Spack¶

#!/bin/bash
rm -rf $HOME/spack-workspace/perlmutter/modules
rm -rf $HOME/spack-workspace/perlmutter/software
module load e4s/23.05
source $SPACK_ROOT/bin/spack-setup.sh
spack env status
spack spec zlib
rm -rf $HOME/e4s-demo
spack env create -d $HOME/e4s-demo spack.yaml
spack env activate -d $HOME/e4s-demo
ls -l $HOME/e4s-demo
spack config list
echo  $SPACK_SYSTEM_CONFIG_PATH
ls -l $SPACK_SYSTEM_CONFIG_PATH
cat $SPACK_ROOT/etc/spack/config.yaml
spack clean -m
spack install
spack location -i papi
cat $SPACK_ROOT/etc/spack/modules.yaml
spack module tcl refresh --delete-tree -y
spack module tcl find --full-path papi
module use $HOME/spack-workspace/perlmutter/modules/$(spack arch)
ml -t av papi

# This is a Spack Environment file.
#
# It describes a set of packages to be installed, along with
# configuration settings.
spack:
  # add package specs to the `specs` list
  specs:
  - papi
  view: true

elvis@login40> bash workflow.sh
_______________________________________________________________________________________________________
 The Extreme-Scale Scientific Software Stack (E4S) is accessible via the Spack package manager.

 In order to access the production stack, you will need to load a spack environment. Here are some tips to get started:


 'spack env list' - List all Spack environments
 'spack env activate gcc' - Activate the "gcc" Spack environment
 'spack env status' - Display the active Spack environment
 'spack load amrex' - Load the "amrex" Spack package into your user environment

 For additional support, please refer to the following references:

   NERSC E4S Documentation: https://docs.nersc.gov/applications/e4s/
   E4S Documentation: https://e4s.readthedocs.io
   Spack Documentation: https://spack.readthedocs.io/en/latest/
   Spack Slack: https://spackpm.slack.com

______________________________________________________________________________________________________

/opt/cray/pe/lmod/lmod/init/bash: line 197: unalias: spacktivate: not found
Creating python virtual environment in /global/homes/e/elvis/.spack-pyenv
WARNING: You are using pip version 20.0.2; however, version 21.3.1 is available.
You should consider upgrading via the '/global/homes/e/elvis/.spack-pyenv/bin/python3 -m pip install --upgrade pip' command.
Package    Version
---------- -------
cffi       1.15.1
clingo     5.6.2
pip        20.0.2
pycparser  2.21
setuptools 44.1.1
WARNING: You are using pip version 20.0.2; however, version 21.3.1 is available.
You should consider upgrading via the '/global/homes/e/elvis/.spack-pyenv/bin/python3 -m pip install --upgrade pip' command.
Your python interpreter used by spack is /global/homes/e/elvis/.spack-pyenv/bin/python
==> No active environment
Input spec
--------------------------------
zlib

Concretized
--------------------------------
zlib@1.2.13%gcc@11.2.0+optimize+pic+shared build_system=makefile arch=linux-sles15-zen3

==> Created environment in /global/homes/e/elvis/e4s-demo
==> You can activate this environment with:
==>   spack env activate /global/homes/e/elvis/e4s-demo
total 1
-rw-rw-r-- 1 elvis elvis 205 Sep  8 12:44 spack.yaml
compilers concretizer mirrors repos packages modules config upstreams bootstrap ci cdash
/global/common/software/spackecp/perlmutter/spack_settings
total 10
-rw-rw-r-- 1 e4s spackecp 3108 Aug 11 12:31 compilers.yaml
-rw-rw-r-- 1 e4s spackecp 4931 Aug 11 12:31 packages.yaml
config:
  build_stage: $HOME/spack-workspace/perlmutter/build_stage
  misc_cache: $HOME/spack-workspace/perlmutter/misc_cache
  install_tree:
    root: $HOME/spack-workspace/perlmutter/software
  source_cache: $HOME/.spack/cache

==> Removing cached information on repositories
==> Concretized papi
 -   frkekrt  papi@6.0.0.1%gcc@11.2.0~cuda+example~infiniband~lmsensors~nvml~powercap~rapl~rocm~rocm_smi~sde+shared~static_tools build_system=autotools arch=linux-sles15-zen3

==> Installing papi-6.0.0.1-frkekrtdhzrwqsr2nvuntrddpju7etpt
==> Fetching file:///global/common/software/spackecp/mirrors/perlmutter-e4s-23.05/build_cache/linux-sles15-zen3-gcc-11.2.0-papi-6.0.0.1-frkekrtdhzrwqsr2nvuntrddpju7etpt.spec.json.sig
gpg: Signature made Mon 31 Jul 2023 03:05:53 PM PDT
gpg:                using RSA key B5FDE18F615783AF078ED29C3BD6B0E9935AEB8F
gpg: Good signature from "GPG Key - e4s <shahzebsiddiqui@lbl.gov>" [ultimate]
==> Fetching file:///global/common/software/spackecp/mirrors/perlmutter-e4s-23.05/build_cache/linux-sles15-zen3/gcc-11.2.0/papi-6.0.0.1/linux-sles15-zen3-gcc-11.2.0-papi-6.0.0.1-frkekrtdhzrwqsr2nvuntrddpju7etpt.spack
==> Extracting papi-6.0.0.1-frkekrtdhzrwqsr2nvuntrddpju7etpt from binary cache
==> papi: Successfully installed papi-6.0.0.1-frkekrtdhzrwqsr2nvuntrddpju7etpt
  Search: 0.00s.  Fetch: 1.02s.  Install: 1.33s.  Total: 2.36s
[+] /global/homes/s/elvis/spack-workspace/perlmutter/software/linux-sles15-zen3/gcc-11.2.0/papi-6.0.0.1-frkekrtdhzrwqsr2nvuntrddpju7etpt
==> Updating view at /global/homes/e/elvis/e4s-demo/.spack-env/view
==> Warning: detected custom TCL modules configuration in /global/common/software/spackecp/perlmutter/e4s-23.05/89639/spack/etc/spack/modules.yaml, while TCL module file generation for the default module set is disabled. In Spack v0.20 module file generation has been disabled by default. To enable it run:

    $ spack config add 'modules:default:enable:[tcl]'

/global/homes/e/elvis/spack-workspace/perlmutter/software/linux-sles15-zen3/gcc-11.2.0/papi-6.0.0.1-frkekrtdhzrwqsr2nvuntrddpju7etpt
modules:
  default:
    roots:
      tcl: $HOME/spack-workspace/perlmutter/modules
    tcl:
      naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
      all:
        conflict:
        - '{name}'
        environment:
          set:
            '{name}_ROOT': '{prefix}'
==> Regenerating tcl module files
/global/homes/e/elvis/spack-workspace/perlmutter/modules/linux-sles15-zen3/papi/6.0.0.1-gcc-11.2.0-frkekrt
/global/homes/e/elvis/spack-workspace/perlmutter/modules/linux-sles15-zen3:
papi/6.0.0.1-gcc-11.2.0-frkekrt
/opt/cray/pe/lmod/modulefiles/core:
papi/6.0.0.16
papi/7.0.0.1

adiak@0.2.1%gcc@9.3.0: ~ipo+mpi+shared build_type=RelWithDebInfo
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adlbx@1.0.0%gcc@9.3.0:
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aml@0.1.0%gcc@9.3.0:
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amrex@21.11%gcc@9.3.0: ~amrdata~cuda~eb~fortran~hdf5~hypre~ipo+linear_solvers+mpi~openmp~particles~petsc~pic~plotfile_tools~rocm~shared~sundials amdgpu_target=none build_type=RelWithDebInfo cuda_arch=none dimensions=3 precision=double
amrex@21.11%gcc@9.3.0: ~amrdata+cuda~eb~fortran~hdf5~hypre~ipo+linear_solvers+mpi~openmp~particles~petsc~pic~plotfile_tools~rocm~shared~sundials amdgpu_target=none build_type=RelWithDebInfo cuda_arch=70 dimensions=3 precision=double
amrex@21.11%gcc@9.3.0: ~amrdata+cuda~eb~fortran~hdf5~hypre~ipo+linear_solvers+mpi~openmp~particles~petsc~pic~plotfile_tools~rocm~shared~sundials amdgpu_target=none build_type=RelWithDebInfo cuda_arch=80 dimensions=3 precision=double
ant@1.10.7%gcc@9.3.0:
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argobots@1.1%gcc@9.3.0: ~affinity~debug+perf~stackunwind~tool~valgrind stackguard=none
arpack-ng@3.8.0%gcc@9.3.0: +mpi+shared
ascent@0.7.1%gcc@9.3.0: ~adios~adios2~babelflow~cuda~doc~dray~fides+fortran~ipo~mfem+mpi+openmp~python+serial+shared+test+vtkh build_type=RelWithDebInfo cuda_arch=none
asio@1.20.0%gcc@9.3.0: ~boost_coroutine~boost_regex~separate_compilation cxxstd=17
assimp@5.0.1%gcc@9.3.0: ~ipo+shared build_type=RelWithDebInfo
autoconf@2.69%gcc@9.3.0:  patches=35c449281546376449766f92d49fc121ca50e330e60fefcfc9be2af3253082c2,7793209b33013dc0f81208718c68440c5aae80e7a1c4b8d336e382525af791a7,a49dd5bac3b62daa0ff688ab4d508d71dbd2f4f8d7e2a02321926346161bf3ee
autoconf-archive@2019.01.06%gcc@9.3.0:
automake@1.16.3%gcc@9.3.0:
axl@0.3.0%gcc@9.3.0: +bbapi~bbapi_fallback~dw~ipo+shared async_api=daemon build_type=RelWithDebInfo
axl@0.5.0%gcc@9.3.0: +bbapi~bbapi_fallback~dw~ipo+shared async_api=daemon build_type=RelWithDebInfo
axom@0.5.0%gcc@9.3.0: +cpp14~cuda~debug~devtools+examples+fortran+hdf5~ipo+lua~mfem+mpi+openmp~python+raja~scr+shared+tools+umpire build_type=RelWithDebInfo cuda_arch=none
berkeley-db@18.1.40%gcc@9.3.0: +cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522
berkeley-db@18.1.40%gcc@11.1.0: +cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522
binutils@2.33.1%gcc@9.3.0: ~gas+gold+headers~interwork+ld+libiberty~lto~nls+plugins libs=shared,static
binutils@2.36.1%gcc@9.3.0: ~gas+gold+headers~interwork+ld+libiberty~lto~nls+plugins libs=shared,static patches=a51b7bf4607645235be01683a3e2deb3a87d767cc124ea4ef6febf9f32abf4a7
binutils@2.36.1%gcc@11.1.0: ~gas+gold+headers~interwork+ld+libiberty~lto~nls+plugins libs=shared,static patches=a51b7bf4607645235be01683a3e2deb3a87d767cc124ea4ef6febf9f32abf4a7
bison@3.8.2%gcc@9.3.0:
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blaspp@2021.04.01%gcc@9.3.0: ~cuda~ipo+openmp~rocm+shared amdgpu_target=none build_type=RelWithDebInfo cuda_arch=none
blaspp@2021.04.01%gcc@9.3.0: +cuda~ipo+openmp~rocm+shared amdgpu_target=none build_type=RelWithDebInfo cuda_arch=none
blt@0.4.1%gcc@9.3.0:
bmi@main%gcc@9.3.0:
bolt@2.0%gcc@9.3.0: ~ipo build_type=RelWithDebInfo
boost@1.77.0%gcc@9.3.0: +atomic+chrono~clanglibcpp~container~context~coroutine+date_time~debug+exception~fiber+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave cxxstd=17 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=global
boost@1.77.0%gcc@9.3.0: +atomic+chrono~clanglibcpp~container~context~coroutine+date_time~debug+exception~fiber+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy~pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave cxxstd=98 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=global
butterflypack@2.0.0%gcc@9.3.0: ~ipo+shared build_type=RelWithDebInfo
bzip2@1.0.8%gcc@9.3.0: ~debug~pic+shared
bzip2@1.0.8%gcc@11.1.0: ~debug~pic+shared
c-blosc@1.21.0%gcc@9.3.0: +avx2~ipo build_type=RelWithDebInfo
cabana@0.4.0%gcc@9.3.0: ~arborx~cuda~heffte~hypre~ipo+mpi~openmp~pthread~rocm+serial+shared~sycl build_type=RelWithDebInfo
caliper@2.7.0%gcc@9.3.0: +adiak~cuda~fortran+gotcha~ipo+libdw~libpfm+libunwind+mpi+papi+sampler+shared~sosflow build_type=RelWithDebInfo cuda_arch=none
caliper@2.7.0%gcc@9.3.0: +adiak+cuda~fortran+gotcha~ipo+libdw~libpfm+libunwind+mpi+papi+sampler+shared~sosflow build_type=RelWithDebInfo cuda_arch=70
caliper@2.7.0%gcc@9.3.0: +adiak+cuda~fortran+gotcha~ipo+libdw~libpfm+libunwind+mpi+papi+sampler+shared~sosflow build_type=RelWithDebInfo cuda_arch=80
camp@0.1.0%gcc@9.3.0: ~cuda~ipo~rocm~tests amdgpu_target=none build_type=RelWithDebInfo cuda_arch=none
camp@0.2.2%gcc@9.3.0: ~cuda~ipo~rocm~tests amdgpu_target=none build_type=RelWithDebInfo cuda_arch=none
camp@0.2.2%gcc@9.3.0: +cuda~ipo~rocm~tests amdgpu_target=none build_type=RelWithDebInfo cuda_arch=70
camp@0.2.2%gcc@9.3.0: +cuda~ipo~rocm~tests amdgpu_target=none build_type=RelWithDebInfo cuda_arch=80
catalyst@5.6.0%gcc@9.3.0: ~essentials~extras~ipo+osmesa~python~python3+rendering build_type=RelWithDebInfo
chai@2.4.0%gcc@9.3.0: ~benchmarks~cuda~enable_pick+examples~ipo~openmp~raja~rocm+shared~tests amdgpu_target=none build_type=RelWithDebInfo cuda_arch=none
chai@2.4.0%gcc@9.3.0: ~benchmarks+cuda~enable_pick+examples~ipo~openmp~raja~rocm+shared~tests amdgpu_target=none build_type=RelWithDebInfo cuda_arch=70
chai@2.4.0%gcc@9.3.0: ~benchmarks+cuda~enable_pick+examples~ipo~openmp~raja~rocm+shared~tests amdgpu_target=none build_type=RelWithDebInfo cuda_arch=80
charliecloud@0.25%gcc@9.3.0: ~docs
cinch@master%gcc@9.3.0:
cmake@3.21.4%gcc@9.3.0: ~doc+ncurses+openssl+ownlibs~qt build_type=Release
cmake@3.21.4%gcc@11.1.0: ~doc+ncurses+openssl+ownlibs~qt build_type=Release
conduit@0.7.2%gcc@9.3.0: ~adios~doc~doxygen+fortran+hdf5+hdf5_compat~ipo+mpi~parmetis~python+shared~silo+test~zfp build_type=RelWithDebInfo patches=89d1829ad52f503f6179e43efddf998c239a95c14ca1f248463a3f61ad7d5cf7
conduit@0.7.2%gcc@9.3.0: ~adios~doc~doxygen+fortran+hdf5+hdf5_compat~ipo+mpi~parmetis~python+shared~silo+test~zfp build_type=RelWithDebInfo patches=89d1829ad52f503f6179e43efddf998c239a95c14ca1f248463a3f61ad7d5cf7
cub@1.12.0-rc0%gcc@9.3.0:
cuda@11.4.2%gcc@9.3.0: ~dev
cuda@11.4.2%gcc@11.1.0: ~dev
curl@7.79.0%gcc@9.3.0: ~gssapi~ldap~libidn2~librtmp~libssh~libssh2~nghttp2 tls=openssl
czmq@4.1.1%gcc@9.3.0:
darshan-runtime@3.3.1%gcc@9.3.0: ~apmpi~apmpi_sync~apxc~hdf5+mpi scheduler=NONE
darshan-util@3.3.1%gcc@9.3.0: ~apmpi~apxc~bzip2
datatransferkit@3.1-rc3%gcc@9.3.0: ~external-arborx~ipo~openmp+serial+shared build_type=RelWithDebInfo
diffutils@3.8%gcc@9.3.0:
diffutils@3.8%gcc@11.1.0:
double-conversion@3.1.5%gcc@9.3.0: ~ipo build_type=RelWithDebInfo
doxygen@1.8.20%gcc@9.3.0: ~graphviz~ipo~mscgen build_type=RelWithDebInfo
dtcmp@1.1.3%gcc@9.3.0: +shared
dyninst@11.0.1%gcc@9.3.0: ~ipo+openmp~stat_dysect~static build_type=RelWithDebInfo
eigen@3.4.0%gcc@9.3.0: ~ipo build_type=RelWithDebInfo
elfutils@0.185%gcc@9.3.0: +bzip2~debuginfod~nls+xz patches=d786d49c28d7f0c8fc27bab39ca8714e5f4d128c7f09bb18533a8ec99b38dbf8
er@0.1.0%gcc@9.3.0: ~ipo+shared build_type=RelWithDebInfo
exaworks@0.1.0%gcc@9.3.0:
exmcutils@0.6.0%gcc@9.3.0:
expat@2.4.1%gcc@9.3.0: +libbsd
expat@2.4.1%gcc@11.1.0: +libbsd
faodel@1.2108.1%gcc@9.3.0: ~hdf5~ipo+mpi+shared+tcmalloc build_type=RelWithDebInfo logging=stdout network=nnti serializer=xdr
fftw@3.3.10%gcc@9.3.0: +mpi+openmp~pfft_patches precision=double,float
findutils@4.8.0%gcc@9.3.0:
flecsi@1.4.2%gcc@9.3.0: ~coverage~cuda~debug_backend~disable_metis~doc~doxygen+external_cinch~flecstan~flog~graphviz+hdf5~ipo~kokkos~openmp+shared~tutorial~unit_tests backend=mpi build_type=RelWithDebInfo caliper_detail=none cuda_arch=none
flecsi@2.1.0%gcc@9.3.0: ~coverage+cuda~debug_backend~disable_metis~doc~doxygen~external_cinch~flecstan~flog~graphviz+hdf5~ipo~kokkos~openmp+shared~tutorial~unit_tests backend=mpi build_type=RelWithDebInfo caliper_detail=none cuda_arch=70
flecsi@2.1.0%gcc@9.3.0: ~coverage+cuda~debug_backend~disable_metis~doc~doxygen~external_cinch~flecstan~flog~graphviz+hdf5~ipo~kokkos~openmp+shared~tutorial~unit_tests backend=mpi build_type=RelWithDebInfo caliper_detail=none cuda_arch=80
flex@2.6.3%gcc@9.3.0: +lex~nls
flit@2.1.0%gcc@9.3.0:
flux-core@0.30.0%gcc@9.3.0: ~cuda~docs patches=0329f4b38b5ce4e1a3dee212cb93ce40388d1bde47c82a7a8e73bc7c38274c81
flux-sched@0.19.0%gcc@9.3.0: ~cuda
fortrilinos@2.0.0%gcc@9.3.0: +hl~ipo+shared build_type=RelWithDebInfo
freetype@2.11.0%gcc@9.3.0:
gasnet@2021.9.0%gcc@9.3.0: ~debug conduits=smp
gawk@5.1.0%gcc@9.3.0:
gdbm@1.19%gcc@9.3.0:
gdbm@1.19%gcc@11.1.0:
gettext@0.21%gcc@9.3.0: +bzip2+curses+git~libunistring+libxml2+tar+xz
gettext@0.21%gcc@11.1.0: +bzip2+curses+git~libunistring+libxml2+tar+xz
ginkgo@1.4.0%gcc@9.3.0: ~cuda~develtools~full_optimizations~hwloc~ipo+openmp+rocm+shared amdgpu_target=gfx908 build_type=Release cuda_arch=none patches=43e571a49ea774793d89d145571c95ae7cdf991f5220d8fe84db217a3c613a32
ginkgo@1.4.0%gcc@9.3.0: ~cuda~develtools~full_optimizations~hwloc~ipo+openmp~rocm+shared amdgpu_target=none build_type=Release cuda_arch=none patches=43e571a49ea774793d89d145571c95ae7cdf991f5220d8fe84db217a3c613a32
ginkgo@1.4.0%gcc@9.3.0: +cuda~develtools~full_optimizations~hwloc~ipo+openmp~rocm+shared amdgpu_target=none build_type=Release cuda_arch=70 patches=43e571a49ea774793d89d145571c95ae7cdf991f5220d8fe84db217a3c613a32
ginkgo@1.4.0%gcc@9.3.0: +cuda~develtools~full_optimizations~hwloc~ipo+openmp~rocm+shared amdgpu_target=none build_type=Release cuda_arch=80 patches=43e571a49ea774793d89d145571c95ae7cdf991f5220d8fe84db217a3c613a32
git@2.31.1%gcc@9.3.0: +man+nls+perl~svn~tcltk
glib@2.70.0%gcc@9.3.0: ~libmount patches=8547954e50d0a720fa9794b84c31569df6a7419319b95ac9de0ed861d8969ffd tracing=none
globalarrays@5.8%gcc@9.3.0: ~scalapack armci=mpi-ts
glproto@1.4.17%gcc@9.3.0:
gmake@4.3%gcc@9.3.0: ~guile+nls
gmp@6.2.1%gcc@9.3.0:
googletest@1.8.1%gcc@9.3.0: +gmock~ipo+pthreads+shared build_type=RelWithDebInfo
gotcha@1.0.3%gcc@9.3.0: ~ipo~test build_type=RelWithDebInfo
gperftools@2.9.1%gcc@9.3.0: +debugalloc~dynamic_sized_delete_support+libunwind~sized_delete
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