Merge branch 'master' of gitlab.inria.fr:guix-hpc/guix-hpc-non-free into master

.gitlab-ci.yml

@@ -42,3 +42,33 @@ chameleon_mkl_mt:
   script:
     - .channels/guix-hpc/bin/guix describe
     - .channels/guix-hpc/bin/guix build -L . chameleon-mkl-mt
+    
+mumps_mkl:
+  stage: build
+  script:
+    - .channels/guix-hpc/bin/guix describe
+    - .channels/guix-hpc/bin/guix build -L . mumps-mkl
+
+mumps_mkl_metis:
+  stage: build
+  script:
+    - .channels/guix-hpc/bin/guix describe
+    - .channels/guix-hpc/bin/guix build -L . mumps-mkl-metis
+
+mumps_mkl_openmpi:
+  stage: build
+  script:
+    - .channels/guix-hpc/bin/guix describe
+    - .channels/guix-hpc/bin/guix build -L . mumps-mkl-openmpi
+
+mumps_mkl_metis_openmpi:
+  stage: build
+  script:
+    - .channels/guix-hpc/bin/guix describe
+    - .channels/guix-hpc/bin/guix build -L . mumps-mkl-metis-openmpi
+
+pastix_5_mkl:
+  stage: build
+  script:
+    - .channels/guix-hpc/bin/guix describe
+    - .channels/guix-hpc/bin/guix build -L . pastix-5-mkl

README.md

@@ -15,12 +15,10 @@ invite you not to share it widely.
 
 ## How does it work?
 
-The package recipes in this repo _extend_ [those that come with
-Guix](https://gnu.org/s/guix/packages) and
-[Guix-HPC](https://gitlab.inria.fr/guix-hpc/guix-hpc).  To make them
-visible to the `guix` command-line tools, and assuming you’re using
-Guix >= 0.16.0, create a `~/.config/guix/channels.scm` file with the
-following snippet:
+The package definitions in this repo _extend_ [those that come with
+Guix](https://hpc.guix.info/browse).  To make them visible to the
+`guix` command-line tools, create the `~/.config/guix/channels.scm` file
+with the following snippet to request the `guix-hpc` _channel_:
 
 ```scheme
 (cons (channel
@@ -30,7 +28,7 @@ following snippet:
 ```
 
 That way, `guix pull` will systematically pull not only Guix, but also
-Guix-HPC.
+Guix-HPC-non-free and Guix-HPC.
 
 See [Guix-HPC](https://gitlab.inria.fr/guix-hpc/guix-hpc), for more
 information.

hacky/mumps-mkl.scm

@@ -7,6 +7,7 @@
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module (gnu packages mpi)
+  #:use-module (gnu packages llvm)
   #:use-module (gnu packages maths)
   #:use-module (srfi srfi-1)
   #:use-module (non-free mkl))
@@ -17,6 +18,7 @@
    (name "mumps-mkl")
    (inputs
     `(("blas" ,mkl)
+      ("libomp" ,libomp)
       ,@(alist-delete "openblas" (package-inputs mumps))))
    (arguments
     (substitute-keyword-arguments
@@ -55,11 +57,13 @@ SCALAP      += -lscalapack~]
 LIBOTHERS    = -pthread
 CDEFS        = -DAdd_
 PIC          = -fPIC
-OPTF         = -O2 -DALLOW_NON_INIT $(PIC)
-OPTL         = -O2 $(PIC)
+OPTF         = -O2 -DALLOW_NON_INIT -DBLR_MT -fopenmp $(PIC)
+OPTL         = -O2 -fopenmp $(PIC)
 OPTC         = -O2 $(PIC)
 INCS         = $(INCSEQ)
-LIBS         = $(SCALAP) $(LIBSEQ)
+OMPDIR       = ~a
+LIBOMP       = -L$(OMPDIR)/lib -lgomp
+LIBS         = $(SCALAP) $(LIBSEQ) $(LIBOMP)
 LPORDDIR     = $(topdir)/PORD/lib
 IPORD        = -I$(topdir)/PORD/include
 LPORD        = $(LPORDDIR)/libpord.a
@@ -74,12 +78,13 @@ LSCOTCH      = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps
 LSCOTCH     += -lscotch -lscotcherr
 ORDERINGSF  += ~a~}~]
 ORDERINGSC   = $(ORDERINGSF)
-LORDERINGS   = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
-IORDERINGSF  = $(ISCOTCH)
-IORDERINGSC  = $(IPORD) $(IMETIS) $(ISCOTCH)"
+LORDERINGS   = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ) $(LIBOMP)
+IORDERINGSF  = $(ISCOTCH) $(LIBOMP)
+IORDERINGSC  = $(IPORD) $(IMETIS) $(ISCOTCH) $(LIBOMP)"
                         (assoc-ref inputs "mpi")
                         (assoc-ref inputs "blas")
                         (assoc-ref inputs "scalapack")
+                        (assoc-ref inputs "libomp")
                         (assoc-ref inputs "metis")
                         (match (list (assoc-ref inputs "pt-scotch")
                                      (assoc-ref inputs "scotch"))
@@ -91,8 +96,8 @@ IORDERINGSC  = $(IPORD) $(IMETIS) $(ISCOTCH)"
                            `((,ptscotch
                               "-lptesmumps -lptscotch -lptscotcherr "
                               "-Dptscotch")))))))))))))
-   (synopsis "Multifrontal sparse direct solver (using Intel® MKL instead of
-OpenBLAS)")))
+   (synopsis "Multifrontal sparse direct solver (compiled with OpenMP
+directives-based multi-threading support and Intel® MKL instead of OpenBLAS)")))
 
 (define-public mumps-mkl-metis
   (package
@@ -121,8 +126,8 @@ OpenBLAS)")))
                                (lambda _
                                  ((assoc-ref ,phases 'check)
                                   #:exec-prefix '("mpirun" "-n" "2"))))))))
-   (synopsis "Multifrontal sparse direct solver (using Intel® MKL instead of
-OpenBLAS and MPI)")))
+   (synopsis "Multifrontal sparse direct solver (compiled with combined MPI and
+OpenMP multi-threading support and Intel® MKL instead of OpenBLAS)")))
 
 (define-public mumps-mkl-metis-openmpi
   (package

hacky/pastix-mkl.scm → hacky/pastix-5-mkl.scm

@@ -3,7 +3,7 @@
 ;;;
 ;;; Copyright © 2020 Inria
 
-(define-module (hacky pastix-mkl)
+(define-module (hacky pastix-5-mkl)
   #:use-module (guix packages)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1)
@@ -24,7 +24,7 @@
       (#:phases phases)
       `(modify-phases ,phases
                       (replace 'configure
-                               (lambda _
+                               (lambda* (#:key inputs #:allow-other-keys)
                                (call-with-output-file "config.in"
                                  (lambda (port)
                                    (format port "
@@ -33,12 +33,12 @@ VERSIONBIT  = _32bit
 EXEEXT      =
 OBJEXT      = .o
 LIBEXT      = .a
-CCPROG      = gcc -Wall
-CFPROG      = gfortran
-CF90PROG    = gfortran -ffree-form
-CXXPROG     = g++
+CCPROG      = gcc -Wall -g
+CFPROG      = gfortran -g
+CF90PROG    = gfortran -ffree-form -g
+CXXPROG     = g++ -g
 
-MCFPROG     = mpif90
+MCFPROG     = mpif90 -g
 CF90CCPOPT  = -ffree-form -x f95-cpp-input
 # Compilation options for optimization (make expor)
 CCFOPT      = -O3
@@ -136,7 +136,7 @@ CCTYPESFLT := $(CCTYPESFLT) -DTYPE_COMPLEX
 
 # Uncomment the following line if your MPI doesn't support MPI_THREAD_MULTIPLE,
 # level then use IPARM_THREAD_COMM_MODE
-CCPASTIX   := $(CCPASTIX) -DPASTIX_FUNNELED
+#CCPASTIX   := $(CCPASTIX) -DPASTIX_FUNNELED
 
 # Uncomment the following line if your MPI doesn't support MPI_Datatype
 # correctly
@@ -172,7 +172,7 @@ NVCCOPT    := $(NVCCOPT) -arch sm_20
 CCPASTIX   := $(CCPASTIX) -DMEMORY_USAGE
 
 # Show memory usage statistics in solver
-CCPASTIX   := $(CCPASTIX) -DSTATS_SOPALIN
+#CCPASTIX   := $(CCPASTIX) -DSTATS_SOPALIN
 
 # Uncomment following line for dynamic thread scheduling support
 #CCPASTIX   := $(CCPASTIX) -DPASTIX_DYNSCHED
@@ -191,9 +191,9 @@ CCPASTIX   := $(CCPASTIX) -DSTATS_SOPALIN
 #EXTRALIB   := $(EXTRALIB) -L$(METIS_HOME) -lmetis
 
 # Scotch always needed to compile
-SCOTCH_HOME ?= ${HOME}/scotch_5.1/
-SCOTCH_INC ?= $(SCOTCH_HOME)/include
-SCOTCH_LIB ?= $(SCOTCH_HOME)/lib
+SCOTCH_HOME  = ~a
+SCOTCH_INC  ?= $(SCOTCH_HOME)/include
+SCOTCH_LIB  ?= $(SCOTCH_HOME)/lib
 # Uncomment on of this blocks
 #scotch
 CCPASTIX   := $(CCPASTIX) -I$(SCOTCH_INC) -DWITH_SCOTCH
@@ -210,7 +210,7 @@ EXTRALIB   := $(EXTRALIB) -L$(SCOTCH_LIB) -lscotch -lscotcherrexit
 ###################################################################
 # By default PaStiX uses hwloc to bind threads,
 # comment this lines if you don't want it (not recommended)
-HWLOC_HOME ?= /opt/hwloc/
+HWLOC_HOME  = ~a
 HWLOC_INC  ?= $(HWLOC_HOME)/include
 HWLOC_LIB  ?= $(HWLOC_HOME)/lib
 CCPASTIX   := $(CCPASTIX) -I$(HWLOC_INC) -DWITH_HWLOC
@@ -245,8 +245,8 @@ EXTRALIB   := $(EXTRALIB) -lpthread
 #---- Gotoblas ----
 #BLASLIB  = -L${BLAS_HOME} -lgoto
 #----  MKL     ----
-BLASLIB  = -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64
-BLASLIB += -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl
+BLASLIB  = -L~a/lib -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_gnu_thread
+BLASLIB += -lmkl_core -lgomp -lpthread -lm -ldl
 #----  Acml    ----
 #BLASLIB  = -L$(BLAS_HOME) -lacml
 
@@ -281,6 +281,9 @@ FFLAGS   = $(CCFOPT)
 LDFLAGS  = $(EXTRALIB) $(BLASLIB)
 CTAGS    = $(CTAGSPROG)
 "
+                                           (assoc-ref inputs "scotch32")
+                                           (assoc-ref inputs "hwloc")
+                                           (assoc-ref inputs "mkl")
                                            ))) #t))))))
    (synopsis "Sparse matrix direct solver (using Intel® MKL instead of
 OpenBLAS)")))

inria/experimental.scm

@@ -74,7 +74,7 @@
      (inputs `(("openblas" ,openblas)
                ("perl" ,perl)
                ;; ("scotch" ,pt-scotch)
-               ("scotch" ,scotch)
+               ("scotch32" ,scotch32)
 	       ("ssh" ,openssh)
                ("metis" ,metis)
                ("starpu" ,starpu)))

inria/hou10ni.scm

+;;; This module extends GNU Guix and is licensed under the same terms, those
+;;; of the GNU GPL version 3 or (at your option) any later version.
+;;;
+;;; Copyright © 2020 Inria
+
+(define-module (inria hou10ni)
+               #:use-module (guix)
+               #:use-module (guix git)                         ;for 'git-checkout'
+               #:use-module (guix git-download)
+               #:use-module (guix build-system cmake)
+               #:use-module ((guix licenses) #:prefix license:)
+               #:use-module (inria mpi)
+               #:use-module (gnu packages algebra)
+               #:use-module (gnu packages gcc)
+               #:use-module (gnu packages maths)
+               #:use-module (inria hiepacs)
+               #:use-module (inria storm)
+               #:use-module (gnu packages linux)
+               #:use-module (gnu packages ssh)
+               #:use-module (gnu packages mpi)
+               #:use-module (gnu packages fabric-management))
+(define-public hou10ni
+               (let ((commit "f12d26f704e6be0b17c2e144021eef4edba6dc1d")
+                     (revision "0"))
+                 (package
+                   (name "hou10ni")
+                   (version "0.5")
+                   (home-page "git@gitlab.inria.fr:hou10ni/hou10ni2d.git")
+
+                   ;; This will clone the repository over SSH on the client side, provided
+                   ;; you have permissions to do so.license:bsd-3
+                   (source (git-checkout
+                             (url "git@gitlab.inria.fr:hou10ni/hou10ni2d.git")
+                             (commit commit)))
+
+                   (build-system cmake-build-system)
+                   (arguments
+                     `(#:phases (modify-phases %standard-phases
+                                               (add-after 'build 'mpi-setup
+                                                          ;; Set the test environment for Open MPI.
+                                                          ,%openmpi-setup))
+
+                       #:tests? #f
+                       #:build-type "Release"))                            ;FIXME
+                   (native-inputs
+                     `(("gfortran" ,gfortran)))
+                   (inputs
+                     `(("mumps-openmpi" ,mumps-openmpi)
+                       ("metis" ,metis)
+                       ("openblas" ,openblas)
+                       ("maphys", maphys)
+                       ("pastix", pastix)
+                       ("starpu", starpu)
+                       ("scalapack" ,scalapack)
+                       ("pt-scotch" ,pt-scotch)
+                       ("scotch" ,scotch)
+                       ("openmpi" ,openmpi)
+                       ("openssh" ,openssh)
+                       ("arb" ,arb)))
+                   (synopsis "Hou10ni")
+                   (description
+                     "hou10ni is a DG wave propagation simulating library ")
+                   (license #f))))

inria/tainted/storm.scm

@@ -67,12 +67,8 @@ implicit GCC."
   (package
     (inherit starpu)
     (name "starpu-cuda")
-    ;; "host_config.h" in 'cuda-toolkit' says "gcc versions later than 5 are
-    ;; not supported".  Thus, provide GCC 5.x.
-    (build-system (gnu-build-system-with-compiler gcc-5))
     (native-inputs
-     `(("no-float128" ,no-float128)
-       ("gfortran" ,gfortran-sans-libstdc++)
+     `(("gfortran" ,gfortran-sans-libstdc++)
        ,@(alist-delete "gfortran" (package-native-inputs starpu))))
     (inputs
      `(("cuda" ,cuda)
@@ -81,6 +77,7 @@ implicit GCC."
      (substitute-keyword-arguments (package-arguments starpu)
        ((#:configure-flags flags '())
         `(append (list "--enable-cuda"
+                       "--disable-opencl"
                        (string-append "--with-cuda-dir="
                                       (assoc-ref %build-inputs "cuda"))
                        (string-append "--with-cuda-lib-dir="

non-free/cuda.scm

@@ -6,7 +6,7 @@
 ;;; are detrimental to user freedom and to proper scientific review and
 ;;; experimentation.  As such, we kindly invite you not to share it.
 ;;;
-;;; Copyright © 2018, 2019 Inria
+;;; Copyright © 2018, 2019, 2020 Inria
 
 (define-module (non-free cuda)
   #:use-module (guix)
@@ -126,6 +126,8 @@ libraries for NVIDIA GPUs, all of which are proprietary.")
     (supported-systems '("x86_64-linux"))))
 
 (define-syntax-rule (cuda-source url hash)
+  ;; Visit
+  ;; <https://developer.nvidia.com/cuda-10.2-download-archive?target_os=Linux&target_arch=x86_64&target_distro=Fedora&target_version=29&target_type=runfilelocal> or similar to get the actual URL.
   (origin
     (uri url)
     (sha256 (base32 hash))
@@ -137,9 +139,109 @@ libraries for NVIDIA GPUs, all of which are proprietary.")
               "https://developer.nvidia.com/compute/cuda/8.0/Prod2/local_installers/cuda_8.0.61_375.26_linux-run"
               "1i4xrsqbad283qffvysn88w2pmxzxbbby41lw0j1113z771akv4w")))
 
+(define-public cuda-11.0
+  (package
+    (inherit cuda-8.0)
+    (version "11.0.3")
+    (source
+     (cuda-source
+      "https://developer.download.nvidia.com/compute/cuda/11.0.3/local_installers/cuda_11.0.3_450.51.06_linux.run"
+      "1h4c69nfrgm09jzv8xjnjcvpq8n4gnlii17v3wzqry5d13jc8ydh"))
+    (outputs '("out"))                         ;XXX: no documentation for now
+    (arguments
+     (substitute-keyword-arguments (package-arguments cuda-8.0)
+       ((#:modules modules)
+        `((guix build utils)
+          (guix build gnu-build-system)
+          (ice-9 match)
+          (ice-9 ftw)))                           ;for 'scandir'
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (replace 'unpack
+             (lambda* (#:key inputs #:allow-other-keys)
+               (define libc
+                 (assoc-ref inputs "libc"))
+               (define ld.so
+                 (string-append libc ,(glibc-dynamic-linker)))
+
+               (let ((source (assoc-ref inputs "source")))
+                 (invoke "sh" source "--keep" "--noexec")
+                 (chdir "pkg")
+                 #t)))
+           (add-after 'unpack 'remove-superfluous-stuff
+             (lambda _
+               ;; Remove things we have no use for.
+               (with-directory-excursion "builds"
+                 (for-each delete-file-recursively
+                           '("nsight_compute" "nsight_systems" "cuda_gdb")))
+               #t))
+           (replace 'install
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out")))
+                 (define (copy-from-directory directory)
+                   (for-each (lambda (entry)
+                               (define sub-directory
+                                 (string-append directory "/" entry))
+
+                               (define target
+                                 (string-append out "/" (basename entry)))
+
+                               (when (file-exists? sub-directory)
+                                 (copy-recursively sub-directory target)))
+                             '("bin" "targets/x86_64-linux/lib"
+                               "targets/x86_64-linux/include"
+                               "nvvm/bin" "nvvm/include"
+                               "nvvm/lib64")))
+
+                 (setenv "COLUMNS" "200")         ;wide backtraces!
+                 (with-directory-excursion "builds"
+                   (for-each copy-from-directory
+                             (scandir "." (match-lambda
+                                            ((or "." "..") #f)
+                                            (_ #t))))
+
+                   ;; 'cicc' needs that directory.
+                   (copy-recursively "cuda_nvcc/nvvm/libdevice"
+                                     (string-append out "/nvvm/libdevice")))
+                 #t)))
+           ;; XXX: No documentation for now.
+           (delete 'move-documentation)))))
+    (native-inputs
+     `(("which" ,which)
+       ,@(package-native-inputs cuda-8.0)))))
+
+(define-public cuda-10.2
+  (package
+    (inherit cuda-11.0)
+    (version "10.2.89")
+    (source
+     (cuda-source
+      "https://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda_10.2.89_440.33.01_linux.run"
+      "04fasl9sjkb1jvchvqgaqxprnprcz7a8r52249zp2ijarzyhf3an"))
+    (arguments
+     (substitute-keyword-arguments (package-arguments cuda-11.0)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           ;; This phase doesn't work as is for 10.2.
+           (delete 'remove-superfluous-stuff)
+
+           (add-after 'install 'really-install-libdevice
+             (lambda* (#:key outputs #:allow-other-keys)
+               ;; XXX: The 'install' phase of CUDA 11.0 looks for libdevice
+               ;; in a location that's different from that of libdevice in
+               ;; CUDA 10.  Copy it from the right place here.
+               (let ((out (assoc-ref outputs "out")))
+                 ;; 'cicc' needs that directory.
+                 (copy-recursively "builds/cuda-toolkit/nvvm/libdevice/"
+                                   (string-append out "/nvvm/libdevice"))
+                 #t)))))))))
+
 (define-public cuda
   ;; Default version.
-  cuda-8.0)
+  ;;
+  ;; Note: Pick a version that matches the actual "driver"--i.e.,
+  ;; /usr/lib64/libcuda.so available on the target machine.
+  cuda-10.2)
 
 (define-public no-float128
   ;; FIXME: We cannot simply add it to 'propagated-inputs' of cuda-toolkit
@@ -171,7 +273,7 @@ libraries for NVIDIA GPUs, all of which are proprietary.")
     (description
      "This package provides a @file{<bits/floatn.h>} header to override that
 of glibc and disable float128 support.  This is required allow the use of
-@command{nvcc} with glibc 2.26+.  Otherwise, @command{nvcc} fails like this:
+@command{nvcc} with CUDA 8.0 and glibc 2.26+.  Otherwise, @command{nvcc} fails like this:
 
 @example
 /gnu/store/…-glibc-2.26.105-g0890d5379c/include/bits/floatn.h(61): error: invalid argument to attribute \"__mode__\"