* [bug#39862] [PATCH v2 0/6] Update Dune finite element packages
2020-03-02 21:56 ` Felix Gruber
@ 2020-03-10 19:29 ` Felix Gruber
2020-03-12 10:46 ` Ludovic Courtès
2020-03-10 19:29 ` [bug#39862] [PATCH v2 1/6] gnu: dune-*: set up MPI for tests Felix Gruber
` (5 subsequent siblings)
6 siblings, 1 reply; 25+ messages in thread
From: Felix Gruber @ 2020-03-10 19:29 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, zimoun
The first four patches in this patch set are identical to v1. I've added
two new patches that remove the openmpi dependency from all dune-*
packages and add new dedicated dune-*-openmpi packages instead.
To create these openmpi variants of the dune-* packages without a lot of
duplication, I've added a helper function add-openmpi-to-dune-package
that takes a dune-* package and returns its openmpi variant with the
correct dependencies and the setup code necessary to make Dune's tests
work with openmpi.
Felix Gruber (6):
gnu: dune-*: set up MPI for tests
gnu: add dune-uggrid 2.6.0
gnu: Add dune-subgrid
gnu: dune-istl: Build with suitesparse
gnu: dune-*: remove openmpi dependency
gnu: define dune-*-openmpi packages
gnu/packages/maths.scm | 285 +++++++++++++++++++++++++----------------
1 file changed, 172 insertions(+), 113 deletions(-)
--
2.25.1
^ permalink raw reply [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v2 0/6] Update Dune finite element packages
2020-03-10 19:29 ` [bug#39862] [PATCH v2 0/6] Update " Felix Gruber
@ 2020-03-12 10:46 ` Ludovic Courtès
0 siblings, 0 replies; 25+ messages in thread
From: Ludovic Courtès @ 2020-03-12 10:46 UTC (permalink / raw)
To: Felix Gruber; +Cc: zimoun, 39862
Hi Felix,
Felix Gruber <felgru@posteo.net> skribis:
> The first four patches in this patch set are identical to v1. I've added
> two new patches that remove the openmpi dependency from all dune-*
> packages and add new dedicated dune-*-openmpi packages instead.
> To create these openmpi variants of the dune-* packages without a lot of
> duplication, I've added a helper function add-openmpi-to-dune-package
> that takes a dune-* package and returns its openmpi variant with the
> correct dependencies and the setup code necessary to make Dune's tests
> work with openmpi.
>
> Felix Gruber (6):
> gnu: dune-*: set up MPI for tests
> gnu: add dune-uggrid 2.6.0
> gnu: Add dune-subgrid
> gnu: dune-istl: Build with suitesparse
I applied all these.
> gnu: dune-*: remove openmpi dependency
> gnu: define dune-*-openmpi packages
I’ll comment on these separately.
Thank you!
Ludo’.
^ permalink raw reply [flat|nested] 25+ messages in thread
* [bug#39862] [PATCH v2 1/6] gnu: dune-*: set up MPI for tests
2020-03-02 21:56 ` Felix Gruber
2020-03-10 19:29 ` [bug#39862] [PATCH v2 0/6] Update " Felix Gruber
@ 2020-03-10 19:29 ` Felix Gruber
2020-03-10 19:29 ` [bug#39862] [PATCH v2 2/6] gnu: add dune-uggrid 2.6.0 Felix Gruber
` (4 subsequent siblings)
6 siblings, 0 replies; 25+ messages in thread
From: Felix Gruber @ 2020-03-10 19:29 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, zimoun
* gnu/packages/maths.scm (dune-common, dune-grid, dune-istl,
dune-alugrid): [arguments]: correctly set up MPI instead of disabling
tests that require MPI.
---
gnu/packages/maths.scm | 110 ++++-------------------------------------
1 file changed, 10 insertions(+), 100 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index a990ffc45e..bec490ebc3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4583,36 +4583,8 @@ linear algebra primitives specifically targeting graph analytics.")
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags)))
- ;; These tests fail because they require a fully functional MPI
- ;; environment.
- (add-after 'unpack 'disable-failing-tests
- (lambda _
- (setenv "ARGS"
- (string-append "--exclude-regex '("
- (string-join
- (list
- "remoteindicestest"
- "remoteindicestest-mpi-2"
- "syncertest"
- "syncertest-mpi-2"
- "variablesizecommunicatortest"
- "variablesizecommunicatortest-mpi-2"
- "arithmetictestsuitetest"
- "assertandreturntest"
- "assertandreturntest_ndebug"
- "concept"
- "debugaligntest"
- "mpicollectivecommunication"
- "mpicollectivecommunication-mpi-2"
- "mpiguardtest"
- "mpiguardtest-mpi-2"
- "mpihelpertest"
- "mpihelpertest-mpi-2"
- "mpihelpertest2"
- "mpihelpertest2-mpi-2")
- "|")
- ")'"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("gmp" ,gmp)
("metis" ,metis)
@@ -4693,54 +4665,8 @@ This package contains the basic DUNE geometry classes.")
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags)))
- ;; These tests fail because they require a fully functional MPI
- ;; environment.
- (add-after 'unpack 'disable-failing-tests
- (lambda _
- (setenv "ARGS"
- (string-append "--exclude-regex '("
- (string-join
- (list
- "scsgmappertest"
- "conformvolumevtktest"
- "gnuplottest"
- "nonconformboundaryvtktest"
- "subsamplingvtktest"
- "vtktest"
- "vtktest-mpi-2"
- "vtksequencetest"
- "gmshtest-onedgrid"
- "test-dgf-yasp"
- "test-dgf-yasp-offset"
- "test-dgf-oned"
- "test-geogrid-yaspgrid"
- "test-gridinfo"
- "test-identitygrid"
- "testiteratorranges"
- "test-hierarchicsearch"
- "test-parallel-ug-mpi-2"
- "test-yaspgrid-backuprestore-equidistant"
- "test-yaspgrid-backuprestore-equidistant-mpi-2"
- "test-yaspgrid-backuprestore-equidistantoffset"
- "test-yaspgrid-backuprestore-equidistantoffset-mpi-2"
- "test-yaspgrid-backuprestore-tensor"
- "test-yaspgrid-backuprestore-tensor-mpi-2"
- "test-yaspgrid-tensorgridfactory"
- "test-yaspgrid-tensorgridfactory-mpi-2"
- "test-yaspgrid-yaspfactory-1d"
- "test-yaspgrid-yaspfactory-1d-mpi-2"
- "test-yaspgrid-yaspfactory-2d"
- "test-yaspgrid-yaspfactory-2d-mpi-2"
- "test-yaspgrid-yaspfactory-3d"
- "test-yaspgrid-yaspfactory-3d-mpi-2"
- "globalindexsettest"
- "persistentcontainertest"
- "structuredgridfactorytest"
- "tensorgridfactorytest"
- "vertexordertest")
- "|")
- ")'"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
@@ -4783,24 +4709,8 @@ This package contains the basic DUNE grid classes.")
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags)))
- ;; These tests fail because they require a fully functional MPI
- ;; environment.
- (add-after 'unpack 'disable-failing-tests
- (lambda _
- (setenv "ARGS"
- (string-append "--exclude-regex '("
- (string-join
- (list
- "galerkintest"
- "hierarchytest"
- "pamgtest"
- "pamg_comm_repart_test"
- "matrixredisttest"
- "vectorcommtest"
- "matrixmarkettest")
- "|")
- ")'"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("dune-common" ,dune-common)
("openmpi" ,openmpi)
@@ -4886,9 +4796,7 @@ assemble global function spaces on finite-element grids.")
"1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj"))))
(build-system cmake-build-system)
(arguments
- `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI
- ; environment
- #:phases
+ `(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-include
(lambda _
@@ -4900,7 +4808,9 @@ assemble global function spaces on finite-element grids.")
(lambda* (#:key inputs make-flags #:allow-other-keys)
(setenv "CPLUS_INCLUDE_PATH"
(string-append (assoc-ref inputs "dune-grid") "/share"))
- (apply invoke "make" "build_tests" make-flags))))))
+ (apply invoke "make" "build_tests" make-flags)))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v2 2/6] gnu: add dune-uggrid 2.6.0
2020-03-02 21:56 ` Felix Gruber
2020-03-10 19:29 ` [bug#39862] [PATCH v2 0/6] Update " Felix Gruber
2020-03-10 19:29 ` [bug#39862] [PATCH v2 1/6] gnu: dune-*: set up MPI for tests Felix Gruber
@ 2020-03-10 19:29 ` Felix Gruber
2020-03-10 19:29 ` [bug#39862] [PATCH v2 3/6] gnu: Add dune-subgrid Felix Gruber
` (3 subsequent siblings)
6 siblings, 0 replies; 25+ messages in thread
From: Felix Gruber @ 2020-03-10 19:29 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, zimoun
* gnu/packages/maths.scm (dune-uggrid): New variable.
* gnu/packages/maths.scm (dune-grid): [propagated-inputs]: Add
dune-uggrid dependency, so that the UGGrid class in dune-grid can be
used by packages that have dune-grid as input.
* gnu/packages/maths.scm (dune-functions): [arguments]: enable tests
that previously weren't built as they require dune-uggrid.
---
gnu/packages/maths.scm | 53 +++++++++++++++++++++++++++++++++++++++++-
1 file changed, 52 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index bec490ebc3..3f89efeff4 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4646,6 +4646,42 @@ This package contains the basic DUNE geometry classes.")
;; GPL version 2 with "runtime exception"
(license license:gpl2)))
+(define-public dune-uggrid
+ (package
+ (name "dune-uggrid")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://dune-project.org/download/"
+ version "/dune-uggrid-" version ".tar.gz"))
+ (sha256
+ (base32
+ "05l7a1gb78mny49anyxk6rjvn66rhgm30y72v5cjg0m5kfgr1a1f"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'build-tests
+ (lambda* (#:key make-flags #:allow-other-keys)
+ (apply invoke "make" "build_tests" make-flags))))))
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("openmpi" ,openmpi)))
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://dune-project.org/")
+ (synopsis "Distributed and Unified Numerics Environment")
+ (description "DUNE, the Distributed and Unified Numerics Environment is a
+modular toolbox for solving @dfn{partial differential equations} (PDEs) with
+grid-based methods. It supports the easy implementation of methods like
+@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite
+Differences} (FD).
+
+This package contains the DUNE UG grid classes.")
+ (license license:lgpl2.1)))
+
(define-public dune-grid
(package
(name "dune-grid")
@@ -4675,6 +4711,8 @@ This package contains the basic DUNE geometry classes.")
("openblas" ,openblas)
("openmpi" ,openmpi)
("python" ,python)))
+ (propagated-inputs
+ `(("dune-uggrid" ,dune-uggrid)))
(native-inputs
`(("gfortran" ,gfortran)
("pkg-config" ,pkg-config)))
@@ -4888,7 +4926,20 @@ operating on statically typed trees of objects.")
(base32
"1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200"))))
(build-system cmake-build-system)
- (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'disable-failing-tests
+ (lambda _
+ (setenv "ARGS"
+ ;; unable to load GMSH file in this test
+ "--exclude-regex gridviewfunctionspacebasistest")
+ #t))
+ (add-after 'build 'build-tests
+ (lambda* (#:key make-flags #:allow-other-keys)
+ (apply invoke "make" "build_tests" make-flags)))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(inputs
`(("dune-common" ,dune-common)
("dune-istl" ,dune-istl)
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v2 3/6] gnu: Add dune-subgrid
2020-03-02 21:56 ` Felix Gruber
` (2 preceding siblings ...)
2020-03-10 19:29 ` [bug#39862] [PATCH v2 2/6] gnu: add dune-uggrid 2.6.0 Felix Gruber
@ 2020-03-10 19:29 ` Felix Gruber
2020-03-10 19:29 ` [bug#39862] [PATCH v2 4/6] gnu: dune-istl: Build with suitesparse Felix Gruber
` (2 subsequent siblings)
6 siblings, 0 replies; 25+ messages in thread
From: Felix Gruber @ 2020-03-10 19:29 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, zimoun
* gnu/packages/maths.scm (dune-subgrid): New variable.
---
gnu/packages/maths.scm | 43 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 43 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 3f89efeff4..9da38aad68 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4871,6 +4871,49 @@ implementation of the DUNE grid interface supporting either simplices or
cubes.")
(license license:gpl2+)))
+(define-public dune-subgrid
+ (package
+ (name "dune-subgrid")
+ (version "2.6.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
+ (commit "releases/2.6-1")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1gcv35rx3knqd54r4pp9rzd639db4j8w2r2ibq43w1mgwdcqhs64"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'build-tests
+ (lambda* (#:key make-flags #:allow-other-keys)
+ (apply invoke "make" "build_tests" make-flags)))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
+ (inputs
+ `(("dune-common" ,dune-common)
+ ("dune-geometry" ,dune-geometry)
+ ("dune-grid" ,dune-grid)
+ ("openmpi" ,openmpi)
+ ;; Optional
+ ("metis" ,metis)
+ ("openblas" ,openblas)
+ ("gmp" ,gmp)))
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php")
+ (synopsis "Distributed and Unified Numerics Environment")
+ (description "The dune-subgrid module allows to mark elements of
+another hierarchical dune grid. The set of marked elements can then be
+accessed as a hierarchical dune grid in its own right. Dune-Subgrid
+provides the full grid interface including adaptive mesh refinement.")
+ (license license:gpl2+)))
+
(define-public dune-typetree
(package
(name "dune-typetree")
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v2 4/6] gnu: dune-istl: Build with suitesparse
2020-03-02 21:56 ` Felix Gruber
` (3 preceding siblings ...)
2020-03-10 19:29 ` [bug#39862] [PATCH v2 3/6] gnu: Add dune-subgrid Felix Gruber
@ 2020-03-10 19:29 ` Felix Gruber
2020-03-10 19:29 ` [bug#39862] [PATCH v2 5/6] gnu: dune-*: remove openmpi dependency Felix Gruber
2020-03-10 19:29 ` [bug#39862] [PATCH v2 6/6] gnu: define dune-*-openmpi packages Felix Gruber
6 siblings, 0 replies; 25+ messages in thread
From: Felix Gruber @ 2020-03-10 19:29 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, zimoun
* gnu/packages/maths.scm (dune-istl)[inputs]: Add suitesparse to build
additional solvers in dune-istl.
---
gnu/packages/maths.scm | 1 +
1 file changed, 1 insertion(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 9da38aad68..2c03c00366 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4754,6 +4754,7 @@ This package contains the basic DUNE grid classes.")
("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
+ ("suitesparse" ,suitesparse)
("superlu" ,superlu)
("openblas" ,openblas)
("gmp" ,gmp)
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v2 5/6] gnu: dune-*: remove openmpi dependency
2020-03-02 21:56 ` Felix Gruber
` (4 preceding siblings ...)
2020-03-10 19:29 ` [bug#39862] [PATCH v2 4/6] gnu: dune-istl: Build with suitesparse Felix Gruber
@ 2020-03-10 19:29 ` Felix Gruber
2020-03-10 19:29 ` [bug#39862] [PATCH v2 6/6] gnu: define dune-*-openmpi packages Felix Gruber
6 siblings, 0 replies; 25+ messages in thread
From: Felix Gruber @ 2020-03-10 19:29 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, zimoun
* gnu/packages/maths.scm (dune-*)[inputs]: Remove openmpi dependency.
[arguments]: remove code to setup openmpi for tests.
---
gnu/packages/maths.scm | 37 +++++++------------------------------
1 file changed, 7 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2c03c00366..33a5efd2f0 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4582,13 +4582,10 @@ linear algebra primitives specifically targeting graph analytics.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("gmp" ,gmp)
("metis" ,metis)
- ("openmpi" ,openmpi)
("openblas" ,openblas)
("python" ,python)
("superlu" ,superlu)))
@@ -4626,7 +4623,6 @@ Differences} (FD).")
(apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)
;; Optional
("openblas" ,openblas)
("gmp" ,gmp)
@@ -4666,8 +4662,7 @@ This package contains the basic DUNE geometry classes.")
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags))))))
(inputs
- `(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)))
+ `(("dune-common" ,dune-common)))
(native-inputs
`(("gfortran" ,gfortran)
("pkg-config" ,pkg-config)))
@@ -4700,16 +4695,13 @@ This package contains the DUNE UG grid classes.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
("gmp" ,gmp)
("metis" ,metis)
("openblas" ,openblas)
- ("openmpi" ,openmpi)
("python" ,python)))
(propagated-inputs
`(("dune-uggrid" ,dune-uggrid)))
@@ -4746,12 +4738,9 @@ This package contains the basic DUNE grid classes.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("suitesparse" ,suitesparse)
@@ -4799,7 +4788,6 @@ aggregation-based algebraic multigrid.")
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("superlu" ,superlu)
@@ -4847,14 +4835,11 @@ assemble global function spaces on finite-element grids.")
(lambda* (#:key inputs make-flags #:allow-other-keys)
(setenv "CPLUS_INCLUDE_PATH"
(string-append (assoc-ref inputs "dune-grid") "/share"))
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
("dune-grid" ,dune-grid)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("openblas" ,openblas)
@@ -4892,14 +4877,11 @@ cubes.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
("dune-grid" ,dune-grid)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("openblas" ,openblas)
@@ -4938,7 +4920,6 @@ provides the full grid interface including adaptive mesh refinement.")
(apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)
;; Optional
("openblas" ,openblas)
("python" ,python)
@@ -4981,9 +4962,7 @@ operating on statically typed trees of objects.")
#t))
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-istl" ,dune-istl)
@@ -4991,7 +4970,6 @@ operating on statically typed trees of objects.")
("dune-grid" ,dune-grid)
("dune-geometry" ,dune-geometry)
("dune-typetree" ,dune-typetree)
- ("openmpi" ,openmpi)
("openblas" ,openblas)
("metis" ,metis)
("python" ,python)
@@ -5032,7 +5010,6 @@ implemented as callable objects, and bases of finite element spaces.")
("dune-grid" ,dune-grid)
("dune-typetree" ,dune-typetree)
("dune-functions" ,dune-functions)
- ("openmpi" ,openmpi)
;; Optional
("openblas" ,openblas)
("eigen" ,eigen)
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v2 6/6] gnu: define dune-*-openmpi packages
2020-03-02 21:56 ` Felix Gruber
` (5 preceding siblings ...)
2020-03-10 19:29 ` [bug#39862] [PATCH v2 5/6] gnu: dune-*: remove openmpi dependency Felix Gruber
@ 2020-03-10 19:29 ` Felix Gruber
2020-03-12 12:42 ` Ludovic Courtès
6 siblings, 1 reply; 25+ messages in thread
From: Felix Gruber @ 2020-03-10 19:29 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, zimoun
* gnu/packages/maths.scm (dune-*-openmpi): New variables.
* gnu/packages/maths.scm (add-openmpi-to-dune-package): New function to
add openmpi to the inputs of a dune-* package and replace all dune-*
packages in its input with the corresponding dune-*-openmpi package.
---
gnu/packages/maths.scm | 79 +++++++++++++++++++++++++++++++++++++++++-
1 file changed, 78 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 33a5efd2f0..e904ca1bd8 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -126,7 +126,9 @@
#:use-module (gnu packages version-control)
#:use-module (gnu packages wxwidgets)
#:use-module (gnu packages xml)
- #:use-module (srfi srfi-1))
+ #:use-module (srfi srfi-1)
+ #:use-module (srfi srfi-34)
+ #:use-module (srfi srfi-35))
(define-public aris
(package
@@ -5027,6 +5029,81 @@ built on top of DUNE, the Distributed and Unified Numerics Environment.")
;; Either GPL version 2 with "runtime exception" or LGPLv3+.
(license (list license:lgpl3+ license:gpl2))))
+(define add-openmpi-to-dune-package
+ (let ((transformed-packages '()))
+ (lambda (p)
+ (let* ((p-name (package-name p))
+ (replace-package
+ (lambda (mapping)
+ (let* ((name (car mapping))
+ (p (cadr mapping))
+ (new-p
+ (match (assoc-ref transformed-packages name)
+ (#f
+ (if (string-prefix? "dune-" name)
+ (raise (condition
+ (&message
+ (message
+ (format #f "Need to call \
+add-openmpi-to-dune-package on '~a' before '~a'."
+ name p-name)))))
+ p))
+ (transformed-p transformed-p))))
+ `(,name ,new-p))))
+ (substitute-mpi-packages (lambda (inputs)
+ (map replace-package inputs)))
+ (mpi-p
+ (package (inherit p)
+ (name (string-append p-name "-openmpi"))
+ (inputs `(,@(substitute-mpi-packages (package-inputs p))
+ ("openmpi" ,openmpi)))
+ (propagated-inputs
+ (substitute-mpi-packages (package-propagated-inputs p)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments p)
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
+ (synopsis (string-append (package-synopsis p) " (with MPI support)")))))
+ (begin
+ (set! transformed-packages
+ (acons p-name mpi-p transformed-packages))
+ mpi-p)))))
+
+(define-public dune-common-openmpi
+ (add-openmpi-to-dune-package dune-common))
+
+(define-public dune-geometry-openmpi
+ (add-openmpi-to-dune-package dune-geometry))
+
+(define-public dune-istl-openmpi
+ (add-openmpi-to-dune-package dune-istl))
+
+(define-public dune-typetree-openmpi
+ (add-openmpi-to-dune-package dune-typetree))
+
+(define-public dune-uggrid-openmpi
+ (add-openmpi-to-dune-package dune-uggrid))
+
+(define-public dune-grid-openmpi
+ (add-openmpi-to-dune-package dune-grid))
+
+(define-public dune-alugrid-openmpi
+ (add-openmpi-to-dune-package dune-alugrid))
+
+(define-public dune-subgrid-openmpi
+ (add-openmpi-to-dune-package dune-subgrid))
+
+(define-public dune-localfunctions-openmpi
+ (add-openmpi-to-dune-package dune-localfunctions))
+
+(define-public dune-functions-openmpi
+ (add-openmpi-to-dune-package dune-functions))
+
+(define-public dune-pdelab-openmpi
+ (add-openmpi-to-dune-package dune-pdelab))
+
(define-public mlucas
(package
(name "mlucas")
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v2 6/6] gnu: define dune-*-openmpi packages
2020-03-10 19:29 ` [bug#39862] [PATCH v2 6/6] gnu: define dune-*-openmpi packages Felix Gruber
@ 2020-03-12 12:42 ` Ludovic Courtès
2020-03-12 21:05 ` [bug#39862] [PATCH v3 0/2] Add " Felix Gruber
` (2 more replies)
0 siblings, 3 replies; 25+ messages in thread
From: Ludovic Courtès @ 2020-03-12 12:42 UTC (permalink / raw)
To: Felix Gruber; +Cc: zimoun, 39862
Hi again,
Felix Gruber <felgru@posteo.net> skribis:
> +(define add-openmpi-to-dune-package
> + (let ((transformed-packages '()))
> + (lambda (p)
> + (let* ((p-name (package-name p))
> + (replace-package
> + (lambda (mapping)
> + (let* ((name (car mapping))
> + (p (cadr mapping))
> + (new-p
> + (match (assoc-ref transformed-packages name)
> + (#f
> + (if (string-prefix? "dune-" name)
> + (raise (condition
> + (&message
> + (message
> + (format #f "Need to call \
> +add-openmpi-to-dune-package on '~a' before '~a'."
> + name p-name)))))
> + p))
> + (transformed-p transformed-p))))
> + `(,name ,new-p))))
> + (substitute-mpi-packages (lambda (inputs)
> + (map replace-package inputs)))
> + (mpi-p
> + (package (inherit p)
> + (name (string-append p-name "-openmpi"))
> + (inputs `(,@(substitute-mpi-packages (package-inputs p))
> + ("openmpi" ,openmpi)))
> + (propagated-inputs
> + (substitute-mpi-packages (package-propagated-inputs p)))
> + (arguments
> + (substitute-keyword-arguments (package-arguments p)
> + ((#:phases phases '%standard-phases)
> + `(modify-phases ,phases
> + (add-before 'check 'mpi-setup
> + ,%openmpi-setup)))))
> + (synopsis (string-append (package-synopsis p) " (with MPI support)")))))
> + (begin
> + (set! transformed-packages
> + (acons p-name mpi-p transformed-packages))
> + mpi-p)))))
I think it’s a good idea to add those “-openmpi” packages. However, I
have suggestions regarding the code above. :-)
A general note: set!, car, cdr, etc. are frowned upon in Guix:
https://guix.gnu.org/manual/en/html_node/Coding-Style.html
It seems to me that ‘replace-package’ above is overly generic: since
it’s an internal procedure, we don’t need to add error cases, messages,
etc.
Last, could it be written in terms of ‘package-mapping’? That takes
care of graph traversal and memoization.
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v3 0/2] Add dune-*-openmpi packages
2020-03-12 12:42 ` Ludovic Courtès
@ 2020-03-12 21:05 ` Felix Gruber
2020-03-12 21:05 ` [bug#39862] [PATCH v3 1/2] gnu: dune-*: remove openmpi dependency Felix Gruber
2020-03-12 21:05 ` [bug#39862] [PATCH v3 2/2] gnu: define dune-*-openmpi packages Felix Gruber
2 siblings, 0 replies; 25+ messages in thread
From: Felix Gruber @ 2020-03-12 21:05 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, Ludovic Courtès
Hi Ludo’,
thanks for your suggestions regarding the creation of the dune-*-openmpi
packages. I've rewritten the add-openmpi-to-dune-package in terms of
package-mapping as you suggested.
You'll find the modified version of my last two patches in the following
two emails.
Many thanks,
Felix
Felix Gruber (2):
gnu: dune-*: remove openmpi dependency
gnu: define dune-*-openmpi packages
gnu/packages/maths.scm | 90 ++++++++++++++++++++++++++++--------------
1 file changed, 60 insertions(+), 30 deletions(-)
--
2.25.1
^ permalink raw reply [flat|nested] 25+ messages in thread
* [bug#39862] [PATCH v3 1/2] gnu: dune-*: remove openmpi dependency
2020-03-12 12:42 ` Ludovic Courtès
2020-03-12 21:05 ` [bug#39862] [PATCH v3 0/2] Add " Felix Gruber
@ 2020-03-12 21:05 ` Felix Gruber
2020-03-12 21:05 ` [bug#39862] [PATCH v3 2/2] gnu: define dune-*-openmpi packages Felix Gruber
2 siblings, 0 replies; 25+ messages in thread
From: Felix Gruber @ 2020-03-12 21:05 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, Ludovic Courtès
* gnu/packages/maths.scm (dune-*)[inputs]: Remove openmpi dependency.
[arguments]: remove code to setup openmpi for tests.
---
gnu/packages/maths.scm | 37 +++++++------------------------------
1 file changed, 7 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2c03c00366..33a5efd2f0 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4582,13 +4582,10 @@ linear algebra primitives specifically targeting graph analytics.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("gmp" ,gmp)
("metis" ,metis)
- ("openmpi" ,openmpi)
("openblas" ,openblas)
("python" ,python)
("superlu" ,superlu)))
@@ -4626,7 +4623,6 @@ Differences} (FD).")
(apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)
;; Optional
("openblas" ,openblas)
("gmp" ,gmp)
@@ -4666,8 +4662,7 @@ This package contains the basic DUNE geometry classes.")
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags))))))
(inputs
- `(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)))
+ `(("dune-common" ,dune-common)))
(native-inputs
`(("gfortran" ,gfortran)
("pkg-config" ,pkg-config)))
@@ -4700,16 +4695,13 @@ This package contains the DUNE UG grid classes.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
("gmp" ,gmp)
("metis" ,metis)
("openblas" ,openblas)
- ("openmpi" ,openmpi)
("python" ,python)))
(propagated-inputs
`(("dune-uggrid" ,dune-uggrid)))
@@ -4746,12 +4738,9 @@ This package contains the basic DUNE grid classes.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("suitesparse" ,suitesparse)
@@ -4799,7 +4788,6 @@ aggregation-based algebraic multigrid.")
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("superlu" ,superlu)
@@ -4847,14 +4835,11 @@ assemble global function spaces on finite-element grids.")
(lambda* (#:key inputs make-flags #:allow-other-keys)
(setenv "CPLUS_INCLUDE_PATH"
(string-append (assoc-ref inputs "dune-grid") "/share"))
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
("dune-grid" ,dune-grid)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("openblas" ,openblas)
@@ -4892,14 +4877,11 @@ cubes.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
("dune-grid" ,dune-grid)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("openblas" ,openblas)
@@ -4938,7 +4920,6 @@ provides the full grid interface including adaptive mesh refinement.")
(apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)
;; Optional
("openblas" ,openblas)
("python" ,python)
@@ -4981,9 +4962,7 @@ operating on statically typed trees of objects.")
#t))
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-istl" ,dune-istl)
@@ -4991,7 +4970,6 @@ operating on statically typed trees of objects.")
("dune-grid" ,dune-grid)
("dune-geometry" ,dune-geometry)
("dune-typetree" ,dune-typetree)
- ("openmpi" ,openmpi)
("openblas" ,openblas)
("metis" ,metis)
("python" ,python)
@@ -5032,7 +5010,6 @@ implemented as callable objects, and bases of finite element spaces.")
("dune-grid" ,dune-grid)
("dune-typetree" ,dune-typetree)
("dune-functions" ,dune-functions)
- ("openmpi" ,openmpi)
;; Optional
("openblas" ,openblas)
("eigen" ,eigen)
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v3 2/2] gnu: define dune-*-openmpi packages
2020-03-12 12:42 ` Ludovic Courtès
2020-03-12 21:05 ` [bug#39862] [PATCH v3 0/2] Add " Felix Gruber
2020-03-12 21:05 ` [bug#39862] [PATCH v3 1/2] gnu: dune-*: remove openmpi dependency Felix Gruber
@ 2020-03-12 21:05 ` Felix Gruber
2020-03-13 9:42 ` Ludovic Courtès
2 siblings, 1 reply; 25+ messages in thread
From: Felix Gruber @ 2020-03-12 21:05 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, Ludovic Courtès
* gnu/packages/maths.scm (dune-*-openmpi): New variables.
* gnu/packages/maths.scm (add-openmpi-to-dune-package): New function to
add openmpi to the inputs of a dune-* package and replace all dune-*
packages in its input with the corresponding dune-*-openmpi package.
---
gnu/packages/maths.scm | 53 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 33a5efd2f0..ac89064a7f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5027,6 +5027,59 @@ built on top of DUNE, the Distributed and Unified Numerics Environment.")
;; Either GPL version 2 with "runtime exception" or LGPLv3+.
(license (list license:lgpl3+ license:gpl2))))
+(define add-openmpi-to-dune-package
+ (let ((dune-package?
+ (lambda (p) (string-prefix? "dune-" (package-name p)))))
+ (package-mapping
+ (lambda (p)
+ (if (dune-package? p)
+ (package (inherit p)
+ (name (string-append (package-name p) "-openmpi"))
+ (inputs `(,@(package-inputs p)
+ ("openmpi" ,openmpi)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments p)
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
+ (synopsis (string-append (package-synopsis p) " (with MPI support)")))
+ p))
+ (lambda (p) (not (dune-package? p))))))
+
+(define-public dune-common-openmpi
+ (add-openmpi-to-dune-package dune-common))
+
+(define-public dune-geometry-openmpi
+ (add-openmpi-to-dune-package dune-geometry))
+
+(define-public dune-istl-openmpi
+ (add-openmpi-to-dune-package dune-istl))
+
+(define-public dune-typetree-openmpi
+ (add-openmpi-to-dune-package dune-typetree))
+
+(define-public dune-uggrid-openmpi
+ (add-openmpi-to-dune-package dune-uggrid))
+
+(define-public dune-grid-openmpi
+ (add-openmpi-to-dune-package dune-grid))
+
+(define-public dune-alugrid-openmpi
+ (add-openmpi-to-dune-package dune-alugrid))
+
+(define-public dune-subgrid-openmpi
+ (add-openmpi-to-dune-package dune-subgrid))
+
+(define-public dune-localfunctions-openmpi
+ (add-openmpi-to-dune-package dune-localfunctions))
+
+(define-public dune-functions-openmpi
+ (add-openmpi-to-dune-package dune-functions))
+
+(define-public dune-pdelab-openmpi
+ (add-openmpi-to-dune-package dune-pdelab))
+
(define-public mlucas
(package
(name "mlucas")
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v3 2/2] gnu: define dune-*-openmpi packages
2020-03-12 21:05 ` [bug#39862] [PATCH v3 2/2] gnu: define dune-*-openmpi packages Felix Gruber
@ 2020-03-13 9:42 ` Ludovic Courtès
2020-03-13 17:26 ` Felix Gruber
` (2 more replies)
0 siblings, 3 replies; 25+ messages in thread
From: Ludovic Courtès @ 2020-03-13 9:42 UTC (permalink / raw)
To: Felix Gruber; +Cc: 39862
Hi Felix,
Felix Gruber <felgru@posteo.net> skribis:
> * gnu/packages/maths.scm (dune-*-openmpi): New variables.
> * gnu/packages/maths.scm (add-openmpi-to-dune-package): New function to
> add openmpi to the inputs of a dune-* package and replace all dune-*
> packages in its input with the corresponding dune-*-openmpi package.
Nitpick: no need to repeat the file name above. It would also be great
if you could list all the new variables.
> + (lambda (p) (not (dune-package? p))))))
You can replace the lambda with:
(negate dune-package?)
One last thing: could you look at the output of, say, ‘guix graph
dune-geometry-openmpi’ and ensure we’re not duplicating more nodes than
needed in the graph?
For example, you can compare node counts with:
guix graph dune-geometry | grep 'label =' | wc -l
guix graph dune-geometry-openmpi | grep 'label =' | wc -l
The difference should be less than:
guix graph openmpi | grep 'label =' | wc -l
If that works well, please send an updated patch and we should be ready
to go!
Thanks,
Ludo’.
^ permalink raw reply [flat|nested] 25+ messages in thread* [bug#39862] [PATCH v3 2/2] gnu: define dune-*-openmpi packages
2020-03-13 9:42 ` Ludovic Courtès
@ 2020-03-13 17:26 ` Felix Gruber
2020-03-13 21:28 ` Ludovic Courtès
2020-03-13 17:30 ` [bug#39862] [PATCH v4 1/2] gnu: dune-*: remove openmpi dependency Felix Gruber
2020-03-13 17:30 ` [bug#39862] [PATCH v4 2/2] gnu: define dune-*-openmpi packages Felix Gruber
2 siblings, 1 reply; 25+ messages in thread
From: Felix Gruber @ 2020-03-13 17:26 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: 39862
Hi Ludo’,
On 3/13/20 10:42 AM, Ludovic Courtès wrote:
> Felix Gruber <felgru@posteo.net> skribis:
>
>> * gnu/packages/maths.scm (dune-*-openmpi): New variables.
>> * gnu/packages/maths.scm (add-openmpi-to-dune-package): New function to
>> add openmpi to the inputs of a dune-* package and replace all dune-*
>> packages in its input with the corresponding dune-*-openmpi package.
>
> Nitpick: no need to repeat the file name above. It would also be great
> if you could list all the new variables.
Sure, no problem.
>> + (lambda (p) (not (dune-package? p))))))
>
> You can replace the lambda with:
>
> (negate dune-package?)
Thanks for this hint, as I'm new to Scheme, my knowledge of its standard
library is still pretty limited. The negate function is quite useful.
> One last thing: could you look at the output of, say, ‘guix graph
> dune-geometry-openmpi’ and ensure we’re not duplicating more nodes than
> needed in the graph?
>
> For example, you can compare node counts with:
>
> guix graph dune-geometry | grep 'label =' | wc -l
> guix graph dune-geometry-openmpi | grep 'label =' | wc -l
>
> The difference should be less than:
>
> guix graph openmpi | grep 'label =' | wc -l
>
> If that works well, please send an updated patch and we should be ready
> to go!
I get the following numbers:
graph dune-geometry | grep 'label =' | wc -l
70
guix graph dune-geometry-openmpi | grep 'label =' | wc -l
143
guix graph openmpi | grep 'label =' | wc -l
137
The difference seems to be OK: 143 - 70 = 73 < 137.
I'll send the updated patch ASAP.
Best Regards,
Felix
^ permalink raw reply [flat|nested] 25+ messages in thread
* [bug#39862] [PATCH v3 2/2] gnu: define dune-*-openmpi packages
2020-03-13 17:26 ` Felix Gruber
@ 2020-03-13 21:28 ` Ludovic Courtès
0 siblings, 0 replies; 25+ messages in thread
From: Ludovic Courtès @ 2020-03-13 21:28 UTC (permalink / raw)
To: Felix Gruber; +Cc: 39862
Hi,
Felix Gruber <felgru@posteo.net> skribis:
>>> + (lambda (p) (not (dune-package? p))))))
>>
>> You can replace the lambda with:
>>
>> (negate dune-package?)
>
> Thanks for this hint, as I'm new to Scheme, my knowledge of its standard
> library is still pretty limited.
Sure, I think sharing knowledge is one of the goals of review.
>> One last thing: could you look at the output of, say, ‘guix graph
>> dune-geometry-openmpi’ and ensure we’re not duplicating more nodes than
>> needed in the graph?
>>
>> For example, you can compare node counts with:
>>
>> guix graph dune-geometry | grep 'label =' | wc -l
>> guix graph dune-geometry-openmpi | grep 'label =' | wc -l
>>
>> The difference should be less than:
>>
>> guix graph openmpi | grep 'label =' | wc -l
>>
>> If that works well, please send an updated patch and we should be ready
>> to go!
>
> I get the following numbers:
>
> graph dune-geometry | grep 'label =' | wc -l
> 70
>
> guix graph dune-geometry-openmpi | grep 'label =' | wc -l
> 143
>
> guix graph openmpi | grep 'label =' | wc -l
> 137
>
> The difference seems to be OK: 143 - 70 = 73 < 137.
Looks good, thanks!
Ludo’.
^ permalink raw reply [flat|nested] 25+ messages in thread
* [bug#39862] [PATCH v4 1/2] gnu: dune-*: remove openmpi dependency
2020-03-13 9:42 ` Ludovic Courtès
2020-03-13 17:26 ` Felix Gruber
@ 2020-03-13 17:30 ` Felix Gruber
2020-03-14 16:55 ` bug#39862: " Ludovic Courtès
2020-03-13 17:30 ` [bug#39862] [PATCH v4 2/2] gnu: define dune-*-openmpi packages Felix Gruber
2 siblings, 1 reply; 25+ messages in thread
From: Felix Gruber @ 2020-03-13 17:30 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, Ludovic Courtès
* gnu/packages/maths.scm (dune-*)[inputs]: Remove openmpi dependency.
[arguments]: remove code to setup openmpi for tests.
---
gnu/packages/maths.scm | 37 +++++++------------------------------
1 file changed, 7 insertions(+), 30 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2c03c00366..33a5efd2f0 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4582,13 +4582,10 @@ linear algebra primitives specifically targeting graph analytics.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("gmp" ,gmp)
("metis" ,metis)
- ("openmpi" ,openmpi)
("openblas" ,openblas)
("python" ,python)
("superlu" ,superlu)))
@@ -4626,7 +4623,6 @@ Differences} (FD).")
(apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)
;; Optional
("openblas" ,openblas)
("gmp" ,gmp)
@@ -4666,8 +4662,7 @@ This package contains the basic DUNE geometry classes.")
(lambda* (#:key make-flags #:allow-other-keys)
(apply invoke "make" "build_tests" make-flags))))))
(inputs
- `(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)))
+ `(("dune-common" ,dune-common)))
(native-inputs
`(("gfortran" ,gfortran)
("pkg-config" ,pkg-config)))
@@ -4700,16 +4695,13 @@ This package contains the DUNE UG grid classes.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
("gmp" ,gmp)
("metis" ,metis)
("openblas" ,openblas)
- ("openmpi" ,openmpi)
("python" ,python)))
(propagated-inputs
`(("dune-uggrid" ,dune-uggrid)))
@@ -4746,12 +4738,9 @@ This package contains the basic DUNE grid classes.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("suitesparse" ,suitesparse)
@@ -4799,7 +4788,6 @@ aggregation-based algebraic multigrid.")
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("superlu" ,superlu)
@@ -4847,14 +4835,11 @@ assemble global function spaces on finite-element grids.")
(lambda* (#:key inputs make-flags #:allow-other-keys)
(setenv "CPLUS_INCLUDE_PATH"
(string-append (assoc-ref inputs "dune-grid") "/share"))
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
("dune-grid" ,dune-grid)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("openblas" ,openblas)
@@ -4892,14 +4877,11 @@ cubes.")
(modify-phases %standard-phases
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-geometry" ,dune-geometry)
("dune-grid" ,dune-grid)
- ("openmpi" ,openmpi)
;; Optional
("metis" ,metis)
("openblas" ,openblas)
@@ -4938,7 +4920,6 @@ provides the full grid interface including adaptive mesh refinement.")
(apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
- ("openmpi" ,openmpi)
;; Optional
("openblas" ,openblas)
("python" ,python)
@@ -4981,9 +4962,7 @@ operating on statically typed trees of objects.")
#t))
(add-after 'build 'build-tests
(lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags)))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (apply invoke "make" "build_tests" make-flags))))))
(inputs
`(("dune-common" ,dune-common)
("dune-istl" ,dune-istl)
@@ -4991,7 +4970,6 @@ operating on statically typed trees of objects.")
("dune-grid" ,dune-grid)
("dune-geometry" ,dune-geometry)
("dune-typetree" ,dune-typetree)
- ("openmpi" ,openmpi)
("openblas" ,openblas)
("metis" ,metis)
("python" ,python)
@@ -5032,7 +5010,6 @@ implemented as callable objects, and bases of finite element spaces.")
("dune-grid" ,dune-grid)
("dune-typetree" ,dune-typetree)
("dune-functions" ,dune-functions)
- ("openmpi" ,openmpi)
;; Optional
("openblas" ,openblas)
("eigen" ,eigen)
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread* bug#39862: [PATCH v4 1/2] gnu: dune-*: remove openmpi dependency
2020-03-13 17:30 ` [bug#39862] [PATCH v4 1/2] gnu: dune-*: remove openmpi dependency Felix Gruber
@ 2020-03-14 16:55 ` Ludovic Courtès
0 siblings, 0 replies; 25+ messages in thread
From: Ludovic Courtès @ 2020-03-14 16:55 UTC (permalink / raw)
To: Felix Gruber; +Cc: 39862-done
Hi,
Felix Gruber <felgru@posteo.net> skribis:
> * gnu/packages/maths.scm (dune-*)[inputs]: Remove openmpi dependency.
> [arguments]: remove code to setup openmpi for tests.
[...]
> * gnu/packages/maths.scm (dune-common-openmpi, dune-geometry-openmpi,
> dune-istl-openmpi, dune-typetree-openmpi, dune-uggrid-openmpi,
> dune-grid-openmpi, dune-alugrid-openmpi, dune-subgrid-openmpi,
> dune-localfunctions-openmpi, dune-functions-openmpi,
> dune-pdelab-openmpi): New variables.
> (add-openmpi-to-dune-package): New function to add openmpi to the
> inputs of a dune-* package and replace all dune-* packages in its
> input with the corresponding dune-*-openmpi package.
Pushed, thanks!
Ludo’.
^ permalink raw reply [flat|nested] 25+ messages in thread
* [bug#39862] [PATCH v4 2/2] gnu: define dune-*-openmpi packages
2020-03-13 9:42 ` Ludovic Courtès
2020-03-13 17:26 ` Felix Gruber
2020-03-13 17:30 ` [bug#39862] [PATCH v4 1/2] gnu: dune-*: remove openmpi dependency Felix Gruber
@ 2020-03-13 17:30 ` Felix Gruber
2 siblings, 0 replies; 25+ messages in thread
From: Felix Gruber @ 2020-03-13 17:30 UTC (permalink / raw)
To: 39862; +Cc: Felix Gruber, Ludovic Courtès
* gnu/packages/maths.scm (dune-common-openmpi, dune-geometry-openmpi,
dune-istl-openmpi, dune-typetree-openmpi, dune-uggrid-openmpi,
dune-grid-openmpi, dune-alugrid-openmpi, dune-subgrid-openmpi,
dune-localfunctions-openmpi, dune-functions-openmpi,
dune-pdelab-openmpi): New variables.
(add-openmpi-to-dune-package): New function to add openmpi to the
inputs of a dune-* package and replace all dune-* packages in its
input with the corresponding dune-*-openmpi package.
---
gnu/packages/maths.scm | 53 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 33a5efd2f0..6c2813f100 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5027,6 +5027,59 @@ built on top of DUNE, the Distributed and Unified Numerics Environment.")
;; Either GPL version 2 with "runtime exception" or LGPLv3+.
(license (list license:lgpl3+ license:gpl2))))
+(define add-openmpi-to-dune-package
+ (let ((dune-package?
+ (lambda (p) (string-prefix? "dune-" (package-name p)))))
+ (package-mapping
+ (lambda (p)
+ (if (dune-package? p)
+ (package (inherit p)
+ (name (string-append (package-name p) "-openmpi"))
+ (inputs `(,@(package-inputs p)
+ ("openmpi" ,openmpi)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments p)
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
+ (synopsis (string-append (package-synopsis p) " (with MPI support)")))
+ p))
+ (negate dune-package?))))
+
+(define-public dune-common-openmpi
+ (add-openmpi-to-dune-package dune-common))
+
+(define-public dune-geometry-openmpi
+ (add-openmpi-to-dune-package dune-geometry))
+
+(define-public dune-istl-openmpi
+ (add-openmpi-to-dune-package dune-istl))
+
+(define-public dune-typetree-openmpi
+ (add-openmpi-to-dune-package dune-typetree))
+
+(define-public dune-uggrid-openmpi
+ (add-openmpi-to-dune-package dune-uggrid))
+
+(define-public dune-grid-openmpi
+ (add-openmpi-to-dune-package dune-grid))
+
+(define-public dune-alugrid-openmpi
+ (add-openmpi-to-dune-package dune-alugrid))
+
+(define-public dune-subgrid-openmpi
+ (add-openmpi-to-dune-package dune-subgrid))
+
+(define-public dune-localfunctions-openmpi
+ (add-openmpi-to-dune-package dune-localfunctions))
+
+(define-public dune-functions-openmpi
+ (add-openmpi-to-dune-package dune-functions))
+
+(define-public dune-pdelab-openmpi
+ (add-openmpi-to-dune-package dune-pdelab))
+
(define-public mlucas
(package
(name "mlucas")
--
2.25.1
^ permalink raw reply related [flat|nested] 25+ messages in thread