Spackless by mankoff · Pull Request #1 · NASA-GISS/spack

mankoff · 2023-07-03T19:50:29Z

Spackless can be interpreted two different ways. This PR is, for now, an attempt at less spack. OS/system tools are moved out of spack. Unused packages (e.g, modele-control) are also removed.

Eventually, this may grow to no spack - the different definition of spackless.

See NASA-GISS/landice#42

At each step, the entire (remaining) spack dependency graph will be built, and then LIME run for 2 days to check that it gets past NASA-GISS/landice#25

Spack dependency graph prior to this PR is (from $SPACK/bin/spack -e $SPENV concretize -f):

$SPACK/bin/spack -e $SPENV concretize -f
==> Concretizing modele
[+]  b3sftn2  modele@master%intel@20.0.166~aux build_type=RelWithDebInfo copy=standard ~diags+everytrace~fexception~ic+icebin+model~mods+mpi+pnetcdf+tests arch=linux-sles12-x86_64 
[+]  5yvhmqt      ^cmake@3.12.4%intel@20.0.166~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-sles12-x86_64 
[+]  jue5yne          ^ncurses@6.2%intel@20.0.166~symlinks~termlib arch=linux-sles12-x86_64 
[+]  okxsecl              ^pkgconf@1.5.4%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  uc7xsp6          ^openssl@1.1.1%intel@20.0.166+systemcerts arch=linux-sles12-x86_64 
[+]  zmxapgz              ^perl@5.26.2%intel@20.0.166+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-sles12-x86_64 
[+]  5l4h3it                  ^gdbm@1.18.1%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  bqg277o                      ^readline@7.0%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  ke6zypu              ^zlib@1.2.11%intel@20.0.166+optimize+pic+shared arch=linux-sles12-x86_64 
[+]  qdgdt4q      ^everytrace@0.2.2%intel@20.0.166 build_type=RelWithDebInfo copy=standard +cxx+fortran+mpi arch=linux-sles12-x86_64 
[+]  2xi6red          ^intel-mpi@2020.0.166%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  4dsr5dv      ^icebin@0.2.1%intel@20.0.166 build_type=RelWithDebInfo copy=standard +coupler~doc+googletest+gridgen+modele+pism+python arch=linux-sles12-x86_64 
[+]  cvkbo7u          ^blitz@1.0.2%intel@20.0.166 build_type=RelWithDebInfo arch=linux-sles12-x86_64 
[+]  beblqlk              ^papi@5.6.0%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  efa2lug          ^boost@1.69.0%intel@20.0.166+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math+mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 ~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-sles12-x86_64 
[+]  xaawq2h              ^bzip2@1.0.6%intel@20.0.166+shared arch=linux-sles12-x86_64 
[+]  caytrce                  ^diffutils@3.6%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  7jo7skd          ^cgal@4.12%intel@20.0.166 build_type=Release ~core~demos~imageio+shared arch=linux-sles12-x86_64 
[+]  bv2habw              ^gmp@6.1.2%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  f5drweh                  ^autoconf@2.69%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  mggfrkm                      ^m4@1.4.18%intel@20.0.166 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-sles12-x86_64 
[+]  mp32mnc                          ^libsigsegv@2.11%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  r3jixou                  ^automake@1.16.1%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  3i5x62q                  ^libtool@2.4.6%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  pgnl3sw              ^mpfr@4.0.1%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  jebbewu          ^eigen@3.2.10%intel@20.0.166 build_type=RelWithDebInfo +fftw+metis+mpfr+scotch~suitesparse arch=linux-sles12-x86_64 
[+]  d7e54rb              ^fftw@3.3.8%intel@20.0.166+double+float~fma+long_double+mpi~openmp~pfft_patches~quad simd=avx,avx2,sse2 arch=linux-sles12-x86_64 
[+]  z6mlokq              ^metis@5.1.0%intel@20.0.166 build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1 +real64+shared arch=linux-sles12-x86_64 
[+]  cko7hy3              ^scotch@6.0.6%intel@20.0.166+compression~esmumps~int64+metis+mpi+shared arch=linux-sles12-x86_64 
[+]  aontsm3                  ^bison@3.0.5%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  5zbs7ul                      ^help2man@1.47.4%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  pbbexlk                          ^gettext@0.19.8.1%intel@20.0.166+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-sles12-x86_64 
[+]  dkojgty                              ^libxml2@2.9.8%intel@20.0.166~python arch=linux-sles12-x86_64 
[+]  pqlypfo                                  ^libiconv@1.15%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  ggtut6p                                  ^xz@5.2.4%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  sndz6j7                              ^tar@1.30%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  3pndf5i                  ^flex@2.6.1%intel@20.0.166+lex arch=linux-sles12-x86_64 
[+]  5zdscwl          ^googletest@1.8.1%intel@20.0.166 build_type=RelWithDebInfo ~gmock+pthreads+shared arch=linux-sles12-x86_64 
[+]  cj5ztki          ^ibmisc@0.2.0%intel@20.0.166+blitz+boost build_type=RelWithDebInfo copy=standard ~doc+everytrace+googletest+netcdf+proj+python+udunits2 arch=linux-sles12-x86_64 
[+]  iwz6754              ^netcdf@4.4.0%intel@20.0.166~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+pic+shared arch=linux-sles12-x86_64 
[+]  zynd7jq                  ^hdf5@1.8.18%intel@20.0.166~cxx~debug+fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-sles12-x86_64 
[+]  psi4jl3                      ^numactl@2.0.12%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  vgod2gf              ^netcdf-cxx4@4.3.0%intel@20.0.166 build_type=RelWithDebInfo arch=linux-sles12-x86_64 
[+]  bjtjj74              ^proj@5.0.1%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  r2o2cec              ^py-cython@0.23.5%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  jtxg6er                  ^python@3.5.2%intel@20.0.166+dbm~optimizations patches=123082ab3483ded78e86d7c809e98a804b3465b4683c96bd79a2fd799f572244 +pic~pythoncmd+shared~tk~ucs4 arch=linux-sles12-x86_64 
[+]  ldsspvx                      ^sqlite@3.26.0%intel@20.0.166~functions arch=linux-sles12-x86_64 
[+]  d3pqkvr              ^py-numpy@1.15.2%intel@20.0.166+blas+lapack arch=linux-sles12-x86_64 
[+]  mwxuopu                  ^intel-mkl@2020.0.166%intel@20.0.166~ilp64+shared threads=none arch=linux-sles12-x86_64 
[+]  x3yw3lq                  ^py-setuptools@40.4.3%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  puztwus              ^udunits2@2.2.24%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  nemt6wp                  ^expat@2.2.5%intel@20.0.166+libbsd arch=linux-sles12-x86_64 
[+]  3t7idzu                      ^libbsd@0.9.1%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  26ctvho          ^petsc@3.7.7%intel@20.0.166~X clanguage=C ~complex~debug+double~fortran+hdf5+hypre~int64~metis+mpi~mumps patches=22392530068e375ce8b62a1f552b43fbfd2e20822002c69dbafab4d3fa787cbb +shared~suite-sparse~superlu-dist~trilinos arch=linux-sles12-x86_64 
[+]  73pp27y              ^hypre@2.13.0%intel@20.0.166~debug~int64~internal-superlu+mpi+shared arch=linux-sles12-x86_64 
[+]  36odvrq          ^pism@icebin%intel@20.0.166 build_type=RelWithDebInfo copy=standard ~doc+everytrace+examples~extra+icebin~parallel-hdf5~parallel-netcdf3~parallel-netcdf4+proj~python+shared arch=linux-sles12-x86_64 
[+]  3o5fsty              ^gsl@2.5%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  odov7tx          ^tclap@1.2.2%intel@20.0.166 arch=linux-sles12-x86_64 
[+]  fmti6pa      ^netcdf-fortran@4.4.4%intel@20.0.166+pic arch=linux-sles12-x86_64 
[+]  cxqo2je      ^parallel-netcdf@1.11.0%intel@20.0.166~cxx+fortran+pic arch=linux-sles12-x86_64 
[+]  up6gtt5      ^pfunit@3.2.9%intel@20.0.166 build_type=RelWithDebInfo ~docs+mpi~openmp+shared~use_comm_world arch=linux-sles12-x86_64

mankoff · 2023-07-03T20:23:12Z

$SPACK/bin/spack -e $SPENV concretize -f output after above changes:

==> Concretizing modele
 -   3d3rxen  modele@master%intel@20.0.166~aux build_type=RelWithDebInfo copy=standard ~diags+everytrace~fexception~ic+icebin+model~mods+mpi+pnetcdf+tests arch=linux-sles12-x86_64 
[+]  7honbyu      ^cmake@3.23.1%intel@20.0.166~doc+ncurses+openssl+ownlibs~qt arch=linux-sles12-x86_64 
[+]  nzmt7pp      ^everytrace@0.2.2%intel@20.0.166 build_type=RelWithDebInfo copy=standard +cxx+fortran+mpi arch=linux-sles12-x86_64 
 -   qggjmmy      ^icebin@0.2.1%intel@20.0.166 build_type=RelWithDebInfo copy=standard +coupler~doc+googletest+gridgen+modele+pism+python arch=linux-sles12-x86_64 
 -   cvkbo7u          ^blitz@1.0.2%intel@20.0.166 build_type=RelWithDebInfo arch=linux-sles12-x86_64 
 -   beblqlk              ^papi@5.6.0%intel@20.0.166 arch=linux-sles12-x86_64 
 -   svstrr3          ^boost@1.69.0%intel@20.0.166+atomic+chrono~clanglibcpp cxxstd=default +date_time~debug+exception+filesystem+graph~icu+iostreams+locale+log+math+mpi+multithreaded~numpy patches=2ab6c72d03dec6a4ae20220a9dfd5c8c572c5294252155b85c6874d97c323199 ~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave arch=linux-sles12-x86_64 
 -   ce4eb25              ^bzip2@1.0.6%intel@20.0.166+shared arch=linux-sles12-x86_64 
 -   2xi6red              ^intel-mpi@2020.0.166%intel@20.0.166 arch=linux-sles12-x86_64 
 -   ke6zypu              ^zlib@1.2.11%intel@20.0.166+optimize+pic+shared arch=linux-sles12-x86_64 
 -   l7lxjzy          ^cgal@4.12%intel@20.0.166 build_type=Release ~core~demos~imageio+shared arch=linux-sles12-x86_64 
 -   bv2habw              ^gmp@6.1.2%intel@20.0.166 arch=linux-sles12-x86_64 
 -   53yav7x                  ^autoconf@2.69%intel@20.0.166 arch=linux-sles12-x86_64 
 -   hjoa6a7                  ^automake@1.16.1%intel@20.0.166 arch=linux-sles12-x86_64 
 -   3i5x62q                  ^libtool@2.4.6%intel@20.0.166 arch=linux-sles12-x86_64 
 -   mggfrkm                      ^m4@1.4.18%intel@20.0.166 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-sles12-x86_64 
 -   mp32mnc                          ^libsigsegv@2.11%intel@20.0.166 arch=linux-sles12-x86_64 
 -   pgnl3sw              ^mpfr@4.0.1%intel@20.0.166 arch=linux-sles12-x86_64 
 -   jebbewu          ^eigen@3.2.10%intel@20.0.166 build_type=RelWithDebInfo +fftw+metis+mpfr+scotch~suitesparse arch=linux-sles12-x86_64 
 -   d7e54rb              ^fftw@3.3.8%intel@20.0.166+double+float~fma+long_double+mpi~openmp~pfft_patches~quad simd=avx,avx2,sse2 arch=linux-sles12-x86_64 
 -   z6mlokq              ^metis@5.1.0%intel@20.0.166 build_type=Release ~gdb~int64 patches=4991da938c1d3a1d3dea78e49bbebecba00273f98df2a656e38b83d55b281da1 +real64+shared arch=linux-sles12-x86_64 
 -   cko7hy3              ^scotch@6.0.6%intel@20.0.166+compression~esmumps~int64+metis+mpi+shared arch=linux-sles12-x86_64 
 -   vvtvn3q                  ^bison@3.0.5%intel@20.0.166 arch=linux-sles12-x86_64 
 -   vp3hizk                  ^flex@2.6.1%intel@20.0.166+lex arch=linux-sles12-x86_64 
 -   5zdscwl          ^googletest@1.8.1%intel@20.0.166 build_type=RelWithDebInfo ~gmock+pthreads+shared arch=linux-sles12-x86_64 
 -   ioljpaf          ^ibmisc@0.2.0%intel@20.0.166+blitz+boost build_type=RelWithDebInfo copy=standard ~doc+everytrace+googletest+netcdf+proj+python+udunits2 arch=linux-sles12-x86_64 
 -   iwz6754              ^netcdf@4.4.0%intel@20.0.166~dap~hdf4 maxdims=1024 maxvars=8192 +mpi~parallel-netcdf+pic+shared arch=linux-sles12-x86_64 
 -   zynd7jq                  ^hdf5@1.8.18%intel@20.0.166~cxx~debug+fortran+hl+mpi+pic+shared~szip~threadsafe arch=linux-sles12-x86_64 
 -   psi4jl3                      ^numactl@2.0.12%intel@20.0.166 arch=linux-sles12-x86_64 
 -   vgod2gf              ^netcdf-cxx4@4.3.0%intel@20.0.166 build_type=RelWithDebInfo arch=linux-sles12-x86_64 
 -   bjtjj74              ^proj@5.0.1%intel@20.0.166 arch=linux-sles12-x86_64 
 -   6hnqtky              ^py-cython@0.23.5%intel@20.0.166 arch=linux-sles12-x86_64 
 -   3lam3ci                  ^python@3.5.2%intel@20.0.166+dbm~optimizations patches=123082ab3483ded78e86d7c809e98a804b3465b4683c96bd79a2fd799f572244 +pic~pythoncmd+shared~tk~ucs4 arch=linux-sles12-x86_64 
 -   5l4h3it                      ^gdbm@1.18.1%intel@20.0.166 arch=linux-sles12-x86_64 
 -   bqg277o                          ^readline@7.0%intel@20.0.166 arch=linux-sles12-x86_64 
 -   jue5yne                              ^ncurses@6.2%intel@20.0.166~symlinks~termlib arch=linux-sles12-x86_64 
 -   okxsecl                                  ^pkgconf@1.5.4%intel@20.0.166 arch=linux-sles12-x86_64 
 -   uc7xsp6                      ^openssl@1.1.1%intel@20.0.166+systemcerts arch=linux-sles12-x86_64 
 -   rfy575j                          ^perl@5.26.2%intel@20.0.166+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-sles12-x86_64 
 -   ldsspvx                      ^sqlite@3.26.0%intel@20.0.166~functions arch=linux-sles12-x86_64 
 -   sg23jjy              ^py-numpy@1.15.2%intel@20.0.166+blas+lapack arch=linux-sles12-x86_64 
 -   mwxuopu                  ^intel-mkl@2020.0.166%intel@20.0.166~ilp64+shared threads=none arch=linux-sles12-x86_64 
 -   wzelhfa                  ^py-setuptools@40.4.3%intel@20.0.166 arch=linux-sles12-x86_64 
 -   puztwus              ^udunits2@2.2.24%intel@20.0.166 arch=linux-sles12-x86_64 
 -   nemt6wp                  ^expat@2.2.5%intel@20.0.166+libbsd arch=linux-sles12-x86_64 
 -   3t7idzu                      ^libbsd@0.9.1%intel@20.0.166 arch=linux-sles12-x86_64 
 -   d2lmna7          ^petsc@3.5.3%intel@20.0.166~X clanguage=C ~complex~debug+double~fortran+hdf5+hypre~int64~metis+mpi~mumps+shared~suite-sparse~superlu-dist~trilinos arch=linux-sles12-x86_64 
 -   73pp27y              ^hypre@2.13.0%intel@20.0.166~debug~int64~internal-superlu+mpi+shared arch=linux-sles12-x86_64 
 -   z42rxj5          ^pism@icebin%intel@20.0.166 build_type=RelWithDebInfo copy=standard ~doc+everytrace+examples~extra+icebin~parallel-hdf5~parallel-netcdf3~parallel-netcdf4+proj~python+shared arch=linux-sles12-x86_64 
 -   3o5fsty              ^gsl@2.5%intel@20.0.166 arch=linux-sles12-x86_64 
 -   odov7tx          ^tclap@1.2.2%intel@20.0.166 arch=linux-sles12-x86_64 
 -   fmti6pa      ^netcdf-fortran@4.4.4%intel@20.0.166+pic arch=linux-sles12-x86_64 
 -   cxqo2je      ^parallel-netcdf@1.11.0%intel@20.0.166~cxx+fortran+pic arch=linux-sles12-x86_64 
 -   yikzrfe      ^pfunit@3.2.9%intel@20.0.166 build_type=RelWithDebInfo ~docs+mpi~openmp+shared~use_comm_world arch=linux-sles12-x86_64

mankoff added 5 commits July 3, 2023 11:21

Don't build modele-control, modele-utils, py-pillow, nco, or ncview

fb4a561

Use system cmake

946f62d

Use manually built everytrace

02c1541

Use system tools: autmake, autoconf, bison,flex, bzip2 & perl

765323a

Correct cmake path

8fcc992

mankoff mentioned this pull request Jul 3, 2023

spackless: fftw #2

Closed

mankoff marked this pull request as draft July 3, 2023 21:44

mankoff self-assigned this Jul 3, 2023

Clean spackless env. Otherwise link failure from other packages

02cd535

mankoff mentioned this pull request Jul 7, 2023

Spackless #3

Open

mankoff added 2 commits July 8, 2023 18:13

Work in new YAML file; System tools now moved to mamba env

20b7922

cython, python, and udunits

1eb26cb

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Spackless#1

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mankoff wants to merge 8 commits intoefischer/giss2from
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