* [bug#74572] [PATCH 1/6] gnu: openmpi-5: Update to 5.0.6.
2024-11-28 6:24 [bug#74572] [PATCH 0/6] ] Python bindings, reduced size for OpenPMIx/OpenMPI Maxim Cournoyer
@ 2024-11-28 7:47 ` Maxim Cournoyer
2024-11-28 7:47 ` [bug#74572] [PATCH 2/6] gnu: openpmix: Enable Python bindings Maxim Cournoyer
` (4 subsequent siblings)
5 siblings, 0 replies; 7+ messages in thread
From: Maxim Cournoyer @ 2024-11-28 7:47 UTC (permalink / raw)
To: 74572; +Cc: Maxim Cournoyer, Maxim Cournoyer
* gnu/packages/mpi.scm (openmpi-5): Update to 5.0.6.
Change-Id: I132b1aaeee4d7a760301582013575a5ea99f03a1
---
gnu/packages/mpi.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 20497242e5..41e57c3012 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -318,7 +318,7 @@ (define-public openmpi openmpi-4)
(define-public openmpi-5
(package
(inherit openmpi)
- (version "5.0.3")
+ (version "5.0.6")
(source
(origin
(method url-fetch)
@@ -326,7 +326,7 @@ (define-public openmpi-5
(version-major+minor version)
"/downloads/openmpi-" version ".tar.bz2"))
(sha256
- (base32 "02x9xmpggw77mdpikjjx83j6i4v3gkqbncda73lk5axk0vr841cr"))))
+ (base32 "0mw1z4ppnlvxngwd58kl5q26qmvf3bgjkd4r8wjpqis3pky86hdx"))))
(inputs (modify-inputs (package-inputs openmpi)
;; As of Open MPI 5.0.X, PMIx is used to communicate
--
2.46.0
^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#74572] [PATCH 2/6] gnu: openpmix: Enable Python bindings.
2024-11-28 6:24 [bug#74572] [PATCH 0/6] ] Python bindings, reduced size for OpenPMIx/OpenMPI Maxim Cournoyer
2024-11-28 7:47 ` [bug#74572] [PATCH 1/6] gnu: openmpi-5: Update to 5.0.6 Maxim Cournoyer
@ 2024-11-28 7:47 ` Maxim Cournoyer
2024-11-28 7:47 ` [bug#74572] [PATCH 3/6] gnu: openpmix: Fix indentation Maxim Cournoyer
` (3 subsequent siblings)
5 siblings, 0 replies; 7+ messages in thread
From: Maxim Cournoyer @ 2024-11-28 7:47 UTC (permalink / raw)
To: 74572; +Cc: Maxim Cournoyer, Maxim Cournoyer
* gnu/packages/parallel.scm (openpmix)
[arguments] <configure-flags>: Add '--enable-python-bindings'.
<phases>: Add set-LDFLAGS phase.
[native-inputs]: Add python-cython.
Change-Id: I6910ed9c3c7b47b3a76085b95b1f251286a48077
---
gnu/packages/parallel.scm | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index e508dc6493..6a16f0e4c0 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -16,6 +16,7 @@
;;; Copyright © 2024 David Elsing <david.elsing@posteo.net>
;;; Copyright © 2024 Romain Garbage <romain.garbage@inria.fr>
;;; Copyright © 2024 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -709,14 +710,20 @@ (define-public openpmix
(arguments
(list #:configure-flags
#~(list (string-append "--with-hwloc="
- (ungexp (this-package-input "hwloc") "lib")))
+ (ungexp (this-package-input "hwloc") "lib"))
+ "--enable-python-bindings") ;disabled by default
;; Don't keep a reference to GCC.
#:disallowed-references (and (not (%current-target-system))
(list (canonical-package gcc)))
-
#:phases
#~(modify-phases %standard-phases
+ (add-after 'unpack 'set-LDFLAGS
+ (lambda _
+ ;; The Cython-compiled shared library would fail the
+ ;; validate-runpath phase otherwise.
+ (setenv "LDFLAGS"
+ (string-append "-Wl,-rpath=" #$output "/lib"))))
(add-before 'configure 'strip-pmix-cc-absolute
(lambda _
;; The 'pmix_info' program prints the 'configure' command
@@ -733,7 +740,7 @@ (define-public openpmix
(("#define PMIX_CONFIGURE_CLI .*")
"#define PMIX_CONFIGURE_CLI \"[scrubbed]\"\n")))))))
(inputs (list libevent `(,hwloc "lib") zlib))
- (native-inputs (list perl python))
+ (native-inputs (list perl python python-cython))
(synopsis "PMIx library")
(description
"PMIx is an application programming interface standard that provides
--
2.46.0
^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#74572] [PATCH 3/6] gnu: openpmix: Fix indentation.
2024-11-28 6:24 [bug#74572] [PATCH 0/6] ] Python bindings, reduced size for OpenPMIx/OpenMPI Maxim Cournoyer
2024-11-28 7:47 ` [bug#74572] [PATCH 1/6] gnu: openmpi-5: Update to 5.0.6 Maxim Cournoyer
2024-11-28 7:47 ` [bug#74572] [PATCH 2/6] gnu: openpmix: Enable Python bindings Maxim Cournoyer
@ 2024-11-28 7:47 ` Maxim Cournoyer
2024-11-28 7:47 ` [bug#74572] [PATCH 4/6] gnu: openpmix: Do not install HTML documentation Maxim Cournoyer
` (2 subsequent siblings)
5 siblings, 0 replies; 7+ messages in thread
From: Maxim Cournoyer @ 2024-11-28 7:47 UTC (permalink / raw)
To: 74572; +Cc: Maxim Cournoyer, Maxim Cournoyer
* gnu/packages/parallel.scm (openpmix): Fix indentation.
Change-Id: I05751408847343ac593e666afc5f1efbbef94a79
---
gnu/packages/parallel.scm | 106 +++++++++++++++++++-------------------
1 file changed, 53 insertions(+), 53 deletions(-)
diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 6a16f0e4c0..3e50a75047 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -696,61 +696,61 @@ (define-public psimd
(define-public openpmix
(package
- (name "openpmix")
- (version "4.2.8")
- (source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/openpmix/openpmix/releases/download/v"
- version "/pmix-" version ".tar.bz2"))
- (sha256
- (base32
- "1j9xlhqrrmgjdkwakamn78y5gj756adi53hn25zksgr3is3l5d09"))))
- (build-system gnu-build-system)
- (arguments
- (list #:configure-flags
- #~(list (string-append "--with-hwloc="
- (ungexp (this-package-input "hwloc") "lib"))
- "--enable-python-bindings") ;disabled by default
-
- ;; Don't keep a reference to GCC.
- #:disallowed-references (and (not (%current-target-system))
- (list (canonical-package gcc)))
- #:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'set-LDFLAGS
- (lambda _
- ;; The Cython-compiled shared library would fail the
- ;; validate-runpath phase otherwise.
- (setenv "LDFLAGS"
- (string-append "-Wl,-rpath=" #$output "/lib"))))
- (add-before 'configure 'strip-pmix-cc-absolute
- (lambda _
- ;; The 'pmix_info' program prints the 'configure' command
- ;; line, compiler absolute file name, etc., which causes it
- ;; to keep references to many build-time packages. Scrub
- ;; these.
- (substitute* "configure"
- (("PMIX_CC_ABSOLUTE=\"(.*)\"" _ cc)
- (string-append "PMIX_CC_ABSOLUTE=\"$(basename \""
- cc "\")\"\n")))))
- (add-after 'configure 'strip-pmix-config-header
- (lambda _
- (substitute* "src/include/pmix_config.h"
- (("#define PMIX_CONFIGURE_CLI .*")
- "#define PMIX_CONFIGURE_CLI \"[scrubbed]\"\n")))))))
- (inputs (list libevent `(,hwloc "lib") zlib))
- (native-inputs (list perl python python-cython))
- (synopsis "PMIx library")
- (description
- "PMIx is an application programming interface standard that provides
+ (name "openpmix")
+ (version "4.2.8")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/openpmix/openpmix/releases/download/v"
+ version "/pmix-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "1j9xlhqrrmgjdkwakamn78y5gj756adi53hn25zksgr3is3l5d09"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:configure-flags
+ #~(list (string-append "--with-hwloc="
+ (ungexp (this-package-input "hwloc") "lib"))
+ "--enable-python-bindings") ;disabled by default
+
+ ;; Don't keep a reference to GCC.
+ #:disallowed-references (and (not (%current-target-system))
+ (list (canonical-package gcc)))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'set-LDFLAGS
+ (lambda _
+ ;; The Cython-compiled shared library would fail the
+ ;; validate-runpath phase otherwise.
+ (setenv "LDFLAGS"
+ (string-append "-Wl,-rpath=" #$output "/lib"))))
+ (add-before 'configure 'strip-pmix-cc-absolute
+ (lambda _
+ ;; The 'pmix_info' program prints the 'configure' command line,
+ ;; compiler absolute file name, etc., which causes it to keep
+ ;; references to many build-time packages. Scrub these.
+ (substitute* "configure"
+ (("PMIX_CC_ABSOLUTE=\"(.*)\"" _ cc)
+ (string-append "PMIX_CC_ABSOLUTE=\"$(basename \""
+ cc "\")\"\n")))))
+ (add-after 'configure 'strip-pmix-config-header
+ (lambda _
+ (substitute* "src/include/pmix_config.h"
+ (("#define PMIX_CONFIGURE_CLI .*")
+ "#define PMIX_CONFIGURE_CLI \"[scrubbed]\"\n")))))))
+ (inputs (list libevent `(,hwloc "lib") zlib))
+ (native-inputs (list perl python python-cython))
+ (synopsis "PMIx library")
+ (description
+ "PMIx is an application programming interface standard that provides
libraries and programming models with portable and well-defined access to
commonly needed services in distributed and parallel computing systems.")
- (home-page "https://pmix.org/")
- ;; configure: WARNING: PMIx does not support 32 bit builds.
- (supported-systems %64bit-supported-systems)
- ;; The provided license is kind of BSD-style but specific.
- (license (license:fsf-free "https://github.com/openpmix/openpmix?tab=License-1-ov-file#License-1-ov-file"))))
+ (home-page "https://pmix.org/")
+ ;; configure: WARNING: PMIx does not support 32 bit builds.
+ (supported-systems %64bit-supported-systems)
+ ;; The provided license is kind of BSD-style but specific.
+ (license (license:fsf-free "https://github.com/openpmix/openpmix?tab=License-1-ov-file#License-1-ov-file"))))
(define-public prrte
(package
--
2.46.0
^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#74572] [PATCH 4/6] gnu: openpmix: Do not install HTML documentation.
2024-11-28 6:24 [bug#74572] [PATCH 0/6] ] Python bindings, reduced size for OpenPMIx/OpenMPI Maxim Cournoyer
` (2 preceding siblings ...)
2024-11-28 7:47 ` [bug#74572] [PATCH 3/6] gnu: openpmix: Fix indentation Maxim Cournoyer
@ 2024-11-28 7:47 ` Maxim Cournoyer
2024-11-28 7:47 ` [bug#74572] [PATCH 5/6] gnu: openmpi-5: Reformat Maxim Cournoyer
2024-11-28 7:47 ` [bug#74572] [PATCH 6/6] gnu: openmpi-5: Streamline source and do not install HTML doc Maxim Cournoyer
5 siblings, 0 replies; 7+ messages in thread
From: Maxim Cournoyer @ 2024-11-28 7:47 UTC (permalink / raw)
To: 74572; +Cc: Maxim Cournoyer, Maxim Cournoyer
This reduces the package size from 9 MiB to 5 MiB.
* gnu/packages/parallel.scm (openpmix) [source]: Add snippet.
Change-Id: I36e4a1e456225588df96f5eb70ed607505dae493
---
gnu/packages/parallel.scm | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/parallel.scm b/gnu/packages/parallel.scm
index 3e50a75047..a6119743ce 100644
--- a/gnu/packages/parallel.scm
+++ b/gnu/packages/parallel.scm
@@ -705,7 +705,11 @@ (define-public openpmix
version "/pmix-" version ".tar.bz2"))
(sha256
(base32
- "1j9xlhqrrmgjdkwakamn78y5gj756adi53hn25zksgr3is3l5d09"))))
+ "1j9xlhqrrmgjdkwakamn78y5gj756adi53hn25zksgr3is3l5d09"))
+ (snippet
+ '(begin (use-modules (guix build utils))
+ ;; Remove ~5 MiB of pre-built HTML doc.
+ (delete-file-recursively "docs/_build/html")))))
(build-system gnu-build-system)
(arguments
(list
--
2.46.0
^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#74572] [PATCH 5/6] gnu: openmpi-5: Reformat.
2024-11-28 6:24 [bug#74572] [PATCH 0/6] ] Python bindings, reduced size for OpenPMIx/OpenMPI Maxim Cournoyer
` (3 preceding siblings ...)
2024-11-28 7:47 ` [bug#74572] [PATCH 4/6] gnu: openpmix: Do not install HTML documentation Maxim Cournoyer
@ 2024-11-28 7:47 ` Maxim Cournoyer
2024-11-28 7:47 ` [bug#74572] [PATCH 6/6] gnu: openmpi-5: Streamline source and do not install HTML doc Maxim Cournoyer
5 siblings, 0 replies; 7+ messages in thread
From: Maxim Cournoyer @ 2024-11-28 7:47 UTC (permalink / raw)
To: 74572; +Cc: Maxim Cournoyer, Maxim Cournoyer
Better comply to our 80 characters maximum width guideline.
* gnu/packages/mpi.scm (openmpi-5): Reformat.
Change-Id: Ib164c4d7dae7bece60738787fd950003fb75e057
---
gnu/packages/mpi.scm | 103 ++++++++++++++++++++++---------------------
1 file changed, 53 insertions(+), 50 deletions(-)
diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 41e57c3012..67e12657db 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -328,59 +328,62 @@ (define-public openmpi-5
(sha256
(base32 "0mw1z4ppnlvxngwd58kl5q26qmvf3bgjkd4r8wjpqis3pky86hdx"))))
- (inputs (modify-inputs (package-inputs openmpi)
- ;; As of Open MPI 5.0.X, PMIx is used to communicate
- ;; with SLURM, so SLURM'S PMI is no longer needed.
- (delete "slurm")
- (append ucx) ;for Infiniband support
- (append openpmix) ;for PMI support (launching via "srun")
- (append prrte))) ;for PMI support (launching via "srun")
- (native-inputs (modify-inputs (package-native-inputs openmpi)
- (append python)))
+ (inputs
+ (modify-inputs (package-inputs openmpi)
+ ;; As of Open MPI 5.0.X, PMIx is used to communicate with SLURM, so
+ ;; SLURM'S PMI is no longer needed.
+ (delete "slurm")
+ (append ucx) ;for Infiniband support
+ (append openpmix) ;for PMI support (launching via "srun")
+ (append prrte))) ;for PMI support (launching via "srun")
+ (native-inputs
+ (modify-inputs (package-native-inputs openmpi)
+ (append python)))
(outputs '("out" "debug"))
(arguments
- (list #:configure-flags
- #~(list "--enable-mpi-ext=affinity" ;cr doesn't work
- "--with-sge"
- "--disable-static"
-
- #$@(if (package? (this-package-input "valgrind"))
- #~("--enable-memchecker"
- "--with-valgrind")
- #~("--without-valgrind"))
-
- "--with-hwloc=external"
- "--with-libevent"
-
- ;; This replaces --enable-mpirun-prefix-by-default wich is deprecated
- ;; since 5.x.
- "--enable-prte-prefix-by-default"
-
- ;; Enable support for the 'Process Management Interface for Exascale'
- ;; (PMIx) used e.g. by Slurm for the management communication and
- ;; coordination of MPI processes.
- (string-append "--with-pmix=" #$(this-package-input "openpmix"))
- (string-append "--with-prrte=" #$(this-package-input "prrte"))
-
- ;; Since 5.x, Infiniband support is provided by ucx.
- ;; See https://docs.open-mpi.org/en/main/release-notes/networks.html#miscellaneous-network-notes
- (string-append "--with-ucx=" #$(this-package-input "ucx")))
-
- #:phases
- #~(modify-phases %standard-phases
- (add-before 'build 'remove-absolute
- (lambda _
- ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE
- ;; etc.) to reduce the closure size. See
- ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html>
- ;; and
- ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>.
- (substitute* '("oshmem/tools/oshmem_info/param.c"
- "ompi/tools/ompi_info/param.c")
- (("_ABSOLUTE") "")))))
-
- #:disallowed-references (list (canonical-package gcc))))))
+ (list
+ #:configure-flags
+ #~(list "--enable-mpi-ext=affinity" ;cr doesn't work
+ "--with-sge"
+ "--disable-static"
+
+ #$@(if (package? (this-package-input "valgrind"))
+ #~("--enable-memchecker"
+ "--with-valgrind")
+ #~("--without-valgrind"))
+
+ "--with-hwloc=external"
+ "--with-libevent"
+
+ ;; This replaces --enable-mpirun-prefix-by-default wich is
+ ;; deprecated since 5.x.
+ "--enable-prte-prefix-by-default"
+
+ ;; Enable support for the 'Process Management Interface for
+ ;; Exascale' (PMIx) used e.g. by Slurm for the management
+ ;; communication and coordination of MPI processes.
+ (string-append "--with-pmix=" #$(this-package-input "openpmix"))
+ (string-append "--with-prrte=" #$(this-package-input "prrte"))
+
+ ;; Since 5.x, Infiniband support is provided by ucx. See
+ ;; https://docs.open-mpi.org/en/main/release-notes/networks.html#miscellaneous-network-notes
+ (string-append "--with-ucx=" #$(this-package-input "ucx")))
+
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'build 'remove-absolute
+ (lambda _
+ ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE etc.)
+ ;; to reduce the closure size. See
+ ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html>
+ ;; and
+ ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>.
+ (substitute* '("oshmem/tools/oshmem_info/param.c"
+ "ompi/tools/ompi_info/param.c")
+ (("_ABSOLUTE") "")))))
+
+ #:disallowed-references (list (canonical-package gcc))))))
(define-public openmpi-c++
(package/inherit openmpi
--
2.46.0
^ permalink raw reply related [flat|nested] 7+ messages in thread* [bug#74572] [PATCH 6/6] gnu: openmpi-5: Streamline source and do not install HTML doc.
2024-11-28 6:24 [bug#74572] [PATCH 0/6] ] Python bindings, reduced size for OpenPMIx/OpenMPI Maxim Cournoyer
` (4 preceding siblings ...)
2024-11-28 7:47 ` [bug#74572] [PATCH 5/6] gnu: openmpi-5: Reformat Maxim Cournoyer
@ 2024-11-28 7:47 ` Maxim Cournoyer
5 siblings, 0 replies; 7+ messages in thread
From: Maxim Cournoyer @ 2024-11-28 7:47 UTC (permalink / raw)
To: 74572; +Cc: Maxim Cournoyer, Maxim Cournoyer
This reduces the installed package size by 63 MiB.
* gnu/packages/mpi.scm (openmpi-5) [source]: Add modules, snippet fields.
Change-Id: Ie3dc365a2e4e48dc4c385dd447d3c64b7db065ca
---
gnu/packages/mpi.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 67e12657db..2f37364ef3 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -325,6 +325,31 @@ (define-public openmpi-5
(uri (string-append "https://www.open-mpi.org/software/ompi/v"
(version-major+minor version)
"/downloads/openmpi-" version ".tar.bz2"))
+ (modules '((guix build utils)
+ (ice-9 ftw)
+ (srfi srfi-26)))
+ (snippet
+ '(begin
+ ;; XXX: 'delete-all-but' is copied from the turbovnc package.
+ (define (delete-all-but directory . preserve)
+ (define (directory? x)
+ (and=> (stat x #f)
+ (compose (cut eq? 'directory <>) stat:type)))
+ (with-directory-excursion directory
+ (let* ((pred
+ (negate (cut member <> (append '("." "..") preserve))))
+ (items (scandir "." pred)))
+ (for-each (lambda (item)
+ (if (directory? item)
+ (delete-file-recursively item)
+ (delete-file item)))
+ items))))
+ ;; Delete as many bundled libraries as permitted by the build
+ ;; system.
+ (delete-all-but "3rd-party" "treematch" "Makefile.in" "Makefile.am")
+ ;; Do not install 64 MiB worth fo pre-generated HTML
+ ;; documentation.
+ (delete-file-recursively "docs/html")))
(sha256
(base32 "0mw1z4ppnlvxngwd58kl5q26qmvf3bgjkd4r8wjpqis3pky86hdx"))))
--
2.46.0
^ permalink raw reply related [flat|nested] 7+ messages in thread