Installing your Spack environment¶
As in the previous example, we need to spec and then install our
environment.
Spack find¶
Let's look at the output of spack find in the activated environment:
spack find output
[spack-python] $ spack find -x -p
==> In environment /data/scratch/abc123/spack-environments/spack-python
==> 3 root specs
- libsndfile - py-pip - python@3.12
==> 0 installed packages
So, in the context of the environment, the "root specs" are listed but not yet
installed ("==> 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 run a spec command in the activated environment:
spack spec output (click to expand)
[spack-python] $ spack spec
- libsndfile@1.2.2%gcc@12.2.0~alsa~external-libs~sqlite 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@12.2.0 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
[^] ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] py-pip@23.1.2%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
[^] ^python-venv@1.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] python@3.12.1%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 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
[^] ^diffutils@3.10%gcc@11.4.1 build_system=autotools 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
[^] ^gdbm@1.23%gcc@11.4.1 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
[^] ^libxml2@2.10.3%gcc@11.4.1+pic~python+shared 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
[^] ^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
[^] ^ncurses@6.5%gcc@11.4.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc 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
[^] ^readline@8.2%gcc@11.4.1 build_system=autotools patches=bbf97f1 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
[^] ^xz@5.4.6%gcc@11.4.1~pic build_system=autotools libs=shared,static 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
This time everything is already in upstream ([^]) apart from libsndfile,
which in the output above is marked with - meaning that it is missing and
needs to be installed personally.
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, you should 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-python] $ spack install -j $NSLOTS
==> Concretized 3 specs
- ls6bwub libsndfile@1.2.2%gcc@12.2.0~alsa~external-libs~sqlite 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] q2367ne ^glibc@2.34%gcc@12.2.0 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
[^] 7wg26bz ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] inullmb py-pip@23.1.2%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
[^] fcsyl32 ^python-venv@1.0%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] sd2mpei python@3.12.1%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 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
[^] 7zermel ^diffutils@3.10%gcc@11.4.1 build_system=autotools 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
[^] bx77xc6 ^gdbm@1.23%gcc@11.4.1 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
[^] q6zmsq6 ^libxml2@2.10.3%gcc@11.4.1+pic~python+shared 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
[^] 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
[^] 4n2uzha ^ncurses@6.5%gcc@11.4.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc 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
[^] ea7drzj ^readline@8.2%gcc@11.4.1 build_system=autotools patches=bbf97f1 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
[^] rwn7pno ^xz@5.4.6%gcc@11.4.1~pic build_system=autotools libs=shared,static 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
[+] /usr (external glibc-2.34-xri56vcyzs7kkvakhoku3fefc46nw25y)
[+] /usr (external glibc-2.34-q2367nemoxqj6j3fg54cg4mjlkvc7f5n)
[+] /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/xz/5.4.6-rwn7pno
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/zstd/1.5.6-my7tyw6
[+] /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/pkgconf/2.2.0-7wg26bz
[+] /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/zlib-ng/2.1.6-g2yruc3
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/bzip2/1.0.8-uj4wyhx
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libxcrypt/4.4.35-4mszlpj
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libmd/1.0.4-y6ppafl
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libffi/3.4.6-yc4oqfz
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/util-linux-uuid/2.38.1-nkfrifq
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/readline/8.2-ea7drzj
==> Installing libsndfile-1.2.2-ls6bwubs4onvwu3wk5xps47p4r5t3l5q [17/29]
==> No binary for libsndfile-1.2.2-ls6bwubs4onvwu3wk5xps47p4r5t3l5q found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/37/3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e.tar.xz
==> No patches needed for libsndfile
==> libsndfile: Executing phase: 'autoreconf'
==> libsndfile: Executing phase: 'configure'
==> libsndfile: Executing phase: 'build'
==> libsndfile: Executing phase: 'install'
==> libsndfile: Successfully installed libsndfile-1.2.2-ls6bwubs4onvwu3wk5xps47p4r5t3l5q
Stage: 0.17s. Autoreconf: 0.00s. Configure: 22.36s. Build: 5.59s. Install: 0.75s. Post-install: 0.11s. Total: 29.26s
[+] /data/scratch/abc123/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libsndfile/1.2.2-ls6bwub
[+] /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-11.4.1/pigz/2.8-somkvv4
[+] /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/libbsd/0.12.1-zb23l3j
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gdbm/1.23-bx77xc6
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/sqlite/3.43.2-t5xgpdh
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/tar/1.34-ivzmnos
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/expat/2.6.2-je4ggnn
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gettext/0.22.5-udcuonu
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/python/3.12.1-sd2mpei
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/python-venv/1.0-fcsyl32
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/py-pip/23.1.2-inullmb
==> Updating view at /data/scratch/abc123/spack-environments/spack-python/.spack-env/view
Spack has
concretized
the environment specs and then used upstream or existing personal installs for
everything except libsndfile, 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-python] $ spack find -x -p
==> In environment /data/scratch/abc123/spack-environments/spack-python
==> 3 root specs
[+] libsndfile [^] py-pip [^] python@3.12
-- linux-rocky9-x86_64_v4 / gcc@12.2.0 --------------------------
libsndfile@1.2.2 /data/scratch/abc123/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libsndfile/1.2.2-ls6bwub
openssl@3.3.0 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openssl/3.3.0-filwsx6
python@3.12.1 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/python/3.12.1-sd2mpei
sqlite@3.43.2 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/sqlite/3.43.2-t5xgpdh
==> 4 installed packages
==> 0 concretized packages to be installed (show with `spack find -c`)