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Jean-François GUILLAUME 2022-05-02 12:07:45 +02:00
parent 7b5d3e5a65
commit 3bcb54d6a1
5 changed files with 138 additions and 222 deletions
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11
glicid/packages/clam.scm
View file

@ -550,8 +550,6 @@
) )
(define-public glicid-clam (define-public glicid-clam
(package (package
(name "glicid-clam") (name "glicid-clam")
@ -573,7 +571,6 @@
) )
) )
) )
; (build-system python-build-system) ; (build-system python-build-system)
(build-system copy-build-system) (build-system copy-build-system)
;; XXX: The git repository has no tags, and the PyPI releases do not ;; XXX: The git repository has no tags, and the PyPI releases do not
@ -582,7 +579,6 @@
;#:tests? #f ;#:tests? #f
; #:use-setuptools? #f ; uses custom distutils 'install' command ; #:use-setuptools? #f ; uses custom distutils 'install' command
#:phases #:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-before 'reset-gzip-timestamps 'make-files-writable (add-before 'reset-gzip-timestamps 'make-files-writable
@ -591,15 +587,8 @@
(for-each make-file-writable (for-each make-file-writable
(find-files out "\\.gz$")) (find-files out "\\.gz$"))
#t)))))) #t))))))
; ) ; )
; ) ; )
(propagated-inputs `(("python-keycloak-client" , python-keycloak-client-0.2.3) (propagated-inputs `(("python-keycloak-client" , python-keycloak-client-0.2.3)
("python-ecdsa", python-ecdsa) ("python-ecdsa", python-ecdsa)
("python-django", python-django) ("python-django", python-django)

4
glicid/packages/fabric-management.scm
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@ -52,12 +52,9 @@
) )
) )
(define local-ucx ucx-upstream-1.12.1) (define local-ucx ucx-upstream-1.12.1)
(define-public ucx-latest (latest-version local-ucx gnu:ucx)) (define-public ucx-latest (latest-version local-ucx gnu:ucx))
(define-public ucx-latest-rdma (define-public ucx-latest-rdma
(transform-package (transform-package
( (
@ -67,7 +64,6 @@
) )
) )
(define-public ucx-latest-glicid (define-public ucx-latest-glicid
(transform-package (transform-package
( (

262
glicid/packages/glicid.scm
View file

@ -4,11 +4,10 @@
#:use-module (guix git-download) #:use-module (guix git-download)
#:use-module (guix build-system gnu) #:use-module (guix build-system gnu)
#:use-module (guix build-system cmake) #: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 gawk)
#:use-module (gnu packages gcc) #:use-module (gnu packages gcc)
#:use-module (gnu packages commencement) #:use-module (gnu packages commencement)
#:use-module (guix build-system python)
#:use-module ((guix licenses) #:prefix license:) #:use-module ((guix licenses) #:prefix license:)
#:use-module ((guix utils) #:select (target-64bit?)) #:use-module ((guix utils) #:select (target-64bit?))
#:use-module (gnu packages) #:use-module (gnu packages)
@ -57,7 +56,7 @@
#:use-module (gnu packages maths) #:use-module (gnu packages maths)
#:use-module (guix utils) #:use-module (guix utils)
#:use-module (gnu packages cmake) #: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 boost)
#:use-module (gnu packages curl) #:use-module (gnu packages curl)
#:use-module (gnu packages cryptsetup) #:use-module (gnu packages cryptsetup)
@ -87,156 +86,145 @@
#:use-module (gnu packages sphinx) #:use-module (gnu packages sphinx)
#:use-module (gnu packages tls) #:use-module (gnu packages tls)
#:use-module (gnu packages web) #:use-module (gnu packages web)
;; #:use-module (gnu packages glicid)
#:use-module (gnu packages pretty-print) #:use-module (gnu packages pretty-print)
#:use-module (gnu packages virtualization) #:use-module (gnu packages virtualization)
;; #:use-module (glicid packages storage)
#:use-module (glicid packages mpi) #:use-module (glicid packages mpi)
#:use-module (glicid packages gcc) #:use-module (glicid packages gcc)
) )
;;;;;;;;
(define-public glicid-librdkafka-09 (define-public glicid-librdkafka-09
(package (package
(inherit librdkafka) (inherit librdkafka)
(name "glicid-librdkafka-09") (name "glicid-librdkafka-09")
(version "0.9.2") (version "0.9.2")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://github.com/edenhill/librdkafka/archive/v" version ".tar.gz")) (uri (string-append "https://github.com/edenhill/librdkafka/archive/v" version ".tar.gz"))
(sha256 (base32 "0938yn1msaq8xcj5z7b3jcdy6rslh9kxmvz01r8rdcgbarlvchy2")) (sha256 (base32 "0938yn1msaq8xcj5z7b3jcdy6rslh9kxmvz01r8rdcgbarlvchy2"))
)) )
)) )
)
)
(define-public glicid-x2go (define-public glicid-x2go
(package (package
(name "glicid-x2go") (name "glicid-x2go")
(version "4.1.0.3") (version "4.1.0.3")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://code.x2go.org/releases/source/x2goserver/x2goserver-" version ".tar.gz")) (uri (string-append "https://code.x2go.org/releases/source/x2goserver/x2goserver-" version ".tar.gz"))
(sha256 (base32 "1l6wd708kbipib4ldprfiihqmj4895nifg0bkws4x97majislxk7")) (sha256 (base32 "1l6wd708kbipib4ldprfiihqmj4895nifg0bkws4x97majislxk7"))
)) )
)
(native-inputs (native-inputs
`(("autoconf" ,autoconf) (autoconf automake libtool)
("automake" ,automake) )
("libtool" ,libtool))) (inputs
(perl)
(inputs )
`(("perl" , perl))) (build-system gnu-build-system)
(synopsis "X2go")
(build-system gnu-build-system) (description "X2go")
(synopsis "X2go") (license "not checked")
(description "X2go") (home-page "https://wiki.x2go.org")
(license "not checked")
(home-page "https://wiki.x2go.org")
) )
) )
(define-public glicid-gromacs-openmpi (define-public glicid-gromacs-openmpi
(package (package
(inherit gromacs) (inherit gromacs)
(name "glicid-gromacs-openmpi") (name "glicid-gromacs-openmpi")
(inputs `(("openmpi", openmpi) (inputs
;; ("openssh", openssh) ;; only for tests... disabled now `(
,@(package-inputs gromacs))) ("openmpi", openmpi)
(build-system cmake-build-system) ,@(package-inputs gromacs)
)
(arguments )
`(#:configure-flags )
(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests (build-system cmake-build-system)
;; Unbundling (arguments
"-DGMX_USE_LMFIT=EXTERNAL" `(#:configure-flags
"-DGMX_BUILD_OWN_FFTW=off" (list
"-DGMX_EXTERNAL_BLAS=on" "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
"-DGMX_EXTERNAL_LAPACK=on" ;; Unbundling
"-DGMX_EXTERNAL_TNG=on" "-DGMX_USE_LMFIT=EXTERNAL"
"-DGMX_EXTERNAL_ZLIB=on" "-DGMX_BUILD_OWN_FFTW=off"
"-DGMX_EXTERNAL_TINYXML2=on" "-DGMX_EXTERNAL_BLAS=on"
;; special glicid "-DGMX_EXTERNAL_LAPACK=on"
"-DGMX_MPI=on" "-DGMX_EXTERNAL_TNG=on"
"-DCMAKE_C_COMPILER=mpicc" "-DGMX_EXTERNAL_ZLIB=on"
"-DCMAKE_CXX_COMPILER=mpicxx" "-DGMX_EXTERNAL_TINYXML2=on"
"-DGMX_DOUBLE=off" ;; special glicid
"-DGMX_OPENMP=on" "-DGMX_MPI=on"
"-DGMX_SIMD=AVX2_256" "-DCMAKE_C_COMPILER=mpicc"
(string-append "-DTinyXML2_DIR=" "-DCMAKE_CXX_COMPILER=mpicxx"
(assoc-ref %build-inputs "tinyxml2")) "-DGMX_DOUBLE=off"
;; Workaround for cmake/FindSphinx.cmake version parsing that does "-DGMX_OPENMP=on"
;; not understand the guix-wrapped `sphinx-build --version' answer "-DGMX_SIMD=AVX2_256"
(string-append "-DSPHINX_EXECUTABLE_VERSION=" (string-append "-DTinyXML2_DIR=" (assoc-ref %build-inputs "tinyxml2"))
,(package-version python-sphinx))) ;; Workaround for cmake/FindSphinx.cmake version parsing that does
#:tests? #f ;; not understand the guix-wrapped `sphinx-build --version' answer
#:phases (string-append "-DSPHINX_EXECUTABLE_VERSION=",(package-version python-sphinx))
(modify-phases %standard-phases )
(add-after 'unpack 'fixes #:tests? #f
(lambda* (#:key inputs #:allow-other-keys) #:phases
;; Still bundled: part of gromacs, source behind registration (modify-phases %standard-phases
;; but free software anyways (add-after 'unpack 'fixes
;;(delete-file-recursively "src/external/vmd_molfile") (lambda* (#:key inputs #:allow-other-keys)
;; Still bundled: threads-based OpenMPI-compatible fallback ;; Still bundled: part of gromacs, source behind registration
;; designed to be bundled like that ;; but free software anyways
;;(delete-file-recursively "src/external/thread_mpi") ;;(delete-file-recursively "src/external/vmd_molfile")
;; Unbundling ;; Still bundled: threads-based OpenMPI-compatible fallback
(delete-file-recursively "src/external/lmfit") ;; designed to be bundled like that
(delete-file-recursively "src/external/clFFT") ;;(delete-file-recursively "src/external/thread_mpi")
(delete-file-recursively "src/external/fftpack") ;; Unbundling
(delete-file-recursively "src/external/build-fftw") (delete-file-recursively "src/external/lmfit")
(delete-file-recursively "src/external/tng_io") (delete-file-recursively "src/external/clFFT")
(delete-file-recursively "src/external/tinyxml2") (delete-file-recursively "src/external/fftpack")
(delete-file-recursively "src/external/googletest") (delete-file-recursively "src/external/build-fftw")
(copy-recursively (assoc-ref inputs "googletest-source") (delete-file-recursively "src/external/tng_io")
"src/external/googletest") (delete-file-recursively "src/external/tinyxml2")
;; This test warns about the build host hardware, disable (delete-file-recursively "src/external/googletest")
(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" (copy-recursively (assoc-ref inputs "googletest-source") "src/external/googletest")
(("TEST\\(HardwareTopologyTest, HwlocExecute\\)") ;; This test warns about the build host hardware, disable
"void __guix_disabled()")) (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") "void __guix_disabled()"))
#t))))) #t
)
)
)
)
) )
) )
(define-public glicid-python-nbxmpp (define-public glicid-python-nbxmpp
(package (package
(inherit python-nbxmpp) (inherit python-nbxmpp)
(name "glicid-python-nbxmpp") (name "glicid-python-nbxmpp")
(version "1.0.2") (version "1.0.2")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "nbxmpp" version)) (uri (pypi-uri "nbxmpp" version))
(sha256 (sha256 (base32 "0vw5drr077w9ks4crnw6pwa4735ycyjdcm54knc3w4in4x5027wr"))
(base32 )
"0vw5drr077w9ks4crnw6pwa4735ycyjdcm54knc3w4in4x5027wr")))) )
)
)) )
(define-public glicid-specific-hdf5 (define-public glicid-specific-hdf5
(package (package
(inherit hdf5-1.12) (inherit hdf5-1.12)
(name "glicid-specific-hdf5") (name "glicid-specific-hdf5")
; (arguments (native-inputs
; `(#:tests? #f) `(
; ) ("gcc",gcc-11)
(native-inputs `( ("gfortran",gfortran-11)
("gcc",gcc-11) ,@(package-native-inputs hdf5-1.12)
("gfortran",gfortran-11) )
,@(package-native-inputs hdf5-1.12))) )
) )
) )
@ -256,9 +244,7 @@
(arguments (arguments
`(#:make-flags `(#:make-flags
;; #:make-flags
(list (string-append "PREFIX=" %output) (list (string-append "PREFIX=" %output)
; (string-append "CC=" ,(cc-for-target))
;; Xft.h #includes <ft2build.h> without ‘freetype2/’. The Makefile ;; Xft.h #includes <ft2build.h> without ‘freetype2/’. The Makefile
;; works around this by hard-coding /usr/include & $PREFIX. ;; works around this by hard-coding /usr/include & $PREFIX.
(string-append "CPPFLAGS=-I" (string-append "CPPFLAGS=-I"
@ -278,12 +264,10 @@
("flex" ,flex) ("flex" ,flex)
("bison" ,bison) ("bison" ,bison)
("libxt" ,libxt))) ("libxt" ,libxt)))
(synopsis "Motif") (synopsis "Motif")
(description "Motif ") (description "Motif ")
(home-page "https://sourceforge.net/untested") (home-page "https://sourceforge.net/untested")
(license " ") (license " ")
) )
) )
@ -329,16 +313,12 @@
("fontconfig", fontconfig) ("fontconfig", fontconfig)
("gfortran", gfortran) ("gfortran", gfortran)
("libjpeg-turbo", libjpeg-turbo) ("libjpeg-turbo", libjpeg-turbo)
;; ("libxmhtml", libxmhtml)
) )
) )
(synopsis "Xmgrace") (synopsis "Xmgrace")
(description "xmgrace") (description "xmgrace")
(home-page "https://sourceforge.net/untested") (home-page "https://sourceforge.net/untested")
(license " ") (license " ")
) )
) )
@ -346,9 +326,6 @@
(use-modules (guix download)) (use-modules (guix download))
(use-modules (gnu packages ruby)) (use-modules (gnu packages ruby))
(use-modules (guix build-system ruby)) (use-modules (guix build-system ruby))
;(use-modules (guix licenses))
(define-public ruby-asciidoctor-revealjs (define-public ruby-asciidoctor-revealjs
(package (package
@ -366,7 +343,6 @@
'(#:tests? #f)) '(#:tests? #f))
(propagated-inputs (propagated-inputs
`(("ruby-asciidoctor" ,ruby-asciidoctor) `(("ruby-asciidoctor" ,ruby-asciidoctor)
; ("ruby-concurrent-ruby" ,ruby-concurrent-ruby)
("ruby-concurrent" ,ruby-concurrent) ("ruby-concurrent" ,ruby-concurrent)
("ruby-asciidoctor-kroki", ruby-asciidoctor-kroki) ("ruby-asciidoctor-kroki", ruby-asciidoctor-kroki)
("ruby-thread-safe" ,ruby-thread-safe))) ("ruby-thread-safe" ,ruby-thread-safe)))
@ -404,7 +380,3 @@
(license license:expat) (license license:expat)
) )
) )
;; python-glances is now upstreamed as glances in python-xyz
;;; glicid.scm ends here

1
glicid/packages/maths.scm
View file

@ -40,6 +40,7 @@
) )
) )
) )
(define local:scalapack scalapack-upstream) (define local:scalapack scalapack-upstream)
(define-public scalapack-latest (latest-version local:scalapack gnu:scalapack)) (define-public scalapack-latest (latest-version local:scalapack gnu:scalapack))

82
glicid/packages/mpi.scm
View file

@ -10,22 +10,21 @@
#:use-module (gnu packages) #:use-module (gnu packages)
) )
(define-public openmpi-upstream-4.1.2 (define-public openmpi-upstream-4.1.2
(package (package
(inherit gnu:openmpi) (inherit gnu:openmpi)
(name "openmpi-upstream") (name "openmpi-upstream")
(version "4.1.2") (version "4.1.2")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://www.open-mpi.org/software/ompi/v" (uri (string-append "https://www.open-mpi.org/software/ompi/v"
(version-major+minor version) (version-major+minor version)
"/downloads/openmpi-" version ".tar.bz2")) "/downloads/openmpi-" version ".tar.bz2"))
(sha256 (sha256 (base32 "09xmlr4mfs02kwcf5cmdgkcdjj81fjwjmpa3rz2k28f3gz7wfy4v"))
(base32 "09xmlr4mfs02kwcf5cmdgkcdjj81fjwjmpa3rz2k28f3gz7wfy4v")) (patches (search-patches "openmpi-mtl-priorities.patch"))
(patches (search-patches "openmpi-mtl-priorities.patch")))) )
)
) )
) )
@ -35,77 +34,39 @@
(define-public openmpi-glicid (define-public openmpi-glicid
(package (package
(inherit (inherit
(transform-package (transform-package ((instead-of "slurm" slurm-glicid) openmpi-latest) "glicid")
( )
(instead-of "slurm" slurm-glicid) openmpi-latest
) "glicid"
) )
)
)
) )
(define-public openmpi-glicid-libfabric (define-public openmpi-glicid-libfabric
(transform-package (transform-package ((instead-of "libfabric" libfabric-latest) openmpi-glicid) "libfabric")
(
(instead-of "libfabric" libfabric-latest)
openmpi-glicid
) "libfabric"
)
) )
(define-public openmpi-glicid-rdma (define-public openmpi-glicid-rdma
(transform-package (transform-package ((instead-of "rdma-core" rdma-core-latest) openmpi-glicid) "rdma-core")
(
(instead-of "rdma-core" rdma-core-latest)
openmpi-glicid
) "rdma-core"
)
) )
(define-public openmpi-glicid-ucx (define-public openmpi-glicid-ucx
(transform-package (transform-package ((instead-of "ucx" ucx-latest-glicid) openmpi-glicid) "ucx" )
(
(instead-of "ucx" ucx-latest-glicid) openmpi-glicid
) "ucx"
)
) )
(define-public openmpi-glicid-libfabric-rdma (define-public openmpi-glicid-libfabric-rdma
(transform-package (transform-package ((instead-of "rdma-core" rdma-core-latest) openmpi-glicid-libfabric) "rdma")
(
(instead-of "rdma-core" rdma-core-latest)
openmpi-glicid-libfabric
) "rdma"
)
) )
(define-public openmpi-glicid-libfabric-ucx (define-public openmpi-glicid-libfabric-ucx
(transform-package (transform-package ((instead-of "ucx" ucx-latest-glicid) openmpi-glicid-libfabric) "ucx")
(
(instead-of "ucx" ucx-latest-glicid)
openmpi-glicid-libfabric
) "ucx"
)
) )
(define-public openmpi-glicid-libfabric-rdma-ucx (define-public openmpi-glicid-libfabric-rdma-ucx
(transform-package (transform-package ((instead-of "ucx" ucx-latest-glicid) openmpi-glicid-libfabric-rdma) "ucx")
(
(instead-of "ucx" ucx-latest-glicid)
openmpi-glicid-libfabric-rdma
) "ucx"
)
) )
(define-public openmpi-glicid-libfabric-rdma-ucx-ccipl (define-public openmpi-glicid-libfabric-rdma-ucx-ccipl
(transform-package (transform-package ((instead-of "slurm-glicid" slurm-ccipl) openmpi-glicid-libfabric-rdma-ucx) "ccipl")
(
(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" )) (name (string-append (package-name openmpi-glicid-transform-gcc-11) "-gcc-11" ))
) )
) )
;openmpi-glicid-libfabric-rdma-ucx-ccipl