242 lines
10 KiB
Scheme
242 lines
10 KiB
Scheme
;;; 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, 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, 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.
|
|
;;;
|
|
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
|
;;; under the terms of the GNU General Public License as published by
|
|
;;; the Free Software Foundation; either version 3 of the License, or (at
|
|
;;; your option) any later version.
|
|
;;;
|
|
;;; GNU Guix is distributed in the hope that it will be useful, but
|
|
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
;;; GNU General Public License for more details.
|
|
;;;
|
|
;;; You should have received a copy of the GNU General Public License
|
|
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
(define-module (gnu packages parallel)
|
|
#: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 packages)
|
|
#:use-module (gnu packages)
|
|
#:use-module (gnu packages admin)
|
|
#:use-module (gnu packages autotools)
|
|
#:use-module (gnu packages base)
|
|
#:use-module (gnu packages freeipmi)
|
|
#:use-module (gnu packages linux)
|
|
#:use-module (gnu packages mpi)
|
|
#:use-module (gnu packages perl)
|
|
#:use-module (gnu packages pkg-config)
|
|
#:use-module (gnu packages python)
|
|
#:use-module (gnu packages python-xyz)
|
|
#:use-module (gnu packages readline)
|
|
#:use-module (gnu packages tcl)
|
|
#:use-module (gnu packages tls)
|
|
#:use-module (gnu packages web))
|
|
|
|
(define-public parallel
|
|
(package
|
|
(name "parallel")
|
|
(version "20190522")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/parallel/parallel-"
|
|
version ".tar.bz2"))
|
|
(sha256
|
|
(base32 "0y3z9wybs3gak3zwgsby8r5gg6dwd3qlrkch0q4fn0i1j1jhmijv"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'patch-bin-sh
|
|
(lambda _
|
|
(for-each
|
|
(lambda (file)
|
|
(substitute* file
|
|
;; 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"))))
|
|
(list "src/parallel" "src/sem"))
|
|
#t))
|
|
(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)
|
|
(invoke (string-append
|
|
(assoc-ref outputs "out") "/bin/parallel")
|
|
"echo"
|
|
":::" "1" "2" "3"))))))
|
|
(inputs
|
|
`(("perl" ,perl)
|
|
("procps" ,procps)))
|
|
(home-page "https://www.gnu.org/software/parallel/")
|
|
(synopsis "Build and execute command lines in parallel")
|
|
(description
|
|
"GNU Parallel is a tool for executing shell jobs in parallel using one
|
|
or more computers. Jobs can consist of single commands or of scripts
|
|
and they are executed on lists of files, hosts, users or other items.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public slurm
|
|
(package
|
|
(name "slurm")
|
|
(version "17.11.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://download.schedmd.com/slurm/slurm-"
|
|
version ".tar.bz2"))
|
|
(sha256
|
|
(base32
|
|
"1x3i6z03d9m46fvj1cslrapm1drvgyqch9pn4xf23kvbz4gkhaps"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
(substitute* "configure.ac"
|
|
(("^[[:space:]]+contribs/.*$") ""))
|
|
(delete-file-recursively "contribs")
|
|
#t))))
|
|
;; FIXME: More optional inputs could be added,
|
|
;; in particular mysql and gtk+.
|
|
(inputs `(("expect" ,expect)
|
|
("freeipmi" ,freeipmi)
|
|
("hwloc" ,hwloc "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)))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:configure-flags
|
|
(list "--enable-pam" "--sysconfdir=/etc/slurm"
|
|
(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")))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'autoconf
|
|
(lambda _ (invoke "autoconf")))))) ; configure.ac was patched
|
|
(home-page "https://slurm.schedmd.com/")
|
|
(synopsis "Workload manager for cluster computing")
|
|
(description
|
|
"SLURM is a fault-tolerant and highly scalable cluster management and job
|
|
scheduling system for large and small clusters. It allocates access to
|
|
resources (computer nodes) to users for some duration of time, provides a
|
|
framework for starting, executing, and monitoring work (typically a parallel
|
|
job) on a set of allocated nodes, and arbitrates contention for resources
|
|
by managing a queue of pending work.")
|
|
(license (list license:bsd-2 ; src/common/log.[ch], src/common/uthash
|
|
license:expat ; slurm/pmi.h
|
|
license:isc ; src/common/strlcpy.c
|
|
license:lgpl2.1+ ; hilbert.[ch], src/common/slurm_time.h
|
|
license:zlib ; src/common/strnatcmp.c
|
|
license:gpl2+)))) ; the rest, often with OpenSSL exception
|
|
|
|
(define-public slurm-drmaa
|
|
(package
|
|
(name "slurm-drmaa")
|
|
(version "1.0.7")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri "http://apps.man.poznan.pl/trac/slurm-drmaa/downloads/9")
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0grw55hmny2mc4nc0y1arnvxd2k0dcdfn476kzs180fibjxgfw14"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("slurm" ,slurm)))
|
|
(native-inputs
|
|
`(("which" ,which)))
|
|
(home-page "http://apps.man.poznan.pl/trac/slurm-drmaa")
|
|
(synopsis "Distributed resource management application API for SLURM")
|
|
(description
|
|
"PSNC DRMAA for Simple Linux Utility for Resource Management (SLURM) is
|
|
an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource
|
|
Management Application API) specification for submission and control of jobs
|
|
to SLURM. Using DRMAA, grid applications builders, portal developers and ISVs
|
|
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))))
|