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Tricks and handy spack commands

To get a list of available versions not the full info (see below), use

$ spack versions samtools
==> Safe versions (already checksummed):
  1.13  1.12  1.10  1.9  1.8  1.7  1.6  1.5  1.4  1.3.1  1.2  0.1.8
==> Remote versions (not yet checksummed):
  1.15.1  1.15  1.14  1.11

Show the specs of installed packages

$ spack find
==> 60 installed packages
-- linux-rhel8-skylake_avx512 / gcc@8.4.1 -----------------------
autoconf@2.69                gcc@10.3.0       m4@1.4.19      readline@8.1
. . . .

$ spack find --long --deps angsd
==> 1 installed package
-- linux-rhel8-skylake_avx512 / gcc@10.3.0 ----------------------
7rrgjas angsd@0.935
w3oy6q3     curl@7.79.0
sniyjil         openssl@1.1.1l
3fym6nw             zlib@1.2.11
dzhwvps     htslib@1.13
hknpl5u         bzip2@1.0.8
bz7ofpl         xz@5.2.5
cwmudc6     lzma@4.32.7
bjvrnkj     r@4.1.1
wjwgcz3         icu4c@67.1
uyfgcqr         ncurses@6.2
aeg3qbt         openjdk@11.0.12_7
3sf7sri         pcre2@10.36
4una6ug         readline@8.1

Regenerate module files to update content or layout with refresh. Use --delete-tree to delete the module file tree before refresh. Add -y option if you are sure and don't want to be prompted to confirm

$ spack module lmod refresh --delete-tree

Garbage Collector command: uninstall all unneeded packages

$  spack gc

These two were gleaned from Slack. Someone wanted to run spack uninstall --all and was getting an error.

$ spack clean -a
$ spack reindex

were suggested to get things back on track.

To get detailed information about a package use spack info package_name.

$ spack info blat

Full output

To see the depencies of a package, use

$ spack dependencies -i plink-ng
==> Dependencies of plink-ng@220503%gcc@10.3.0/zgl226z
-- linux-rhel8-haswell / gcc@10.3.0 -----------------------------
3ntlyrq cblas@2015-06-06  d5sydgn zlib@1.2.11
mslmaxc openblas@0.3.18   z6it5pz zstd@1.5.0

To see what depends on a package (its dependents), use

$ spack dependents -i openblas@0.3.18
==> Dependents of openblas@0.3.18%gcc@10.3.0/mslmaxc
-- linux-rhel8-haswell / gcc@10.3.0 -----------------------------
3ntlyrq cblas@2015-06-06  zgl226z plink-ng@220503

To refresh modules, we currently have to blast the module tree and regenerate,

spack module lmod refresh -y --delete-tree

There is a bug that gives permission denied to anyone who didn't create the tree.