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
==> 7 root specs
- 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%gcc@12.2.0 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
[^] ^gcc-runtime@11.4.1%gcc@11.4.1 build_system=generic 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
[^] ^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
[^] ^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
[^] ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools 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
[^] blast-plus@2.14.1%gcc@12.2.0+bzip2+freetype+gnutls+jpeg+lzo+openssl+pcre+perl+png+python~static+zlib build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^cpio@2.15%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^freetype@2.13.2%gcc@12.2.0+pic+shared 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
[^] ^gnutls@3.8.3%gcc@12.2.0~guile+zlib build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libidn2@2.3.7%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libunistring@1.2%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^nettle@3.9.1%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^gmp@6.2.1%gcc@11.4.1+cxx build_system=autotools libs=shared,static patches=69ad2e2 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
[^] ^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
[^] ^libsigsegv@2.14%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libjpeg-turbo@3.0.0%gcc@12.2.0~ipo~jpeg8~partial_decoder+pic build_system=cmake build_type=Release generator=make libs=shared,static arch=linux-rocky9-x86_64_v4
[^] ^nasm@2.15.05%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ^libpng@1.6.39%gcc@12.2.0~ipo~pic build_system=cmake build_type=Release generator=make libs=shared,static arch=linux-rocky9-x86_64_v4
[^] ^lmdb@0.9.31%gcc@12.2.0 build_system=makefile arch=linux-rocky9-x86_64_v4
[^] ^lzo@2.10%gcc@12.2.0 build_system=autotools libs=shared,static 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
[^] ^pcre@8.45%gcc@12.2.0~jit+multibyte+pic+shared+static+utf build_system=autotools 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
[^] ^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
[^] bowtie2@2.5.2%gcc@12.2.0 build_system=makefile arch=linux-rocky9-x86_64_v4
[^] ^intel-tbb@2021.9.0%gcc@12.2.0~ipo+shared+tm build_system=cmake build_type=Release cxxstd=default generator=make patches=91755c6 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
[^] ^readline@8.2%gcc@11.4.1 build_system=autotools patches=bbf97f1 arch=linux-rocky9-x86_64_v4
[^] gatk@4.5.0.0%gcc@12.2.0~r build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^openjdk@17.0.8.1_1%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] qctool@2.2.0%gcc@12.2.0 build_system=waf arch=linux-rocky9-x86_64_v4
[^] ^zlib@1.3.1%gcc@12.2.0+optimize+pic+shared build_system=makefile arch=linux-rocky9-x86_64_v4
[^] samtools@1.19.2%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] ^htslib@1.19.1%gcc@12.2.0+libcurl+libdeflate build_system=autotools 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
[^] ^libdeflate@1.18%gcc@12.2.0~ipo build_system=cmake build_type=Release generator=make arch=linux-rocky9-x86_64_v4
[^] ^gzip@1.13%gcc@12.2.0 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
[^] spades@3.15.5%gcc@12.2.0~ipo build_system=cmake build_type=Release generator=make 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
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 $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 7 specs
[^] pifiw4t bedtools2@2.31.1%gcc@12.2.0 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
[^] llid4hw ^gcc-runtime@11.4.1%gcc@11.4.1 build_system=generic 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
[^] 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
[^] 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
[^] 7wg26bz ^pkgconf@2.2.0%gcc@11.4.1 build_system=autotools 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
[^] ozy63do blast-plus@2.14.1%gcc@12.2.0+bzip2+freetype+gnutls+jpeg+lzo+openssl+pcre+perl+png+python~static+zlib build_system=autotools arch=linux-rocky9-x86_64_v4
[^] xkf76pr ^cpio@2.15%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] d62qmki ^freetype@2.13.2%gcc@12.2.0+pic+shared 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
[^] fwxsw34 ^gnutls@3.8.3%gcc@12.2.0~guile+zlib build_system=autotools arch=linux-rocky9-x86_64_v4
[^] qtzguez ^libidn2@2.3.7%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] 2xc2pfo ^libunistring@1.2%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ipyura5 ^nettle@3.9.1%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] ibyfd4t ^gmp@6.2.1%gcc@11.4.1+cxx build_system=autotools libs=shared,static patches=69ad2e2 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
[^] 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
[^] m2gvtuy ^libsigsegv@2.14%gcc@11.4.1 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] wclh6t6 ^libjpeg-turbo@3.0.0%gcc@12.2.0~ipo~jpeg8~partial_decoder+pic build_system=cmake build_type=Release generator=make libs=shared,static arch=linux-rocky9-x86_64_v4
[^] x3t4wcw ^nasm@2.15.05%gcc@12.2.0 build_system=autotools arch=linux-rocky9-x86_64_v4
[^] p2dnxbj ^libpng@1.6.39%gcc@12.2.0~ipo~pic build_system=cmake build_type=Release generator=make libs=shared,static arch=linux-rocky9-x86_64_v4
[^] bl6hurk ^lmdb@0.9.31%gcc@12.2.0 build_system=makefile arch=linux-rocky9-x86_64_v4
[^] azktqak ^lzo@2.10%gcc@12.2.0 build_system=autotools libs=shared,static 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
[^] 5grzchz ^pcre@8.45%gcc@12.2.0~jit+multibyte+pic+shared+static+utf build_system=autotools 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
[^] 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
[^] a7zexua bowtie2@2.5.2%gcc@12.2.0 build_system=makefile arch=linux-rocky9-x86_64_v4
[^] 7fsrvwa ^intel-tbb@2021.9.0%gcc@12.2.0~ipo+shared+tm build_system=cmake build_type=Release cxxstd=default generator=make patches=91755c6 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
[^] ea7drzj ^readline@8.2%gcc@11.4.1 build_system=autotools patches=bbf97f1 arch=linux-rocky9-x86_64_v4
[^] 6uwwf26 gatk@4.5.0.0%gcc@12.2.0~r build_system=generic arch=linux-rocky9-x86_64_v4
[^] qk5wpoh ^openjdk@17.0.8.1_1%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] h7j7hde qctool@2.2.0%gcc@12.2.0 build_system=waf arch=linux-rocky9-x86_64_v4
[^] 4wxzrgl ^zlib@1.3.1%gcc@12.2.0+optimize+pic+shared build_system=makefile arch=linux-rocky9-x86_64_v4
[^] z5llbnv samtools@1.19.2%gcc@12.2.0 build_system=generic arch=linux-rocky9-x86_64_v4
[^] x6h2y4a ^htslib@1.19.1%gcc@12.2.0+libcurl+libdeflate build_system=autotools 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
[^] frfbkda ^libdeflate@1.18%gcc@12.2.0~ipo build_system=cmake build_type=Release generator=make arch=linux-rocky9-x86_64_v4
[^] eysmsnu ^gzip@1.13%gcc@12.2.0 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
[^] ap7kfa4 spades@3.15.5%gcc@12.2.0~ipo build_system=cmake build_type=Release generator=make 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
[+] /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/libjpeg-turbo/3.0.0-wclh6t6
[+] /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/pcre/8.45-5grzchz
[+] /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-12.2.0/libmd/1.0.4-y6ppafl
[+] /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/libpciaccess/0.17-tpopwgn
[+] /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/zlib/1.3.1-4wxzrgl
[+] /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/libunistring/1.2-2xc2pfo
[+] /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/libxcrypt/4.4.35-4mszlpj
[+] /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/ncurses/6.5-4n2uzha
[+] /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/xz/5.4.6-rwn7pno
[+] /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/zstd/1.5.6-my7tyw6
[+] /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-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-h7j7hde
[+] /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-11.4.1/readline/8.2-ea7drzj
[+] /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/libpng/1.6.39-p2dnxbj
[+] /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/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-12.2.0/bedtools2/2.31.1-pifiw4t
[+] /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/expat/2.6.2-je4ggnn
[+] /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/hwloc/2.9.1-zqnfdoq
[+] /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-11.4.1/tar/1.34-ivzmnos
[+] /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/perl/5.38.0-eyk53wh
[+] /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/gettext/0.22.5-udcuonu
[+] /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-12.2.0/python/3.11.7-rj3pox3
[+] /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/spades/3.15.5-ap7kfa4
[+] /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/samtools/1.19.2-z5llbnv
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/gatk/4.5.0.0-6uwwf26
[+] /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/blast-plus/2.14.1-ozy63do
==> Updating view at /data/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 /data/scratch/abc123/spack-environments/spack-only
==> 7 root specs
[^] 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 / gcc@12.2.0 --------------------------
bedtools2@2.31.1 /share/apps/rocky9/spack/apps/linux-rocky9-x86_64_v4/gcc-12.2.0/bedtools2/2.31.1-pifiw4t
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-h7j7hde
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`)