[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
commit: e0a89fd9e8bf7f3939ffc6eefaf7ce059a3ab13a
Author: Matthias Maier gentoo org>
AuthorDate: Thu May 26 00:05:35 2022 +
Commit: Matthias Maier gentoo org>
CommitDate: Thu May 26 01:26:54 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e0a89fd9
sci-mathematics/petsc: drop 3.13.1, 3.14.6, 3.15.0, 3.15.0-r1
Signed-off-by: Matthias Maier gentoo.org>
sci-mathematics/petsc/Manifest | 3 -
.../files/petsc-3.13.0-do_not_run_mpiexec.patch| 34
.../files/petsc-3.13.0-fix_sandbox_violation.patch | 18 --
.../files/petsc-3.13.0-make_hypre_configure.patch | 90 --
sci-mathematics/petsc/petsc-3.13.1.ebuild | 196 -
sci-mathematics/petsc/petsc-3.14.6.ebuild | 194
sci-mathematics/petsc/petsc-3.15.0-r1.ebuild | 194
sci-mathematics/petsc/petsc-3.15.0.ebuild | 190
8 files changed, 919 deletions(-)
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index a53a6158e9b6..8a1dcafa8362 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,6 +1,3 @@
-DIST petsc-3.13.1.tar.gz 35097687 BLAKE2B
fccf64fd3694deffdd0dc561069ffa7e9342fe279b5c9123edeb011df931874083839d27b7b9a0c63faea6487b104b54fd4ce68a88a074c82de91e8baaf270b0
SHA512
41c3138a6ae6c1f2d9077b464c6aeda96287e5a76849582b8f432e2ee93d2594a78ba2181eac0054a77b6165692be5f1a057049313f2be9743d4246383dfdc77
-DIST petsc-3.14.6.tar.gz 39719179 BLAKE2B
d3047baf87c67eb64ef02c0c54d6313ea06f091b377b3cdf6dcf6d96c7d68cec5958a007ddd84b52a3ab39bfc0adf146307fa1785a10f39386393371186a3fba
SHA512
9766e164446ac5a69b8bf761a0e8a235b1a2b85ed9c96a7fd59e668ae4cceb9d9559a38b175b4aa9747e78d7b44d0018a3c02748dcd3d783d28f861f8382d44c
-DIST petsc-3.15.0.tar.gz 15976488 BLAKE2B
babfbeb05321c9cb2f7d70ef8ffca974a016eae73ca1a3359d9a8d38aa5aa90ff34571169a5711627d738b93f89fdee3d0a0ff1bd0e51cb7300bbb9b0a8675cb
SHA512
d1565823d8a5ce5e1c2c576bbe1b4ebf467cef20bbd8e0cf6c303c6c2af2bf902b66c79468f4e125496f9242be4bd6ac162535ee30252cfb902c0d906a6f27c0
DIST petsc-3.16.0-fftw-without-mpi.patch.bz2 5824 BLAKE2B
59615b1bbaf8ca1da92d7d193a45a2dd434f762cd741d711d4f408183a201a276ac3c968a3e7d740d19212120271701bce52bb7b0f4e311268f40915c81f9dcb
SHA512
8e07dfe56a9150ce9a3a5ab8012657875ef84e6e7daa60560bbdd9062078c876a826057f3f3eaf1697ce046a82756ee6eb6a8b819eb51245367c9d5c8a72ee8e
DIST petsc-3.16.0.tar.gz 16748960 BLAKE2B
87f9fdb79a9c44e5f476fa4746ad0cbe72f3eda9f6039f2e4743105626701d7c8d6c010fdb9d89becf8619288d0b7a60c8bc4e2fc0793eac5b39030b02c04fd9
SHA512
5280032fb4ec4d058733788bb0ae674e7400565e204133bd10ed88a2965230ec7adeaca2d498267ce661377ca7e6f9d948992206b1d679587606cb422c004655
DIST petsc-3.17.1.tar.gz 17082265 BLAKE2B
de1bfe45f93e18e32181499e59912df9225c8e24d75f52e641e552fd43e4d5be48d549d284365b173aa93e51603f5b7740eaac0557ff8c7c96b370f4683257f6
SHA512
8c81cc148b1a899a55e54a013d61519ec7b44f98f7ae30c3f8d0e83ba285b23f4b4d9e2cd483c531d337bc41887e4079b727ba73676b1b653910140291e93575
diff --git a/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
b/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
deleted file mode 100644
index 4c46658dec71..
--- a/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-diff --git a/config/BuildSystem/config/packages/MPI.py
b/config/BuildSystem/config/packages/MPI.py
-index 7e424e71..ee502bd2 100644
a/config/BuildSystem/config/packages/MPI.py
-+++ b/config/BuildSystem/config/packages/MPI.py
-@@ -210,28 +210,11 @@ shared libraries and run with
--known-mpi-shared-libraries=1')
- raise RuntimeError('Could not locate MPIEXEC - please specify
--with-mpiexec option')
- # Support for spaces and () in executable names; also needs to handle
optional arguments at the end
- # TODO: This support for spaces and () should be moved to core
BuildSystem
-- self.mpiexec = self.mpiexec.replace(' ', '\\ ').replace('(',
'\\(').replace(')', '\\)').replace('\ -',' -')
-- if (hasattr(self, 'ompi_major_version') and
int(self.ompi_major_version) >= 3):
--(out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -help
all', checkCommand = noCheck, timeout = 60, log = self.log, threads = 1)
--if out.find('--oversubscribe') >=0:
-- self.mpiexec = self.mpiexec + ' --oversubscribe'
-+ self.mpiexec = self.mpiexec + ' --oversubscribe'
-
- # using mpiexec environmental variables make sure mpiexec matches the MPI
libraries and save the variables for testing in PetscInitialize()
- # the variable HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE is not currently used.
PetscInitialize() can check the existence of the environmental variable to
- # determine if the program has been started with the correct mpiexec
(will only be set for parallel runs so not clear how to check appropriately
[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
commit: 2c0aea17b396af99413234f7a84607817f31dbd3
Author: Fabio Rossi inwind it>
AuthorDate: Wed Dec 1 18:04:37 2021 +
Commit: Sam James gentoo org>
CommitDate: Wed Dec 1 21:25:12 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2c0aea17
sci-mathematics/petsc: version bump to 3.16.0 and bugfix
The latest release is needed to backport the patch from upstream
to solve the issue of Gentoo bug #827185 (build issue with
USE="fftw -mpi").
Upstream fix is at https://gitlab.com/petsc/petsc/-/merge_requests/4604
Closes: https://bugs.gentoo.org/827185
Signed-off-by: Fabio Rossi inwind.it>
Closes: https://github.com/gentoo/gentoo/pull/23136
Signed-off-by: Sam James gentoo.org>
sci-mathematics/petsc/Manifest | 2 +
.../files/petsc-3.16.0-fix_sandbox_violation.patch | 15 ++
sci-mathematics/petsc/petsc-3.16.0.ebuild | 192 +
3 files changed, 209 insertions(+)
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index b8a099ec30dc..66543b456f86 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,3 +1,5 @@
DIST petsc-3.13.1.tar.gz 35097687 BLAKE2B
fccf64fd3694deffdd0dc561069ffa7e9342fe279b5c9123edeb011df931874083839d27b7b9a0c63faea6487b104b54fd4ce68a88a074c82de91e8baaf270b0
SHA512
41c3138a6ae6c1f2d9077b464c6aeda96287e5a76849582b8f432e2ee93d2594a78ba2181eac0054a77b6165692be5f1a057049313f2be9743d4246383dfdc77
DIST petsc-3.14.6.tar.gz 39719179 BLAKE2B
d3047baf87c67eb64ef02c0c54d6313ea06f091b377b3cdf6dcf6d96c7d68cec5958a007ddd84b52a3ab39bfc0adf146307fa1785a10f39386393371186a3fba
SHA512
9766e164446ac5a69b8bf761a0e8a235b1a2b85ed9c96a7fd59e668ae4cceb9d9559a38b175b4aa9747e78d7b44d0018a3c02748dcd3d783d28f861f8382d44c
DIST petsc-3.15.0.tar.gz 15976488 BLAKE2B
babfbeb05321c9cb2f7d70ef8ffca974a016eae73ca1a3359d9a8d38aa5aa90ff34571169a5711627d738b93f89fdee3d0a0ff1bd0e51cb7300bbb9b0a8675cb
SHA512
d1565823d8a5ce5e1c2c576bbe1b4ebf467cef20bbd8e0cf6c303c6c2af2bf902b66c79468f4e125496f9242be4bd6ac162535ee30252cfb902c0d906a6f27c0
+DIST petsc-3.16.0-fftw-without-mpi.patch.bz2 5824 BLAKE2B
59615b1bbaf8ca1da92d7d193a45a2dd434f762cd741d711d4f408183a201a276ac3c968a3e7d740d19212120271701bce52bb7b0f4e311268f40915c81f9dcb
SHA512
8e07dfe56a9150ce9a3a5ab8012657875ef84e6e7daa60560bbdd9062078c876a826057f3f3eaf1697ce046a82756ee6eb6a8b819eb51245367c9d5c8a72ee8e
+DIST petsc-3.16.0.tar.gz 16748960 BLAKE2B
87f9fdb79a9c44e5f476fa4746ad0cbe72f3eda9f6039f2e4743105626701d7c8d6c010fdb9d89becf8619288d0b7a60c8bc4e2fc0793eac5b39030b02c04fd9
SHA512
5280032fb4ec4d058733788bb0ae674e7400565e204133bd10ed88a2965230ec7adeaca2d498267ce661377ca7e6f9d948992206b1d679587606cb422c004655
diff --git
a/sci-mathematics/petsc/files/petsc-3.16.0-fix_sandbox_violation.patch
b/sci-mathematics/petsc/files/petsc-3.16.0-fix_sandbox_violation.patch
new file mode 100644
index ..d1ed880bddfd
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.16.0-fix_sandbox_violation.patch
@@ -0,0 +1,15 @@
+--- a/config/PETSc/options/installDir.py
b/config/PETSc/options/installDir.py
+@@ -40,13 +40,7 @@ class Configure(config.base.Configure):
+ self.dir =
os.path.abspath(os.path.expanduser(self.framework.argDB['prefix']))
+ self.petscDir = self.dir
+ self.petscArch = ''
+- try:
+-os.makedirs(os.path.join(self.dir,'PETScTestDirectory'))
+-os.rmdir(os.path.join(self.dir,'PETScTestDirectory'))
+- except Exception as e:
+-self.logPrint('Error trying to to test write permissions on directory
'+str(e))
+-self.installSudo = 'sudo '
+ else:
+ self.dir = os.path.abspath(os.path.join(self.petscdir.dir,
self.arch.arch))
+ self.petscDir = self.petscdir.dir
diff --git a/sci-mathematics/petsc/petsc-3.16.0.ebuild
b/sci-mathematics/petsc/petsc-3.16.0.ebuild
new file mode 100644
index ..f39f87d8c281
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.16.0.ebuild
@@ -0,0 +1,192 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
+
+DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
+HOMEPAGE="https://www.mcs.anl.gov/petsc/";
+SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${P}.tar.gz";
+SRC_URI+="
https://dev.gentoo.org/~sam/distfiles/${CATEGORY}/${PN}/${P}-fftw-without-mpi.patch.bz2";
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="afterimage boost complex-scalars cxx debug fftw
+ fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
+
+# hypre and superlu curretly exclude each other due to missing linking to hypre
+# if both are enabled
+REQUIRED_USE="
+ afterimage? ( X )
+ complex-scalars? ( !hypre !superlu )
+ hdf5? ( mpi )
+ hypre? ( cxx mpi !superlu )
+ mumps? ( mpi
[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
commit: 53490294521a32eb37e6131b1f9931930368e70c
Author: Matthias Maier gentoo org>
AuthorDate: Wed Apr 29 21:07:13 2020 +
Commit: Matthias Maier gentoo org>
CommitDate: Wed Apr 29 21:35:37 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=53490294
sci-mathematics/petsc: drop old
Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Matthias Maier gentoo.org>
sci-mathematics/petsc/Manifest | 2 -
.../files/petsc-3.12.1-do_not_run_mpiexec.patch| 32
.../files/petsc-3.12.1-make_hypre_configure.patch | 90 --
.../files/petsc-3.9.0-fix_sandbox_violation.patch | 17 --
sci-mathematics/petsc/petsc-3.11.3.ebuild | 193
sci-mathematics/petsc/petsc-3.12.1.ebuild | 195 -
6 files changed, 529 deletions(-)
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index f7372ecf5e1..c224c776882 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,3 +1 @@
-DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B
870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b
SHA512
e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa
-DIST petsc-3.12.1.tar.gz 34592587 BLAKE2B
b48056a1fe1d507338f7d145f5fceeab2b2f576470d8af90c9d7828de9b775daadf11198fecc46b5e48fcf1eb38addb366e3a908dab5c4ffaf7f9b71ff17b3d8
SHA512
df33170922c0b34136d2fd5bdc3c68a80d3a5873d66bfb03b2cea4a6456393c7181a8da673911b89ea0fcb51d5fd89b5b4c8b76ddb1df573180a92d029fbc1fb
DIST petsc-3.13.0.tar.gz 35080264 BLAKE2B
0ac58e53751dbc6e053e3591cdf2363194e0cf7a493f252d879031e0135da16fa24e66974dd7bf07ce18558a75f8dd794e87f96590ad9e550d11edfeb462f727
SHA512
0590bb63d9c6dfd6ac03b1b88e5a8c11d42a0fd014084603d4d085060b126aa4341b4ec3a4d2b12146b971da327ccc7ede370e5633282bf44f269465aea32953
diff --git a/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch
b/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch
deleted file mode 100644
index 9c3d5047b0a..000
--- a/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-diff --git a/config/BuildSystem/config/packages/MPI.py
b/config/BuildSystem/config/packages/MPI.py
-index c85bb504..7720eba9 100644
a/config/BuildSystem/config/packages/MPI.py
-+++ b/config/BuildSystem/config/packages/MPI.py
-@@ -209,26 +209,11 @@ shared libraries and run with
--known-mpi-shared-libraries=1')
- raise RuntimeError('Could not locate MPIEXEC - please specify
--with-mpiexec option')
- # Support for spaces and () in executable names; also needs to handle
optional arguments at the end
- # TODO: This support for spaces and () should be moved to core
BuildSystem
-- self.mpiexec = self.mpiexec.replace(' ', '\\ ').replace('(',
'\\(').replace(')', '\\)').replace('\ -',' -')
-- if (hasattr(self, 'ompi_major_version') and
int(self.ompi_major_version) >= 3):
--(out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -help
all', checkCommand = noCheck, timeout = 10, log = self.log)
--if out.find('--oversubscribe') >=0:
-- self.mpiexec = self.mpiexec + ' --oversubscribe'
-+ self.mpiexec = self.mpiexec + ' --oversubscribe'
-
- # using mpiexec environmental variables make sure mpiexec matches the MPI
libraries and save the variables for testing in PetscInitialize()
- # the variable HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE is not currently used.
PetscInitialize() can check the existence of the environmental variable to
- # determine if the program has been started with the correct mpiexec
(will only be set for parallel runs so not clear how to check appropriately)
--(out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -n 1
printenv', checkCommand = noCheck, timeout = 10, log = self.log)
--if ret: raise RuntimeError('Unable to run '+self.mpiexec+' with option
"-n 1"\n'+err)
--if out.find('MPIR_CVAR_CH3') > -1:
-- if hasattr(self,'ompi_major_version'): raise RuntimeError("Your
libraries are from OpenMPI but it appears your mpiexec is from MPICH");
-- self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPIR_CVAR_CH3')
--elif out.find('MPIR_CVAR_CH3') > -1:
-- if hasattr(self,'ompi_major_version'): raise RuntimeError("Your
libraries are from OpenMPI but it appears your mpiexec is from MPICH");
-- self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPICH')
--elif out.find('OMPI_COMM_WORLD_SIZE') > -1:
-- if hasattr(self,'mpich_numversion'): raise RuntimeError("Your libraries
are from MPICH but it appears your mpiexec is from OpenMPI");
-- self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'OMP')
- self.addMakeMacro('MPIEXEC', self.mpiexec)
- self.mpiexec = self.mpiexec + '
[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
commit: e50be8a41d664ed38d2903406bac8f3f28ffb695
Author: Matthias Maier gentoo org>
AuthorDate: Wed Apr 29 20:45:17 2020 +
Commit: Matthias Maier gentoo org>
CommitDate: Wed Apr 29 21:35:33 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e50be8a4
sci-mathematics/petsc: version bump to 13.0
Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Matthias Maier gentoo.org>
sci-mathematics/petsc/Manifest | 1 +
.../files/petsc-3.13.0-do_not_run_mpiexec.patch| 34
.../files/petsc-3.13.0-fix_sandbox_violation.patch | 18 ++
.../files/petsc-3.13.0-make_hypre_configure.patch | 90 ++
sci-mathematics/petsc/petsc-3.13.0.ebuild | 189 +
5 files changed, 332 insertions(+)
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index 35342d214c5..f7372ecf5e1 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,2 +1,3 @@
DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B
870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b
SHA512
e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa
DIST petsc-3.12.1.tar.gz 34592587 BLAKE2B
b48056a1fe1d507338f7d145f5fceeab2b2f576470d8af90c9d7828de9b775daadf11198fecc46b5e48fcf1eb38addb366e3a908dab5c4ffaf7f9b71ff17b3d8
SHA512
df33170922c0b34136d2fd5bdc3c68a80d3a5873d66bfb03b2cea4a6456393c7181a8da673911b89ea0fcb51d5fd89b5b4c8b76ddb1df573180a92d029fbc1fb
+DIST petsc-3.13.0.tar.gz 35080264 BLAKE2B
0ac58e53751dbc6e053e3591cdf2363194e0cf7a493f252d879031e0135da16fa24e66974dd7bf07ce18558a75f8dd794e87f96590ad9e550d11edfeb462f727
SHA512
0590bb63d9c6dfd6ac03b1b88e5a8c11d42a0fd014084603d4d085060b126aa4341b4ec3a4d2b12146b971da327ccc7ede370e5633282bf44f269465aea32953
diff --git a/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
b/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
new file mode 100644
index 000..4c46658dec7
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
@@ -0,0 +1,34 @@
+diff --git a/config/BuildSystem/config/packages/MPI.py
b/config/BuildSystem/config/packages/MPI.py
+index 7e424e71..ee502bd2 100644
+--- a/config/BuildSystem/config/packages/MPI.py
b/config/BuildSystem/config/packages/MPI.py
+@@ -210,28 +210,11 @@ shared libraries and run with
--known-mpi-shared-libraries=1')
+ raise RuntimeError('Could not locate MPIEXEC - please specify
--with-mpiexec option')
+ # Support for spaces and () in executable names; also needs to handle
optional arguments at the end
+ # TODO: This support for spaces and () should be moved to core
BuildSystem
+- self.mpiexec = self.mpiexec.replace(' ', '\\ ').replace('(',
'\\(').replace(')', '\\)').replace('\ -',' -')
+- if (hasattr(self, 'ompi_major_version') and
int(self.ompi_major_version) >= 3):
+-(out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -help
all', checkCommand = noCheck, timeout = 60, log = self.log, threads = 1)
+-if out.find('--oversubscribe') >=0:
+- self.mpiexec = self.mpiexec + ' --oversubscribe'
++ self.mpiexec = self.mpiexec + ' --oversubscribe'
+
+ # using mpiexec environmental variables make sure mpiexec matches the MPI
libraries and save the variables for testing in PetscInitialize()
+ # the variable HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE is not currently used.
PetscInitialize() can check the existence of the environmental variable to
+ # determine if the program has been started with the correct mpiexec
(will only be set for parallel runs so not clear how to check appropriately)
+-(out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -n 1
printenv', checkCommand = noCheck, timeout = 60, threads = 1, log = self.log)
+-if ret:
+- self.logWrite('Unable to run '+self.mpiexec+' with option "-n 1
printenv"\nThis could be ok, some MPI implementations such as SGI produce a
non-zero status with non-MPI programs\n'+out+err)
+-else:
+- if out.find('MPIR_CVAR_CH3') > -1:
+-if hasattr(self,'ompi_major_version'): raise RuntimeError("Your
libraries are from OpenMPI but it appears your mpiexec is from MPICH");
+-self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPIR_CVAR_CH3')
+- elif out.find('MPIR_CVAR_CH3') > -1:
+-if hasattr(self,'ompi_major_version'): raise RuntimeError("Your
libraries are from OpenMPI but it appears your mpiexec is from MPICH");
+-self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPICH')
+- elif out.find('OMPI_COMM_WORLD_SIZE') > -1:
+-if hasattr(self,'mpich_numversion'): raise RuntimeError("Your
libraries are from MPICH but it appears your mpiexec is from OpenMPI");
+-self.addDefine('HAVE_MPIEXEC_ENVIRONME
[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
commit: 44c266fd90ff2510b3d5ee74ed1dcff364eebcb1 Author: Matthias Maier gentoo org> AuthorDate: Mon Aug 5 04:48:15 2019 + Commit: Matthias Maier gentoo org> CommitDate: Mon Aug 5 06:51:11 2019 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=44c266fd sci-mathematics/petsc: package migration from ::science overlay After years in ::science it is stable enough to be hosted in ::gentoo. Package-Manager: Portage-2.3.70, Repoman-2.3.16 Signed-off-by: Matthias Maier gentoo.org> sci-mathematics/petsc/Manifest | 1 + .../petsc/files/petsc-3.7.0-disable-rpath.patch| 18 ++ .../files/petsc-3.9.0-fix_sandbox_violation.patch | 17 ++ sci-mathematics/petsc/metadata.xml | 23 +++ sci-mathematics/petsc/petsc-3.11.3.ebuild | 193 + 5 files changed, 252 insertions(+) diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest new file mode 100644 index 000..3be30d7421f --- /dev/null +++ b/sci-mathematics/petsc/Manifest @@ -0,0 +1 @@ +DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B 870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b SHA512 e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch new file mode 100644 index 000..8d0d993309b --- /dev/null +++ b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch @@ -0,0 +1,18 @@ +diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py +index 219a35b..ad2ed8c 100644 +--- a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py +@@ -1385,12 +1385,7 @@ class Configure(config.base.Configure): + for language in languages: + flag = '-L' + self.pushLanguage(language) +- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options. +- if not Configure.isDarwin(self.log): +-testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,'] +- else: +-testFlags = ['-Wl,-rpath,'] +- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not. ++ testFlags = [] + if self.isSun(self.framework.getCompiler(), self.log): + testFlags.insert(0,'-R') + for testFlag in testFlags: diff --git a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch new file mode 100644 index 000..97f8dfed4d7 --- /dev/null +++ b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch @@ -0,0 +1,17 @@ +diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py +index 92f190d..047c85b 100644 +--- a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py +@@ -41,12 +41,6 @@ class Configure(config.base.Configure): + self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix'])) + self.petscDir = self.dir + self.petscArch = '' +- try: +-os.makedirs(os.path.join(self.dir,'PETScTestDirectory')) +-os.rmdir(os.path.join(self.dir,'PETScTestDirectory')) +- except: +-self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs' +-self.installSudo = 'sudo ' + else: + self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) + self.petscDir = self.petscdir.dir diff --git a/sci-mathematics/petsc/metadata.xml b/sci-mathematics/petsc/metadata.xml new file mode 100644 index 000..8c9c01d8326 --- /dev/null +++ b/sci-mathematics/petsc/metadata.xml @@ -0,0 +1,23 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + + tam...@gentoo.org + Matthias Maier + + + sci-mathemat...@gentoo.org + Gentoo Mathematics Project + + + Use Afterstep image library (media-libs/libafterimage) + Use boost (dev-libs/boost) + Use HYPRE (sci-mathematics/hypre) and for preconditioning + Make scalars complex + Add support for metis (sci-libs/parmetis) + Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization + Use superlu (sci-libs/superlu) for preconditioning + Add support for mumps (sci-libs/mumps) + Add support for scotch (sci-libs/scotch) + + diff --git a/sci-mathematics/petsc/petsc-3.11.3.ebuild b/sci-mathematics/petsc/petsc-3.11.
