The package rpms/gromacs.git has added or updated architecture specific content in its
spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s):
https://src.fedoraproject.org/cgit/rpms/gromacs.git/commit/?id=a024f613b2....
Change:
+ExcludeArch: i686 armv7hl s390x
Thanks.
Full change:
============
commit c78d91a6d9bf48f4c1563c35563d3dfa4469a5ec
Author: Christoph Junghans <junghans(a)votca.org>
Date: Wed Jan 24 15:10:22 2024 -0700
Version bump to v2023.4 (bug#2260114)
diff --git a/.gitignore b/.gitignore
index fefacf6..4e8e2eb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -107,3 +107,6 @@ manual-4.0.pdf
/gromacs-2023.3.tar.gz
/manual-2023.3.pdf
/regressiontests-2023.3.tar.gz
+/gromacs-2023.4.tar.gz
+/manual-2023.4.pdf
+/regressiontests-2023.4.tar.gz
diff --git a/3900.patch b/3900.patch
deleted file mode 100644
index bef42a3..0000000
--- a/3900.patch
+++ /dev/null
@@ -1,93 +0,0 @@
-From e70245fa143080eef222f0d4dde367f28c5780e7 Mon Sep 17 00:00:00 2001
-From: Berk Hess <hess(a)kth.se>
-Date: Tue, 7 Nov 2023 19:20:06 +0100
-Subject: [PATCH 1/3] Increase tolerance for one continuation test
-
-The conserved energy quantity for the largest system for
-the mdrun continuation test, alanine_vacuo, already had
-a higher tolerance for single precision. Now a uniform
-increase is used. This needs a higher tolerance because
-the conserved energy is relatively small due to the sum
-of (negative) potential energy and (positive) kinetic energy.
-
-Fixes #4725
----
- src/programs/mdrun/tests/exactcontinuation.cpp | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/src/programs/mdrun/tests/exactcontinuation.cpp
b/src/programs/mdrun/tests/exactcontinuation.cpp
-index dc8f83a9909..47d93fde704 100644
---- a/src/programs/mdrun/tests/exactcontinuation.cpp
-+++ b/src/programs/mdrun/tests/exactcontinuation.cpp
-@@ -433,9 +433,10 @@ TEST_P(MdrunNoAppendContinuationIsExact, WithinTolerances)
- if (simulationName == "alanine_vacuo")
- {
- // This is slightly less reproducible
-+ const int factor = 4;
- energyTermsToCompare.insert({ interaction_function[F_ECONSERVED].longname,
- relativeToleranceAsPrecisionDependentUlp(
-- 10.0, ulpToleranceInMixed * 2,
ulpToleranceInDouble) });
-+ 10.0, factor * ulpToleranceInMixed,
factor * ulpToleranceInDouble) });
- }
- else
- {
---
-GitLab
-
-
-From 5b8ba16192047ea08ef3c74db2036b4412b6ff9e Mon Sep 17 00:00:00 2001
-From: Berk Hess <hess(a)kth.se>
-Date: Tue, 7 Nov 2023 19:28:33 +0100
-Subject: [PATCH 2/3] Clang-format
-
----
- src/programs/mdrun/tests/exactcontinuation.cpp | 7 ++++---
- 1 file changed, 4 insertions(+), 3 deletions(-)
-
-diff --git a/src/programs/mdrun/tests/exactcontinuation.cpp
b/src/programs/mdrun/tests/exactcontinuation.cpp
-index 47d93fde704..81cc2e34840 100644
---- a/src/programs/mdrun/tests/exactcontinuation.cpp
-+++ b/src/programs/mdrun/tests/exactcontinuation.cpp
-@@ -434,9 +434,10 @@ TEST_P(MdrunNoAppendContinuationIsExact, WithinTolerances)
- {
- // This is slightly less reproducible
- const int factor = 4;
-- energyTermsToCompare.insert({ interaction_function[F_ECONSERVED].longname,
-- relativeToleranceAsPrecisionDependentUlp(
-- 10.0, factor * ulpToleranceInMixed,
factor * ulpToleranceInDouble) });
-+ energyTermsToCompare.insert(
-+ { interaction_function[F_ECONSERVED].longname,
-+ relativeToleranceAsPrecisionDependentUlp(
-+ 10.0, factor * ulpToleranceInMixed, factor *
ulpToleranceInDouble) });
- }
- else
- {
---
-GitLab
-
-
-From 6bc0c66d8b69612abcef50f8bdbbdc2bdc382e66 Mon Sep 17 00:00:00 2001
-From: Mark Abraham <mark.j.abraham(a)gmail.com>
-Date: Tue, 7 Nov 2023 21:40:03 +0000
-Subject: [PATCH 3/3] Apply 1 suggestion(s) to 1 file(s)
-
----
- src/programs/mdrun/tests/exactcontinuation.cpp | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/programs/mdrun/tests/exactcontinuation.cpp
b/src/programs/mdrun/tests/exactcontinuation.cpp
-index 81cc2e34840..b5f8d2eef04 100644
---- a/src/programs/mdrun/tests/exactcontinuation.cpp
-+++ b/src/programs/mdrun/tests/exactcontinuation.cpp
-@@ -433,6 +433,8 @@ TEST_P(MdrunNoAppendContinuationIsExact, WithinTolerances)
- if (simulationName == "alanine_vacuo")
- {
- // This is slightly less reproducible
-+ // Wider tolerance is needed because of sum of negative PE
-+ // with positive KE producing small conserved energy.
- const int factor = 4;
- energyTermsToCompare.insert(
- { interaction_function[F_ECONSERVED].longname,
---
-GitLab
-
diff --git a/gromacs.spec b/gromacs.spec
index d94ec64..5e4759c 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -30,8 +30,8 @@ ExcludeArch: i686 armv7hl s390x
%endif
Name: gromacs
-Version: 2023.3
-Release: 3%{?dist}
+Version: 2023.4
+Release: 1%{?dist}
Summary: Fast, Free and Flexible Molecular Dynamics
License: GPLv2+
URL:
http://www.gromacs.org
@@ -42,7 +42,6 @@
Source2:
https://ftp.gromacs.org/regressiontests/regressiontests-%{version}%{?_r
Source3: gromacs-README.fedora
# increase some test tolerances:
https://gitlab.com/gromacs/gromacs/-/merge_requests/3900
# drop in v2023.4
-Patch0: 3900.patch
BuildRequires: gcc-c++
BuildRequires: cmake3 >= 3.4.3
BuildRequires: %{blaslib}-devel
@@ -226,8 +225,7 @@ This package single and double precision binaries and libraries.
%prep
-%setup -q %{?SOURCE2:-a 2} -n gromacs-%{version}%{?_rc}
-%patch 0 -p1
+%autosetup -p1 %{?SOURCE2:-a 2} -n gromacs-%{version}%{?_rc}
install -Dpm644 %{SOURCE1} ./serial/docs/manual/gromacs.pdf
# Delete bundled stuff so that it doesn't get used accidentally
# Don't remove tinyxml2 as gromacs needs an old version to build
@@ -379,6 +377,9 @@ done
%{_libdir}/mpich/bin/gmx_mpich*
%changelog
+* Wed Jan 24 2024 Christoph Junghans <junghans(a)votca.org> - 2023.4-1
+- Version bump to v2023.4 (bug#2260114)
+
* Wed Jan 24 2024 Fedora Release Engineering <releng(a)fedoraproject.org> - 2023.3-3
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
diff --git a/sources b/sources
index f679e9c..f342057 100644
--- a/sources
+++ b/sources
@@ -1,3 +1,3 @@
-SHA512 (gromacs-2023.3.tar.gz) =
016181be78887b0e31bc7fd124ac7c25c923c6bab1ffe43d3b4a744ae68203bb9d9f976c4c81bce344f4ea8e9d610ebd5b631b2202fcd6cfefd8c1ad0ebfe10d
-SHA512 (manual-2023.3.pdf) =
144220f18bfab6fefec738a7af743bd01733a896c853963ce113354da05514941862412786f0e2183de77634b31b334814d42daae87a9009ec0211118ed87685
-SHA512 (regressiontests-2023.3.tar.gz) =
0a5bd7a502973c2f658faca159ed0677907a1ca30eae3912a624e58e7cae9965c17c94ce65e94886d92444d34eb63b5b88a578459e6063687c43188031c0f836
+SHA512 (gromacs-2023.4.tar.gz) =
7913348d0da25e095b795123894f4e2007f66cf2455664edeb7bc1edc09f2e0da9911bc9501e3001278ab59917ccef838c485e6b6533c1c816c54c6dbd56350c
+SHA512 (manual-2023.4.pdf) =
b42e53f405a8ff4387970e4a1a199452bcb11befbf492cbd78b81229db2b0991e5c0c549162937e83eec79b15c71b441474b1338ed9050fdd132ae2ba09175b6
+SHA512 (regressiontests-2023.4.tar.gz) =
27c3dfbe5423bd5e7ed6ae14976e4d0cddd4c6b138070a7b72fec6ebc0e4d56b0b3e6e5c361986b1f354788ce2e9e665999b2fdc6ff6455d7f9012860f9b80ad
commit 4e73cde6c3003a12171f0f15877552f5e1cdb465
Author: Fedora Release Engineering <releng(a)fedoraproject.org>
Date: Wed Jan 24 21:03:50 2024 +0000
Rebuilt for
https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
diff --git a/gromacs.spec b/gromacs.spec
index 6021425..d94ec64 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -31,7 +31,7 @@ ExcludeArch: i686 armv7hl s390x
Name: gromacs
Version: 2023.3
-Release: 2%{?dist}
+Release: 3%{?dist}
Summary: Fast, Free and Flexible Molecular Dynamics
License: GPLv2+
URL:
http://www.gromacs.org
@@ -379,6 +379,9 @@ done
%{_libdir}/mpich/bin/gmx_mpich*
%changelog
+* Wed Jan 24 2024 Fedora Release Engineering <releng(a)fedoraproject.org> - 2023.3-3
+- Rebuilt for
https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
* Sat Jan 20 2024 Fedora Release Engineering <releng(a)fedoraproject.org> - 2023.3-2
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
commit bc1378bc18778b6d4537bcb8b24f1cbf96ddcf2d
Author: Fedora Release Engineering <releng(a)fedoraproject.org>
Date: Sat Jan 20 21:32:35 2024 +0000
Rebuilt for
https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
diff --git a/gromacs.spec b/gromacs.spec
index cb4c6d8..6021425 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -31,7 +31,7 @@ ExcludeArch: i686 armv7hl s390x
Name: gromacs
Version: 2023.3
-Release: 1%{?dist}
+Release: 2%{?dist}
Summary: Fast, Free and Flexible Molecular Dynamics
License: GPLv2+
URL:
http://www.gromacs.org
@@ -379,6 +379,9 @@ done
%{_libdir}/mpich/bin/gmx_mpich*
%changelog
+* Sat Jan 20 2024 Fedora Release Engineering <releng(a)fedoraproject.org> - 2023.3-2
+- Rebuilt for
https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
* Fri Nov 10 2023 Christoph Junghans <junghans(a)votca.org> - 2023.3-1
- Version bump v2023.3 (bug #2143353)
commit a024f613b2024cb348e3a607e6609b5772499b66
Author: Christoph Junghans <junghans(a)votca.org>
Date: Sat Nov 11 20:22:25 2023 -0700
Version bump v2023.3 (bug #2143353)
diff --git a/.gitignore b/.gitignore
index f918998..fefacf6 100644
--- a/.gitignore
+++ b/.gitignore
@@ -101,3 +101,9 @@ manual-4.0.pdf
/gromacs-2022.3.tar.gz
/manual-2022.3.pdf
/regressiontests-2022.3.tar.gz
+/gromacs-2023.tar.gz
+/manual-2023.pdf
+/regressiontests-2023.tar.gz
+/gromacs-2023.3.tar.gz
+/manual-2023.3.pdf
+/regressiontests-2023.3.tar.gz
diff --git a/3900.patch b/3900.patch
new file mode 100644
index 0000000..bef42a3
--- /dev/null
+++ b/3900.patch
@@ -0,0 +1,93 @@
+From e70245fa143080eef222f0d4dde367f28c5780e7 Mon Sep 17 00:00:00 2001
+From: Berk Hess <hess(a)kth.se>
+Date: Tue, 7 Nov 2023 19:20:06 +0100
+Subject: [PATCH 1/3] Increase tolerance for one continuation test
+
+The conserved energy quantity for the largest system for
+the mdrun continuation test, alanine_vacuo, already had
+a higher tolerance for single precision. Now a uniform
+increase is used. This needs a higher tolerance because
+the conserved energy is relatively small due to the sum
+of (negative) potential energy and (positive) kinetic energy.
+
+Fixes #4725
+---
+ src/programs/mdrun/tests/exactcontinuation.cpp | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/src/programs/mdrun/tests/exactcontinuation.cpp
b/src/programs/mdrun/tests/exactcontinuation.cpp
+index dc8f83a9909..47d93fde704 100644
+--- a/src/programs/mdrun/tests/exactcontinuation.cpp
++++ b/src/programs/mdrun/tests/exactcontinuation.cpp
+@@ -433,9 +433,10 @@ TEST_P(MdrunNoAppendContinuationIsExact, WithinTolerances)
+ if (simulationName == "alanine_vacuo")
+ {
+ // This is slightly less reproducible
++ const int factor = 4;
+ energyTermsToCompare.insert({ interaction_function[F_ECONSERVED].longname,
+ relativeToleranceAsPrecisionDependentUlp(
+- 10.0, ulpToleranceInMixed * 2,
ulpToleranceInDouble) });
++ 10.0, factor * ulpToleranceInMixed,
factor * ulpToleranceInDouble) });
+ }
+ else
+ {
+--
+GitLab
+
+
+From 5b8ba16192047ea08ef3c74db2036b4412b6ff9e Mon Sep 17 00:00:00 2001
+From: Berk Hess <hess(a)kth.se>
+Date: Tue, 7 Nov 2023 19:28:33 +0100
+Subject: [PATCH 2/3] Clang-format
+
+---
+ src/programs/mdrun/tests/exactcontinuation.cpp | 7 ++++---
+ 1 file changed, 4 insertions(+), 3 deletions(-)
+
+diff --git a/src/programs/mdrun/tests/exactcontinuation.cpp
b/src/programs/mdrun/tests/exactcontinuation.cpp
+index 47d93fde704..81cc2e34840 100644
+--- a/src/programs/mdrun/tests/exactcontinuation.cpp
++++ b/src/programs/mdrun/tests/exactcontinuation.cpp
+@@ -434,9 +434,10 @@ TEST_P(MdrunNoAppendContinuationIsExact, WithinTolerances)
+ {
+ // This is slightly less reproducible
+ const int factor = 4;
+- energyTermsToCompare.insert({ interaction_function[F_ECONSERVED].longname,
+- relativeToleranceAsPrecisionDependentUlp(
+- 10.0, factor * ulpToleranceInMixed,
factor * ulpToleranceInDouble) });
++ energyTermsToCompare.insert(
++ { interaction_function[F_ECONSERVED].longname,
++ relativeToleranceAsPrecisionDependentUlp(
++ 10.0, factor * ulpToleranceInMixed, factor *
ulpToleranceInDouble) });
+ }
+ else
+ {
+--
+GitLab
+
+
+From 6bc0c66d8b69612abcef50f8bdbbdc2bdc382e66 Mon Sep 17 00:00:00 2001
+From: Mark Abraham <mark.j.abraham(a)gmail.com>
+Date: Tue, 7 Nov 2023 21:40:03 +0000
+Subject: [PATCH 3/3] Apply 1 suggestion(s) to 1 file(s)
+
+---
+ src/programs/mdrun/tests/exactcontinuation.cpp | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/programs/mdrun/tests/exactcontinuation.cpp
b/src/programs/mdrun/tests/exactcontinuation.cpp
+index 81cc2e34840..b5f8d2eef04 100644
+--- a/src/programs/mdrun/tests/exactcontinuation.cpp
++++ b/src/programs/mdrun/tests/exactcontinuation.cpp
+@@ -433,6 +433,8 @@ TEST_P(MdrunNoAppendContinuationIsExact, WithinTolerances)
+ if (simulationName == "alanine_vacuo")
+ {
+ // This is slightly less reproducible
++ // Wider tolerance is needed because of sum of negative PE
++ // with positive KE producing small conserved energy.
+ const int factor = 4;
+ energyTermsToCompare.insert(
+ { interaction_function[F_ECONSERVED].longname,
+--
+GitLab
+
diff --git a/gromacs.spec b/gromacs.spec
index 757e39d..cb4c6d8 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -7,8 +7,10 @@
%global blaslib openblas
%endif
+# 32-bit arch
#
https://gitlab.com/gromacs/gromacs/-/merge_requests/2453
-ExcludeArch: i686 armv7hl
+# openmpi 5 & s390x
+ExcludeArch: i686 armv7hl s390x
%global with_opencl 1
@@ -28,8 +30,8 @@ ExcludeArch: i686 armv7hl
%endif
Name: gromacs
-Version: 2022.3
-Release: 4%{?dist}
+Version: 2023.3
+Release: 1%{?dist}
Summary: Fast, Free and Flexible Molecular Dynamics
License: GPLv2+
URL:
http://www.gromacs.org
@@ -38,6 +40,9 @@
Source0:
https://ftp.gromacs.org/pub/gromacs/gromacs-%{version}%{?_rc}.tar.gz
Source1:
https://ftp.gromacs.org/pub/manual/manual-%{version}%{?_rc}.pdf
Source2:
https://ftp.gromacs.org/regressiontests/regressiontests-%{version}%{?_rc}...
Source3: gromacs-README.fedora
+# increase some test tolerances:
https://gitlab.com/gromacs/gromacs/-/merge_requests/3900
+# drop in v2023.4
+Patch0: 3900.patch
BuildRequires: gcc-c++
BuildRequires: cmake3 >= 3.4.3
BuildRequires: %{blaslib}-devel
@@ -222,6 +227,7 @@ This package single and double precision binaries and libraries.
%prep
%setup -q %{?SOURCE2:-a 2} -n gromacs-%{version}%{?_rc}
+%patch 0 -p1
install -Dpm644 %{SOURCE1} ./serial/docs/manual/gromacs.pdf
# Delete bundled stuff so that it doesn't get used accidentally
# Don't remove tinyxml2 as gromacs needs an old version to build
@@ -373,6 +379,9 @@ done
%{_libdir}/mpich/bin/gmx_mpich*
%changelog
+* Fri Nov 10 2023 Christoph Junghans <junghans(a)votca.org> - 2023.3-1
+- Version bump v2023.3 (bug #2143353)
+
* Thu Jul 20 2023 Fedora Release Engineering <releng(a)fedoraproject.org> - 2022.3-4
- Rebuilt for
https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
diff --git a/sources b/sources
index 24d63a0..f679e9c 100644
--- a/sources
+++ b/sources
@@ -1,3 +1,3 @@
-SHA512 (gromacs-2022.3.tar.gz) =
1a6a1674ed17dfd93dcd51537cd13c9df5bb9bd91c3a26601032f83b788a93689bac8070eb8e495a786d41cc9d474885538cbaffa4229da70dfa640ee42b7c60
-SHA512 (manual-2022.3.pdf) =
f634eac722d4a6f77820ef46024d9209de97fb6afb52333f200c2717049d8d09e31f0ef7bac8f154d79ae43fa31541ed6c3d839dd088433222ebdace298b5fae
-SHA512 (regressiontests-2022.3.tar.gz) =
98888ad908705ac29ae958591368e994b091a1619782b49601e41f576c821eb3c96a713449151b8db59d46bc6dd3bcb363f5d0cda354ce6b39a9bb93ba31f913
+SHA512 (gromacs-2023.3.tar.gz) =
016181be78887b0e31bc7fd124ac7c25c923c6bab1ffe43d3b4a744ae68203bb9d9f976c4c81bce344f4ea8e9d610ebd5b631b2202fcd6cfefd8c1ad0ebfe10d
+SHA512 (manual-2023.3.pdf) =
144220f18bfab6fefec738a7af743bd01733a896c853963ce113354da05514941862412786f0e2183de77634b31b334814d42daae87a9009ec0211118ed87685
+SHA512 (regressiontests-2023.3.tar.gz) =
0a5bd7a502973c2f658faca159ed0677907a1ca30eae3912a624e58e7cae9965c17c94ce65e94886d92444d34eb63b5b88a578459e6063687c43188031c0f836