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 /gpfs/scratch/abc123/spack-environments/spack-only
==> 7 root specs
-- no arch / no compilers ---------------------------------------
- bedtools2@2.31.1 - blast-plus@2.14.1 - bowtie2@2.5.2 - gatk@4.5.0.0 - qctool@2.2.0 - samtools@1.19.2 - spades@3.15.5
==> 0 installed packages
==> 0 concretized packages to be installed (show with `spack find -c`)
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
[^] bedtools2@2.31.1 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] ^bzip2@1.0.8~debug~pic+shared build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] ^diffutils@3.10 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^gcc-runtime@11.4.1 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] ^gcc-runtime@12.2.0 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[e] ^glibc@2.34 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^python@3.11.7+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 platform=linux os=rocky9 target=x86_64_v4
[^] ^expat@2.6.2+libbsd build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libbsd@0.12.1 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libmd@1.0.4 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^gdbm@1.23 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^gettext@0.22.5+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libxml2@2.10.3+pic~python+shared build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^tar@1.34 build_system=autotools zip=pigz platform=linux os=rocky9 target=x86_64_v4
[^] ^pigz@2.8 build_system=makefile platform=linux os=rocky9 target=x86_64_v4
[^] ^zstd@1.5.6+programs build_system=makefile compression:=none libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] ^libffi@3.4.6 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libxcrypt@4.4.35~obsolete_api build_system=autotools patches:=4885da3 platform=linux os=rocky9 target=x86_64_v4
[^] ^pkgconf@2.2.0 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^sqlite@3.43.2+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^util-linux-uuid@2.38.1 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^xz@5.4.6~pic build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] ^zlib-ng@2.1.6+compat+new_strategies+opt+pic+shared build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] blast-plus@2.14.1+bzip2+freetype+gnutls+jpeg+lzo+openssl+pcre+perl+png+python~static+zlib build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^cpio@2.15 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^freetype@2.13.2+pic+shared build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^gmake@4.4.1~guile build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] ^gnutls@3.8.3~guile+zlib build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libidn2@2.3.7 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libunistring@1.2 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^nettle@3.9.1 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^gmp@6.2.1+cxx build_system=autotools libs:=shared,static patches:=69ad2e2 platform=linux os=rocky9 target=x86_64_v4
[^] ^autoconf@2.72 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^automake@1.16.5 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libtool@2.4.7 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^findutils@4.9.0 build_system=autotools patches:=440b954 platform=linux os=rocky9 target=x86_64_v4
[^] ^m4@1.4.19+sigsegv build_system=autotools patches:=9dc5fbd,bfdffa7 platform=linux os=rocky9 target=x86_64_v4
[^] ^libsigsegv@2.14 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libjpeg-turbo@3.0.0~ipo~jpeg8~partial_decoder+pic build_system=cmake build_type=Release generator=make libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] ^nasm@2.15.05 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libpng@1.6.39~ipo~pic build_system=cmake build_type=Release generator=make libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] ^lmdb@0.9.31 build_system=makefile platform=linux os=rocky9 target=x86_64_v4
[^] ^lzo@2.10 build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] ^openssl@3.3.0~docs+shared build_system=generic certs=mozilla platform=linux os=rocky9 target=x86_64_v4
[^] ^ca-certificates-mozilla@2023-05-30 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] ^pcre@8.45~jit+multibyte+pic+shared+static+utf build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^perl@5.38.0+cpanm+opcode+open+shared+threads build_system=generic patches:=714e4d1 platform=linux os=rocky9 target=x86_64_v4
[^] ^berkeley-db@18.1.40+cxx~docs+stl build_system=autotools patches:=26090f4,b231fcc platform=linux os=rocky9 target=x86_64_v4
[^] bowtie2@2.5.2 build_system=makefile platform=linux os=rocky9 target=x86_64_v4
[^] ^intel-tbb@2021.9.0~ipo+shared+tm build_system=cmake build_type=Release cxxstd=default generator=make patches:=91755c6 platform=linux os=rocky9 target=x86_64_v4
[^] ^hwloc@2.9.1~cairo~cuda~gl~libudev+libxml2~netloc~nvml~oneapi-level-zero~opencl+pci~rocm build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] ^libpciaccess@0.17 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^util-macros@1.19.3 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^readline@8.2 build_system=autotools patches:=bbf97f1 platform=linux os=rocky9 target=x86_64_v4
[^] gatk@4.5.0.0~r build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] ^openjdk@17.0.8.1_1 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] qctool@2.2.0 build_system=waf platform=linux os=rocky9 target=x86_64_v4
[^] ^python@3.12.1+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] ^zlib@1.3.1+optimize+pic+shared build_system=makefile platform=linux os=rocky9 target=x86_64_v4
[^] samtools@1.19.2 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] ^htslib@1.19.1+libcurl+libdeflate build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^curl@8.7.1~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs:=shared,static tls:=openssl platform=linux os=rocky9 target=x86_64_v4
[^] ^nghttp2@1.57.0 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^libdeflate@1.18~ipo build_system=cmake build_type=Release generator=make platform=linux os=rocky9 target=x86_64_v4
[^] ^gzip@1.13 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ^ncurses@6.5~symlinks+termlib abi=none build_system=autotools patches:=7a351bc platform=linux os=rocky9 target=x86_64_v4
[^] spades@3.15.5~ipo build_system=cmake build_type=Release generator=make platform=linux os=rocky9 target=x86_64_v4
[^] ^cmake@3.27.9~doc+ncurses+ownlibs build_system=generic build_type=Release platform=linux os=rocky9 target=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 (nothing is missing so this doesn't appear above)[^]means that the listed application/library is already installed in upstream and will be used to avoid re-installation (in this environment, that is almost all packages)[e]means that the listed application/library is marked as external.glibcis always marked as external
You'll notice then, that everything is already available from our upstream already.
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 ${SLURM_NTASKS} to your command to ensure that you match the
installation process threading to your salloc core request:
spack install output (click to expand)
[spack-only] $ spack install -j ${SLURM_NTASKS}
==> Concretized 7 specs
[^] km7j5kp bedtools2@2.31.1 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] uj4wyhx ^bzip2@1.0.8~debug~pic+shared build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] 7zermel ^diffutils@3.10 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] llid4hw ^gcc-runtime@11.4.1 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] w77gg5r ^gcc-runtime@12.2.0 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[e] xri56vc ^glibc@2.34 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] rj3pox3 ^python@3.11.7+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 platform=linux os=rocky9 target=x86_64_v4
[^] je4ggnn ^expat@2.6.2+libbsd build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] zb23l3j ^libbsd@0.12.1 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] y6ppafl ^libmd@1.0.4 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] bx77xc6 ^gdbm@1.23 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] udcuonu ^gettext@0.22.5+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] q6zmsq6 ^libxml2@2.10.3+pic~python+shared build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ivzmnos ^tar@1.34 build_system=autotools zip=pigz platform=linux os=rocky9 target=x86_64_v4
[^] somkvv4 ^pigz@2.8 build_system=makefile platform=linux os=rocky9 target=x86_64_v4
[^] my7tyw6 ^zstd@1.5.6+programs build_system=makefile compression:=none libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] yc4oqfz ^libffi@3.4.6 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] 4mszlpj ^libxcrypt@4.4.35~obsolete_api build_system=autotools patches:=4885da3 platform=linux os=rocky9 target=x86_64_v4
[^] 7wg26bz ^pkgconf@2.2.0 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] t5xgpdh ^sqlite@3.43.2+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] nkfrifq ^util-linux-uuid@2.38.1 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] rwn7pno ^xz@5.4.6~pic build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] g2yruc3 ^zlib-ng@2.1.6+compat+new_strategies+opt+pic+shared build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ozy63do blast-plus@2.14.1+bzip2+freetype+gnutls+jpeg+lzo+openssl+pcre+perl+png+python~static+zlib build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] xkf76pr ^cpio@2.15 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] d62qmki ^freetype@2.13.2+pic+shared build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] xchit5a ^gmake@4.4.1~guile build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] fwxsw34 ^gnutls@3.8.3~guile+zlib build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] qtzguez ^libidn2@2.3.7 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] 2xc2pfo ^libunistring@1.2 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ipyura5 ^nettle@3.9.1 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ibyfd4t ^gmp@6.2.1+cxx build_system=autotools libs:=shared,static patches:=69ad2e2 platform=linux os=rocky9 target=x86_64_v4
[^] h32ralr ^autoconf@2.72 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] y5sqj65 ^automake@1.16.5 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] c43op4r ^libtool@2.4.7 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] 62lolye ^findutils@4.9.0 build_system=autotools patches:=440b954 platform=linux os=rocky9 target=x86_64_v4
[^] fdljdyg ^m4@1.4.19+sigsegv build_system=autotools patches:=9dc5fbd,bfdffa7 platform=linux os=rocky9 target=x86_64_v4
[^] m2gvtuy ^libsigsegv@2.14 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] wclh6t6 ^libjpeg-turbo@3.0.0~ipo~jpeg8~partial_decoder+pic build_system=cmake build_type=Release generator=make libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] x3t4wcw ^nasm@2.15.05 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] p2dnxbj ^libpng@1.6.39~ipo~pic build_system=cmake build_type=Release generator=make libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] bl6hurk ^lmdb@0.9.31 build_system=makefile platform=linux os=rocky9 target=x86_64_v4
[^] azktqak ^lzo@2.10 build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] filwsx6 ^openssl@3.3.0~docs+shared build_system=generic certs=mozilla platform=linux os=rocky9 target=x86_64_v4
[^] muc5zmk ^ca-certificates-mozilla@2023-05-30 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] 5grzchz ^pcre@8.45~jit+multibyte+pic+shared+static+utf build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] eyk53wh ^perl@5.38.0+cpanm+opcode+open+shared+threads build_system=generic patches:=714e4d1 platform=linux os=rocky9 target=x86_64_v4
[^] cogxxtx ^berkeley-db@18.1.40+cxx~docs+stl build_system=autotools patches:=26090f4,b231fcc platform=linux os=rocky9 target=x86_64_v4
[^] a7zexua bowtie2@2.5.2 build_system=makefile platform=linux os=rocky9 target=x86_64_v4
[^] 7fsrvwa ^intel-tbb@2021.9.0~ipo+shared+tm build_system=cmake build_type=Release cxxstd=default generator=make patches:=91755c6 platform=linux os=rocky9 target=x86_64_v4
[^] zqnfdoq ^hwloc@2.9.1~cairo~cuda~gl~libudev+libxml2~netloc~nvml~oneapi-level-zero~opencl+pci~rocm build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v4
[^] tpopwgn ^libpciaccess@0.17 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] twcm7s7 ^util-macros@1.19.3 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] ea7drzj ^readline@8.2 build_system=autotools patches:=bbf97f1 platform=linux os=rocky9 target=x86_64_v4
[^] 6uwwf26 gatk@4.5.0.0~r build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] qk5wpoh ^openjdk@17.0.8.1_1 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] 7ih5mnd qctool@2.2.0 build_system=waf platform=linux os=rocky9 target=x86_64_v4
[^] sd2mpei ^python@3.12.1+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] 4wxzrgl ^zlib@1.3.1+optimize+pic+shared build_system=makefile platform=linux os=rocky9 target=x86_64_v4
[^] z5llbnv samtools@1.19.2 build_system=generic platform=linux os=rocky9 target=x86_64_v4
[^] x6h2y4a ^htslib@1.19.1+libcurl+libdeflate build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] v4za2y6 ^curl@8.7.1~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs:=shared,static tls:=openssl platform=linux os=rocky9 target=x86_64_v4
[^] 4ntqcoo ^nghttp2@1.57.0 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] frfbkda ^libdeflate@1.18~ipo build_system=cmake build_type=Release generator=make platform=linux os=rocky9 target=x86_64_v4
[^] eysmsnu ^gzip@1.13 build_system=autotools platform=linux os=rocky9 target=x86_64_v4
[^] 4n2uzha ^ncurses@6.5~symlinks+termlib abi=none build_system=autotools patches:=7a351bc platform=linux os=rocky9 target=x86_64_v4
[^] ap7kfa4 spades@3.15.5~ipo build_system=cmake build_type=Release generator=make platform=linux os=rocky9 target=x86_64_v4
[^] o3vtj26 ^cmake@3.27.9~doc+ncurses+ownlibs build_system=generic build_type=Release platform=linux os=rocky9 target=x86_64_v4
[+] /usr (external glibc-2.34-xri56vcyzs7kkvakhoku3fefc46nw25y)
[+] /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/gcc-runtime/11.4.1-llid4hw
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh
[+] /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-12.2.0/lzo/2.10-azktqak
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libunistring/1.2-2xc2pfo
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gzip/1.13-eysmsnu
[+] /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/zlib/1.3.1-4wxzrgl
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/pcre/8.45-5grzchz
[+] /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/libjpeg-turbo/3.0.0-wclh6t6
[+] /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/lmdb/0.9.31-bl6hurk
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/nghttp2/1.57.0-4ntqcoo
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/gmp/6.2.1-ibyfd4t
[+] /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-11.4.1/zlib-ng/2.1.6-g2yruc3
[+] /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/berkeley-db/18.1.40-cogxxtx
[+] /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-12.2.0/libidn2/2.3.7-qtzguez
[+] /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-12.2.0/qctool/2.2.0-7ih5mnd
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/nettle/3.9.1-ipyura5
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libdeflate/1.18-frfbkda
[+] /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-11.4.1/pigz/2.8-somkvv4
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libpng/1.6.39-p2dnxbj
[+] /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/bedtools2/2.31.1-km7j5kp
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/readline/8.2-ea7drzj
[+] /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-12.2.0/curl/8.7.1-v4za2y6
[+] /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/freetype/2.13.2-d62qmki
[+] /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-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-12.2.0/htslib/1.19.1-x6h2y4a
[+] /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/intel-tbb/2021.9.0-7fsrvwa
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-11.4.1/perl/5.38.0-eyk53wh
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gnutls/3.8.3-fwxsw34
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/python/3.11.7-rj3pox3
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/samtools/1.19.2-z5llbnv
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/spades/3.15.5-ap7kfa4
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gatk/4.5.0.0-6uwwf26
==> Updating view at /gpfs/scratch/abc123/spack-environments/spack-only/.spack-env/view
Spack has
concretized
the environment specs and then used upstream installs for everything.
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 /gpfs/scratch/abc123/spack-environments/spack-only
==> 7 root specs
-- no arch / no compilers ---------------------------------------
[^] bedtools2@2.31.1 [^] blast-plus@2.14.1 [^] bowtie2@2.5.2 [^] gatk@4.5.0.0 [^] qctool@2.2.0 [^] samtools@1.19.2 [^] spades@3.15.5
-- linux-rocky9-x86_64_v4 / no compilers ------------------------
bedtools2@2.31.1 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-km7j5kp
blast-plus@2.14.1 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do
bowtie2@2.5.2 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bowtie2/2.5.2-a7zexua
cmake@3.27.9 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/cmake/3.27.9-o3vtj26
gatk@4.5.0.0 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gatk/4.5.0.0-6uwwf26
htslib@1.19.1 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/htslib/1.19.1-x6h2y4a
intel-tbb@2021.9.0 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/intel-tbb/2021.9.0-7fsrvwa
libpng@1.6.39 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/libpng/1.6.39-p2dnxbj
openjdk@17.0.8.1_1 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openjdk/17.0.8.1_1-qk5wpoh
openssl@3.3.0 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/openssl/3.3.0-filwsx6
python@3.11.7 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/python/3.11.7-rj3pox3
python@3.12.1 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/python/3.12.1-sd2mpei
qctool@2.2.0 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/qctool/2.2.0-7ih5mnd
samtools@1.19.2 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/samtools/1.19.2-z5llbnv
spades@3.15.5 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/spades/3.15.5-ap7kfa4
sqlite@3.43.2 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/sqlite/3.43.2-t5xgpdh
==> 16 installed packages
==> 0 concretized packages to be installed (show with `spack find -c`)