diff options
Diffstat (limited to 'gnu/packages/mpi.scm')
| -rw-r--r-- | gnu/packages/mpi.scm | 211 |
1 files changed, 110 insertions, 101 deletions
diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm index 70b14c30b3..baef62616f 100644 --- a/gnu/packages/mpi.scm +++ b/gnu/packages/mpi.scm @@ -25,6 +25,7 @@ ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. (define-module (gnu packages mpi) + #:use-module (guix gexp) #:use-module (guix packages) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) @@ -53,8 +54,6 @@ #:use-module (ice-9 match)) (define-public hwloc-1 - ;; Note: For now we keep 1.x as the default because many packages have yet - ;; to migrate to 2.0. (package (name "hwloc") (version "1.11.13") @@ -140,7 +139,6 @@ bind processes, and much more.") (license license:bsd-3))) (define-public hwloc-2 - ;; Note: 2.x isn't the default yet, see above. (package (inherit hwloc-1) (version "2.9.0") @@ -167,10 +165,19 @@ bind processes, and much more.") (substitute* "tests/hwloc/linux-libnuma.c" (("numa_available\\(\\)") "-1")))) - (add-before 'check 'skip-test-that-requires-/sys + (add-before 'check 'skip-tests-that-require-/sys (lambda _ ;; 'test-gather-topology.sh' requires /sys as of 2.9.0; skip it. - (setenv "HWLOC_TEST_GATHER_TOPOLOGY" "0"))) + (setenv "HWLOC_TEST_GATHER_TOPOLOGY" "0") + + ;; 'hwloc_backends' also requires /sys on non-x86 systems, for + ;; which hwloc lacks a topology backend not reliant on the + ;; operating system; skip it also on these machines. + (substitute* "tests/hwloc/hwloc_backends.c" + ,@(if (not (target-x86?)) + '((("putenv\\(\\(char \\*\\) \"HWLOC_L" all) + (string-append "exit (77);\n" all))) + '())))) (add-before 'check 'skip-test-that-fails-on-qemu (lambda _ ;; Skip test that fails on emulated hardware due to QEMU bug: @@ -191,13 +198,13 @@ bind processes, and much more.") (version "4.1.4") (source (origin - (method url-fetch) - (uri (string-append "https://www.open-mpi.org/software/ompi/v" - (version-major+minor version) - "/downloads/openmpi-" version ".tar.bz2")) - (sha256 - (base32 "03ckngrff1cl0l81vfvrfhp99rbgk7s0633kr1l468yibwbjx4cj")) - (patches (search-patches "openmpi-mtl-priorities.patch")))) + (method url-fetch) + (uri (string-append "https://www.open-mpi.org/software/ompi/v" + (version-major+minor version) + "/downloads/openmpi-" version ".tar.bz2")) + (sha256 + (base32 "03ckngrff1cl0l81vfvrfhp99rbgk7s0633kr1l468yibwbjx4cj")) + (patches (search-patches "openmpi-mtl-priorities.patch")))) (properties ;; Tell the 'generic-html' updater to monitor this URL for updates. @@ -228,68 +235,69 @@ bind processes, and much more.") (list pkg-config perl)) (outputs '("out" "debug")) (arguments - `(#:configure-flags `("--enable-mpi-ext=affinity" ;cr doesn't work - "--with-sge" - - ,@(if ,(package? (this-package-input "valgrind")) - `("--enable-memchecker" - "--with-valgrind") - `("--without-valgrind")) - - "--with-hwloc=external" - "--with-libevent" - - ;; Help 'orterun' and 'mpirun' find their tools - ;; under $prefix by default. - "--enable-mpirun-prefix-by-default" - - ;; InfiniBand support - "--enable-openib-control-hdr-padding" - "--enable-openib-dynamic-sl" - "--enable-openib-udcm" - "--enable-openib-rdmacm" - "--enable-openib-rdmacm-ibaddr" - - ;; Enable support for SLURM's Process Manager - ;; Interface (PMI). - ,(string-append "--with-pmi=" - (assoc-ref %build-inputs "slurm"))) - #:phases (modify-phases %standard-phases - ;; opensm is needed for InfiniBand support. - (add-after 'unpack 'find-opensm-headers - (lambda* (#:key inputs #:allow-other-keys) - (setenv "C_INCLUDE_PATH" - (search-input-directory inputs - "/include/infiniband")) - (setenv "CPLUS_INCLUDE_PATH" - (search-input-directory inputs - "/include/infiniband")))) - (add-before 'build 'remove-absolute - (lambda _ - ;; Remove compiler absolute file names (OPAL_FC_ABSOLUTE - ;; etc.) to reduce the closure size. See - ;; <https://lists.gnu.org/archive/html/guix-devel/2017-07/msg00388.html> - ;; and - ;; <https://www.mail-archive.com/users@lists.open-mpi.org//msg31397.html>. - (substitute* '("orte/tools/orte-info/param.c" - "oshmem/tools/oshmem_info/param.c" - "ompi/tools/ompi_info/param.c") - (("_ABSOLUTE") "")) - ;; Avoid valgrind (which pulls in gdb etc.). - (substitute* - '("./ompi/mca/io/romio321/src/io_romio321_component.c") - (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS") - "\"[elided to reduce closure]\"")))) - (add-before 'build 'scrub-timestamps ;reproducibility - (lambda _ - (substitute* '("ompi/tools/ompi_info/param.c" - "orte/tools/orte-info/param.c" - "oshmem/tools/oshmem_info/param.c") - ((".*(Built|Configured) on.*") "")))) - (add-after 'install 'remove-logs ;reproducibility - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (for-each delete-file (find-files out "config.log")))))))) + (list + #:configure-flags #~`("--enable-mpi-ext=affinity" ;cr doesn't work + "--with-sge" + + #$@(if (package? (this-package-input "valgrind")) + #~("--enable-memchecker" + "--with-valgrind") + #~("--without-valgrind")) + + "--with-hwloc=external" + "--with-libevent" + + ;; Help 'orterun' and 'mpirun' find their tools + ;; under $prefix by default. + "--enable-mpirun-prefix-by-default" + + ;; InfiniBand support + "--enable-openib-control-hdr-padding" + "--enable-openib-dynamic-sl" + "--enable-openib-udcm" + "--enable-openib-rdmacm" + "--enable-openib-rdmacm-ibaddr" + + ;; Enable support for SLURM's Process Manager + ;; Interface (PMI). + ,(string-append "--with-pmi=" + #$(this-package-input "slurm"))) + #:phases #~(modify-phases %standard-phases + ;; opensm is needed for InfiniBand support. + (add-after 'unpack 'find-opensm-headers + (lambda* (#:key inputs #:allow-other-keys) + (setenv "C_INCLUDE_PATH" + (search-input-directory inputs + "/include/infiniband")) + (setenv "CPLUS_INCLUDE_PATH" + (search-input-directory inputs + "/include/infiniband")))) + (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* '("orte/tools/orte-info/param.c" + "oshmem/tools/oshmem_info/param.c" + "ompi/tools/ompi_info/param.c") + (("_ABSOLUTE") "")) + ;; Avoid valgrind (which pulls in gdb etc.). + (substitute* + '("./ompi/mca/io/romio321/src/io_romio321_component.c") + (("MCA_io_romio321_COMPLETE_CONFIGURE_FLAGS") + "\"[elided to reduce closure]\"")))) + (add-before 'build 'scrub-timestamps ;reproducibility + (lambda _ + (substitute* '("ompi/tools/ompi_info/param.c" + "orte/tools/orte-info/param.c" + "oshmem/tools/oshmem_info/param.c") + ((".*(Built|Configured) on.*") "")))) + (add-after 'install 'remove-logs ;reproducibility + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each delete-file (find-files out "config.log")))))))) (home-page "https://www.open-mpi.org") (synopsis "MPI-3 implementation") (description @@ -309,7 +317,7 @@ software vendors, application developers and computer science researchers.") (arguments (substitute-keyword-arguments (package-arguments openmpi) ((#:configure-flags flags) - `(cons "--enable-mpi-cxx" ,flags)))) + #~(cons "--enable-mpi-cxx" #$flags)))) (synopsis "C++ bindings for MPI"))) ;; TODO: javadoc files contain timestamps. @@ -325,34 +333,35 @@ software vendors, application developers and computer science researchers.") ,@(package-native-inputs openmpi))) (outputs '("out")) (arguments - `(#:modules ((guix build gnu-build-system) + (cons* + #:modules '((guix build gnu-build-system) ((guix build ant-build-system) #:prefix ant:) (guix build utils)) - #:imported-modules ((guix build ant-build-system) + #:imported-modules `((guix build ant-build-system) ,@%gnu-build-system-modules) - ,@(substitute-keyword-arguments (package-arguments openmpi) - ((#:configure-flags flags) - `(cons "--enable-mpi-java" ,flags)) - ((#:make-flags flags ''()) - `(append '("-C" "ompi/mpi/java") - ,flags)) - ((#:phases phases) - `(modify-phases ,phases - ;; We could provide the location of the JDK in the configure - ;; flags, but since the configure flags are embedded in the - ;; info binaries that would leave a reference to the JDK in - ;; the "out" output. To avoid this we set JAVA_HOME. - (add-after 'unpack 'set-JAVA_HOME - (lambda* (#:key inputs #:allow-other-keys) - (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) - #t)) - (add-after 'unpack 'link-with-existing-mpi-libraries - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "ompi/mpi/java/c/Makefile.in" - (("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la") - (search-input-file inputs "/lib/libmpi.la"))))) - (add-after 'install 'strip-jar-timestamps - (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))))) + (substitute-keyword-arguments (package-arguments openmpi) + ((#:configure-flags flags) + #~(cons "--enable-mpi-java" #$flags)) + ((#:make-flags flags ''()) + #~(append '("-C" "ompi/mpi/java") + #$flags)) + ((#:phases phases) + #~(modify-phases #$phases + ;; We could provide the location of the JDK in the configure + ;; flags, but since the configure flags are embedded in the + ;; info binaries that would leave a reference to the JDK in + ;; the "out" output. To avoid this we set JAVA_HOME. + (add-after 'unpack 'set-JAVA_HOME + (lambda* (#:key inputs #:allow-other-keys) + (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) + #t)) + (add-after 'unpack 'link-with-existing-mpi-libraries + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "ompi/mpi/java/c/Makefile.in" + (("\\$\\(top_builddir\\)/ompi/lib@OMPI_LIBMPI_NAME@.la") + (search-input-file inputs "/lib/libmpi.la"))))) + (add-after 'install 'strip-jar-timestamps + (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))))) (synopsis "Java bindings for MPI"))) (define-public openmpi-thread-multiple @@ -361,7 +370,7 @@ software vendors, application developers and computer science researchers.") (arguments (substitute-keyword-arguments (package-arguments openmpi) ((#:configure-flags flags) - `(cons "--enable-mpi-thread-multiple" ,flags)))) + #~(cons "--enable-mpi-thread-multiple" #$flags)))) (description "This version of Open@tie{}MPI has an implementation of @code{MPI_Init_thread} that provides @code{MPI_THREAD_MULTIPLE}. This won't work correctly with all transports (such as @code{openib}), and the |