diff --git a/glicid/packages/clam.scm b/glicid/packages/clam.scm index 30180bd..9633719 100644 --- a/glicid/packages/clam.scm +++ b/glicid/packages/clam.scm @@ -550,8 +550,6 @@ ) - - (define-public glicid-clam (package (name "glicid-clam") @@ -573,7 +571,6 @@ ) ) ) - ; (build-system python-build-system) (build-system copy-build-system) ;; XXX: The git repository has no tags, and the PyPI releases do not @@ -582,7 +579,6 @@ ;#:tests? #f ; #:use-setuptools? #f ; uses custom distutils 'install' command - #:phases (modify-phases %standard-phases (add-before 'reset-gzip-timestamps 'make-files-writable @@ -591,15 +587,8 @@ (for-each make-file-writable (find-files out "\\.gz$")) #t)))))) - - - - - - ; ) ; ) - (propagated-inputs `(("python-keycloak-client" , python-keycloak-client-0.2.3) ("python-ecdsa", python-ecdsa) ("python-django", python-django) diff --git a/glicid/packages/fabric-management.scm b/glicid/packages/fabric-management.scm index 09646c5..f1faf6b 100644 --- a/glicid/packages/fabric-management.scm +++ b/glicid/packages/fabric-management.scm @@ -52,12 +52,9 @@ ) ) - - (define local-ucx ucx-upstream-1.12.1) (define-public ucx-latest (latest-version local-ucx gnu:ucx)) - (define-public ucx-latest-rdma (transform-package ( @@ -67,7 +64,6 @@ ) ) - (define-public ucx-latest-glicid (transform-package ( diff --git a/glicid/packages/glicid.scm b/glicid/packages/glicid.scm index 4c01664..1e0ea56 100644 --- a/glicid/packages/glicid.scm +++ b/glicid/packages/glicid.scm @@ -4,11 +4,10 @@ #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) -; #:use-module (guix licenses) + #:use-module (guix build-system python) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) #:use-module (gnu packages commencement) - #:use-module (guix build-system python) #:use-module ((guix licenses) #:prefix license:) #:use-module ((guix utils) #:select (target-64bit?)) #:use-module (gnu packages) @@ -57,7 +56,7 @@ #:use-module (gnu packages maths) #:use-module (guix utils) #:use-module (gnu packages cmake) - #:use-module (gnu packages pretty-print) + #:use-module (gnu packages pretty-print) #:use-module (gnu packages boost) #:use-module (gnu packages curl) #:use-module (gnu packages cryptsetup) @@ -87,156 +86,145 @@ #:use-module (gnu packages sphinx) #:use-module (gnu packages tls) #:use-module (gnu packages web) -;; #:use-module (gnu packages glicid) #:use-module (gnu packages pretty-print) #:use-module (gnu packages virtualization) -;; #:use-module (glicid packages storage) #:use-module (glicid packages mpi) #:use-module (glicid packages gcc) - ) - -;;;;;;;; - - (define-public glicid-librdkafka-09 - (package - (inherit librdkafka) - (name "glicid-librdkafka-09") - (version "0.9.2") - (source - (origin - (method url-fetch) - (uri (string-append "https://github.com/edenhill/librdkafka/archive/v" version ".tar.gz")) - (sha256 (base32 "0938yn1msaq8xcj5z7b3jcdy6rslh9kxmvz01r8rdcgbarlvchy2")) - )) -)) - - + (package + (inherit librdkafka) + (name "glicid-librdkafka-09") + (version "0.9.2") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/edenhill/librdkafka/archive/v" version ".tar.gz")) + (sha256 (base32 "0938yn1msaq8xcj5z7b3jcdy6rslh9kxmvz01r8rdcgbarlvchy2")) + ) + ) + ) +) (define-public glicid-x2go - (package - (name "glicid-x2go") - (version "4.1.0.3") - (source - (origin - (method url-fetch) - (uri (string-append "https://code.x2go.org/releases/source/x2goserver/x2goserver-" version ".tar.gz")) - (sha256 (base32 "1l6wd708kbipib4ldprfiihqmj4895nifg0bkws4x97majislxk7")) - )) - + (package + (name "glicid-x2go") + (version "4.1.0.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://code.x2go.org/releases/source/x2goserver/x2goserver-" version ".tar.gz")) + (sha256 (base32 "1l6wd708kbipib4ldprfiihqmj4895nifg0bkws4x97majislxk7")) + ) + ) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("libtool" ,libtool))) - - (inputs - `(("perl" , perl))) - - (build-system gnu-build-system) - (synopsis "X2go") - (description "X2go") - (license "not checked") - (home-page "https://wiki.x2go.org") + (autoconf automake libtool) + ) + (inputs + (perl) + ) + (build-system gnu-build-system) + (synopsis "X2go") + (description "X2go") + (license "not checked") + (home-page "https://wiki.x2go.org") ) ) - (define-public glicid-gromacs-openmpi - (package - (inherit gromacs) - (name "glicid-gromacs-openmpi") - (inputs `(("openmpi", openmpi) - ;; ("openssh", openssh) ;; only for tests... disabled now - ,@(package-inputs gromacs))) - (build-system cmake-build-system) - - (arguments - `(#:configure-flags - (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests - ;; Unbundling - "-DGMX_USE_LMFIT=EXTERNAL" - "-DGMX_BUILD_OWN_FFTW=off" - "-DGMX_EXTERNAL_BLAS=on" - "-DGMX_EXTERNAL_LAPACK=on" - "-DGMX_EXTERNAL_TNG=on" - "-DGMX_EXTERNAL_ZLIB=on" - "-DGMX_EXTERNAL_TINYXML2=on" - ;; special glicid - "-DGMX_MPI=on" - "-DCMAKE_C_COMPILER=mpicc" - "-DCMAKE_CXX_COMPILER=mpicxx" - "-DGMX_DOUBLE=off" - "-DGMX_OPENMP=on" - "-DGMX_SIMD=AVX2_256" - (string-append "-DTinyXML2_DIR=" - (assoc-ref %build-inputs "tinyxml2")) - ;; Workaround for cmake/FindSphinx.cmake version parsing that does - ;; not understand the guix-wrapped `sphinx-build --version' answer - (string-append "-DSPHINX_EXECUTABLE_VERSION=" - ,(package-version python-sphinx))) - #:tests? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fixes - (lambda* (#:key inputs #:allow-other-keys) - ;; Still bundled: part of gromacs, source behind registration - ;; but free software anyways - ;;(delete-file-recursively "src/external/vmd_molfile") - ;; Still bundled: threads-based OpenMPI-compatible fallback - ;; designed to be bundled like that - ;;(delete-file-recursively "src/external/thread_mpi") - ;; Unbundling - (delete-file-recursively "src/external/lmfit") - (delete-file-recursively "src/external/clFFT") - (delete-file-recursively "src/external/fftpack") - (delete-file-recursively "src/external/build-fftw") - (delete-file-recursively "src/external/tng_io") - (delete-file-recursively "src/external/tinyxml2") - (delete-file-recursively "src/external/googletest") - (copy-recursively (assoc-ref inputs "googletest-source") - "src/external/googletest") - ;; This test warns about the build host hardware, disable - (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" - (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") - "void __guix_disabled()")) - #t))))) - - - + (package + (inherit gromacs) + (name "glicid-gromacs-openmpi") + (inputs + `( + ("openmpi", openmpi) + ,@(package-inputs gromacs) + ) + ) + ) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list + "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ;; Unbundling + "-DGMX_USE_LMFIT=EXTERNAL" + "-DGMX_BUILD_OWN_FFTW=off" + "-DGMX_EXTERNAL_BLAS=on" + "-DGMX_EXTERNAL_LAPACK=on" + "-DGMX_EXTERNAL_TNG=on" + "-DGMX_EXTERNAL_ZLIB=on" + "-DGMX_EXTERNAL_TINYXML2=on" + ;; special glicid + "-DGMX_MPI=on" + "-DCMAKE_C_COMPILER=mpicc" + "-DCMAKE_CXX_COMPILER=mpicxx" + "-DGMX_DOUBLE=off" + "-DGMX_OPENMP=on" + "-DGMX_SIMD=AVX2_256" + (string-append "-DTinyXML2_DIR=" (assoc-ref %build-inputs "tinyxml2")) + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=",(package-version python-sphinx)) + ) + #:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fixes + (lambda* (#:key inputs #:allow-other-keys) + ;; Still bundled: part of gromacs, source behind registration + ;; but free software anyways + ;;(delete-file-recursively "src/external/vmd_molfile") + ;; Still bundled: threads-based OpenMPI-compatible fallback + ;; designed to be bundled like that + ;;(delete-file-recursively "src/external/thread_mpi") + ;; Unbundling + (delete-file-recursively "src/external/lmfit") + (delete-file-recursively "src/external/clFFT") + (delete-file-recursively "src/external/fftpack") + (delete-file-recursively "src/external/build-fftw") + (delete-file-recursively "src/external/tng_io") + (delete-file-recursively "src/external/tinyxml2") + (delete-file-recursively "src/external/googletest") + (copy-recursively (assoc-ref inputs "googletest-source") "src/external/googletest") + ;; This test warns about the build host hardware, disable + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") "void __guix_disabled()")) + #t + ) + ) + ) + ) ) - ) - (define-public glicid-python-nbxmpp - (package - (inherit python-nbxmpp) - (name "glicid-python-nbxmpp") - (version "1.0.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "nbxmpp" version)) - (sha256 - (base32 - "0vw5drr077w9ks4crnw6pwa4735ycyjdcm54knc3w4in4x5027wr")))) - -)) + (package + (inherit python-nbxmpp) + (name "glicid-python-nbxmpp") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "nbxmpp" version)) + (sha256 (base32 "0vw5drr077w9ks4crnw6pwa4735ycyjdcm54knc3w4in4x5027wr")) + ) + ) + ) +) (define-public glicid-specific-hdf5 (package (inherit hdf5-1.12) (name "glicid-specific-hdf5") -; (arguments -; `(#:tests? #f) -; ) - (native-inputs `( - ("gcc",gcc-11) - ("gfortran",gfortran-11) - ,@(package-native-inputs hdf5-1.12))) + (native-inputs + `( + ("gcc",gcc-11) + ("gfortran",gfortran-11) + ,@(package-native-inputs hdf5-1.12) + ) + ) ) ) @@ -256,9 +244,7 @@ (arguments `(#:make-flags -;; #:make-flags (list (string-append "PREFIX=" %output) -; (string-append "CC=" ,(cc-for-target)) ;; Xft.h #includes without ‘freetype2/’. The Makefile ;; works around this by hard-coding /usr/include & $PREFIX. (string-append "CPPFLAGS=-I" @@ -278,12 +264,10 @@ ("flex" ,flex) ("bison" ,bison) ("libxt" ,libxt))) - (synopsis "Motif") (description "Motif ") (home-page "https://sourceforge.net/untested") (license " ") - ) ) @@ -329,16 +313,12 @@ ("fontconfig", fontconfig) ("gfortran", gfortran) ("libjpeg-turbo", libjpeg-turbo) -;; ("libxmhtml", libxmhtml) ) ) - - (synopsis "Xmgrace") (description "xmgrace") (home-page "https://sourceforge.net/untested") (license " ") - ) ) @@ -346,9 +326,6 @@ (use-modules (guix download)) (use-modules (gnu packages ruby)) (use-modules (guix build-system ruby)) -;(use-modules (guix licenses)) - - (define-public ruby-asciidoctor-revealjs (package @@ -366,7 +343,6 @@ '(#:tests? #f)) (propagated-inputs `(("ruby-asciidoctor" ,ruby-asciidoctor) -; ("ruby-concurrent-ruby" ,ruby-concurrent-ruby) ("ruby-concurrent" ,ruby-concurrent) ("ruby-asciidoctor-kroki", ruby-asciidoctor-kroki) ("ruby-thread-safe" ,ruby-thread-safe))) @@ -404,7 +380,3 @@ (license license:expat) ) ) - -;; python-glances is now upstreamed as glances in python-xyz - -;;; glicid.scm ends here diff --git a/glicid/packages/maths.scm b/glicid/packages/maths.scm index 865bf34..e84c313 100644 --- a/glicid/packages/maths.scm +++ b/glicid/packages/maths.scm @@ -40,6 +40,7 @@ ) ) ) + (define local:scalapack scalapack-upstream) (define-public scalapack-latest (latest-version local:scalapack gnu:scalapack)) diff --git a/glicid/packages/mpi.scm b/glicid/packages/mpi.scm index 4e56558..e5694a2 100644 --- a/glicid/packages/mpi.scm +++ b/glicid/packages/mpi.scm @@ -10,22 +10,21 @@ #:use-module (gnu packages) ) - (define-public openmpi-upstream-4.1.2 (package (inherit gnu:openmpi) (name "openmpi-upstream") (version "4.1.2") (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 "09xmlr4mfs02kwcf5cmdgkcdjj81fjwjmpa3rz2k28f3gz7wfy4v")) - (patches (search-patches "openmpi-mtl-priorities.patch")))) - + (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 "09xmlr4mfs02kwcf5cmdgkcdjj81fjwjmpa3rz2k28f3gz7wfy4v")) + (patches (search-patches "openmpi-mtl-priorities.patch")) + ) + ) ) ) @@ -35,77 +34,39 @@ (define-public openmpi-glicid -(package - (inherit - (transform-package - ( - (instead-of "slurm" slurm-glicid) openmpi-latest - ) "glicid" + (package + (inherit + (transform-package ((instead-of "slurm" slurm-glicid) openmpi-latest) "glicid") + ) ) - ) - ) ) (define-public openmpi-glicid-libfabric - (transform-package - ( - (instead-of "libfabric" libfabric-latest) - openmpi-glicid - ) "libfabric" - ) + (transform-package ((instead-of "libfabric" libfabric-latest) openmpi-glicid) "libfabric") ) (define-public openmpi-glicid-rdma - (transform-package - ( - (instead-of "rdma-core" rdma-core-latest) - openmpi-glicid - ) "rdma-core" - ) + (transform-package ((instead-of "rdma-core" rdma-core-latest) openmpi-glicid) "rdma-core") ) (define-public openmpi-glicid-ucx - (transform-package - ( - (instead-of "ucx" ucx-latest-glicid) openmpi-glicid - ) "ucx" - ) + (transform-package ((instead-of "ucx" ucx-latest-glicid) openmpi-glicid) "ucx" ) ) (define-public openmpi-glicid-libfabric-rdma - (transform-package - ( - (instead-of "rdma-core" rdma-core-latest) - openmpi-glicid-libfabric - ) "rdma" - ) + (transform-package ((instead-of "rdma-core" rdma-core-latest) openmpi-glicid-libfabric) "rdma") ) (define-public openmpi-glicid-libfabric-ucx - (transform-package - ( - (instead-of "ucx" ucx-latest-glicid) - openmpi-glicid-libfabric - ) "ucx" - ) + (transform-package ((instead-of "ucx" ucx-latest-glicid) openmpi-glicid-libfabric) "ucx") ) (define-public openmpi-glicid-libfabric-rdma-ucx - (transform-package - ( - (instead-of "ucx" ucx-latest-glicid) - openmpi-glicid-libfabric-rdma - ) "ucx" - ) + (transform-package ((instead-of "ucx" ucx-latest-glicid) openmpi-glicid-libfabric-rdma) "ucx") ) (define-public openmpi-glicid-libfabric-rdma-ucx-ccipl - (transform-package - ( - (instead-of "slurm-glicid" slurm-ccipl) - openmpi-glicid-libfabric-rdma-ucx - ) "ccipl" - ) + (transform-package ((instead-of "slurm-glicid" slurm-ccipl) openmpi-glicid-libfabric-rdma-ucx) "ccipl") ) @@ -117,6 +78,3 @@ (name (string-append (package-name openmpi-glicid-transform-gcc-11) "-gcc-11" )) ) ) - - -;openmpi-glicid-libfabric-rdma-ucx-ccipl