;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2013, 2014, 2020 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
-;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2019, 2020 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
;;;
;;; This file is part of GNU Guix.
;;;
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages parallel)
- #:use-module (guix build-system gnu)
#:use-module (guix download)
+ #:use-module (guix git-download)
+ #:use-module (guix build-system gnu)
+ #:use-module (guix build-system python)
#:use-module ((guix licenses) #:prefix license:)
+ #:use-module ((guix utils) #:select (target-64bit?))
#:use-module (guix packages)
+ #:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (gnu packages admin)
#:use-module (gnu packages autotools)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-science)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
(define-public parallel
(package
(name "parallel")
- (version "20190422")
+ (version "20210322")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/parallel/parallel-"
version ".tar.bz2"))
(sha256
- (base32 "0xdl5fnh1vpjp3zpmqsrbbgjixazlhl4d9awk42nz4snzynysjxl"))))
+ (base32 "152np0jg4n94sbl2p2fzxjfnssiyp5sg7r5wx6s8p893b921pxwq"))))
(build-system gnu-build-system)
(arguments
`(#:phases
and they are executed on lists of files, hosts, users or other items.")
(license license:gpl3+)))
+(define-public xe
+ (package
+ (name "xe")
+ (version "0.11")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/leahneukirchen/xe")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "04jr8f6jcijr0bsmn8ajm0aj35qh9my3xjsaq64h8lwg5bpyn29x"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f
+ #:make-flags (list (string-append "CC=" ,(cc-for-target))
+ (string-append "PREFIX=" %output))
+ #:phases (modify-phases %standard-phases
+ (delete 'configure))))
+ (synopsis "Execute a command for every argument")
+ (description
+ "The xe utility constructs command lines from specified arguments,
+combining some of the best features of xargs(1) and apply(1). Parallel
+execution is also possible.")
+ (home-page "https://github.com/leahneukirchen/xe")
+ (license license:public-domain)))
+
(define-public slurm
(package
(name "slurm")
- (version "17.11.3")
+ (version "20.11.3")
(source (origin
(method url-fetch)
(uri (string-append
version ".tar.bz2"))
(sha256
(base32
- "1x3i6z03d9m46fvj1cslrapm1drvgyqch9pn4xf23kvbz4gkhaps"))
+ "1s70x6yh60sx63dgmp5rlhq8jcz7kxv9pk8gbs9v1jg8zps5h5bk"))
(modules '((guix build utils)))
(snippet
'(begin
+ ;; According to
+ ;; <https://lists.gnu.org/archive/html/guix-devel/2016-02/msg00534.html>
+ ;; there are non-free bits under contribs/, though it's not
+ ;; clear which ones. libpmi is clearly free (it used to be
+ ;; under src/api/), so remove all of contribs/ except
+ ;; contribs/pmi/.
(substitute* "configure.ac"
- (("^[[:space:]]+contribs/.*$") ""))
+ (("^[[:space:]]+contribs/(.*)$" all directory)
+ (if (and (string-prefix? "pmi" directory)
+ (not (string-prefix? "pmi2" directory)))
+ all
+ "")))
+
+ (rename-file "contribs/pmi" "tmp-pmi")
(delete-file-recursively "contribs")
+ (mkdir "contribs")
+ (rename-file "tmp-pmi" "contribs/pmi")
#t))))
;; FIXME: More optional inputs could be added,
;; in particular mysql and gtk+.
- (inputs `(("expect" ,expect)
- ("freeipmi" ,freeipmi)
- ("hwloc" ,hwloc "lib")
+ (inputs `(("freeipmi" ,freeipmi)
+ ("hwloc" ,hwloc-2 "lib")
("json-c" ,json-c)
("linux-pam" , linux-pam)
("munge" ,munge)
("numactl" ,numactl)
- ("openssl" ,openssl)
- ("perl" ,perl)
- ("python" ,python-wrapper)
("readline" ,readline)))
(native-inputs
`(("autoconf" ,autoconf)
- ("pkg-config" ,pkg-config)))
+ ("expect" ,expect)
+ ("perl" ,perl)
+ ("pkg-config" ,pkg-config)
+ ("python" ,python-wrapper)))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
(list "--enable-pam" "--sysconfdir=/etc/slurm"
+ "--disable-static"
(string-append "--with-freeipmi=" (assoc-ref %build-inputs "freeipmi"))
(string-append "--with-hwloc=" (assoc-ref %build-inputs "hwloc"))
(string-append "--with-json=" (assoc-ref %build-inputs "json-c"))
(string-append "--with-munge=" (assoc-ref %build-inputs "munge"))
- (string-append "--with-ssl=" (assoc-ref %build-inputs "openssl")))
+
+ ;; 32-bit support is marked as deprecated and needs to be
+ ;; explicitly enabled.
+ ,@(if (target-64bit?) '() '("--enable-deprecated")))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autoconf
- (lambda _ (invoke "autoconf")))))) ; configure.ac was patched
+ (lambda _ (invoke "autoconf"))) ;configure.ac was patched
+ (add-after 'install 'install-libpmi
+ (lambda _
+ ;; Open MPI expects libpmi to be provided by Slurm so install it.
+ (invoke "make" "install" "-C" "contribs/pmi"))))))
(home-page "https://slurm.schedmd.com/")
(synopsis "Workload manager for cluster computing")
(description
license:zlib ; src/common/strnatcmp.c
license:gpl2+)))) ; the rest, often with OpenSSL exception
+;; The SLURM client/daemon protocol and file format changes from time to time
+;; in incompatible ways, as noted in
+;; <https://slurm.schedmd.com/troubleshoot.html#network>. Thus, keep older
+;; releases here. See also <https://issues.guix.gnu.org/44387>.
+;; As noted in the link, YY.MM is the release scheme, and the 'maintenance'
+;; digit does not introduce incompatibilities.
+
+(define-public slurm-20.02
+ (package
+ (inherit slurm)
+ (version "20.02.6-1")
+ (source (origin
+ (inherit (package-source slurm))
+ (method url-fetch)
+ (uri (string-append
+ "https://download.schedmd.com/slurm/slurm-"
+ version ".tar.bz2"))
+ (sha256
+ (base32
+ "0qj4blfymrd2ry2qmb58l3jbr4jwygc3adcfw7my27rippcijlyc"))))))
+
+(define-public slurm-19.05
+ (package
+ (inherit slurm)
+ (version "19.05.8")
+ (source (origin
+ (inherit (package-source slurm))
+ (method url-fetch)
+ (uri (string-append
+ "https://download.schedmd.com/slurm/slurm-"
+ version ".tar.bz2"))
+ (sha256
+ (base32
+ "10c9j4a9a6d4ibpf75006mn03p8xgpaprc247x2idakysjf2fw43"))))))
+
+;; Same as Debian 10
+(define-public slurm-18.08
+ (package
+ (inherit slurm)
+ (version "18.08.9")
+ (source
+ (origin
+ (inherit (package-source slurm))
+ (uri (string-append
+ "https://download.schedmd.com/slurm/slurm-"
+ version ".tar.bz2"))
+ (sha256
+ (base32
+ "1bgrpz75m7l4xhirsd0fvnkzlkrl8v2qpmjcz60barc5qm2kn457"))))))
+
(define-public slurm-drmaa
(package
(name "slurm-drmaa")
- (version "1.0.7")
+ (version "1.1.2")
(source (origin
(method url-fetch)
- (uri "http://apps.man.poznan.pl/trac/slurm-drmaa/downloads/9")
- (file-name (string-append name "-" version ".tar.gz"))
+ (uri (string-append
+ "https://github.com/natefoo/slurm-drmaa/releases/download/"
+ version "/slurm-drmaa-" version ".tar.gz"))
(sha256
(base32
- "0grw55hmny2mc4nc0y1arnvxd2k0dcdfn476kzs180fibjxgfw14"))))
+ "0dn8ypqxdaq3k4jqwwx7msckxnmr6n2z5j68yffp50yy07ajbzjv"))))
(build-system gnu-build-system)
+ (arguments `(#:tests? #f)) ; The tests require "bats".
(inputs
`(("slurm" ,slurm)))
(native-inputs
`(("which" ,which)))
- (home-page "http://apps.man.poznan.pl/trac/slurm-drmaa")
+ (home-page "https://github.com/natefoo/slurm-drmaa")
(synopsis "Distributed resource management application API for SLURM")
(description
"PSNC DRMAA for Simple Linux Utility for Resource Management (SLURM) is
can use the same high-level API to link their software with different
cluster/resource management systems.")
(license license:gpl3+)))
+
+(define-public python-slurm-magic
+ (let ((commit "73dd1a2b85799f7dae4b3f1cd9027536eff0c4d7")
+ (revision "0"))
+ (package
+ (name "python-slurm-magic")
+ (version (git-version "0.0" revision commit))
+ (home-page "https://github.com/NERSC/slurm-magic")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page)
+ (commit commit)))
+ (sha256
+ (base32
+ "19pp2vs0wm8mx0arz9n6lw9wgyv70w9wyi4y6b91qc5j3bz5igfs"))
+ (file-name (git-file-name name version))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases (modify-phases %standard-phases
+ (add-before 'build 'set-slurm-path
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; The '_execute' method tries to exec 'salloc'
+ ;; etc. from $PATH. Record the absolute file name
+ ;; instead.
+ (let ((slurm (assoc-ref inputs "slurm")))
+ (substitute* "slurm_magic.py"
+ (("name = (.*)$" _ value)
+ (string-append "name = \""
+ slurm "/bin/\" + "
+ value "\n")))
+ #t))))))
+ (inputs
+ `(("slurm" ,slurm)))
+ (propagated-inputs
+ `(("python-ipython" ,python-ipython)
+ ("python-pandas" ,python-pandas)))
+ (synopsis "Control the SLURM batch scheduler from Jupyter Notebook")
+ (description
+ "This package implements Jupyter/IPython
+@uref{http://ipython.readthedocs.io/en/stable/interactive/magics.html, magic
+commands} for interacting with the SLURM workload manager. SLURM magic simply
+wraps command-line executables and the commands themselves should look like
+their command-line counterparts. Commands are spawned via @code{subprocess}
+and output captured in the notebook. Whatever arguments are accepted by a
+SLURM command line executable are also accepted by the corresponding magic
+command---e.g., @code{%salloc}, @code{%sbatch}, etc.")
+ (license license:bsd-3))))
HCoop / jackhill / guix / guix.git / blobdiff