Installing your Spack environment¶
Once your environment is activated, you can follow a similar workflow as we saw in the "Putting it all together" section of the Spack Custom Scopes tutorial.
However, things are slightly different in the context of a Spack environment.
The most important thing is that we no longer need to specify a directory
containing configuration files using -C; the active Spack environment now
knows all the configuration options we have set in our
spack.yaml file already.
Spack find¶
Much as we did when installing personal variants in a custom scope, let's see
what packages are available (remember no need for -C):
spack find output
[spack-only] $ spack find -x -p
==> In environment /data/scratch/abc123/spack-environments/spack-only
==> 3 root specs
- gromacs +plumed - lammps +kokkos - nano@6.3
==> 0 installed packages
Unlike a custom configuration scope, existing upstream and personal packages
won’t be listed. Only those packages "installed" inside the Spack environment
("root specs") are listed. At the moment, they aren’t actually installed,
hence why it says "==> 0 installed packages".
Speccing the environment¶
Always run a spec command before install!
You should always check what is about to be installed using the spec
command as detailed below and then move onto the install command.
Let's see what happens when we run a spec command in the activated
environment:
spack spec output (click to expand)
[spack-only] $ spack spec
Input spec
--------------------------------
- nano@6.3
Concretized
--------------------------------
[+] nano@6.3%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^gcc-runtime@12.2.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[e] ^glibc@2.34%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^gmake@4.4.1%gcc@11.4.1~guile build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^gcc-runtime@11.4.1%gcc@11.4.1 build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^ncurses@6.5%gcc@11.4.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-rocky9-x86_64_v4
[^] ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
Input spec
--------------------------------
- lammps+kokkos
- ^openmpi
Concretized
--------------------------------
- lammps@20230802.3%gcc@12.2.0~adios~amoeba~asphere~atc~awpmd~bocs~body~bpm~brownian~cg-dna~cg-spica~class2~colloid~colvars~compress~coreshell~cuda~cuda_mps~dielectric~diffraction~dipole~dpd-basic~dpd-meso~dpd-react~dpd-smooth~drude~eff~electrode~extra-compute~extra-dump~extra-fix~extra-molecule~extra-pair~fep~ffmpeg~granular~h5md~intel~interlayer~ipo~jpeg~kim+kokkos+kspace~latboltz~lepton+lib~machdyn~manifold+manybody~mc~meam~mesont~mgpt~misc~ml-hdnnp~ml-iap~ml-pod~ml-rann~ml-snap~mofff+molecule~molfile+mpi~netcdf~opencl+openmp~openmp-package~opt~orient~peri~phonon~plugin~plumed~png~poems~ptm~python~qeq~qtb~reaction~reaxff~replica+rigid~rocm~shock~smtbq~sph~spin~srd~tally~uef~voronoi~vtk~yaff build_system=cmake build_type=Release fftw_precision=double generator=make lammps_sizes=smallbig arch=linux-rocky9-x86_64_v4
[^] ^cmake@3.27.9%gcc@12.2.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rocky9-x86_64_v4
[^] ^curl@8.7.1%gcc@12.2.0~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-rocky9-x86_64_v4
[^] ^nghttp2@1.57.0%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^diffutils@3.10%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^openssl@3.3.0%gcc@12.2.0~docs+shared build_system=generic certs=mozilla arch=linux-rocky9-x86_64_v4
[^] ^ca-certificates-mozilla@2023-05-30%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^perl@5.38.0%gcc@11.4.1+cpanm+opcode+open+shared+threads build_system=generic patches=714e4d1 arch=linux-rocky9-x86_64_v4
[^] ^berkeley-db@18.1.40%gcc@11.4.1+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-rocky9-x86_64_v4
[^] ^bzip2@1.0.8%gcc@11.4.1~debug~pic+shared build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^gdbm@1.23%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^readline@8.2%gcc@11.4.1 build_system=autotools patches=bbf97f1 arch=linux-rocky9-x86_64_v4
[^] ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^ncurses@6.5%gcc@11.4.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-rocky9-x86_64_v4
[^] ^zlib-ng@2.1.6%gcc@11.4.1+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^fftw@3.3.10%gcc@12.2.0+mpi+openmp~pfft_patches+shared build_system=autotools precision=double,float arch=linux-rocky9-x86_64_v4
[^] ^gcc-runtime@12.2.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[e] ^glibc@2.34%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^gmake@4.4.1%gcc@11.4.1~guile build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^gcc-runtime@11.4.1%gcc@11.4.1 build_system=generic arch=linux-rocky9-x86_64_v4
[+] ^kokkos@4.3.00%gcc@12.2.0~aggressive_vectorization~compiler_warnings~cuda~debug~debug_bounds_check~debug_dualview_modify_check~deprecated_code~examples~hpx~hpx_async_dispatch~hwloc~ipo~memkind~numactl~openmp~openmptarget~pic~rocm+serial+shared~sycl~tests~threads~tuning~wrapper build_system=cmake build_type=Release cxxstd=17 generator=make intel_gpu_arch=none arch=linux-rocky9-x86_64_v4
[e] ^openmpi@5.0.3%gcc@12.2.0~atomics~cuda+gpfs~internal-hwloc~internal-libevent~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix~romio+rsh~static+vt+wrapper-rpath build_system=autotools fabrics=none romio-filesystem=none schedulers=none arch=linux-rocky9-x86_64_v4
Input spec
--------------------------------
- gromacs+plumed
- ^fftw+openmp
- ^openmpi
Concretized
--------------------------------
[+] gromacs@2023%gcc@12.2.0~cp2k~cuda~cycle_subcounters~double+gmxapi+hwloc~intel_provided_gcc~ipo~mdrun_only+mpi+nblib~nosuffix~opencl+openmp+plumed~relaxed_double_precision+shared~sycl build_system=cmake build_type=Release generator=make openmp_max_threads=none arch=linux-rocky9-x86_64_v4
[^] ^cmake@3.27.9%gcc@12.2.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rocky9-x86_64_v4
[^] ^curl@8.7.1%gcc@12.2.0~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-rocky9-x86_64_v4
[^] ^nghttp2@1.57.0%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^openssl@3.3.0%gcc@12.2.0~docs+shared build_system=generic certs=mozilla arch=linux-rocky9-x86_64_v4
[^] ^ca-certificates-mozilla@2023-05-30%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^ncurses@6.5%gcc@11.4.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-rocky9-x86_64_v4
[^] ^zlib-ng@2.1.6%gcc@11.4.1+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^fftw@3.3.10%gcc@12.2.0+mpi+openmp~pfft_patches+shared build_system=autotools precision=double,float arch=linux-rocky9-x86_64_v4
[^] ^gcc-runtime@12.2.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[e] ^glibc@2.34%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^gmake@4.4.1%gcc@11.4.1~guile build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^gcc-runtime@11.4.1%gcc@11.4.1 build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^hwloc@2.9.1%gcc@12.2.0~cairo~cuda~gl~libudev+libxml2~netloc~nvml~oneapi-level-zero~opencl+pci~rocm build_system=autotools libs=shared,static arch=linux-rocky9-x86_64_v4
[^] ^libpciaccess@0.17%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^util-macros@1.19.3%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libxml2@2.10.3%gcc@11.4.1+pic~python+shared build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^xz@5.4.6%gcc@11.4.1~pic build_system=autotools libs=shared,static arch=linux-rocky9-x86_64_v4
[^] ^openblas@0.3.26%gcc@12.2.0~bignuma~consistent_fpcsr+dynamic_dispatch+fortran~ilp64+locking+pic+shared build_system=makefile symbol_suffix=none threads=none arch=linux-rocky9-x86_64_v4
[^] ^perl@5.38.0%gcc@11.4.1+cpanm+opcode+open+shared+threads build_system=generic patches=714e4d1 arch=linux-rocky9-x86_64_v4
[^] ^berkeley-db@18.1.40%gcc@11.4.1+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-rocky9-x86_64_v4
[^] ^bzip2@1.0.8%gcc@11.4.1~debug~pic+shared build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^gdbm@1.23%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^readline@8.2%gcc@11.4.1 build_system=autotools patches=bbf97f1 arch=linux-rocky9-x86_64_v4
[e] ^openmpi@5.0.3%gcc@12.2.0~atomics~cuda+gpfs~internal-hwloc~internal-libevent~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix~romio+rsh~static+vt+wrapper-rpath build_system=autotools fabrics=none romio-filesystem=none schedulers=none arch=linux-rocky9-x86_64_v4
[^] ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^plumed@2.9.0%gcc@12.2.0+gsl+mpi+shared arrayfire=none build_system=autotools optional_modules=all arch=linux-rocky9-x86_64_v4
[^] ^autoconf@2.72%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^automake@1.16.5%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^gsl@2.7.1%gcc@12.2.0~external-cblas+pic+shared build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libtool@2.4.7%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^findutils@4.9.0%gcc@11.4.1 build_system=autotools patches=440b954 arch=linux-rocky9-x86_64_v4
[^] ^m4@1.4.19%gcc@11.4.1+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-rocky9-x86_64_v4
[^] ^diffutils@3.10%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libsigsegv@2.14%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^py-cython@3.0.8%gcc@12.2.0 build_system=python_pip arch=linux-rocky9-x86_64_v4
[^] ^py-pip@23.1.2%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^py-setuptools@69.2.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^py-wheel@0.41.2%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^python@3.11.7%gcc@12.2.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rocky9-x86_64_v4
[^] ^expat@2.6.2%gcc@12.2.0+libbsd build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libbsd@0.12.1%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libmd@1.0.4%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^gettext@0.22.5%gcc@11.4.1+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^tar@1.34%gcc@11.4.1 build_system=autotools zip=pigz arch=linux-rocky9-x86_64_v4
[^] ^pigz@2.8%gcc@11.4.1 build_system=makefile arch=linux-rocky9-x86_64_v4
[^] ^zstd@1.5.6%gcc@11.4.1+programs build_system=makefile compression=none libs=shared,static arch=linux-rocky9-x86_64_v4
[^] ^libffi@3.4.6%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libxcrypt@4.4.35%gcc@12.2.0~obsolete_api build_system=autotools patches=4885da3 arch=linux-rocky9-x86_64_v4
[^] ^sqlite@3.43.2%gcc@12.2.0+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^util-linux-uuid@2.38.1%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^python-venv@1.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
This should be very familiar from when you ran a spec command for each of
these packages in the Custom Scopes tutorial previously, but a recap of the
symbols:
-means that the listed application/library is not installed anywhere at all, neither in upstream or personally[^]means that the listed application/library is already installed in upstream and will be used to avoid re-installation[e]means that the listed application/library is marked as external.glibcis marked as external, as is Open MPI as it is defined as such in thepackagessection of ourspack.yamlfile (and also explained in thepackages.yamldocumentation) of the Custom Scopes tutorial
You'll notice then, that almost everything is already in upstream or
personally installed already, except lammps +kokkos ^openmpi, which is going
to be compiled and installed again. This is almost certainly because the
dependency chain is more complex to resolve when you want both
gromacs +plumed ^openmpi ^fftw+openmp and lammps +kokkos ^openmpi in the
same environment.
Whilst it may seem annoying, Spack is actually trying to
improve consistency here, and ensure that all the applications in the same
environment use a consistent dependency chain. This can become very important
when you list several application variants in the specs of your spack.yaml
file and they all depend on a key dependency such as Python or Perl - Spack will
try to make sure as much as possible that the versions of these key dependencies
are consistent across all specs and recompile anything as required.
Installing the environment¶
Once you are happy with the output of the spack spec command above, you can
move onto a spack install command. Remember, we still don't need -C, but you
should still add -j $NSLOTS to your command to ensure that you match the
installation process threading to your qlogin core request:
spack install output (click to expand)
[spack-only] $ spack install -j $NSLOTS
==> Concretized nano@6.3
[+] m7n4nhp nano@6.3%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] w77gg5r ^gcc-runtime@12.2.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[e] xri56vc ^glibc@2.34%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] xchit5a ^gmake@4.4.1%gcc@11.4.1~guile build_system=generic arch=linux-rocky9-x86_64_v4
[^] llid4hw ^gcc-runtime@11.4.1%gcc@11.4.1 build_system=generic arch=linux-rocky9-x86_64_v4
[^] 4n2uzha ^ncurses@6.5%gcc@11.4.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-rocky9-x86_64_v4
[^] 7wg26bz ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
==> Concretized lammps+kokkos ^openmpi
- yfsd7tl lammps@20230802.3%gcc@12.2.0~adios~amoeba~asphere~atc~awpmd~bocs~body~bpm~brownian~cg-dna~cg-spica~class2~colloid~colvars~compress~coreshell~cuda~cuda_mps~dielectric~diffraction~dipole~dpd-basic~dpd-meso~dpd-react~dpd-smooth~drude~eff~electrode~extra-compute~extra-dump~extra-fix~extra-molecule~extra-pair~fep~ffmpeg~granular~h5md~intel~interlayer~ipo~jpeg~kim+kokkos+kspace~latboltz~lepton+lib~machdyn~manifold+manybody~mc~meam~mesont~mgpt~misc~ml-hdnnp~ml-iap~ml-pod~ml-rann~ml-snap~mofff+molecule~molfile+mpi~netcdf~opencl+openmp~openmp-package~opt~orient~peri~phonon~plugin~plumed~png~poems~ptm~python~qeq~qtb~reaction~reaxff~replica+rigid~rocm~shock~smtbq~sph~spin~srd~tally~uef~voronoi~vtk~yaff build_system=cmake build_type=Release fftw_precision=double generator=make lammps_sizes=smallbig arch=linux-rocky9-x86_64_v4
[^] o3vtj26 ^cmake@3.27.9%gcc@12.2.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rocky9-x86_64_v4
[^] v4za2y6 ^curl@8.7.1%gcc@12.2.0~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-rocky9-x86_64_v4
[^] 4ntqcoo ^nghttp2@1.57.0%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] 7zermel ^diffutils@3.10%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] filwsx6 ^openssl@3.3.0%gcc@12.2.0~docs+shared build_system=generic certs=mozilla arch=linux-rocky9-x86_64_v4
[^] muc5zmk ^ca-certificates-mozilla@2023-05-30%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] eyk53wh ^perl@5.38.0%gcc@11.4.1+cpanm+opcode+open+shared+threads build_system=generic patches=714e4d1 arch=linux-rocky9-x86_64_v4
[^] cogxxtx ^berkeley-db@18.1.40%gcc@11.4.1+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-rocky9-x86_64_v4
[^] uj4wyhx ^bzip2@1.0.8%gcc@11.4.1~debug~pic+shared build_system=generic arch=linux-rocky9-x86_64_v4
[^] bx77xc6 ^gdbm@1.23%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ea7drzj ^readline@8.2%gcc@11.4.1 build_system=autotools patches=bbf97f1 arch=linux-rocky9-x86_64_v4
[^] 7wg26bz ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] 4n2uzha ^ncurses@6.5%gcc@11.4.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-rocky9-x86_64_v4
[^] g2yruc3 ^zlib-ng@2.1.6%gcc@11.4.1+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-rocky9-x86_64_v4
[^] 3ptgblf ^fftw@3.3.10%gcc@12.2.0+mpi+openmp~pfft_patches+shared build_system=autotools precision=double,float arch=linux-rocky9-x86_64_v4
[^] w77gg5r ^gcc-runtime@12.2.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[e] xri56vc ^glibc@2.34%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] xchit5a ^gmake@4.4.1%gcc@11.4.1~guile build_system=generic arch=linux-rocky9-x86_64_v4
[^] llid4hw ^gcc-runtime@11.4.1%gcc@11.4.1 build_system=generic arch=linux-rocky9-x86_64_v4
[+] 6dnhfd2 ^kokkos@4.3.00%gcc@12.2.0~aggressive_vectorization~compiler_warnings~cuda~debug~debug_bounds_check~debug_dualview_modify_check~deprecated_code~examples~hpx~hpx_async_dispatch~hwloc~ipo~memkind~numactl~openmp~openmptarget~pic~rocm+serial+shared~sycl~tests~threads~tuning~wrapper build_system=cmake build_type=Release cxxstd=17 generator=make intel_gpu_arch=none arch=linux-rocky9-x86_64_v4
[e] f6rfqov ^openmpi@5.0.3%gcc@12.2.0~atomics~cuda+gpfs~internal-hwloc~internal-libevent~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix~romio+rsh~static+vt+wrapper-rpath build_system=autotools fabrics=none romio-filesystem=none schedulers=none arch=linux-rocky9-x86_64_v4
==> Concretized gromacs+plumed ^fftw+openmp ^openmpi
[+] qpa6jjd gromacs@2023%gcc@12.2.0~cp2k~cuda~cycle_subcounters~double+gmxapi+hwloc~intel_provided_gcc~ipo~mdrun_only+mpi+nblib~nosuffix~opencl+openmp+plumed~relaxed_double_precision+shared~sycl build_system=cmake build_type=Release generator=make openmp_max_threads=none arch=linux-rocky9-x86_64_v4
[^] o3vtj26 ^cmake@3.27.9%gcc@12.2.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rocky9-x86_64_v4
[^] v4za2y6 ^curl@8.7.1%gcc@12.2.0~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-rocky9-x86_64_v4
[^] 4ntqcoo ^nghttp2@1.57.0%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] filwsx6 ^openssl@3.3.0%gcc@12.2.0~docs+shared build_system=generic certs=mozilla arch=linux-rocky9-x86_64_v4
[^] muc5zmk ^ca-certificates-mozilla@2023-05-30%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] 4n2uzha ^ncurses@6.5%gcc@11.4.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-rocky9-x86_64_v4
[^] g2yruc3 ^zlib-ng@2.1.6%gcc@11.4.1+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-rocky9-x86_64_v4
[^] 3ptgblf ^fftw@3.3.10%gcc@12.2.0+mpi+openmp~pfft_patches+shared build_system=autotools precision=double,float arch=linux-rocky9-x86_64_v4
[^] w77gg5r ^gcc-runtime@12.2.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[e] xri56vc ^glibc@2.34%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] xchit5a ^gmake@4.4.1%gcc@11.4.1~guile build_system=generic arch=linux-rocky9-x86_64_v4
[^] llid4hw ^gcc-runtime@11.4.1%gcc@11.4.1 build_system=generic arch=linux-rocky9-x86_64_v4
[^] zqnfdoq ^hwloc@2.9.1%gcc@12.2.0~cairo~cuda~gl~libudev+libxml2~netloc~nvml~oneapi-level-zero~opencl+pci~rocm build_system=autotools libs=shared,static arch=linux-rocky9-x86_64_v4
[^] tpopwgn ^libpciaccess@0.17%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] twcm7s7 ^util-macros@1.19.3%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] q6zmsq6 ^libxml2@2.10.3%gcc@11.4.1+pic~python+shared build_system=autotools arch=linux-rocky9-x86_64_v4
[^] rwn7pno ^xz@5.4.6%gcc@11.4.1~pic build_system=autotools libs=shared,static arch=linux-rocky9-x86_64_v4
[^] nt553wl ^openblas@0.3.26%gcc@12.2.0~bignuma~consistent_fpcsr+dynamic_dispatch+fortran~ilp64+locking+pic+shared build_system=makefile symbol_suffix=none threads=none arch=linux-rocky9-x86_64_v4
[^] eyk53wh ^perl@5.38.0%gcc@11.4.1+cpanm+opcode+open+shared+threads build_system=generic patches=714e4d1 arch=linux-rocky9-x86_64_v4
[^] cogxxtx ^berkeley-db@18.1.40%gcc@11.4.1+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-rocky9-x86_64_v4
[^] uj4wyhx ^bzip2@1.0.8%gcc@11.4.1~debug~pic+shared build_system=generic arch=linux-rocky9-x86_64_v4
[^] bx77xc6 ^gdbm@1.23%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ea7drzj ^readline@8.2%gcc@11.4.1 build_system=autotools patches=bbf97f1 arch=linux-rocky9-x86_64_v4
[e] f6rfqov ^openmpi@5.0.3%gcc@12.2.0~atomics~cuda+gpfs~internal-hwloc~internal-libevent~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix~romio+rsh~static+vt+wrapper-rpath build_system=autotools fabrics=none romio-filesystem=none schedulers=none arch=linux-rocky9-x86_64_v4
[^] 7wg26bz ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] 3fnkekg ^plumed@2.9.0%gcc@12.2.0+gsl+mpi+shared arrayfire=none build_system=autotools optional_modules=all arch=linux-rocky9-x86_64_v4
[^] h32ralr ^autoconf@2.72%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] y5sqj65 ^automake@1.16.5%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ynxvfrc ^gsl@2.7.1%gcc@12.2.0~external-cblas+pic+shared build_system=autotools arch=linux-rocky9-x86_64_v4
[^] c43op4r ^libtool@2.4.7%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] 62lolye ^findutils@4.9.0%gcc@11.4.1 build_system=autotools patches=440b954 arch=linux-rocky9-x86_64_v4
[^] fdljdyg ^m4@1.4.19%gcc@11.4.1+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-rocky9-x86_64_v4
[^] 7zermel ^diffutils@3.10%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] m2gvtuy ^libsigsegv@2.14%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] zcf7xi7 ^py-cython@3.0.8%gcc@12.2.0 build_system=python_pip arch=linux-rocky9-x86_64_v4
[^] 4q7v5jc ^py-pip@23.1.2%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] udom3th ^py-setuptools@69.2.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] y4owcqr ^py-wheel@0.41.2%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] rj3pox3 ^python@3.11.7%gcc@12.2.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rocky9-x86_64_v4
[^] je4ggnn ^expat@2.6.2%gcc@12.2.0+libbsd build_system=autotools arch=linux-rocky9-x86_64_v4
[^] zb23l3j ^libbsd@0.12.1%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] y6ppafl ^libmd@1.0.4%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] udcuonu ^gettext@0.22.5%gcc@11.4.1+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ivzmnos ^tar@1.34%gcc@11.4.1 build_system=autotools zip=pigz arch=linux-rocky9-x86_64_v4
[^] somkvv4 ^pigz@2.8%gcc@11.4.1 build_system=makefile arch=linux-rocky9-x86_64_v4
[^] my7tyw6 ^zstd@1.5.6%gcc@11.4.1+programs build_system=makefile compression=none libs=shared,static arch=linux-rocky9-x86_64_v4
[^] yc4oqfz ^libffi@3.4.6%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] 4mszlpj ^libxcrypt@4.4.35%gcc@12.2.0~obsolete_api build_system=autotools patches=4885da3 arch=linux-rocky9-x86_64_v4
[^] t5xgpdh ^sqlite@3.43.2%gcc@12.2.0+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-rocky9-x86_64_v4
[^] nkfrifq ^util-linux-uuid@2.38.1%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] s6divkp ^python-venv@1.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[+] /usr (external glibc-2.34-xri56vcyzs7kkvakhoku3fefc46nw25y)
[+] /share/apps/rocky9/general/libs/openmpi/gcc/12.2.0/5.0.3 (external openmpi-5.0.3-f6rfqovydeohhtdzs6yl2qiro2hxltpm)
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gcc-runtime/11.4.1-llid4hw
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gcc-runtime/12.2.0-w77gg5r
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/ncurses/6.5-4n2uzha
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gmake/4.4.1-xchit5a
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/xz/5.4.6-rwn7pno
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libpciaccess/0.17-tpopwgn
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gsl/2.7.1-ynxvfrc
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openblas/0.3.26-nt553wl
[+] /data/scratch/abc123/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/nano/6.3-m7n4nhp
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/fftw/3.3.10-openmpi-5.0.3-3ptgblf
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/nghttp2/1.57.0-4ntqcoo
[+] /data/scratch/abc123/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/kokkos/4.3.00-6dnhfd2
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/zlib-ng/2.1.6-g2yruc3
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/libxml2/2.10.3-q6zmsq6
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/plumed/2.9.0-openmpi-5.0.3-3fnkekg
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openssl/3.3.0-filwsx6
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/hwloc/2.9.1-zqnfdoq
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/curl/8.7.1-v4za2y6
[+] /data/scratch/abc123/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gromacs/2023-openmpi-5.0.3-qpa6jjd
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/cmake/3.27.9-o3vtj26
==> Installing lammps-20230802.3-yfsd7tlznfcbdrpbdsth73suz4fsxtj4 [23/23]
==> No binary for lammps-20230802.3-yfsd7tlznfcbdrpbdsth73suz4fsxtj4 found: installing from source
==> Using cached archive: /data/scratch/abc123/spack/cache/_source-cache/archive/66/6666e28cb90d3ff01cbbda6c81bdb85cf436bbb41604a87f2ab2fa559caa8510.tar.gz
==> No patches needed for lammps
==> lammps: Executing phase: 'cmake'
==> lammps: Executing phase: 'build'
==> lammps: Executing phase: 'install'
==> lammps: Successfully installed lammps-20230802.3-yfsd7tlznfcbdrpbdsth73suz4fsxtj4
Stage: 2.78s. Cmake: 8.31s. Build: 1m 34.54s. Install: 2.17s. Post-install: 0.63s. Total: 1m 50.14s
[+] /data/scratch/abc123/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/lammps/20230802.3-openmpi-5.0.3-yfsd7tl
==> Updating view at /data/scratch/abc123/spack-environments/spack-only/.spack-env/view
Spack has
concretized
the environment specs and then used upstream or existing personal installs for
everything except the new variant of LAMMPS, which it has installed into the
install_tree: root: we defined in the config: section of our
spack.yaml file.
If we now run our find command again, we see the "root specs" are now
installed. Also listed as "installed" are any required dependencies that have
been taken from our upstream:
spack find output
[spack-only] $ spack find -x -p
==> In environment /data/home/abc123/scratch/spack-environments/spack-only
==> 3 root specs
[+] gromacs +plumed [+] lammps +kokkos [+] nano@6.3
==> Installed packages
-- linux-rocky9-x86_64_v4 / gcc@12.2.0 --------------------------
cmake@3.27.9 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/cmake/3.27.9-o3vtj26
gromacs@2023 /data/scratch/abc123/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gromacs/2023-openmpi-5.0.3-qpa6jjd
gsl@2.7.1 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gsl/2.7.1-ynxvfrc
lammps@20230802.3 /data/scratch/abc123/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/lammps/20230802.3-openmpi-5.0.3-yfsd7tl
nano@6.3 /data/scratch/abc123/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/nano/6.3-m7n4nhp
openmpi@5.0.3 /share/apps/rocky9/general/libs/openmpi/gcc/12.2.0/5.0.3
openssl@3.3.0 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openssl/3.3.0-filwsx6
plumed@2.9.0 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/plumed/2.9.0-openmpi-5.0.3-3fnkekg
python@3.17 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/python/3.11.7-rj3pox3
sqlite@33.2 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/sqlite/3.43.2-t5xgpdh
==> 10 installed packages