Package: guix-patches;
Reported by: "Paul A. Patience" <paul <at> apatience.com>
Date: Mon, 25 Jul 2022 12:31:02 UTC
Severity: normal
Tags: patch
Done: Ludovic Courtès <ludo <at> gnu.org>
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guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 12:31:02 GMT) Full text and rfc822 format available."Paul A. Patience" <paul <at> apatience.com>:guix-patches <at> gnu.org.
(Mon, 25 Jul 2022 12:31:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: guix-patches <at> gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH 0/6] dealii: Update to 9.4.0 and its Trilinos to 13.4.0. Date: Mon, 25 Jul 2022 12:30:15 +0000
The first patch fixes the failing Trilinos build, which means that dealii-openmpi hasn't been buildable for some time. Paul A. Patience (6): gnu: trilinos-for-dealii-openmpi: Fix build. gnu: dealii: Use G-expressions. gnu: dealii: Update to 9.4.0. gnu: trilinos-for-dealii-openmpi: Remove input labels. gnu: trilinos-for-dealii-openmpi: Use G-expressions. gnu: trilinos-for-dealii-openmpi: Update to 13.4.0. gnu/packages/maths.scm | 269 ++++++++++++++++++++--------------------- 1 file changed, 132 insertions(+), 137 deletions(-) -- 2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 12:34:01 GMT) Full text and rfc822 format available.Message #8 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH 1/6] gnu: trilinos-for-dealii-openmpi: Fix build. Date: Mon, 25 Jul 2022 12:33:07 +0000
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs]:
Add gcc-7 to fix the failing build with newer versions of gcc.
---
gnu/packages/maths.scm | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 458bffee61..948776e9d4 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5153,7 +5153,10 @@ (define trilinos-for-dealii-openmpi
(base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
(build-system cmake-build-system)
(native-inputs
- `(("gfortran" ,gfortran)
+ `(;; The build fails with the current gcc.
+ ;; Use the version from when Trilinos was added.
+ ("gcc" ,gcc-7)
+ ("gfortran" ,gfortran)
;; Trilinos's repository contains several C-shell scripts, but adding
;; tcsh to the native inputs does not result in the check phase running
;; any more tests than without it (nor is tcsh required to build
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 12:34:02 GMT) Full text and rfc822 format available.Message #11 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH 2/6] gnu: dealii: Use G-expressions. Date: Mon, 25 Jul 2022 12:33:12 +0000
* gnu/packages/maths.scm (dealii)[snippet, arguments]: Use
G-expressions.
(dealii-openmpi)[arguments]: Same.
---
gnu/packages/maths.scm | 60 ++++++++++++++++++++++--------------------
1 file changed, 32 insertions(+), 28 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 948776e9d4..7d4049c689 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5287,7 +5287,7 @@ (define-public dealii
(modules '((guix build utils)))
(snippet
;; Remove bundled boost, muparser, TBB and UMFPACK.
- '(delete-file-recursively "bundled"))))
+ #~(delete-file-recursively "bundled"))))
(build-system cmake-build-system)
(outputs '("out" "doc"))
(native-inputs
@@ -5315,32 +5315,36 @@ (define-public dealii
sundials-5
tbb))
(arguments
- `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
- ;; The tests take too long and must be explicitly enabled with "make
- ;; setup_tests".
- ;; See https://www.dealii.org/developer/developers/testsuite.html.
- ;; (They can also be run for an already installed deal.II.)
- #:tests? #f
- #:configure-flags
- (let ((doc (string-append (assoc-ref %outputs "doc")
- "/share/doc/" ,name "-" ,version)))
- `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
- ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
- ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
- ;; Don't compile the examples because the source and CMakeLists.txt
- ;; are installed anyway, allowing users to do so for themselves.
- "-DDEAL_II_COMPILE_EXAMPLES=OFF"
- ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
- #:phases
- (modify-phases %standard-phases
- (add-after 'install 'remove-build-logs
- ;; These build logs leak the name of the build directory by storing
- ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((doc (string-append (assoc-ref outputs "doc")
- "/share/doc/" ,name "-" ,version)))
- (for-each delete-file (map (lambda (f) (string-append doc "/" f))
- '("detailed.log" "summary.log")))))))))
+ (list #:build-type "DebugRelease" ; Only Debug, Release or DebugRelease.
+ ;; The tests take too long and must be explicitly enabled with
+ ;; "make setup_tests".
+ ;; See https://www.dealii.org/developer/developers/testsuite.html.
+ ;; (They can also be run for an already installed deal.II.)
+ #:tests? #f
+ #:configure-flags
+ #~(let ((doc (string-append #$output:doc "/share/doc/"
+ #$name "-" #$version)))
+ (list "-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
+ (string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
+ (string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
+ ;; Don't compile the examples because the source and
+ ;; CMakeLists.txt are installed anyway, allowing users to
+ ;; do so for themselves.
+ "-DDEAL_II_COMPILE_EXAMPLES=OFF"
+ (string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc
+ "/examples")))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'install 'remove-build-logs
+ ;; These build logs leak the name of the build directory by
+ ;; storing the values of CMAKE_SOURCE_DIR and
+ ;; CMAKE_BINARY_DIR.
+ (lambda _
+ (let ((doc (string-append #$output:doc "/share/doc/"
+ #$name "-" #$version)))
+ (for-each delete-file
+ (map (lambda (f) (string-append doc "/" f))
+ '("detailed.log" "summary.log")))))))))
(home-page "https://www.dealii.org/")
(synopsis "Finite element library")
(description
@@ -5373,7 +5377,7 @@ (define-public dealii-openmpi
(arguments
(substitute-keyword-arguments (package-arguments dealii)
((#:configure-flags flags)
- `(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
+ #~(cons "-DDEAL_II_WITH_MPI=ON" #$flags))))
(synopsis "Finite element library (with MPI support)")))
(define-public flann
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 12:34:02 GMT) Full text and rfc822 format available.Message #14 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH 3/6] gnu: dealii: Update to 9.4.0. Date: Mon, 25 Jul 2022 12:33:18 +0000
* gnu/packages/maths.scm (dealii): Update to 9.4.0.
[propagated-inputs]: Replace sundials-5 with sundials.
(dealii-openmpi)[propagated-inputs]: Replace sundials-openmpi-5 with
sundials-openmpi.
---
gnu/packages/maths.scm | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 7d4049c689..a2123d2dc8 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5276,14 +5276,14 @@ (define trilinos-for-dealii-openmpi
(define-public dealii
(package
(name "dealii")
- (version "9.3.3")
+ (version "9.4.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/dealii/dealii/releases/"
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
- (base32 "0a8s4yxcbvzmfgv5qcg27h2ss4fcnyhrhhs35glqj59l9cbmkysx"))
+ (base32 "0v73q6f35f2yrjihaq6vh9lma07qc4cdv75nwmc3c5yrdh07g1i3"))
(modules '((guix build utils)))
(snippet
;; Remove bundled boost, muparser, TBB and UMFPACK.
@@ -5311,8 +5311,7 @@ (define-public dealii
(list boost
hdf5
suitesparse ; For UMFPACK.
- ;; SUNDIALS 6.0.0 and later will be supported in deal.II 9.4.0.
- sundials-5
+ sundials
tbb))
(arguments
(list #:build-type "DebugRelease" ; Only Debug, Release or DebugRelease.
@@ -5372,7 +5371,7 @@ (define-public dealii-openmpi
p4est-openmpi
petsc-openmpi
slepc-openmpi
- sundials-openmpi-5
+ sundials-openmpi
trilinos-for-dealii-openmpi)))
(arguments
(substitute-keyword-arguments (package-arguments dealii)
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 12:34:03 GMT) Full text and rfc822 format available.Message #17 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH 4/6] gnu: trilinos-for-dealii-openmpi: Remove input labels. Date: Mon, 25 Jul 2022 12:33:25 +0000
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs,
inputs, propagated-inputs]: Remove labels.
---
gnu/packages/maths.scm | 53 +++++++++++++++++++++---------------------
1 file changed, 27 insertions(+), 26 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index a2123d2dc8..27b92d369c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5153,34 +5153,35 @@ (define trilinos-for-dealii-openmpi
(base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
(build-system cmake-build-system)
(native-inputs
- `(;; The build fails with the current gcc.
- ;; Use the version from when Trilinos was added.
- ("gcc" ,gcc-7)
- ("gfortran" ,gfortran)
- ;; Trilinos's repository contains several C-shell scripts, but adding
- ;; tcsh to the native inputs does not result in the check phase running
- ;; any more tests than without it (nor is tcsh required to build
- ;; Trilinos).
- ;; It seems that Trilinos has replaced its use of C-shell test scripts
- ;; with CMake's testing facilities.
- ;; For example,
- ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
- ;; states that Zoltan's C-shell test script
- ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
- ;; performed through CMake.
- ;;
- ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
- ;;
- ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
- ("perl" ,perl)
- ("python" ,python-2)))
+ (list
+ ;; The build fails with the current gcc.
+ ;; Use the version from when Trilinos was added.
+ gcc-7
+ gfortran
+ ;; Trilinos's repository contains several C-shell scripts, but adding
+ ;; tcsh to the native inputs does not result in the check phase running
+ ;; any more tests than without it (nor is tcsh required to build
+ ;; Trilinos).
+ ;; It seems that Trilinos has replaced its use of C-shell test scripts
+ ;; with CMake's testing facilities.
+ ;; For example,
+ ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
+ ;; states that Zoltan's C-shell test script
+ ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
+ ;; performed through CMake.
+ ;;
+ ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
+ ;;
+ ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
+ perl
+ python-2))
(inputs
- `(("blas" ,openblas)
- ("lapack" ,lapack)
- ("mumps" ,mumps-openmpi)
- ("scalapack" ,scalapack)))
+ (list openblas
+ lapack
+ mumps-openmpi
+ scalapack))
(propagated-inputs
- `(("mpi" ,openmpi)))
+ (list openmpi))
(arguments
`(#:build-type "Release"
#:configure-flags
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 12:34:03 GMT) Full text and rfc822 format available.Message #20 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH 5/6] gnu: trilinos-for-dealii-openmpi: Use G-expressions. Date: Mon, 25 Jul 2022 12:33:31 +0000
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[arguments]: Use
G-expressions.
<#:phases>: Remove trailing boolean.
---
gnu/packages/maths.scm | 162 +++++++++++++++++++++--------------------
1 file changed, 83 insertions(+), 79 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 27b92d369c..751f1b4fd8 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5183,85 +5183,89 @@ (define trilinos-for-dealii-openmpi
(propagated-inputs
(list openmpi))
(arguments
- `(#:build-type "Release"
- #:configure-flags
- `("-DBUILD_SHARED_LIBS=ON"
- ;; Obtain the equivalent of RelWithDebInfo but with -O3 (the Release
- ;; default) rather than -O2 (the RelWithDebInfo default), to conform
- ;; to candi's trilinos.package's compilation flags, which are -g -O3.
- "-DCMAKE_C_FLAGS=-g"
- "-DCMAKE_CXX_FLAGS=-g"
- "-DCMAKE_Fortran_FLAGS=-g"
-
- ;; Trilinos libraries that deal.II can interface with.
- "-DTrilinos_ENABLE_Amesos=ON"
- "-DTrilinos_ENABLE_AztecOO=ON"
- "-DTrilinos_ENABLE_Epetra=ON"
- "-DTrilinos_ENABLE_EpetraExt=ON"
- "-DTrilinos_ENABLE_Ifpack=ON"
- "-DTrilinos_ENABLE_ML=ON"
- "-DTrilinos_ENABLE_MueLu=ON"
- "-DTrilinos_ENABLE_ROL=ON"
- ;; Optional; required for deal.II's GridIn::read_exodusii, but
- ;; depends on netcdf.
- ;; Enable if and when someone needs it.
- ;;"-DTrilinos_ENABLE_SEACAS=ON"
- "-DTrilinos_ENABLE_Sacado=ON"
- "-DTrilinos_ENABLE_Teuchos=ON"
- "-DTrilinos_ENABLE_Tpetra=ON"
- "-DTrilinos_ENABLE_Zoltan=ON"
-
- ;; Third-party libraries (TPLs) that Trilinos can interface with.
- "-DBLAS_LIBRARY_NAMES=openblas"
- "-DTPL_ENABLE_MPI=ON"
- "-DTPL_ENABLE_MUMPS=ON"
- "-DTPL_ENABLE_SCALAPACK=ON"
-
- ;; Enable the tests but not the examples (which are enabled by
- ;; default when enabling tests).
- ;; Although some examples are run as tests, they are otherwise
- ;; unnecessary since this is a private package meant for
- ;; dealii-openmpi.
- ;; Besides, some MueLu and ROL examples require a lot of memory to
- ;; compile.
- ;;
- ;; (For future reference, note that some ROL and SEACAS examples
- ;; require removing gfortran from CPLUS_INCLUDE_PATH as in the
- ;; dune-istl, dune-localfunctions and dune-alugrid packages.)
- "-DTrilinos_ENABLE_TESTS=ON"
- "-DTrilinos_ENABLE_EXAMPLES=OFF"
- ;; MueLu tests require considerably more time and memory to compile
- ;; than the rest of the tests.
- "-DMueLu_ENABLE_TESTS=OFF"
-
- ;; The following options were gleaned from candi's trilinos.package.
- ;; (We do not enable the complex instantiations, which are anyway
- ;; provided only as an option in trilinos.package, because they are
- ;; costly in compilation time and memory usage, and disk space [1].)
- ;;
- ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types
- "-DTrilinos_ENABLE_Ifpack2=OFF"
- "-DTeuchos_ENABLE_FLOAT=ON"
- "-DTpetra_INST_INT_LONG=ON"
- "-DTPL_ENABLE_Boost=OFF")
- #:phases
- (modify-phases %standard-phases
- (add-after 'configure 'fix-kokkos-config
- (lambda _
- ;; GNU Make 4.3 accidentally leaves the backslash preceding the
- ;; number sign in strings containing a literal backslash–number
- ;; sign (\#) [1, 2].
- ;; This is still an issue in Trilinos 13.0.1, but should be fixed
- ;; in the following version.
- ;; (The latest versions of Kokkos incorporate the fix [2].)
- ;;
- ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
- ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
- (substitute* "KokkosCore_config.h"
- (("\\\\#") "#"))
- #t))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (list #:build-type "Release"
+ #:configure-flags
+ #~(list "-DBUILD_SHARED_LIBS=ON"
+ ;; Obtain the equivalent of RelWithDebInfo but with -O3
+ ;; (the Release default) rather than -O2 (the
+ ;; RelWithDebInfo default), to conform to candi's
+ ;; trilinos.package's compilation flags, which are -g -O3.
+ "-DCMAKE_C_FLAGS=-g"
+ "-DCMAKE_CXX_FLAGS=-g"
+ "-DCMAKE_Fortran_FLAGS=-g"
+
+ ;; Trilinos libraries that deal.II can interface with.
+ "-DTrilinos_ENABLE_Amesos=ON"
+ "-DTrilinos_ENABLE_AztecOO=ON"
+ "-DTrilinos_ENABLE_Epetra=ON"
+ "-DTrilinos_ENABLE_EpetraExt=ON"
+ "-DTrilinos_ENABLE_Ifpack=ON"
+ "-DTrilinos_ENABLE_ML=ON"
+ "-DTrilinos_ENABLE_MueLu=ON"
+ "-DTrilinos_ENABLE_ROL=ON"
+ ;; Optional; required for deal.II's GridIn::read_exodusii,
+ ;; but depends on netcdf.
+ ;; Enable if and when someone needs it.
+ ;;"-DTrilinos_ENABLE_SEACAS=ON"
+ "-DTrilinos_ENABLE_Sacado=ON"
+ "-DTrilinos_ENABLE_Teuchos=ON"
+ "-DTrilinos_ENABLE_Tpetra=ON"
+ "-DTrilinos_ENABLE_Zoltan=ON"
+
+ ;; Third-party libraries (TPLs) that Trilinos can interface
+ ;; with.
+ "-DBLAS_LIBRARY_NAMES=openblas"
+ "-DTPL_ENABLE_MPI=ON"
+ "-DTPL_ENABLE_MUMPS=ON"
+ "-DTPL_ENABLE_SCALAPACK=ON"
+
+ ;; Enable the tests but not the examples (which are enabled
+ ;; by default when enabling tests).
+ ;; Although some examples are run as tests, they are
+ ;; otherwise unnecessary since this is a private package
+ ;; meant for dealii-openmpi.
+ ;; Besides, some MueLu and ROL examples require a lot of
+ ;; memory to compile.
+ ;;
+ ;; (For future reference, note that some ROL and SEACAS
+ ;; examples require removing gfortran from
+ ;; CPLUS_INCLUDE_PATH as in the dune-istl,
+ ;; dune-localfunctions and dune-alugrid packages.)
+ "-DTrilinos_ENABLE_TESTS=ON"
+ "-DTrilinos_ENABLE_EXAMPLES=OFF"
+ ;; MueLu tests require considerably more time and memory to
+ ;; compile than the rest of the tests.
+ "-DMueLu_ENABLE_TESTS=OFF"
+
+ ;; The following options were gleaned from candi's
+ ;; trilinos.package.
+ ;; (We do not enable the complex instantiations, which are
+ ;; anyway provided only as an option in trilinos.package,
+ ;; because they are costly in compilation time and memory
+ ;; usage, and disk space [1].)
+ ;;
+ ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types
+ "-DTrilinos_ENABLE_Ifpack2=OFF"
+ "-DTeuchos_ENABLE_FLOAT=ON"
+ "-DTpetra_INST_INT_LONG=ON"
+ "-DTPL_ENABLE_Boost=OFF")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'configure 'fix-kokkos-config
+ (lambda _
+ ;; GNU Make 4.3 accidentally leaves the backslash preceding
+ ;; the number sign in strings containing a literal
+ ;; backslash–number sign (\#) [1, 2].
+ ;; This is still an issue in Trilinos 13.0.1, but should be
+ ;; fixed in the following version.
+ ;; (The latest versions of Kokkos incorporate the fix [2].)
+ ;;
+ ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
+ ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
+ (substitute* "KokkosCore_config.h"
+ (("\\\\#") "#"))))
+ (add-before 'check 'mpi-setup
+ #$%openmpi-setup))))
(home-page "https://trilinos.github.io/")
(synopsis "Algorithms for engineering and scientific problems")
(description
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 12:34:03 GMT) Full text and rfc822 format available.Message #23 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH 6/6] gnu: trilinos-for-dealii-openmpi: Update to 13.4.0. Date: Mon, 25 Jul 2022 12:33:36 +0000
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi): Update to
13.4.0.
[native-inputs]: Remove gcc-7.
[arguments]: Remove 'fix-kokkos-config' phase.
---
gnu/packages/maths.scm | 58 +++++++++++++++---------------------------
1 file changed, 21 insertions(+), 37 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 751f1b4fd8..73180a1831 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5139,7 +5139,7 @@ (define-public lpsolve
(define trilinos-for-dealii-openmpi
(package
(name "trilinos-for-dealii-openmpi")
- (version "12.18.1")
+ (version "13.4.0")
(source
(origin
(method git-fetch)
@@ -5150,31 +5150,28 @@ (define trilinos-for-dealii-openmpi
(string-replace-substring version "." "-")))))
(file-name (git-file-name "trilinos" version))
(sha256
- (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
+ (base32 "11vkn86dbvyvsf3zipd65y2f8vg5if9n3k7h3i8ybj95d4ck5r2n"))))
(build-system cmake-build-system)
(native-inputs
- (list
- ;; The build fails with the current gcc.
- ;; Use the version from when Trilinos was added.
- gcc-7
- gfortran
- ;; Trilinos's repository contains several C-shell scripts, but adding
- ;; tcsh to the native inputs does not result in the check phase running
- ;; any more tests than without it (nor is tcsh required to build
- ;; Trilinos).
- ;; It seems that Trilinos has replaced its use of C-shell test scripts
- ;; with CMake's testing facilities.
- ;; For example,
- ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
- ;; states that Zoltan's C-shell test script
- ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
- ;; performed through CMake.
- ;;
- ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
- ;;
- ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
- perl
- python-2))
+ (list gfortran
+ ;; Trilinos's repository contains several C-shell scripts, but
+ ;; adding tcsh to the native inputs does not result in the check
+ ;; phase running any more tests than without it (nor is tcsh
+ ;; required to build Trilinos).
+ ;; It seems that Trilinos has replaced its use of C-shell test
+ ;; scripts with CMake's testing facilities.
+ ;; For example,
+ ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
+ ;; states that Zoltan's C-shell test script
+ ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests
+ ;; now performed through CMake.
+ ;;
+ ;; Perl is required for some Zoltan tests and Python 2 for one ML
+ ;; test.
+ ;;
+ ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
+ perl
+ python-2))
(inputs
(list openblas
lapack
@@ -5251,19 +5248,6 @@ (define trilinos-for-dealii-openmpi
"-DTPL_ENABLE_Boost=OFF")
#:phases
#~(modify-phases %standard-phases
- (add-after 'configure 'fix-kokkos-config
- (lambda _
- ;; GNU Make 4.3 accidentally leaves the backslash preceding
- ;; the number sign in strings containing a literal
- ;; backslash–number sign (\#) [1, 2].
- ;; This is still an issue in Trilinos 13.0.1, but should be
- ;; fixed in the following version.
- ;; (The latest versions of Kokkos incorporate the fix [2].)
- ;;
- ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
- ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
- (substitute* "KokkosCore_config.h"
- (("\\\\#") "#"))))
(add-before 'check 'mpi-setup
#$%openmpi-setup))))
(home-page "https://trilinos.github.io/")
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 15:13:02 GMT) Full text and rfc822 format available.Message #26 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH v2 1/6] gnu: trilinos-for-dealii-openmpi: Fix build. Date: Mon, 25 Jul 2022 15:11:54 +0000
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs]:
Add gcc-7 to fix the failing build with newer versions of gcc.
---
gnu/packages/maths.scm | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 458bffee61..948776e9d4 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5153,7 +5153,10 @@ (define trilinos-for-dealii-openmpi
(base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
(build-system cmake-build-system)
(native-inputs
- `(("gfortran" ,gfortran)
+ `(;; The build fails with the current gcc.
+ ;; Use the version from when Trilinos was added.
+ ("gcc" ,gcc-7)
+ ("gfortran" ,gfortran)
;; Trilinos's repository contains several C-shell scripts, but adding
;; tcsh to the native inputs does not result in the check phase running
;; any more tests than without it (nor is tcsh required to build
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 15:13:02 GMT) Full text and rfc822 format available.Message #29 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH v2 0/6] dealii: Update to 9.4.0 and its Trilinos to 13.4.0. Date: Mon, 25 Jul 2022 15:11:49 +0000
Fixed the failing Trilinos 13.4.0 build by disabling Tpetra_INST_INT_LONG_LONG. Paul A. Patience (6): gnu: trilinos-for-dealii-openmpi: Fix build. gnu: dealii: Use G-expressions. gnu: dealii: Update to 9.4.0. gnu: trilinos-for-dealii-openmpi: Remove input labels. gnu: trilinos-for-dealii-openmpi: Use G-expressions. gnu: trilinos-for-dealii-openmpi: Update to 13.4.0. gnu/packages/maths.scm | 281 +++++++++++++++++++++-------------------- 1 file changed, 144 insertions(+), 137 deletions(-) -- 2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 15:13:03 GMT) Full text and rfc822 format available.Message #32 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH v2 2/6] gnu: dealii: Use G-expressions. Date: Mon, 25 Jul 2022 15:12:02 +0000
* gnu/packages/maths.scm (dealii)[snippet, arguments]: Use
G-expressions.
(dealii-openmpi)[arguments]: Same.
---
gnu/packages/maths.scm | 60 ++++++++++++++++++++++--------------------
1 file changed, 32 insertions(+), 28 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 948776e9d4..7d4049c689 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5287,7 +5287,7 @@ (define-public dealii
(modules '((guix build utils)))
(snippet
;; Remove bundled boost, muparser, TBB and UMFPACK.
- '(delete-file-recursively "bundled"))))
+ #~(delete-file-recursively "bundled"))))
(build-system cmake-build-system)
(outputs '("out" "doc"))
(native-inputs
@@ -5315,32 +5315,36 @@ (define-public dealii
sundials-5
tbb))
(arguments
- `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
- ;; The tests take too long and must be explicitly enabled with "make
- ;; setup_tests".
- ;; See https://www.dealii.org/developer/developers/testsuite.html.
- ;; (They can also be run for an already installed deal.II.)
- #:tests? #f
- #:configure-flags
- (let ((doc (string-append (assoc-ref %outputs "doc")
- "/share/doc/" ,name "-" ,version)))
- `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
- ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
- ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
- ;; Don't compile the examples because the source and CMakeLists.txt
- ;; are installed anyway, allowing users to do so for themselves.
- "-DDEAL_II_COMPILE_EXAMPLES=OFF"
- ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
- #:phases
- (modify-phases %standard-phases
- (add-after 'install 'remove-build-logs
- ;; These build logs leak the name of the build directory by storing
- ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((doc (string-append (assoc-ref outputs "doc")
- "/share/doc/" ,name "-" ,version)))
- (for-each delete-file (map (lambda (f) (string-append doc "/" f))
- '("detailed.log" "summary.log")))))))))
+ (list #:build-type "DebugRelease" ; Only Debug, Release or DebugRelease.
+ ;; The tests take too long and must be explicitly enabled with
+ ;; "make setup_tests".
+ ;; See https://www.dealii.org/developer/developers/testsuite.html.
+ ;; (They can also be run for an already installed deal.II.)
+ #:tests? #f
+ #:configure-flags
+ #~(let ((doc (string-append #$output:doc "/share/doc/"
+ #$name "-" #$version)))
+ (list "-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
+ (string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
+ (string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
+ ;; Don't compile the examples because the source and
+ ;; CMakeLists.txt are installed anyway, allowing users to
+ ;; do so for themselves.
+ "-DDEAL_II_COMPILE_EXAMPLES=OFF"
+ (string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc
+ "/examples")))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'install 'remove-build-logs
+ ;; These build logs leak the name of the build directory by
+ ;; storing the values of CMAKE_SOURCE_DIR and
+ ;; CMAKE_BINARY_DIR.
+ (lambda _
+ (let ((doc (string-append #$output:doc "/share/doc/"
+ #$name "-" #$version)))
+ (for-each delete-file
+ (map (lambda (f) (string-append doc "/" f))
+ '("detailed.log" "summary.log")))))))))
(home-page "https://www.dealii.org/")
(synopsis "Finite element library")
(description
@@ -5373,7 +5377,7 @@ (define-public dealii-openmpi
(arguments
(substitute-keyword-arguments (package-arguments dealii)
((#:configure-flags flags)
- `(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
+ #~(cons "-DDEAL_II_WITH_MPI=ON" #$flags))))
(synopsis "Finite element library (with MPI support)")))
(define-public flann
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 15:13:03 GMT) Full text and rfc822 format available.Message #35 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH v2 3/6] gnu: dealii: Update to 9.4.0. Date: Mon, 25 Jul 2022 15:12:08 +0000
* gnu/packages/maths.scm (dealii): Update to 9.4.0.
[propagated-inputs]: Replace sundials-5 with sundials.
(dealii-openmpi)[propagated-inputs]: Replace sundials-openmpi-5 with
sundials-openmpi.
---
gnu/packages/maths.scm | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 7d4049c689..a2123d2dc8 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5276,14 +5276,14 @@ (define trilinos-for-dealii-openmpi
(define-public dealii
(package
(name "dealii")
- (version "9.3.3")
+ (version "9.4.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/dealii/dealii/releases/"
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
- (base32 "0a8s4yxcbvzmfgv5qcg27h2ss4fcnyhrhhs35glqj59l9cbmkysx"))
+ (base32 "0v73q6f35f2yrjihaq6vh9lma07qc4cdv75nwmc3c5yrdh07g1i3"))
(modules '((guix build utils)))
(snippet
;; Remove bundled boost, muparser, TBB and UMFPACK.
@@ -5311,8 +5311,7 @@ (define-public dealii
(list boost
hdf5
suitesparse ; For UMFPACK.
- ;; SUNDIALS 6.0.0 and later will be supported in deal.II 9.4.0.
- sundials-5
+ sundials
tbb))
(arguments
(list #:build-type "DebugRelease" ; Only Debug, Release or DebugRelease.
@@ -5372,7 +5371,7 @@ (define-public dealii-openmpi
p4est-openmpi
petsc-openmpi
slepc-openmpi
- sundials-openmpi-5
+ sundials-openmpi
trilinos-for-dealii-openmpi)))
(arguments
(substitute-keyword-arguments (package-arguments dealii)
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 15:13:03 GMT) Full text and rfc822 format available.Message #38 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH v2 4/6] gnu: trilinos-for-dealii-openmpi: Remove input labels. Date: Mon, 25 Jul 2022 15:12:16 +0000
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[native-inputs,
inputs, propagated-inputs]: Remove labels.
---
gnu/packages/maths.scm | 53 +++++++++++++++++++++---------------------
1 file changed, 27 insertions(+), 26 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index a2123d2dc8..27b92d369c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5153,34 +5153,35 @@ (define trilinos-for-dealii-openmpi
(base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
(build-system cmake-build-system)
(native-inputs
- `(;; The build fails with the current gcc.
- ;; Use the version from when Trilinos was added.
- ("gcc" ,gcc-7)
- ("gfortran" ,gfortran)
- ;; Trilinos's repository contains several C-shell scripts, but adding
- ;; tcsh to the native inputs does not result in the check phase running
- ;; any more tests than without it (nor is tcsh required to build
- ;; Trilinos).
- ;; It seems that Trilinos has replaced its use of C-shell test scripts
- ;; with CMake's testing facilities.
- ;; For example,
- ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
- ;; states that Zoltan's C-shell test script
- ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
- ;; performed through CMake.
- ;;
- ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
- ;;
- ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
- ("perl" ,perl)
- ("python" ,python-2)))
+ (list
+ ;; The build fails with the current gcc.
+ ;; Use the version from when Trilinos was added.
+ gcc-7
+ gfortran
+ ;; Trilinos's repository contains several C-shell scripts, but adding
+ ;; tcsh to the native inputs does not result in the check phase running
+ ;; any more tests than without it (nor is tcsh required to build
+ ;; Trilinos).
+ ;; It seems that Trilinos has replaced its use of C-shell test scripts
+ ;; with CMake's testing facilities.
+ ;; For example,
+ ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
+ ;; states that Zoltan's C-shell test script
+ ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
+ ;; performed through CMake.
+ ;;
+ ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
+ ;;
+ ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
+ perl
+ python-2))
(inputs
- `(("blas" ,openblas)
- ("lapack" ,lapack)
- ("mumps" ,mumps-openmpi)
- ("scalapack" ,scalapack)))
+ (list openblas
+ lapack
+ mumps-openmpi
+ scalapack))
(propagated-inputs
- `(("mpi" ,openmpi)))
+ (list openmpi))
(arguments
`(#:build-type "Release"
#:configure-flags
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 15:13:04 GMT) Full text and rfc822 format available.Message #41 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH v2 5/6] gnu: trilinos-for-dealii-openmpi: Use G-expressions. Date: Mon, 25 Jul 2022 15:12:24 +0000
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi)[arguments]: Use
G-expressions.
<#:phases>: Remove trailing boolean.
---
gnu/packages/maths.scm | 162 +++++++++++++++++++++--------------------
1 file changed, 83 insertions(+), 79 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 27b92d369c..751f1b4fd8 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5183,85 +5183,89 @@ (define trilinos-for-dealii-openmpi
(propagated-inputs
(list openmpi))
(arguments
- `(#:build-type "Release"
- #:configure-flags
- `("-DBUILD_SHARED_LIBS=ON"
- ;; Obtain the equivalent of RelWithDebInfo but with -O3 (the Release
- ;; default) rather than -O2 (the RelWithDebInfo default), to conform
- ;; to candi's trilinos.package's compilation flags, which are -g -O3.
- "-DCMAKE_C_FLAGS=-g"
- "-DCMAKE_CXX_FLAGS=-g"
- "-DCMAKE_Fortran_FLAGS=-g"
-
- ;; Trilinos libraries that deal.II can interface with.
- "-DTrilinos_ENABLE_Amesos=ON"
- "-DTrilinos_ENABLE_AztecOO=ON"
- "-DTrilinos_ENABLE_Epetra=ON"
- "-DTrilinos_ENABLE_EpetraExt=ON"
- "-DTrilinos_ENABLE_Ifpack=ON"
- "-DTrilinos_ENABLE_ML=ON"
- "-DTrilinos_ENABLE_MueLu=ON"
- "-DTrilinos_ENABLE_ROL=ON"
- ;; Optional; required for deal.II's GridIn::read_exodusii, but
- ;; depends on netcdf.
- ;; Enable if and when someone needs it.
- ;;"-DTrilinos_ENABLE_SEACAS=ON"
- "-DTrilinos_ENABLE_Sacado=ON"
- "-DTrilinos_ENABLE_Teuchos=ON"
- "-DTrilinos_ENABLE_Tpetra=ON"
- "-DTrilinos_ENABLE_Zoltan=ON"
-
- ;; Third-party libraries (TPLs) that Trilinos can interface with.
- "-DBLAS_LIBRARY_NAMES=openblas"
- "-DTPL_ENABLE_MPI=ON"
- "-DTPL_ENABLE_MUMPS=ON"
- "-DTPL_ENABLE_SCALAPACK=ON"
-
- ;; Enable the tests but not the examples (which are enabled by
- ;; default when enabling tests).
- ;; Although some examples are run as tests, they are otherwise
- ;; unnecessary since this is a private package meant for
- ;; dealii-openmpi.
- ;; Besides, some MueLu and ROL examples require a lot of memory to
- ;; compile.
- ;;
- ;; (For future reference, note that some ROL and SEACAS examples
- ;; require removing gfortran from CPLUS_INCLUDE_PATH as in the
- ;; dune-istl, dune-localfunctions and dune-alugrid packages.)
- "-DTrilinos_ENABLE_TESTS=ON"
- "-DTrilinos_ENABLE_EXAMPLES=OFF"
- ;; MueLu tests require considerably more time and memory to compile
- ;; than the rest of the tests.
- "-DMueLu_ENABLE_TESTS=OFF"
-
- ;; The following options were gleaned from candi's trilinos.package.
- ;; (We do not enable the complex instantiations, which are anyway
- ;; provided only as an option in trilinos.package, because they are
- ;; costly in compilation time and memory usage, and disk space [1].)
- ;;
- ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types
- "-DTrilinos_ENABLE_Ifpack2=OFF"
- "-DTeuchos_ENABLE_FLOAT=ON"
- "-DTpetra_INST_INT_LONG=ON"
- "-DTPL_ENABLE_Boost=OFF")
- #:phases
- (modify-phases %standard-phases
- (add-after 'configure 'fix-kokkos-config
- (lambda _
- ;; GNU Make 4.3 accidentally leaves the backslash preceding the
- ;; number sign in strings containing a literal backslash–number
- ;; sign (\#) [1, 2].
- ;; This is still an issue in Trilinos 13.0.1, but should be fixed
- ;; in the following version.
- ;; (The latest versions of Kokkos incorporate the fix [2].)
- ;;
- ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
- ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
- (substitute* "KokkosCore_config.h"
- (("\\\\#") "#"))
- #t))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ (list #:build-type "Release"
+ #:configure-flags
+ #~(list "-DBUILD_SHARED_LIBS=ON"
+ ;; Obtain the equivalent of RelWithDebInfo but with -O3
+ ;; (the Release default) rather than -O2 (the
+ ;; RelWithDebInfo default), to conform to candi's
+ ;; trilinos.package's compilation flags, which are -g -O3.
+ "-DCMAKE_C_FLAGS=-g"
+ "-DCMAKE_CXX_FLAGS=-g"
+ "-DCMAKE_Fortran_FLAGS=-g"
+
+ ;; Trilinos libraries that deal.II can interface with.
+ "-DTrilinos_ENABLE_Amesos=ON"
+ "-DTrilinos_ENABLE_AztecOO=ON"
+ "-DTrilinos_ENABLE_Epetra=ON"
+ "-DTrilinos_ENABLE_EpetraExt=ON"
+ "-DTrilinos_ENABLE_Ifpack=ON"
+ "-DTrilinos_ENABLE_ML=ON"
+ "-DTrilinos_ENABLE_MueLu=ON"
+ "-DTrilinos_ENABLE_ROL=ON"
+ ;; Optional; required for deal.II's GridIn::read_exodusii,
+ ;; but depends on netcdf.
+ ;; Enable if and when someone needs it.
+ ;;"-DTrilinos_ENABLE_SEACAS=ON"
+ "-DTrilinos_ENABLE_Sacado=ON"
+ "-DTrilinos_ENABLE_Teuchos=ON"
+ "-DTrilinos_ENABLE_Tpetra=ON"
+ "-DTrilinos_ENABLE_Zoltan=ON"
+
+ ;; Third-party libraries (TPLs) that Trilinos can interface
+ ;; with.
+ "-DBLAS_LIBRARY_NAMES=openblas"
+ "-DTPL_ENABLE_MPI=ON"
+ "-DTPL_ENABLE_MUMPS=ON"
+ "-DTPL_ENABLE_SCALAPACK=ON"
+
+ ;; Enable the tests but not the examples (which are enabled
+ ;; by default when enabling tests).
+ ;; Although some examples are run as tests, they are
+ ;; otherwise unnecessary since this is a private package
+ ;; meant for dealii-openmpi.
+ ;; Besides, some MueLu and ROL examples require a lot of
+ ;; memory to compile.
+ ;;
+ ;; (For future reference, note that some ROL and SEACAS
+ ;; examples require removing gfortran from
+ ;; CPLUS_INCLUDE_PATH as in the dune-istl,
+ ;; dune-localfunctions and dune-alugrid packages.)
+ "-DTrilinos_ENABLE_TESTS=ON"
+ "-DTrilinos_ENABLE_EXAMPLES=OFF"
+ ;; MueLu tests require considerably more time and memory to
+ ;; compile than the rest of the tests.
+ "-DMueLu_ENABLE_TESTS=OFF"
+
+ ;; The following options were gleaned from candi's
+ ;; trilinos.package.
+ ;; (We do not enable the complex instantiations, which are
+ ;; anyway provided only as an option in trilinos.package,
+ ;; because they are costly in compilation time and memory
+ ;; usage, and disk space [1].)
+ ;;
+ ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types
+ "-DTrilinos_ENABLE_Ifpack2=OFF"
+ "-DTeuchos_ENABLE_FLOAT=ON"
+ "-DTpetra_INST_INT_LONG=ON"
+ "-DTPL_ENABLE_Boost=OFF")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'configure 'fix-kokkos-config
+ (lambda _
+ ;; GNU Make 4.3 accidentally leaves the backslash preceding
+ ;; the number sign in strings containing a literal
+ ;; backslash–number sign (\#) [1, 2].
+ ;; This is still an issue in Trilinos 13.0.1, but should be
+ ;; fixed in the following version.
+ ;; (The latest versions of Kokkos incorporate the fix [2].)
+ ;;
+ ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
+ ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
+ (substitute* "KokkosCore_config.h"
+ (("\\\\#") "#"))))
+ (add-before 'check 'mpi-setup
+ #$%openmpi-setup))))
(home-page "https://trilinos.github.io/")
(synopsis "Algorithms for engineering and scientific problems")
(description
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Mon, 25 Jul 2022 15:13:04 GMT) Full text and rfc822 format available.Message #44 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH v2 6/6] gnu: trilinos-for-dealii-openmpi: Update to 13.4.0. Date: Mon, 25 Jul 2022 15:12:33 +0000
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi): Update to
13.4.0.
[native-inputs]: Remove gcc-7.
[arguments]: Remove 'fix-kokkos-config' phase.
---
gnu/packages/maths.scm | 70 ++++++++++++++++++++----------------------
1 file changed, 33 insertions(+), 37 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 751f1b4fd8..d3481da0a6 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5139,7 +5139,7 @@ (define-public lpsolve
(define trilinos-for-dealii-openmpi
(package
(name "trilinos-for-dealii-openmpi")
- (version "12.18.1")
+ (version "13.4.0")
(source
(origin
(method git-fetch)
@@ -5150,31 +5150,28 @@ (define trilinos-for-dealii-openmpi
(string-replace-substring version "." "-")))))
(file-name (git-file-name "trilinos" version))
(sha256
- (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
+ (base32 "11vkn86dbvyvsf3zipd65y2f8vg5if9n3k7h3i8ybj95d4ck5r2n"))))
(build-system cmake-build-system)
(native-inputs
- (list
- ;; The build fails with the current gcc.
- ;; Use the version from when Trilinos was added.
- gcc-7
- gfortran
- ;; Trilinos's repository contains several C-shell scripts, but adding
- ;; tcsh to the native inputs does not result in the check phase running
- ;; any more tests than without it (nor is tcsh required to build
- ;; Trilinos).
- ;; It seems that Trilinos has replaced its use of C-shell test scripts
- ;; with CMake's testing facilities.
- ;; For example,
- ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
- ;; states that Zoltan's C-shell test script
- ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
- ;; performed through CMake.
- ;;
- ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
- ;;
- ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
- perl
- python-2))
+ (list gfortran
+ ;; Trilinos's repository contains several C-shell scripts, but
+ ;; adding tcsh to the native inputs does not result in the check
+ ;; phase running any more tests than without it (nor is tcsh
+ ;; required to build Trilinos).
+ ;; It seems that Trilinos has replaced its use of C-shell test
+ ;; scripts with CMake's testing facilities.
+ ;; For example,
+ ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
+ ;; states that Zoltan's C-shell test script
+ ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests
+ ;; now performed through CMake.
+ ;;
+ ;; Perl is required for some Zoltan tests and Python 2 for one ML
+ ;; test.
+ ;;
+ ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
+ perl
+ python-2))
(inputs
(list openblas
lapack
@@ -5248,22 +5245,21 @@ (define trilinos-for-dealii-openmpi
"-DTrilinos_ENABLE_Ifpack2=OFF"
"-DTeuchos_ENABLE_FLOAT=ON"
"-DTpetra_INST_INT_LONG=ON"
+ ;; Disabling Tpetra_INST_INT_LONG_LONG is required only
+ ;; because Tpetra's CMakeLists.txt [1] is incorrectly
+ ;; testing for
+ ;;
+ ;; DEFINED Tpetra_INST_INT_LONG AND Tpetra_INST_INT_UNSIGNED_LONG
+ ;;
+ ;; instead of
+ ;;
+ ;; DEFINED Tpetra_INST_INT_LONG AND Tpetra_INST_INT_LONG
+ ;;
+ ;; [1]: https://github.com/trilinos/Trilinos/blob/0976cf2a8f9ee2991f4fb479f1056ca569eb22b9/packages/tpetra/CMakeLists.txt#L697
+ "-DTpetra_INST_INT_LONG_LONG=OFF"
"-DTPL_ENABLE_Boost=OFF")
#:phases
#~(modify-phases %standard-phases
- (add-after 'configure 'fix-kokkos-config
- (lambda _
- ;; GNU Make 4.3 accidentally leaves the backslash preceding
- ;; the number sign in strings containing a literal
- ;; backslash–number sign (\#) [1, 2].
- ;; This is still an issue in Trilinos 13.0.1, but should be
- ;; fixed in the following version.
- ;; (The latest versions of Kokkos incorporate the fix [2].)
- ;;
- ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
- ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
- (substitute* "KokkosCore_config.h"
- (("\\\\#") "#"))))
(add-before 'check 'mpi-setup
#$%openmpi-setup))))
(home-page "https://trilinos.github.io/")
--
2.37.1
guix-patches <at> gnu.org:bug#56760; Package guix-patches.
(Tue, 26 Jul 2022 11:42:01 GMT) Full text and rfc822 format available.Message #47 received at 56760 <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: 56760 <at> debbugs.gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: Re: [PATCH v2 6/6] gnu: trilinos-for-dealii-openmpi: Update to 13.4.0. Date: Tue, 26 Jul 2022 11:41:25 +0000
On 2022-07-25 08:12:33-07:00, Paul A. Patience wrote: > * gnu/packages/maths.scm (trilinos-for-dealii-openmpi): Update to > 13.4.0. Actually, 13.4.0 has some linking errors even with the fix to the configure flags. So this patch shouldn't be applied, but the first 5 are ok. Paul
Ludovic Courtès <ludo <at> gnu.org>:"Paul A. Patience" <paul <at> apatience.com>:Message #52 received at 56760-done <at> debbugs.gnu.org (full text, mbox):
From: Ludovic Courtès <ludo <at> gnu.org> To: "Paul A. Patience" <paul <at> apatience.com> Cc: 56760-done <at> debbugs.gnu.org Subject: Re: bug#56760: [PATCH 0/6] dealii: Update to 9.4.0 and its Trilinos to 13.4.0. Date: Mon, 01 Aug 2022 17:22:25 +0200
Hi, "Paul A. Patience" <paul <at> apatience.com> skribis: > gnu: trilinos-for-dealii-openmpi: Fix build. > gnu: dealii: Use G-expressions. > gnu: dealii: Update to 9.4.0. > gnu: trilinos-for-dealii-openmpi: Remove input labels. > gnu: trilinos-for-dealii-openmpi: Use G-expressions. > gnu: trilinos-for-dealii-openmpi: Update to 13.4.0. Pushed everything but the sixth patch, as you suggested. Please resubmit it separately when it’s ready. Thanks! Ludo’.
Debbugs Internal Request <help-debbugs <at> gnu.org>
to internal_control <at> debbugs.gnu.org.
(Tue, 30 Aug 2022 11:24:08 GMT) Full text and rfc822 format available.
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