Spack

What is Spack?

Spack is a package manager for supercomputers. It makes installing scientific software easy. Spack isn’t tied to a particular language; you can build a software stack in Python or R, link to libraries written in C, C++, or Fortran, and easily swap compilers or target specific microarchitectures.

How set up Spack in user environment

<user@cresco7x001 ~> module load spack-0.23.0

To summarize:

System	Spack version	Supported shells	Requirement	Command
CRESCO7	0.23.0	all	none	module load spack-0.23.0
XCRESCO	0.23.0	all	none	module load spack-0.23.0
CRESCO6	0.23.0	/bin/bash /bin/sh	module load scipy39	module load spack-0.23.0

How to use Spack

Search a software

<user@cresco7x001 ~> spack list octave
octave  octave-arduino  octave-control  octave-gsl  octave-instrctl  octave-io  octave-optim  octave-quaternion  octave-signal  octave-splines  octave-statistics  octave-struct  octave-symbolic
==> 13 packages

Get info about a software

<user@cresco7x001 ~> spack info octave
AutotoolsPackage:   octave

Description:
   GNU Octave is a high-level language, primarily intended for numerical
   computations. It provides a convenient command line interface for
   solving linear and nonlinear problems numerically, and for performing
   other numerical experiments using a language that is mostly compatible
   with Matlab. It may also be used as a batch-oriented language.

Homepage: https://www.gnu.org/software/octave/

Preferred version:
   9.1.0    https://ftpmirror.gnu.org/octave/octave-9.1.0.tar.gz

Safe versions:
   9.1.0    https://ftpmirror.gnu.org/octave/octave-9.1.0.tar.gz
   8.4.0    https://ftpmirror.gnu.org/octave/octave-8.4.0.tar.gz
   8.2.0    https://ftpmirror.gnu.org/octave/octave-8.2.0.tar.gz
   8.1.0    https://ftpmirror.gnu.org/octave/octave-8.1.0.tar.gz
   7.3.0    https://ftpmirror.gnu.org/octave/octave-7.3.0.tar.gz
   7.2.0    https://ftpmirror.gnu.org/octave/octave-7.2.0.tar.gz
   7.1.0    https://ftpmirror.gnu.org/octave/octave-7.1.0.tar.gz
   6.4.0    https://ftpmirror.gnu.org/octave/octave-6.4.0.tar.gz
   6.3.0    https://ftpmirror.gnu.org/octave/octave-6.3.0.tar.gz
   6.2.0    https://ftpmirror.gnu.org/octave/octave-6.2.0.tar.gz
   6.1.0    https://ftpmirror.gnu.org/octave/octave-6.1.0.tar.gz
   5.2.0    https://ftpmirror.gnu.org/octave/octave-5.2.0.tar.gz
   5.1.0    https://ftpmirror.gnu.org/octave/octave-5.1.0.tar.gz
   4.4.1    https://ftpmirror.gnu.org/octave/octave-4.4.1.tar.gz
   4.4.0    https://ftpmirror.gnu.org/octave/octave-4.4.0.tar.gz
   4.2.2    https://ftpmirror.gnu.org/octave/octave-4.2.2.tar.gz
   4.2.1    https://ftpmirror.gnu.org/octave/octave-4.2.1.tar.gz
   4.2.0    https://ftpmirror.gnu.org/octave/octave-4.2.0.tar.gz
   4.0.2    https://ftpmirror.gnu.org/octave/octave-4.0.2.tar.gz
   4.0.0    https://ftpmirror.gnu.org/octave/octave-4.0.0.tar.gz

Deprecated versions:
   None

Variants:
   arpack [false]                  false, true
       Use arpack
   build_system [autotools]        autotools
       Build systems supported by the package
   bz2 [true]                      false, true
       Use bzip2
   curl [false]                    false, true
       Use curl
   fftw [false]                    false, true
       Use FFTW3
   fltk [false]                    false, true
       Use FLTK

...

Build Dependencies:
   arpack-ng  bzip2  fftw-api  fontconfig  gl     glpk   gnuconfig  hdf5         java    llvm  pcre2      qhull     qscintilla  readline      texinfo
   blas       curl   fltk      freetype    gl2ps  gmake  gnuplot    imagemagick  lapack  pcre  pkgconfig  qrupdate  qt          suite-sparse  zlib-api

Link Dependencies:
   arpack-ng  bzip2  fftw-api  fontconfig  gl     glpk     hdf5         java    llvm  pcre2  qrupdate    qt        suite-sparse
   blas       curl   fltk      freetype    gl2ps  gnuplot  imagemagick  lapack  pcre  qhull  qscintilla  readline  zlib-api

Run Dependencies:
   None

Licenses:
GPL-3.0-or-later

Install a software

Note

N.B.: Error during ncurses installation on AFS

If a software depends on ncurses package then software installation by means spack will be not completed and an error message will be reported as following:

/usr/sbin/ldconfig: Can't create temporary cache file /etc/ld.so.cache~: Permission denied

This event is known on ncurses documentation by this note:

“USING NCURSES WITH AFS: AFS treats each directory as a separate logical filesystem, you can’t hard-link across them. The –enable-symlinks option copes with this by making tic use symbolic links.”

Workaround: From https://github.com/spack/spack/issues/8675 a simple way to install ncurses via spack is to enabling the the use of symbolic links creation instead hard links, i.e: spack install ncurses+symlinks

By default, spack creates an hidden directory named .spack into user home. Below, an example of octave installation via spack by workaround ncurses error:

  <user@cresco7x001 ~> spack install octave^ncurses+symlinks
  [+] /usr (external glibc-2.34-l3ukyqeboaxys3yum525zfxkzbsuljrh)
  [+] /userhome/.spack/opt/spack/linux-almalinux9-skylake_avx512/gcc-11.3.1/gcc-runtime-11.3.1-aphao5cskj5j7lufcrn23sn7vo3as2jb
  [+] /userhome/.spack/opt/spack/linux-almalinux9-skylake_avx512/gcc-11.3.1/pcre2-10.43-6iugizgfqsvaj5cu7hecjgis72pu5evi
  [+] /userhome/.spack/opt/spack/linux-almalinux9-skylake_avx512/gcc-11.3.1/ncurses-6.5-4la6oeefwiying2qbaq52jg5uk6csnvs
  [+] /userhome/.spack/opt/spack/linux-almalinux9-skylake_avx512/gcc-11.3.1/openblas-0.3.27-u5zltiouimdktyfm2rbpuoh4fcrihc5m
  [+] /userhome/.spack/opt/spack/linux-almalinux9-skylake_avx512/gcc-11.3.1/bzip2-1.0.8-dlk26nltz2kcgtg5rnkwiy3yrdov62cm
  [+] /userhome/.spack/opt/spack/linux-almalinux9-skylake_avx512/gcc-11.3.1/readline-8.2-ikqnu623xqzlzunqonnf3z4reut4ob5b
  [+] /userhome/.spack/opt/spack/linux-almalinux9-skylake_avx512/gcc-11.3.1/octave-9.1.0-x5dmrnjlfmvexwqvlppje2mrp7plql32

  <user@cresco7x001 ~> mv .spack .spack_20241015
  <user@cresco7x001 ~> spack install octave^ncurses+symlinks
  ==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-bhqgwuvef354fwuxq7heeighavunpber.spec.json
  ==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64/gcc-10.2.1/clingo-bootstrap-spack/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-bhqgwuvef354fw
  uxq7heeighavunpber.spack
  ==> Installing "clingo-bootstrap@=spack%gcc@=10.2.1~docs+ipo+optimized+python+static_libstdcpp build_system=cmake build_type=Release generator=make patches=bebb819,ec99431 arch=linux-centos7-x86_64" from
  a buildcache
  [+] /usr (external glibc-2.34-l3ukyqeboaxys3yum525zfxkzbsuljrh)
  ==> Installing gcc-runtime-11.3.1-aphao5cskj5j7lufcrn23sn7vo3as2jb [2/22]

  ...

  ==> octave: Executing phase: 'build'
  ==> octave: Executing phase: 'install'
  ==> octave: Successfully installed octave-9.1.0-x5dmrnjlfmvexwqvlppje2mrp7plql32
Stage: 1.12s.  Autoreconf: 0.00s.  Configure: 1m 5.71s.  Build: 4m 15.51s.  Install: 33.36s.  Post-install: 2.86s.  Total: 5m 59.14s
  [+] /userhome/.spack/opt/spack/linux-almalinux9-skylake_avx512/gcc-11.3.1/octave-9.1.0-x5dmrnjlfmvexwqvlppje2mrp7plql32

Launch a software

<user@cresco7x001 ~> spack load octave
<user@cresco7x001 ~> octave

GNU Octave, version 9.1.0
Copyright (C) 1993-2024 The Octave Project Developers.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  For details, type 'warranty'.

Octave was configured for "x86_64-pc-linux-gnu".

Home page:            https://octave.org
Support resources:    https://octave.org/support
Improve Octave:       https://octave.org/get-involved

For changes from previous versions, type 'news'.

octave:1>

Additional Information

Source URL:

Links

https://spack.readthedocs.io/en/latest/