;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016, 2017, 2018 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 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2017 Rutger Helling <rhelling@mykolab.com>
-;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
+;;; Copyright © 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
;;;
;;; 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 (gnu packages)
#:use-module (gnu packages admin)
#: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 "20180122")
+ (version "20191222")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/parallel/parallel-"
version ".tar.bz2"))
(sha256
- (base32
- "1wkkqghdjp9j2aqnrfh57kad1w41gdg7knhhlciczkm853f4d0sw"))))
+ (base32 "0xvw578440s9cc382n7z2l8npj30nwr6wwmkyxn2pj1pcszfjagy"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(for-each
(lambda (file)
(substitute* file
- ;; Patch hard coded '/bin/sh' in the lin ending in:
+ ;; Patch hard coded '/bin/sh' in the line ending in:
;; $Global::shell = $ENV{'PARALLEL_SHELL'} ||
;; parent_shell($$) || $ENV{'SHELL'} || "/bin/sh";
- (("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))
- ;; Patch call to 'ps' and 'perl' commands.
- ((" ps ") (string-append " " (which "ps") " "))
- ((" perl -") (string-append " " (which "perl") " -"))))
+ (("/bin/sh\\\";\n$") (string-append (which "sh") "\";\n"))))
(list "src/parallel" "src/sem"))
#t))
- (add-after 'install 'post-install-test
+ (add-after 'install 'wrap-program
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (wrap-program (string-append out "/bin/parallel")
+ `("PATH" ":" prefix
+ ,(map (lambda (input)
+ (string-append (assoc-ref inputs input) "/bin"))
+ '("perl"
+ "procps"))))
+ #t)))
+ (add-after 'wrap-program 'post-install-test
(lambda* (#:key outputs #:allow-other-keys)
- (zero? (system* (string-append
- (assoc-ref outputs "out") "/bin/parallel")
- "echo"
- ":::" "1" "2" "3")))))))
+ (invoke (string-append
+ (assoc-ref outputs "out") "/bin/parallel")
+ "echo"
+ ":::" "1" "2" "3"))))))
(inputs
`(("perl" ,perl)
("procps" ,procps)))
(define-public slurm
(package
(name "slurm")
- (version "17.11.2")
+ (version "19.05.3-2")
(source (origin
(method url-fetch)
(uri (string-append
version ".tar.bz2"))
(sha256
(base32
- "18yakb8kmhb16n0cv3zhjv8ahvsk9p0max8mmr2flb2c65fawks6"))
+ "0qj4blfymrd2ry2qmb58l3jbr4jwygc3adcfw7my27rippcijlyc"))
(modules '((guix build utils)))
(snippet
'(begin
+ ;; According to
+ ;; <https://lists.gnu.org/archive/html/guix-devel/2016-02/msg00534.html>
+ ;; there are non-free bits under contribs/, though it's not
+ ;; clear which ones. libpmi is clearly free (it used to be
+ ;; under src/api/), so remove all of contribs/ except
+ ;; contribs/pmi/.
(substitute* "configure.ac"
- (("^[[:space:]]+contribs/.*$") ""))
+ (("^[[: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")
+ ("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)))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
- (list "--enable-pam"
+ (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
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