[bug#74572] [PATCH 0/6] ] Python bindings, reduced size for OpenPMIx/OpenMPI.

[bug#74572] [PATCH 0/6] ] Python bindings, reduced size for OpenPMIx/OpenMPI.

[Maxim Cournoyer]

Maxim Cournoyer (6):
  gnu: openmpi-5: Update to 5.0.6.
  gnu: openpmix: Enable Python bindings.
  gnu: openpmix: Fix indentation.
  gnu: openpmix: Do not install HTML documentation.
  gnu: openmpi-5: Reformat.
  gnu: openmpi-5: Streamline source and do not install HTML doc.

 gnu/packages/mpi.scm      | 134 +++++++++++++++++++++++---------------
 gnu/packages/parallel.scm | 105 ++++++++++++++++-------------
 2 files changed, 139 insertions(+), 100 deletions(-)


base-commit: 5ff9e51e2c4dae0dc74f5c85ec553e89fe1824fd
-- 
2.46.0

[bug#74572] [PATCH 1/6] gnu: openmpi-5: Update to 5.0.6.

[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

[bug#74572] [PATCH 2/6] gnu: openpmix: Enable Python bindings.

[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

[bug#74572] [PATCH 3/6] gnu: openpmix: Fix indentation.

[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

[bug#74572] [PATCH 4/6] gnu: openpmix: Do not install HTML documentation.

[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

[bug#74572] [PATCH 5/6] gnu: openmpi-5: Reformat.

[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

[bug#74572] [PATCH 6/6] gnu: openmpi-5: Streamline source and do not install HTML doc.

[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