3-zechrvnbxhq6sudsnpvumvbu4saealzh;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/intel-tbb-2020.3-4xmnc4rzxvxng5bn4uhivmdyjeg6m2wr;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/ninja-1.11.0-qknagrih6hutxmskdyzqrulrhegqxcse;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktzocshodmzhj6zhocqdc5pra;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/ginkgo-1.4.0-nnmnt3hakr7nvn72g4rckweconcvrerp;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/cuda-11.7.0-e3sjwsuxybpqrnvntdnjxbvdlloy5xpl;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/cuda-11.7.0-e3sjwsuxybpqrnvntdnjxbvdlloy5xpl/targets/x86_64-linux/lib/cmake;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/cgal-5.4.1-s2tm34krddhsxpk4sdutf6vo2dizzud4;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpfr-4.1.0-i2gmqyqybws5l52fkd5gwlvtsgdduq5i;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/gmp-6.2.1-zjvldsvhrgyeyy7t3dvy2r7jjftl373x;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/eigen-3.4.0-xzi4uaegoe3hudch2rizbe4juhmqjnab;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/boost-1.79.0-vdbuo2yqndt4coafs6ip4ojmbdmispke;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/assimp-5.2.4-mbai3dhs6wo5tra7gjusmrzyyosoovrw;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/arpack-ng-3.8.0-ei2k6xl3lbqy7pv2lpj6thfodcrklxfm;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/openblas-0.3.21-uny2vcq2bo7k6v3ai6dmhfx6rmw4tqxc;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/arborx-1.2-kjf2nxv45q5fahyhigl4pgr54h3mxify;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/yaksa-0.2-2ol72alrme5dtjrlamyjc7d2deg7tz5k;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/libfabric-1.15.1-7olaq3xnrau6bp4nqvgdvoh3adrlg5fl;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hwloc-2.8.0-wbbhirbdeqdknqfhr3itix2dz4zelzpz;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/libxml2-2.10.1-qlk2eppdafo5hai72zan53bhpzcub6bc;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/xz-5.2.5-gwvbhfpkxuf4ofixoipzmplz2becfbcx;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/libpciaccess-0.16-dch343zp6cgxxm3jjuhb7eh27sejgiqj;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/kokkos-3.6.01-nnrrfgbwn22ur6tafcmmofm4i75cf2zv;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/cmake-3.24.2-fzllxrl7cwsyvq7aob7yrxqvj6rj2qr6;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/zlib-1.2.12-hdtjtngxfoicw3xoif5xrdopjdngev3h;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/bzip2-1.0.8-3gilvnwrzghzcbkmuhcnnmiixzqre6us;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/libiconv-1.16-nxnzjytuy6fbmlzb4tbzuacyagck7hiz;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/ncurses-6.3-i2hv5jcfp6vaydwc7s6tbdq4lmy5ab6v;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/adol-c-2.7.2-nrwbssdgpmiesk5oc7paimvdz7np36a4' '-DDEAL_II_EXAMPLES_RELDIR:STRING=share/deal.II/examples' '-DDEAL_II_DOCREADME_RELDIR:STRING=share/deal.II/' '-DDEAL_II_DOCHTML_RELDIR:STRING=share/deal.II/doc' '-DBOOST_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/boost-1.79.0-vdbuo2yqndt4coafs6ip4ojmbdmispke' '-DLAPACK_FOUND:BOOL=ON' '-DLAPACK_INCLUDE_DIRS:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/openblas-0.3.21-uny2vcq2bo7k6v3ai6dmhfx6rmw4tqxc/include' '-DLAPACK_LIBRARIES:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/openblas-0.3.21-uny2vcq2bo7k6v3ai6dmhfx6rmw4tqxc/lib/libopenblas.so' '-DUMFPACK_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/suite-sparse-5.10.1-sj5tgusbhex7wq3uaajqftvauozs4mby' '-DZLIB_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/zlib-1.2.12-hdtjtngxfoicw3xoif5xrdopjdngev3h' '-DDEAL_II_ALLOW_BUNDLED:BOOL=OFF' '-DDEAL_II_COMPONENT_DOCUMENTATION:BOOL=OFF' '-DDEAL_II_COMPONENT_EXAMPLES:BOOL=ON' '-DDEAL_II_WITH_64BIT_INDICES:BOOL=OFF' '-DDEAL_II_WITH_CUDA:BOOL=ON' '-DDEAL_II_CUDA_FLAGS:STRING=-arch=sm_80' '-DDEAL_II_WITH_MPI:BOOL=ON' '-DCMAKE_C_COMPILER:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/bin/mpicc' '-DCMAKE_CXX_COMPILER:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/bin/mpic++' '-DCMAKE_Fortran_COMPILER:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/bin/mpif90' '-DMPI_C_COMPILER:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/bin/mpicc' '-DMPI_CXX_COMPILER:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/bin/mpic++' '-DMPI_Fortran_COMPILER:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/bin/mpif90' '-DDEAL_II_MPI_WITH_CUDA_SUPPORT:BOOL=OFF' '-DCUDA_HOST_COMPILER:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/bin/mpic++' '-DDEAL_II_COMPONENT_PYTHON_BINDINGS:BOOL=OFF' '-DDEAL_II_WITH_SIMPLEX_SUPPORT:BOOL=ON' '-DDEAL_II_WITH_TBB:BOOL=ON' '-DTBB_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/intel-tbb-2020.3-4xmnc4rzxvxng5bn4uhivmdyjeg6m2wr' '-DDEAL_II_WITH_GSL:BOOL=ON' '-DGSL_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/gsl-2.7.1-o6l5d3nimrhnqhkkygdajlfe7ocrtes2' '-DDEAL_II_WITH_HDF5:BOOL=ON' '-DHDF5_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktzocshodmzhj6zhocqdc5pra' '-DDEAL_II_WITH_P4EST:BOOL=ON' '-DP4EST_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/p4est-2.8-i4c2nk5r4snu7efkius3qu342hdim5hj' '-DDEAL_II_WITH_PETSC:BOOL=ON' '-DPETSC_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/petsc-3.18.0-bhh4j4aicnl4dqw6tzfwnebqfdlt7e3c' '-DDEAL_II_WITH_SLEPC:BOOL=ON' '-DSLEPC_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/slepc-3.18.0-pe35nul6k64usjxcsqibgwo5fxqcmv66' '-DDEAL_II_WITH_TRILINOS:BOOL=OFF' '-DDEAL_II_WITH_METIS:BOOL=ON' '-DMETIS_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/metis-5.1.0-v3fsq7kdbz7rzxqrv36lutpvcmaxtbw3' '-DDEAL_II_WITH_SUNDIALS:BOOL=ON' '-DSUNDIALS_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/sundials-6.3.0-cwzbfq7yo4aajiqn26rgj2i624o5bft5' '-DDEAL_II_WITH_NANOFLANN:BOOL=OFF' '-DDEAL_II_WITH_ASSIMP:BOOL=ON' '-DASSIMP_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/assimp-5.2.4-mbai3dhs6wo5tra7gjusmrzyyosoovrw' '-DDEAL_II_WITH_GMSH:BOOL=ON' '-DGMSH_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/gmsh-4.8.4-jbl6zyzfkdj347bnzd7ldhdj3gc2pc6l' '-DDEAL_II_WITH_MUPARSER:BOOL=ON' '-DMUPARSER_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/muparser-2.2.6.1-eeqwgpr3a72lzlakb3k6dcamcbrujrwh' '-DDEAL_II_WITH_SYMENGINE:BOOL=ON' '-DSYMENGINE_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/symengine-0.9.0-b4lsi6ex2sce6g25i4q7kyekplykjkm5' '-DDEAL_II_WITH_GINKGO:BOOL=ON' '-DGINKGO_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/ginkgo-1.4.0-nnmnt3hakr7nvn72g4rckweconcvrerp' '-DDEAL_II_WITH_ARBORX:BOOL=ON' '-DARBORX_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/arborx-1.2-kjf2nxv45q5fahyhigl4pgr54h3mxify' '-DDEAL_II_WITH_CGAL:BOOL=ON' '-DCGAL_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/cgal-5.4.1-s2tm34krddhsxpk4sdutf6vo2dizzud4' '-DDEAL_II_WITH_ADOLC:BOOL=ON' '-DADOLC_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/adol-c-2.7.2-nrwbssdgpmiesk5oc7paimvdz7np36a4' '-DDEAL_II_WITH_ARPACK:BOOL=ON' '-DARPACK_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/arpack-ng-3.8.0-ei2k6xl3lbqy7pv2lpj6thfodcrklxfm' '-DDEAL_II_ARPACK_WITH_PARPACK:BOOL=ON' '-DDEAL_II_WITH_NETCDF:BOOL=OFF' '-DDEAL_II_WITH_SCALAPACK:BOOL=ON' '-DSCALAPACK_FOUND:BOOL=ON' '-DSCALAPACK_INCLUDE_DIRS:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/netlib-scalapack-2.2.0-4k3wbeyaaqiuptj5jx2fyuhz4ui2mxmg/include' '-DSCALAPACK_LIBRARIES:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/netlib-scalapack-2.2.0-4k3wbeyaaqiuptj5jx2fyuhz4ui2mxmg/lib/libscalapack.so' '-DDEAL_II_WITH_OPENCASCADE:BOOL=ON' '-DOPENCASCADE_DIR:STRING=/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/oce-0.18.3-zechrvnbxhq6sudsnpvumvbu4saealzh' '-DDEAL_II_CXX_FLAGS:STRING=-march=x86-64 -mtune=generic' '/tmp/root/spack-stage/spack-stage-dealii-9.4.0-u6vf5ou66f6dlpngdw4qqaqasmhegpab/spack-src'

1 error found in build log:
433 -- PETSC_INCLUDE_DIRS: /spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/petsc-3.18.0-bhh4j4aicnl4dqw6tzfwnebqfdlt7e3c/include;/spack/opt/s
pack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hypre-2.25.0-fefm2mcox2q7sdv2froqvmicwkg6usmp/include;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.
1.0/superlu-dist-8.1.1-zf6v5we3hdcbwk6uogg5negj25dzwimq/include;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktzocsho
dmzhj6zhocqdc5pra/include;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/parmetis-4.0.3-voh6wdwpjneknyyrpyi2xn64foj4764x/include;/spack/op
t/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/metis-5.1.0-v3fsq7kdbz7rzxqrv36lutpvcmaxtbw3/include;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-1
1.1.0/zlib-1.2.12-hdtjtngxfoicw3xoif5xrdopjdngev3h/include
434 -- PETSC_USER_INCLUDE_DIRS: /spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/petsc-3.18.0-bhh4j4aicnl4dqw6tzfwnebqfdlt7e3c/include;/spack/
opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hypre-2.25.0-fefm2mcox2q7sdv2froqvmicwkg6usmp/include;/spack/opt/spack/linux-ubuntu20.04-x86_64/gc
c-11.1.0/superlu-dist-8.1.1-zf6v5we3hdcbwk6uogg5negj25dzwimq/include;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktz
ocshodmzhj6zhocqdc5pra/include;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/parmetis-4.0.3-voh6wdwpjneknyyrpyi2xn64foj4764x/include;/spa
ck/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/metis-5.1.0-v3fsq7kdbz7rzxqrv36lutpvcmaxtbw3/include;/spack/opt/spack/linux-ubuntu20.04-x86_64/
gcc-11.1.0/zlib-1.2.12-hdtjtngxfoicw3xoif5xrdopjdngev3h/include
435 -- PETSC_LIBRARIES: /spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/petsc-3.18.0-bhh4j4aicnl4dqw6tzfwnebqfdlt7e3c/lib/libpetsc.so;/spack/
opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hypre-2.25.0-fefm2mcox2q7sdv2froqvmicwkg6usmp/lib/libHYPRE.so;/spack/opt/spack/linux-ubuntu20.04-x
86_64/gcc-11.1.0/superlu-dist-8.1.1-zf6v5we3hdcbwk6uogg5negj25dzwimq/lib/libsuperlu_dist.so;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0
/openblas-0.3.21-uny2vcq2bo7k6v3ai6dmhfx6rmw4tqxc/lib/libopenblas.so;pthread;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-gi
auuz5ktzocshodmzhj6zhocqdc5pra/lib/libhdf5_hl_fortran.so;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktzocshodmzhj6z
hocqdc5pra/lib/libhdf5_hl_f90cstub.so;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktzocshodmzhj6zhocqdc5pra/lib/libh
df5_hl.so;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktzocshodmzhj6zhocqdc5pra/lib/libhdf5_fortran.so;/spack/opt/sp
ack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktzocshodmzhj6zhocqdc5pra/lib/libhdf5_f90cstub.so;/spack/opt/spack/linux-ubuntu20.04-
x86_64/gcc-11.1.0/hdf5-1.10.7-giauuz5ktzocshodmzhj6zhocqdc5pra/lib/libhdf5.so;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/parmetis-4.0.
3-voh6wdwpjneknyyrpyi2xn64foj4764x/lib/libparmetis.so;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/metis-5.1.0-v3fsq7kdbz7rzxqrv36lutpvc
maxtbw3/lib/libmetis.so;/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/zlib-1.2.12-hdtjtngxfoicw3xoif5xrdopjdngev3h/lib/libz.so;/spack/opt
/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/lib/libmpifort.so;/spack/opt/spack/linux-ubuntu20.04-x86
_64/gcc-11.1.0/mpich-4.0.2-ofyvsbaosffov5hbaq2layecszlsq6pe/lib/libmpi.so;gfortran;m;quadmath;dl
436 -- Found PETSC
437 -- Could not find a sufficiently modern PETSc installation: Version >=3.3.0 required!
438 -- DEAL_II_WITH_PETSC has unmet external dependencies.

439 CMake Error at cmake/configure/configure_30_petsc.cmake:141 (MESSAGE):
440
441
442 Could not find the petsc library!
443
444 Could not find a sufficiently modern PETSc installation: Version >=3.3.0
445 required!

spack-build-env.txt
spack-build-out.txt
CMakeError.log

balay · 2022-10-07T20:36:19Z

@eugeneswalker thanks for digging into the logs!

Perhaps @bangerth can help here.

eugeneswalker · 2022-10-08T00:37:41Z

petsc@3.18.0 +rocm CI job is failing because:

Error Log

==> Installing petsc-3.18.0-syhkzc54itgu553lglshibiaaakm6bal
==> No binary for petsc-3.18.0-syhkzc54itgu553lglshibiaaakm6bal found: installing from source
==> Using cached archive: /spack/var/spack/cache/_source-cache/archive/9d/9da802e703ad79fb7ef0007d17f68916573011073ee9712dcd1673537f6a5f68.tar.gz
==> No patches needed for petsc
==> petsc: Executing phase: 'configure'
==> petsc: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'make' 'V=1 MAKE_NP=16'
15 errors found in build log:

...


1018    /tmp/root/spack-stage/spack-stage-petsc-3.18.0-syhkzc54itgu553lglshibiaaakm6bal/spack-src/include/petscdevice_hip.h:26:16: fatal error: hipsolver/hipsolver.h: No s

uch file or directory

1019       26 |       #include <hipsolver/hipsolver.h>

1020          |                ^~~~~~~~~~~~~~~~~~~~~~~

1021    compilation terminated.

1022    make[3]: *** [gmakefile:195: arch-linux-c-opt/obj/sys/objects/device/util/memory.o] Error 1

...

1046    /tmp/root/spack-stage/spack-stage-petsc-3.18.0-syhkzc54itgu553lglshibiaaakm6bal/spack-src/include/petscdevice_hip.h:26:16: fatal error: hipsolver/hipsolver.h: No s

uch file or directory

1047       26 |       #include <hipsolver/hipsolver.h>

1048          |                ^~~~~~~~~~~~~~~~~~~~~~~

1049    compilation terminated.

1050    make[3]: *** [gmakefile:195: arch-linux-c-opt/obj/sys/objects/pinit.o] Error 1

...

1142    make[2]: *** [/tmp/root/spack-stage/spack-stage-petsc-3.18.0-syhkzc54itgu553lglshibiaaakm6bal/spack-src/lib/petsc/conf/rules:56: libs] Error 2

1143    ERROR***********

1144      Error during compile, check arch-linux-c-opt/lib/petsc/conf/make.log

1145      Send it and arch-linux-c-opt/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov

1146    ********************************************************************

1147    make[1]: *** [makefile:34: all] Error 1

1148    make: *** [GNUmakefile:9: all] Error 2

spack-build-env.txt
spack-build-out.txt

eugeneswalker · 2022-10-08T00:40:53Z

pism@1.1.4 CI job is failing because:

Error Log

==> Installing pism-1.1.4-2nuga26xoanjr3tp2nz5wclw7tro5pji
==> No binary for pism-1.1.4-2nuga26xoanjr3tp2nz5wclw7tro5pji found: installing from source
==> Using cached archive: /spack/var/spack/cache/_source-cache/archive/8c/8ccb867af3b37e8d103351dadc1d7e77512e64379519fe8a2592668deb27bc44.tar.gz
==> No patches needed for pism
==> pism: Executing phase: 'cmake'
==> pism: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'make' '-j16'
4 errors found in build log:

...

710    In file included from /spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/petsc-3.18.0-qeeectfmf7kwkjiuiytnpmzihd27wcxn/include/petscsys.h:1274,

711                     from /tmp/root/spack-stage/spack-stage-pism-1.1.4-2nuga26xoanjr3tp2nz5wclw7tro5pji/spack-src/src/util/options.cc:21:

712    /tmp/root/spack-stage/spack-stage-pism-1.1.4-2nuga26xoanjr3tp2nz5wclw7tro5pji/spack-src/src/util/options.cc: In member function 'int pism::options::String::proc

ess(const string&, const string&, const string&, pism::options::ArgumentFlag)':


713    /spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/petsc-3.18.0-qeeectfmf7kwkjiuiytnpmzihd27wcxn/include/petscoptions.h:182:5: error: expected primary-express

ion before 'do'

714      182 |     do { 

     715          |     ^~

716    /tmp/root/spack-stage/spack-stage-pism-1.1.4-2nuga26xoanjr3tp2nz5wclw7tro5pji/spack-src/src/util/options.cc:62:10: note: in expansion of macro 'PetscOptionsBegi

n'

717       62 |   ierr = PetscOptionsBegin(MPI_COMM_SELF, "", "", "");

718          |          ^~~~~~~~~

...

723    make[2]: *** [src/util/CMakeFiles/util.dir/build.make:569: src/util/CMakeFiles/util.dir/options.cc.o] Error 1

...

760    make[1]: *** [CMakeFiles/Makefile2:905: src/util/CMakeFiles/util.dir/all] Error 2

761    make[1]: *** Waiting for unfinished jobs....

762    make[2]: Leaving directory '/tmp/root/spack-stage/spack-stage-pism-1.1.4-2nuga26xoanjr3tp2nz5wclw7tro5pji/spack-build-2nuga26'

763    [ 71%] Built target boundary

764    make[1]: Leaving directory '/tmp/root/spack-stage/spack-stage-pism-1.1.4-2nuga26xoanjr3tp2nz5wclw7tro5pji/spack-build-2nuga26'

765    make: *** [Makefile:149: all] Error 2

spack-build-env.txt
spack-build-out.txt
CMakeOutput.log

eugeneswalker · 2022-10-10T23:26:44Z

If the pism@1.1.4 and dealii@9.4.0 CI issues are due to those packages requiring pre v3.18.0 petsc, we could restrict the petsc versions in those packages' package.py

eugeneswalker · 2022-10-11T14:20:49Z

Looks like the only failing CI job now is petsc+rocm because it can't find hipsolver.h

==> Installing petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4
==> No binary for petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4 found: installing from source
==> Fetching http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.18.0.tar.gz
==> No patches needed for petsc
==> petsc: Executing phase: 'configure'
==> petsc: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'make' 'V=1 MAKE_NP=16'
...
     1013    /spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/mpich-4.0.2-neyedgynkxgmvrznfbtbvc2qp6olr3bn/bin/mpicc -c -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-ty
             pe-mismatch -Wno-stringop-overflow -fstack-protector -fvisibility=hidden -g -O  -I/tmp/root/spack-stage/spack-stage-petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4/spack-src
             /include -I/tmp/root/spack-stage/spack-stage-petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4/spack-src/arch-linux-c-opt/include -I/spack/opt/spack/linux-ubuntu20.04-x86_64/g
             cc-11.1.0/hypre-2.25.0-2sjqteg3nkftywk2hj2434plrrvrsa4n/include -I/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/superlu-dist-7.2.0-jvgwdw2pdqvl4iielmjp2doc5r2gvol2/
             include -I/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hdf5-1.12.2-bxpmr25d3sstz6avn6lvvaghvhxnpjsq/include -I/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/
             parmetis-4.0.3-b7oxl7rlfwrxhrgsrvkvu6uat6sovx3z/include -I/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/metis-5.1.0-oua56og3yq4jwbyl3bv7oeqmeofvtp22/include -I/spac
             k/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/zlib-1.2.12-hdtjtngxfoicw3xoif5xrdopjdngev3h/include -I/spack/opt/spack/linux-ubuntu20.04-x86_64/gcc-11.1.0/hip-5.2.1-tmliz
             irwghv5dl2n33ymhrqkrnxptcs3/include    -MMD -MP /tmp/root/spack-stage/spack-stage-petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4/spack-src/src/sys/objects/pinit.c -o arch-l
             inux-c-opt/obj/sys/objects/pinit.o
     1014    In file included from /tmp/root/spack-stage/spack-stage-petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4/spack-src/src/sys/objects/pinit.c:717:
  >> 1015    /tmp/root/spack-stage/spack-stage-petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4/spack-src/include/petscdevice_hip.h:26:16: fatal error: hipsolver/hipsolver.h: No such file
              or directory
     1016       26 |       #include <hipsolver/hipsolver.h>
     1017          |                ^~~~~~~~~~~~~~~~~~~~~~~
     1018    compilation terminated.
  >> 1019    make[3]: *** [gmakefile:195: arch-linux-c-opt/obj/sys/objects/pinit.o] Error 1
...
     1027    In file included from /tmp/root/spack-stage/spack-stage-petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4/spack-src/include/petscdevice_cupm.h:6,
     1028                     from /tmp/root/spack-stage/spack-stage-petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4/spack-src/src/sys/objects/device/util/memory.c:2:
  >> 1029    /tmp/root/spack-stage/spack-stage-petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4/spack-src/include/petscdevice_hip.h:26:16: fatal error: hipsolver/hipsolver.h: No such file
              or directory
     1030       26 |       #include <hipsolver/hipsolver.h>
     1031          |                ^~~~~~~~~~~~~~~~~~~~~~~
     1032    compilation terminated.
  >> 1033    make[3]: *** [gmakefile:195: arch-linux-c-opt/obj/sys/objects/device/util/memory.o] Error 1
...
  >> 1140    make[2]: *** [/tmp/root/spack-stage/spack-stage-petsc-3.18.0-24ntknzbmozkwp5x25cxit6pwlpt2cz4/spack-src/lib/petsc/conf/rules:56: libs] Error 2
     1141    **************************ERROR*************************************
     1142      Error during compile, check arch-linux-c-opt/lib/petsc/conf/make.log
     1143      Send it and arch-linux-c-opt/lib/petsc/conf/configure.log to petsc-maint@mcs.anl.gov
     1144    ********************************************************************
  >> 1145    make[1]: *** [makefile:34: all] Error 1
  >> 1146    make: *** [GNUmakefile:9: all] Error 2

balay · 2022-10-12T01:08:52Z

@eugeneswalker, @tldahlgren, the CI errors are now fixed. Could you recheck/approve the PR?

eugeneswalker

Thank you!

bangerth · 2022-10-14T03:27:57Z

Did that also fix the dealii issue?

balay · 2022-10-14T05:38:02Z

Did that also fix the dealii issue?

Yes - all CI issues including dealii failure are fixed in this PR.

bangerth · 2022-10-14T05:39:57Z

OK, thanks for the confirmation!

balay · 2022-10-14T13:10:30Z

@eugeneswalker @tldahlgren I think this PR is ready for merge

@spackbot

* py-execnet: 1.9.0 (spack#33282) * py-execnet: 1.9.0 * bounds * add version 1.12.3 of parallel-netcdf (spack#33286) * Add checksum for py-psutil 5.9.2 (spack#33139) * gitlab ci: Print better information about broken specs (spack#33124) When a pipeline generation job is automatically failed because it generated jobs for specs known to be broken on develop, print better information about the broken specs that were encountered. Include at a minimum the hash and the url of the job whose failure caused it to be put on the broken specs list in the first place. * meson: remove slash in path (spack#33292) * Add checksum for py-gitpython 3.1.27 (spack#33285) * Add checksum for py-gitpython 3.1.27 * Update package.py * Update var/spack/repos/builtin/packages/py-gitpython/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * UPC++/GASNet-EX 2022.9.0 update (spack#33277) * gasnet: Add new release hash * upcxx: Add new release hash * gasnet: misc updates * upcxx: misc updates * Fix pika@0.9.0 sha (spack#33307) * hip@5.2.0 onwards: set prefix properly (spack#33257) * hip-set-prefix-rocm5.2.0-onwards * Update var/spack/repos/builtin/packages/hip/package.py Update description Co-authored-by: Satish Balay <balay@mcs.anl.gov> * petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0 (spack#32938) * petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0 * workaround for dealii build failure [with petsc version check] * pism: add compatibility fix to for petsc@3.18 * add in hipsolver dependency * py-libensemble: updating package for v0.9.3 (spack#33298) * commit updating py-libensemble package for 0.9.3 * removed commented-out lines * Add checksum for py-oauthlib 3.2.1 (spack#33201) * Add checksum for py-oauthlib 3.2.1 * Update package.py * [@spackbot] updating style on behalf of iarspider * Update package.py * Update package.py Co-authored-by: iarspider <iarspider@users.noreply.github.com> * ninja: New version 1.11.1 (spack#33215) * seacas: update to latest release (spack#33330) Add checksum for latest tag/release * gptl: new version 8.1.1; use the correct mpi fortran compiler (spack#33235) * gptl: new version 8.1.1; use the correct `mpifc` * add `F90` and `$F77` * glib: add 2.74.0 and 2.72.4 (spack#33332) * depfile: update docs (spack#33279) * rocksdb: add 7.7.3 (spack#33341) * Add checksum for py-seaborn 0.12.0 (spack#33145) * Add checksum for py-seaborn 0.12.0 * Update package.py * Update package.py * [@spackbot] updating style on behalf of iarspider * Update package.py Co-authored-by: iarspider <iarspider@users.noreply.github.com> * CI: allow multiple matches to combine tags (spack#32290) Currently "spack ci generate" chooses the first matching entry in gitlab-ci:mappings to fill attributes for a generated build-job, requiring that the entire configuration matrix is listed out explicitly. This unfortunately causes significant problems in environments with large configuration spaces, for example the environment in spack#31598 (spack.yaml) supports 5 operating systems, 3 architectures and 130 packages with explicit size requirements, resulting in 1300 lines of configuration YAML. This patch adds a configuraiton option to the gitlab-ci schema called "match_behavior"; when it is set to "merge", all matching entries are applied in order to the final build-job, allowing a few entries to cover an entire matrix of configurations. The default for "match_behavior" is "first", which behaves as before this commit (only the runner attributes of the first match are used). In addition, match entries may now include a "remove-attributes" configuration, which allows matches to remove tags that have been aggregated by prior matches. This only makes sense to use with "match_behavior:merge". You can combine "runner-attributes" with "remove-attributes" to effectively override prior tags. * meson: update OneAPI compiler support patch (spack#33293) * py-tensorflow: fix zlib (spack#33349) * py-tensorflow: fix zlib * [@spackbot] updating style on behalf of haampie Co-authored-by: haampie <haampie@users.noreply.github.com> * py-meson-python: add new versions (spack#33294) * tasmanian: disable openmp by default (spack#33345) * octopus: upgrade to 12.1 (spack#33343) * py-sphinx: add v5.3 and v5.2 (spack#33356) * py-setuptools: add v65.5.0 (spack#33353) * libblastrampoline: Add versions 5.1.1, 5.2.0 (spack#33352) * nextflow: add v20.10.0 (spack#33354) * sdl2: add v2.0.22 and v2.24.1 (spack#33351) * mariadb-c-client: add 3.3.2, 3.2.7, 3.1.18, 3.0.10 (spack#33335) * py-tensorflow-hub: zlib, again. (spack#33359) * Add checksum for py-sniffio 1.3.0 (spack#32975) * py-numpy: add v1.23.4 (spack#33260) * py-jupyterlab-pygments: install from wheel to avoid cyclic dependency (spack#33278) * py-jupyterlab-pygments: avoid cyclic dependency * Fix style * Update package.py * Update package.py * [@spackbot] updating style on behalf of iarspider * Update package.py * Flake-8 * fix Co-authored-by: iarspider <iarspider@users.noreply.github.com> * installer.py: show timers for binary install (spack#33305) Print a message of the form ``` Fetch mm:ss. Build: mm:ss. Total: mm:ss ``` when installing from buildcache. Previously this only happened for source builds. * Add checksum for py-astroid 2.12.7, py-astroid 2.12.10, py-setuptools 62.6.0, py-wrapt 1.14.1, py-pylint 2.15.0 (spack#32976) * Add checksum for py-astroid 2.12.7, py-setuptools 62.6.0 * Also add checksum for py-wrapt * Update package.py * Update package.py (spack#57) * Update package.py * Update package.py * Update package.py * gitlab ci: Do not force protected build jobs to run on aws runners (spack#33314) * installer.py: fix/test get_deptypes (spack#33363) Fixing an oversight in spack#32537 `get_deptypes` should depend on new `package/dependencies_cache_only` props. * Add checksum for py-grpcio-tools 1.48.1 (spack#33358) * Add checksum for py-prompt-toolkit 3.0.31 (spack#33362) Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com> Co-authored-by: Jim Edwards <jedwards@ucar.edu> Co-authored-by: iarspider <iarspider@gmail.com> Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Dan Bonachea <dobonachea@lbl.gov> Co-authored-by: Auriane R <48684432+aurianer@users.noreply.github.com> Co-authored-by: eugeneswalker <38933153+eugeneswalker@users.noreply.github.com> Co-authored-by: Satish Balay <balay@mcs.anl.gov> Co-authored-by: John-Luke Navarro <33131245+jlnav@users.noreply.github.com> Co-authored-by: iarspider <iarspider@users.noreply.github.com> Co-authored-by: Erik Schnetter <schnetter@gmail.com> Co-authored-by: Greg Sjaardema <gsjaardema@gmail.com> Co-authored-by: WuK <i@wu-kan.cn> Co-authored-by: Michael Kuhn <michael.kuhn@ovgu.de> Co-authored-by: Jonathon Anderson <17242663+blue42u@users.noreply.github.com> Co-authored-by: haampie <haampie@users.noreply.github.com> Co-authored-by: Miroslav Stoyanov <30537612+mkstoyanov@users.noreply.github.com> Co-authored-by: Hans Fangohr <fangohr@users.noreply.github.com> Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com> Co-authored-by: Diego Alvarez <dialvarezs@gmail.com> Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>

balay requested review from joseeroman and tldahlgren October 1, 2022 20:07

spackbot-app bot added dependencies new-version python update-package labels Oct 1, 2022

spackbot-app bot requested review from BarrySmith and jedbrown October 1, 2022 20:07

joseeroman reviewed Oct 2, 2022

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tldahlgren previously approved these changes Oct 3, 2022

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tldahlgren assigned tldahlgren and joseeroman Oct 3, 2022

balay dismissed tldahlgren’s stale review via e839dc0 October 5, 2022 19:10

balay force-pushed the balay/petsc-slepc-3.18.0 branch from f2679d8 to e839dc0 Compare October 5, 2022 19:10

balay added 3 commits October 10, 2022 18:53

petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0

54d4fd1

workaround for dealii build failure [with petsc version check]

4d0253d

pism: add compatibility fix to for petsc@3.18

ee30487

balay force-pushed the balay/petsc-slepc-3.18.0 branch from e839dc0 to ee30487 Compare October 11, 2022 01:01

spackbot-app bot added the patch label Oct 11, 2022

balay mentioned this pull request Oct 11, 2022

petsc@3.17.4 +rocm configure fails using ROCm 5.2.0 and PrgEnv-gnu/cray/amd on OLCF Crusher #32826

Closed

4 tasks

add in hipsolver dependency

264a5a5

eugeneswalker approved these changes Oct 12, 2022

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joseeroman approved these changes Oct 12, 2022

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eugeneswalker merged commit 6983d52 into develop Oct 14, 2022

eugeneswalker deleted the balay/petsc-slepc-3.18.0 branch October 14, 2022 15:12

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petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0 #32938

petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0 #32938

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petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0 #32938

petsc,py-petsc4py,slepc,py-slepc4py: add version 3.18.0 #32938

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