* [bug#49772] [PATCH] gnu: dealii-openmpi: Add Trilinos dependency.
@ 2021-07-29 16:33 Paul A. Patience
2021-07-30 13:59 ` Paul A. Patience
0 siblings, 1 reply; 3+ messages in thread
From: Paul A. Patience @ 2021-07-29 16:33 UTC (permalink / raw)
To: 49772
[-- Attachment #1: Type: text/plain, Size: 452 bytes --]
Hi,
This patch adds the optional dependency Trilinos to dealii-openmpi.
(Starting from deal.II 10.0.0, the Trilinos interface will require
MPI, and anyway parts of deal.II's Trilinos interface do not compile
properly without MPI even in earlier versions.)
This patch is necessary for me to package Lethe [1] next, which
requires deal.II to be compiled with Trilinos support.
Best regards,
Paul
[1]: https://github.com/lethe-cfd/lethe
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From f0d377b93996d9b08cdd4edb9567b0bc2941e593 Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Thu, 29 Jul 2021 12:16:32 -0400
Subject: [PATCH] gnu: dealii-openmpi: Add Trilinos dependency.
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi): New variable.
(dealii-openmpi)[propagated-inputs]: Add trilinos-for-dealii-openmpi.
---
gnu/packages/maths.scm | 148 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 148 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 13c8338f5c..10996dacc9 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4608,6 +4608,153 @@ specifications.")
revised simplex and the branch-and-bound methods.")
(license license:lgpl2.1+)))
+;; Private Trilinos package for dealii-openmpi (similar to
+;; trilinos-serial-xyce and trilinos-parallel-xyce).
+;; This version is the latest known to be compatible with deal.II [1].
+;; Since the latest version of Trilinos is not necessarily supported by
+;; deal.II, it may be worth keeping this package even if and when Trilinos
+;; gets packaged separately for Guix (unless various versions of Trilinos are
+;; packaged).
+;;
+;; An insightful source of information for building Trilinos for deal.II lies
+;; in the Trilinos package for candi [2], which is a source-based installer
+;; for deal.II and its dependencies.
+;;
+;; [1]: https://www.dealii.org/current/external-libs/trilinos.html
+;; [2]: https://github.com/dealii/candi/blob/master/deal.II-toolchain/packages/trilinos.package
+(define trilinos-for-dealii-openmpi
+ (package
+ (name "trilinos-for-dealii-openmpi")
+ (version "12.18.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/trilinos/Trilinos/")
+ (commit
+ (string-append "trilinos-release-"
+ (string-replace-substring version "." "-")))))
+ (file-name (git-file-name "trilinos" version))
+ (sha256
+ (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("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)))
+ (inputs
+ `(("blas" ,openblas)
+ ("lapack" ,lapack)
+ ("mumps" ,mumps-openmpi)
+ ("scalapack" ,scalapack)))
+ (propagated-inputs
+ `(("mpi" ,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 (the examples are disabled
+ ;; by default).
+ ;; 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"
+ ;; 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))))
+ (home-page "https://trilinos.github.io/")
+ (synopsis "Algorithms for engineering and scientific problems")
+ (description
+ "The Trilinos Project is an effort to develop algorithms and enabling
+technologies within an object-oriented software framework for the solution of
+large-scale, complex multi-physics engineering and scientific problems.
+A unique design feature of Trilinos is its focus on packages.")
+ ;; The packages are variously licensed under more than just BSD-3 and
+ ;; LGPL-2.1+, but all the licenses are either BSD- or LGPL-compatible.
+ ;; See https://trilinos.github.io/license.html.
+ (license (list license:bsd-3 license:lgpl2.1+))))
+
(define-public dealii
(package
(name "dealii")
@@ -4703,6 +4850,7 @@ in finite element programs.")
("p4est" ,p4est-openmpi)
("petsc" ,petsc-openmpi)
("slepc" ,slepc-openmpi)
+ ("trilinos" ,trilinos-for-dealii-openmpi)
,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
(arguments
(substitute-keyword-arguments (package-arguments dealii)
--
2.32.0
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [bug#49772] [PATCH] gnu: dealii-openmpi: Add Trilinos dependency.
2021-07-29 16:33 [bug#49772] [PATCH] gnu: dealii-openmpi: Add Trilinos dependency Paul A. Patience
@ 2021-07-30 13:59 ` Paul A. Patience
2021-08-10 15:32 ` bug#49772: " Ludovic Courtès
0 siblings, 1 reply; 3+ messages in thread
From: Paul A. Patience @ 2021-07-30 13:59 UTC (permalink / raw)
To: 49772
[-- Attachment #1: Type: text/plain, Size: 280 bytes --]
On Thursday, July 29th, 2021 at 12:33, Paul A. Patience <paul@apatience.com> wrote:
> This patch adds the optional dependency Trilinos to dealii-openmpi.
Fixed a minor issue in the patch.
(The examples actually get enabled by default with the tests.)
Best regards,
Paul
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From 3556e260785f1b52d351e041e9fe171df448d73b Mon Sep 17 00:00:00 2001
From: "Paul A. Patience" <paul@apatience.com>
Date: Thu, 29 Jul 2021 12:16:32 -0400
Subject: [PATCH] gnu: dealii-openmpi: Add Trilinos dependency.
* gnu/packages/maths.scm (trilinos-for-dealii-openmpi): New variable.
(dealii-openmpi)[propagated-inputs]: Add trilinos-for-dealii-openmpi.
---
gnu/packages/maths.scm | 149 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 149 insertions(+)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 13c8338f5c..64b6c1dc5b 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4608,6 +4608,154 @@ specifications.")
revised simplex and the branch-and-bound methods.")
(license license:lgpl2.1+)))
+;; Private Trilinos package for dealii-openmpi (similar to
+;; trilinos-serial-xyce and trilinos-parallel-xyce).
+;; This version is the latest known to be compatible with deal.II [1].
+;; Since the latest version of Trilinos is not necessarily supported by
+;; deal.II, it may be worth keeping this package even if and when Trilinos
+;; gets packaged separately for Guix (unless various versions of Trilinos are
+;; packaged).
+;;
+;; An insightful source of information for building Trilinos for deal.II lies
+;; in the Trilinos package for candi [2], which is a source-based installer
+;; for deal.II and its dependencies.
+;;
+;; [1]: https://www.dealii.org/current/external-libs/trilinos.html
+;; [2]: https://github.com/dealii/candi/blob/master/deal.II-toolchain/packages/trilinos.package
+(define trilinos-for-dealii-openmpi
+ (package
+ (name "trilinos-for-dealii-openmpi")
+ (version "12.18.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/trilinos/Trilinos/")
+ (commit
+ (string-append "trilinos-release-"
+ (string-replace-substring version "." "-")))))
+ (file-name (git-file-name "trilinos" version))
+ (sha256
+ (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("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)))
+ (inputs
+ `(("blas" ,openblas)
+ ("lapack" ,lapack)
+ ("mumps" ,mumps-openmpi)
+ ("scalapack" ,scalapack)))
+ (propagated-inputs
+ `(("mpi" ,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))))
+ (home-page "https://trilinos.github.io/")
+ (synopsis "Algorithms for engineering and scientific problems")
+ (description
+ "The Trilinos Project is an effort to develop algorithms and enabling
+technologies within an object-oriented software framework for the solution of
+large-scale, complex multi-physics engineering and scientific problems.
+A unique design feature of Trilinos is its focus on packages.")
+ ;; The packages are variously licensed under more than just BSD-3 and
+ ;; LGPL-2.1+, but all the licenses are either BSD- or LGPL-compatible.
+ ;; See https://trilinos.github.io/license.html.
+ (license (list license:bsd-3 license:lgpl2.1+))))
+
(define-public dealii
(package
(name "dealii")
@@ -4703,6 +4851,7 @@ in finite element programs.")
("p4est" ,p4est-openmpi)
("petsc" ,petsc-openmpi)
("slepc" ,slepc-openmpi)
+ ("trilinos" ,trilinos-for-dealii-openmpi)
,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
(arguments
(substitute-keyword-arguments (package-arguments dealii)
--
2.32.0
^ permalink raw reply related [flat|nested] 3+ messages in thread
* bug#49772: [PATCH] gnu: dealii-openmpi: Add Trilinos dependency.
2021-07-30 13:59 ` Paul A. Patience
@ 2021-08-10 15:32 ` Ludovic Courtès
0 siblings, 0 replies; 3+ messages in thread
From: Ludovic Courtès @ 2021-08-10 15:32 UTC (permalink / raw)
To: Paul A. Patience; +Cc: 49772-done
Hi Paul,
"Paul A. Patience" <paul@apatience.com> skribis:
> From 3556e260785f1b52d351e041e9fe171df448d73b Mon Sep 17 00:00:00 2001
> From: "Paul A. Patience" <paul@apatience.com>
> Date: Thu, 29 Jul 2021 12:16:32 -0400
> Subject: [PATCH] gnu: dealii-openmpi: Add Trilinos dependency.
>
> * gnu/packages/maths.scm (trilinos-for-dealii-openmpi): New variable.
> (dealii-openmpi)[propagated-inputs]: Add trilinos-for-dealii-openmpi.
Applied, thank you!
Ludo’.
^ permalink raw reply [flat|nested] 3+ messages in thread
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2021-07-29 16:33 [bug#49772] [PATCH] gnu: dealii-openmpi: Add Trilinos dependency Paul A. Patience
2021-07-30 13:59 ` Paul A. Patience
2021-08-10 15:32 ` bug#49772: " Ludovic Courtès
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