Architecture specific change in rpms/gromacs.git - Arch-excludes - Fedora mailing-lists

6 Oct 2022

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=6715a1d15bbbf....
Change:
-%ifarch s390x armv7hl
Thanks.
Full change:
============
commit d87762c134d73b7d6a1a59709632d4a10688c075
Author: Christoph Junghans junghans@votca.org
Date:   Wed Sep 28 09:10:29 2022 -0600
Rebuild for muparser

diff --git a/gromacs.spec b/gromacs.spec
index bc3ae62..0242e56 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -29,7 +29,7 @@ ExcludeArch:    i686 armv7hl
Name:		gromacs
 Version:	2022.3
-Release:	1%{?dist}
+Release:	2%{?dist}
 Summary:	Fast, Free and Flexible Molecular Dynamics
 License:	GPLv2+
 URL:		http://www.gromacs.org
@@ -373,6 +373,9 @@ done
 %{_libdir}/mpich/bin/gmx_mpich*
%changelog
+* Wed Sep 28 2022 Christoph Junghans junghans@votca.org - 2022.3-2
+- Rebuild for muparser
+
 * Fri Sep 02 2022 Fedora Release Monitoring release-monitoring@fedoraproject.org - 2022.3-1
 - Update to 2022.3 (#2123647)
commit db2066b5f8dc8718d11fbad9b371d6378a3910a9
Author: Christoph Junghans junghans@votca.org
Date:   Fri Sep 16 09:08:08 2022 -0600
Update to 2022.3 (#2123647)
diff --git a/.gitignore b/.gitignore
index ccf1cc3..f918998 100644
--- a/.gitignore
+++ b/.gitignore
@@ -98,3 +98,6 @@ manual-4.0.pdf
 /gromacs-2022.2.tar.gz
 /manual-2022.2.pdf
 /regressiontests-2022.2.tar.gz
+/gromacs-2022.3.tar.gz
+/manual-2022.3.pdf
+/regressiontests-2022.3.tar.gz
diff --git a/gromacs.spec b/gromacs.spec
index 2512ae6..bc3ae62 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -28,8 +28,8 @@ ExcludeArch:    i686 armv7hl
 %endif
Name:		gromacs
-Version:	2022.2
-Release:	2%{?dist}
+Version:	2022.3
+Release:	1%{?dist}
 Summary:	Fast, Free and Flexible Molecular Dynamics
 License:	GPLv2+
 URL:		http://www.gromacs.org
@@ -373,6 +373,9 @@ done
 %{_libdir}/mpich/bin/gmx_mpich*
%changelog
+* Fri Sep 02 2022 Fedora Release Monitoring release-monitoring@fedoraproject.org - 2022.3-1
+- Update to 2022.3 (#2123647)
+
 * Thu Jul 21 2022 Fedora Release Engineering releng@fedoraproject.org - 2022.2-2
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
diff --git a/sources b/sources
index f1f0886..24d63a0 100644
--- a/sources
+++ b/sources
@@ -1,3 +1,3 @@
-SHA512 (gromacs-2022.2.tar.gz) = 9f33518d2035afb37fc40377e575d497ff32bef2adb702669b35b1b51b1694b1113c5634fa6febd41955b6dfbfd055e7d523e1919bda1bf169a6d0c25700cef7
-SHA512 (manual-2022.2.pdf) = 9b4d9b13547e0210b633394e0c9cba183a827409b08d3b2995a4b64df7b7e7aef0441af240bf4cfcb2e24594ade27c25fee454b9fcf4bb5df0ded464c4f6368d
-SHA512 (regressiontests-2022.2.tar.gz) = 6cd4b59515648aa5f9deec130454b4d667cce20a95d389b46883865d39a164ec23da303a52afb4459dda3c6b6a7804d0763c05424ea512e6c0725ce1ca684dc2
+SHA512 (gromacs-2022.3.tar.gz) = 1a6a1674ed17dfd93dcd51537cd13c9df5bb9bd91c3a26601032f83b788a93689bac8070eb8e495a786d41cc9d474885538cbaffa4229da70dfa640ee42b7c60
+SHA512 (manual-2022.3.pdf) = f634eac722d4a6f77820ef46024d9209de97fb6afb52333f200c2717049d8d09e31f0ef7bac8f154d79ae43fa31541ed6c3d839dd088433222ebdace298b5fae
+SHA512 (regressiontests-2022.3.tar.gz) = 98888ad908705ac29ae958591368e994b091a1619782b49601e41f576c821eb3c96a713449151b8db59d46bc6dd3bcb363f5d0cda354ce6b39a9bb93ba31f913
commit 07770bc5e3e000adbf5158549adff5953d7eea9b
Author: Fedora Release Engineering releng@fedoraproject.org
Date:   Thu Jul 21 13:04:23 2022 +0000
Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
Signed-off-by: Fedora Release Engineering releng@fedoraproject.org
diff --git a/gromacs.spec b/gromacs.spec
index 50ae1d6..2512ae6 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -29,7 +29,7 @@ ExcludeArch:    i686 armv7hl
Name:		gromacs
 Version:	2022.2
-Release:	1%{?dist}
+Release:	2%{?dist}
 Summary:	Fast, Free and Flexible Molecular Dynamics
 License:	GPLv2+
 URL:		http://www.gromacs.org
@@ -373,6 +373,9 @@ done
 %{_libdir}/mpich/bin/gmx_mpich*
%changelog
+* Thu Jul 21 2022 Fedora Release Engineering releng@fedoraproject.org - 2022.2-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
+
 * Fri Jun 17 2022 Christoph Junghans junghans@votca.org - 2022.2-1
 - Version bump to v2022.2 (bug #2097747)
commit acf74d5220de4a05fc8287804db52ed6e8f1760a
Author: Christoph Junghans junghans@votca.org
Date:   Sat Jun 18 07:33:45 2022 -0600
Version bump to v2022.2 (bug #2097747)
diff --git a/.gitignore b/.gitignore
index 085f817..ccf1cc3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -95,3 +95,6 @@ manual-4.0.pdf
 /gromacs-2022.1.tar.gz
 /manual-2022.1.pdf
 /regressiontests-2022.1.tar.gz
+/gromacs-2022.2.tar.gz
+/manual-2022.2.pdf
+/regressiontests-2022.2.tar.gz
diff --git a/2672.patch b/2672.patch
deleted file mode 100644
index c357b5b..0000000
--- a/2672.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-From 7f80f91c67d3bd6127c22758464884ab3c9e406c Mon Sep 17 00:00:00 2001
-From: Christoph Junghans christoph.junghans@gmail.com
-Date: Mon, 25 Apr 2022 17:59:10 +0000
-Subject: [PATCH] cmake: only install pkg-config and cmake target files when
- library is installed
-
----
- src/gromacs/CMakeLists.txt | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
-index 7270e08299..cb33f0983e 100644
---- a/src/gromacs/CMakeLists.txt
-+++ b/src/gromacs/CMakeLists.txt
-@@ -454,10 +454,11 @@ if (BUILD_SHARED_LIBS)
-     if(GMX_INSTALL_LEGACY_API)
-         target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
-     endif()
-+    # only install pkg-config and cmake target files when library is installed
-+    include(InstallLibInfo.cmake)
- endif()
- add_library(Gromacs::libgromacs ALIAS libgromacs)
- 
--include(InstallLibInfo.cmake)
- 
- # Technically, the user could want to do this for an OpenCL build
- # using the CUDA runtime, but currently there's no reason to want to
--- 
-GitLab
-
diff --git a/gromacs-dssp-path.patch b/gromacs-dssp-path.patch
deleted file mode 100644
index d3abfca..0000000
--- a/gromacs-dssp-path.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-diff --git a/src/gromacs/gmxana/gmx_do_dssp.cpp b/src/gromacs/gmxana/gmx_do_dssp.cpp
-index a8aab1bc2..184592b7e 100644
---- a/src/gromacs/gmxana/gmx_do_dssp.cpp
-+++ b/src/gromacs/gmxana/gmx_do_dssp.cpp
-@@ -445,7 +445,7 @@ int gmx_do_dssp(int argc, char *argv[])
-         "calling the dssp program. If you do not have the dssp program,",
-         "get it from http://swift.cmbi.ru.nl/gv/dssp. [THISMODULE] assumes ",
-         "that the dssp executable is located in ",
--        "[TT]/usr/local/bin/dssp[tt]. If this is not the case, then you should",
-+        "[TT]/usr/bin/mkdssp[tt]. If this is not the case, then you should",
-         "set an environment variable [TT]DSSP[tt] pointing to the dssp",
-         "executable, e.g.: [PAR]",
-         "[TT]setenv DSSP /opt/dssp/bin/dssp[tt][PAR]",
-@@ -590,7 +590,7 @@ int gmx_do_dssp(int argc, char *argv[])
- 
-     if ((dptr = getenv("DSSP")) == nullptr)
-     {
--        dptr = "/usr/local/bin/dssp";
-+        dptr = "/usr/bin/mkdssp";
-     }
-     if (!gmx_fexist(dptr))
-     {
diff --git a/gromacs-gcc11.patch b/gromacs-gcc11.patch
deleted file mode 100644
index a5153dd..0000000
--- a/gromacs-gcc11.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/src/gromacs/awh/biasparams.cpp b/src/gromacs/awh/biasparams.cpp
-index f4db497..87e0a40 100644
---- a/src/gromacs/awh/biasparams.cpp
-+++ b/src/gromacs/awh/biasparams.cpp
-@@ -47,6 +47,7 @@
- #include "biasparams.h"
- 
- #include <cmath>
-+#include <limits>
- 
- #include <algorithm>
- 
-diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp
-index 8550271..d259b66 100644
---- a/src/gromacs/mdrun/minimize.cpp
-+++ b/src/gromacs/mdrun/minimize.cpp
-@@ -49,6 +49,7 @@
- #include <cmath>
- #include <cstring>
- #include <ctime>
-+#include <limits>
- 
- #include <algorithm>
- #include <vector>
diff --git a/gromacs-issue-2366.patch b/gromacs-issue-2366.patch
deleted file mode 100644
index 7c08010..0000000
--- a/gromacs-issue-2366.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-diff --git a/src/gromacs/hardware/tests/hardwaretopology.cpp b/src/gromacs/hardware/tests/hardwaretopology.cpp
-index ed7897b01..c31d4b9cd 100644
---- a/src/gromacs/hardware/tests/hardwaretopology.cpp
-+++ b/src/gromacs/hardware/tests/hardwaretopology.cpp
-@@ -185,12 +185,14 @@ TEST(HardwareTopologyTest, NumaCacheSelfconsistency)
-             }
-         }
- 
-+#ifndef __aarch64__
-         // Check cache. The hwloc cache detection is fragile and can report
-         // 0 for line size or associativity (=unknown), so we just check the size.
-         for (auto &c : hwTop.machine().caches)
-         {
-             EXPECT_GT(c.size, 0);
-         }
-+#endif
-     }
- }
- 
diff --git a/gromacs.spec b/gromacs.spec
index 6dc59b5..50ae1d6 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -28,7 +28,7 @@ ExcludeArch:    i686 armv7hl
 %endif
Name:		gromacs
-Version:	2022.1
+Version:	2022.2
 Release:	1%{?dist}
 Summary:	Fast, Free and Flexible Molecular Dynamics
 License:	GPLv2+
@@ -38,7 +38,6 @@ Source0:	https://ftp.gromacs.org/pub/gromacs/gromacs-%%7Bversion%7D%%7B?_rc%7D.tar.gz
 Source1:	https://ftp.gromacs.org/pub/manual/manual-%%7Bversion%7D%%7B?_rc%7D.pdf
 Source2:	https://ftp.gromacs.org/regressiontests/regressiontests-%%7Bversion%7D%%7B?_...
 Source3:	gromacs-README.fedora
-Patch0:		https://gitlab.com/gromacs/gromacs/-/merge_requests/2672.patch
 BuildRequires:	gcc-c++
 BuildRequires:  cmake3 >= 3.4.3
 BuildRequires:	%{blaslib}-devel
@@ -223,7 +222,6 @@ This package single and double precision binaries and libraries.
%prep
 %setup -q %{?SOURCE2:-a 2} -n gromacs-%{version}%{?_rc}
-%patch0 -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
@@ -375,6 +373,9 @@ done
 %{_libdir}/mpich/bin/gmx_mpich*
%changelog
+* Fri Jun 17 2022 Christoph Junghans junghans@votca.org - 2022.2-1
+- Version bump to v2022.2 (bug #2097747)
+
 * Fri Apr 22 2022 Christoph Junghans junghans@votca.org - 2022.1-1
 - Version bump to v2022.1 (bug #2057081)
diff --git a/sources b/sources
index 07653cb..f1f0886 100644
--- a/sources
+++ b/sources
@@ -1,3 +1,3 @@
-SHA512 (gromacs-2022.1.tar.gz) = 80c98badb7ebad171925486d1676b64e787cf8cbfb8f1b1cf1ccab8cbf8d8340f7fdd084dfb7388afc7a3aef23b95d603265305faf82125324307d86460c6f17
-SHA512 (manual-2022.1.pdf) = 73455190aec62aaffe760dddac4de26ea148d825f4c2d0e04d38c88b87fe15b7138b5a872bf9757452ac39e68942943c73e19025730ece8052d4a6a1873ca40e
-SHA512 (regressiontests-2022.1.tar.gz) = 44633e7497601a4cf11dd6af9d043ca132efe43246b6d924c57f879d2e6f7a6379390d9897e03d7a8f645e7bdbb76a81586b56c5e61846d9f40c137a4de216c2
+SHA512 (gromacs-2022.2.tar.gz) = 9f33518d2035afb37fc40377e575d497ff32bef2adb702669b35b1b51b1694b1113c5634fa6febd41955b6dfbfd055e7d523e1919bda1bf169a6d0c25700cef7
+SHA512 (manual-2022.2.pdf) = 9b4d9b13547e0210b633394e0c9cba183a827409b08d3b2995a4b64df7b7e7aef0441af240bf4cfcb2e24594ade27c25fee454b9fcf4bb5df0ded464c4f6368d
+SHA512 (regressiontests-2022.2.tar.gz) = 6cd4b59515648aa5f9deec130454b4d667cce20a95d389b46883865d39a164ec23da303a52afb4459dda3c6b6a7804d0763c05424ea512e6c0725ce1ca684dc2
diff --git a/test_timeout.patch b/test_timeout.patch
deleted file mode 100644
index 0d3f336..0000000
--- a/test_timeout.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- gromacs-2019.6/tests/CMakeLists.txt.orig	2020-08-04 09:01:31.281910583 -0600
-+++ gromacs-2019.6/tests/CMakeLists.txt	2020-08-04 09:03:24.506767821 -0600
-@@ -172,6 +172,7 @@
-             #windows requires the command to be perl and not the script
-             COMMAND perl "${REGRESSIONTEST_PATH}/gmxtest.pl" ${subtest} ${ARGS})
-         set_tests_properties(regressiontests/${subtest} PROPERTIES
-+            TIMEOUT 9000
-             ENVIRONMENT "PATH=${PATH}")
-     endforeach()
- else()
commit befe6fccf17a5db00b414c892294326b6f834141
Author: Christoph Junghans junghans@votca.org
Date:   Tue May 3 17:10:21 2022 -0600
make devel depend on main package
diff --git a/gromacs.spec b/gromacs.spec
index 1b79bcb..6dc59b5 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -149,6 +149,8 @@ This package the manual in PDF format.
 %package devel
 Summary:	GROMACS header files and development libraries
 Requires:	gromacs-libs = %{version}-%{release}
+# cmake files refer to /usr/bin/gmx as well
+Requires:	gromacs = %{version}-%{release}
 Obsoletes:	gromacs-mpich-devel < 2016-0.1.20160318gitbec9c87
 Obsoletes:	gromacs-openmpi-devel < 2016-0.1.20160318gitbec9c87
commit f3a5f4f855aaad7fbaa7883ee1c2bae67569737b
Author: Christoph Junghans junghans@votca.org
Date:   Wed Feb 23 14:13:58 2022 -0700
Version bump to v2022.1 (bug #2057081)
diff --git a/.gitignore b/.gitignore
index 446959e..085f817 100644
--- a/.gitignore
+++ b/.gitignore
@@ -89,3 +89,9 @@ manual-4.0.pdf
 /gromacs-2021.5.tar.gz
 /manual-2021.5.pdf
 /regressiontests-2021.5.tar.gz
+/gromacs-2022.tar.gz
+/manual-2022.pdf
+/regressiontests-2022.tar.gz
+/gromacs-2022.1.tar.gz
+/manual-2022.1.pdf
+/regressiontests-2022.1.tar.gz
diff --git a/2672.patch b/2672.patch
new file mode 100644
index 0000000..c357b5b
--- /dev/null
+++ b/2672.patch
@@ -0,0 +1,30 @@
+From 7f80f91c67d3bd6127c22758464884ab3c9e406c Mon Sep 17 00:00:00 2001
+From: Christoph Junghans christoph.junghans@gmail.com
+Date: Mon, 25 Apr 2022 17:59:10 +0000
+Subject: [PATCH] cmake: only install pkg-config and cmake target files when
+ library is installed
+
+---
+ src/gromacs/CMakeLists.txt | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
+index 7270e08299..cb33f0983e 100644
+--- a/src/gromacs/CMakeLists.txt
++++ b/src/gromacs/CMakeLists.txt
+@@ -454,10 +454,11 @@ if (BUILD_SHARED_LIBS)
+     if(GMX_INSTALL_LEGACY_API)
+         target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
+     endif()
++    # only install pkg-config and cmake target files when library is installed
++    include(InstallLibInfo.cmake)
+ endif()
+ add_library(Gromacs::libgromacs ALIAS libgromacs)
+ 
+-include(InstallLibInfo.cmake)
+ 
+ # Technically, the user could want to do this for an OpenCL build
+ # using the CUDA runtime, but currently there's no reason to want to
+-- 
+GitLab
+
diff --git a/gromacs.spec b/gromacs.spec
index 5003bd5..1b79bcb 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -28,7 +28,7 @@ ExcludeArch:    i686 armv7hl
 %endif
Name:		gromacs
-Version:	2021.5
+Version:	2022.1
 Release:	1%{?dist}
 Summary:	Fast, Free and Flexible Molecular Dynamics
 License:	GPLv2+
@@ -38,6 +38,7 @@ Source0:	https://ftp.gromacs.org/pub/gromacs/gromacs-%%7Bversion%7D%%7B?_rc%7D.tar.gz
 Source1:	https://ftp.gromacs.org/pub/manual/manual-%%7Bversion%7D%%7B?_rc%7D.pdf
 Source2:	https://ftp.gromacs.org/regressiontests/regressiontests-%%7Bversion%7D%%7B?_...
 Source3:	gromacs-README.fedora
+Patch0:		https://gitlab.com/gromacs/gromacs/-/merge_requests/2672.patch
 BuildRequires:	gcc-c++
 BuildRequires:  cmake3 >= 3.4.3
 BuildRequires:	%{blaslib}-devel
@@ -47,6 +48,7 @@ BuildRequires:	hwloc
 BuildRequires:	hwloc-devel
 BuildRequires:	libX11-devel
 BuildRequires:	lmfit-devel >= 6.0
+BuildRequires:	muParser-devel
 %if %{with_opencl}
 BuildRequires:	ocl-icd-devel
 BuildRequires:	opencl-headers
@@ -219,26 +221,28 @@ This package single and double precision binaries and libraries.
%prep
 %setup -q %{?SOURCE2:-a 2} -n gromacs-%{version}%{?_rc}
+%patch0 -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
 # test, see: https://redmine.gromacs.org/issues/2389
-rm -r src/external/{fftpack,tng_io,lmfit}
+rm -r src/external/{fftpack,tng_io,lmfit,muparser}
# increase timeout of tests
 sed -i 's/set(_timeout [0-9]*)/set(_timeout 9000)/' src/testutils/TestMacros.cmake
%build
 # Default options, used for all compilations
+# note: Fedora's tinyxml2 is too new, so use the bundled one to build the test (only)
 %global defopts \\
  -DBUILD_TESTING:BOOL=ON \\
  -DCMAKE_SKIP_INSTALL_RPATH=ON \\
  -DGMX_BLAS_USER=%{blaslib} \\
  -DGMX_BUILD_UNITTESTS:BOOL=ON \\
- -DGMX_EXTERNAL_LMFIT:BOOL=ON \\
- -DGMX_USE_LMFIT=external \\
+ -DGMX_USE_LMFIT=EXTERNAL \\
  -DGMX_EXTERNAL_TNG:BOOL=ON \\
  -DGMX_EXTERNAL_TINYXML2:BOOL=OFF \\
+ -DGMX_USE_MUPARSER=EXTERNAL \\
  -DGMX_LAPACK_USER=%{blaslib} \\
  -DGMX_USE_RDTSCP=OFF \\
  -DGMX_INSTALL_LEGACY_API=ON \\
@@ -251,7 +255,7 @@ sed -i 's/set(_timeout [0-9]*)/set(_timeout 9000)/' src/testutils/TestMacros.cma
 %global single -DGMX_GPU=OpenCL
 %endif
 %global double -DGMX_DOUBLE:BOOL=ON
-%global mpi -DGMX_BUILD_MDRUN_ONLY:BOOL=ON -DGMX_MPI:BOOL=ON -DGMX_THREAD_MPI:BOOL=OFF -DGMX_DEFAULT_SUFFIX:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF
+%global mpi -DGMX_MPI:BOOL=ON -DGMX_THREAD_MPI:BOOL=OFF -DGMX_DEFAULT_SUFFIX:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF
 %global _vpath_srcdir ..
. /etc/profile.d/modules.sh
@@ -262,7 +266,7 @@ for p in '' _d ; do
     pushd ${mpi:-serial}${p}
     test -z "${mpi}" && cp -al ../regressiontests* tests/ # use with -DREGRESSIONTEST_PATH=${PWD}/tests below
     %{cmake3} %{defopts} \
-      $(test -n "${mpi}" && echo %{mpi} -DGMX_BINARY_SUFFIX=${MPI_SUFFIX}${p} -DGMX_LIBS_SUFFIX=${MPI_SUFFIX}${p} -DCMAKE_INSTALL_BINDIR=${MPI_BIN} || echo -DGMX_X11=ON) \
+      $(test -n "${mpi}" && echo %{mpi} -DGMX_BINARY_SUFFIX=${MPI_SUFFIX}${p} -DGMX_LIBS_SUFFIX=${MPI_SUFFIX}${p} -DCMAKE_INSTALL_BINDIR=${MPI_BIN} -DCMAKE_INSTALL_LIBDIR=${MPI_LIB} || echo -DGMX_X11=ON) \
       $(test -z "${mpi}" && echo "-DREGRESSIONTEST_PATH=${PWD}/tests") \
       $(test -n "$p" && echo %{double} || echo %{?single})
     %cmake_build
@@ -293,6 +297,9 @@ pushd %{buildroot}
 # rm GMXRC, not needed when installed in /usr
 rm ./%{_bindir}/GMXRC*
+# serial stuff in mpi-versoin
+rm ./%{_libdir}/*mpi*/bin/GMXRC* ./%{_libdir}/*mpi*/bin/*.pl
+
 for bin in demux.pl xplor2gmx.pl; do
   mv ./%{_bindir}/$bin ./%{_bindir}/g_${bin}
 done
@@ -303,7 +310,7 @@ for bin in gmx{,_d}; do
   cat ./%{_bindir}/gmx-completion{,-$bin}.bash > ./%{compdir}/${bin}
   rm ./%{_bindir}/gmx-completion-${bin}.bash
 done
-rm ./%{_bindir}/gmx-completion.bash ./%{_libdir}/*mpi*/bin/gmx-completion-*mpi*.bash
+rm ./%{_bindir}/gmx-completion.bash ./%{_libdir}/*mpi*/bin/gmx-completion*.bash
%ldconfig_scriptlets libs
@@ -336,7 +343,6 @@ done
 %exclude %{_datadir}/%{name}/opencl
%files opencl
-%doc docs/OpenCLTODOList.txt
 %{_datadir}/%{name}/opencl
 %endif
@@ -361,12 +367,15 @@ done
 %{_datadir}/cmake/gmxapi*
%files openmpi
-%{_libdir}/openmpi/bin/mdrun_openmpi*
+%{_libdir}/openmpi/bin/gmx_openmpi*
%files mpich
-%{_libdir}/mpich/bin/mdrun_mpich*
+%{_libdir}/mpich/bin/gmx_mpich*
%changelog
+* Fri Apr 22 2022 Christoph Junghans junghans@votca.org - 2022.1-1
+- Version bump to v2022.1 (bug #2057081)
+
 * Sat Jan 29 2022 Christoph Junghans junghans@votca.org - 2021.5-1
 - Version bump to v2021.5 (bug #1787785)
diff --git a/sources b/sources
index 01978a2..07653cb 100644
--- a/sources
+++ b/sources
@@ -1,3 +1,3 @@
-SHA512 (gromacs-2021.5.tar.gz) = 56c1b312fc8e52ec6f86e445d2fa2d07107c461b35d4dc8cdf95580f05fd8e6c5fd671d0e72b2b9e74e3232bc8c41db496fe4bcaf2b9a3ae3c2cfa93489a31c5
-SHA512 (manual-2021.5.pdf) = 7635108c935e4953d722df6a16ee43edf97eef7e49f047218728f68f61f8f185192ff1d8b13a573b643b040955af211355a7b560c8a894c858d7f71249d41296
-SHA512 (regressiontests-2021.5.tar.gz) = 3605d04b2602339fb7d33e2776da2ada337ca58a3802472d47f490d4e8dd04249a950bf34608a498eedebf69f344c0311bac8f7fcb58ce0ebbb6d608ee39aa2e
+SHA512 (gromacs-2022.1.tar.gz) = 80c98badb7ebad171925486d1676b64e787cf8cbfb8f1b1cf1ccab8cbf8d8340f7fdd084dfb7388afc7a3aef23b95d603265305faf82125324307d86460c6f17
+SHA512 (manual-2022.1.pdf) = 73455190aec62aaffe760dddac4de26ea148d825f4c2d0e04d38c88b87fe15b7138b5a872bf9757452ac39e68942943c73e19025730ece8052d4a6a1873ca40e
+SHA512 (regressiontests-2022.1.tar.gz) = 44633e7497601a4cf11dd6af9d043ca132efe43246b6d924c57f879d2e6f7a6379390d9897e03d7a8f645e7bdbb76a81586b56c5e61846d9f40c137a4de216c2
commit 6715a1d15bbbf0a2912e13581b7b88ce2b2cfbb5
Author: Christoph Junghans junghans@votca.org
Date:   Mon Jan 31 17:21:56 2022 -0700
Version bump to v2021.5 (bug #1787785)
diff --git a/.gitignore b/.gitignore
index 7613f65..446959e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -86,3 +86,6 @@ manual-4.0.pdf
 /gromacs-2019.6.tar.gz
 /manual-2019.6.pdf
 /regressiontests-2019.6.tar.gz
+/gromacs-2021.5.tar.gz
+/manual-2021.5.pdf
+/regressiontests-2021.5.tar.gz
diff --git a/gromacs.spec b/gromacs.spec
index 9beceec..5003bd5 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -7,54 +7,37 @@
 %global blaslib openblas
 %endif
+# https://gitlab.com/gromacs/gromacs/-/merge_requests/2453
+ExcludeArch:    i686 armv7hl
+
 %global with_opencl 1
-# compilation of OpenCL support is failing only on ppc64le (retested 15 Feb 2019)
-# only 64-bit archs: https://redmine.gromacs.org/issues/2821
-%ifarch i686 %arm ppc64le
-%global with_opencl 0
-%endif
%global simd None
 %ifarch x86_64
 %global simd SSE2
 %endif
-%ifarch i686
-%global simd SSE2
-%endif
 %ifarch ppc64p7
 %global simd IBM_VMX
 %endif
-# https://bugzilla.redhat.com/show_bug.cgi?id=1799473#c4
+# IBM_VSX is broken with >=gcc-9
 #ifarch ppc64le
 #global simd IBM_VSX
 #endif
-%ifarch armv7hnl
-%global simd ARM_NEON
-%endif
 %ifarch aarch64
 %global simd ARM_NEON_ASIMD
 %endif
Name:		gromacs
-Version:	2019.6
-Release:	11%{?dist}
+Version:	2021.5
+Release:	1%{?dist}
 Summary:	Fast, Free and Flexible Molecular Dynamics
 License:	GPLv2+
 URL:		http://www.gromacs.org
-Source0:	ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}%{?_rc}.tar.gz
-Source1:	ftp://ftp.gromacs.org/pub/manual/manual-%{version}%{?_rc}.pdf
-# Too britle sind 2018.2
-Source2:	http://gerrit.gromacs.org/download/regressiontests-%%7Bversion%7D%%7B?_rc%7D...
+Source0:	https://ftp.gromacs.org/pub/gromacs/gromacs-%%7Bversion%7D%%7B?_rc%7D.tar.gz
+Source1:	https://ftp.gromacs.org/pub/manual/manual-%%7Bversion%7D%%7B?_rc%7D.pdf
+Source2:	https://ftp.gromacs.org/regressiontests/regressiontests-%%7Bversion%7D%%7B?_...
 Source3:	gromacs-README.fedora
-# fix path to packaged dssp
-# https://bugzilla.redhat.com/show_bug.cgi?id=1203754
-Patch0:		gromacs-dssp-path.patch
-# enable some test on aarch64 - https://redmine.gromacs.org/issues/2366
-# bug#1558206
-Patch1:		gromacs-issue-2366.patch
-Patch2:         test_timeout.patch 
-Patch3:         gromacs-gcc11.patch
 BuildRequires:	gcc-c++
 BuildRequires:  cmake3 >= 3.4.3
 BuildRequires:	%{blaslib}-devel
@@ -71,7 +54,6 @@ Recommends:	gromacs-opencl = %{version}-%{release}
 %endif
 BuildRequires:	tng-devel
 BuildRequires:	bash-completion
-%ifnarch i686 %arm ppc64le
 # Dependencies used for regressiontest
 BuildRequires:	perl(Carp)
 BuildRequires:	perl(Cwd)
@@ -83,7 +65,6 @@ BuildRequires:	perl(lib)
 BuildRequires:	perl(List::Util)
 BuildRequires:	perl(strict)
 BuildRequires:	perl(vars)
-%endif
 %define compdir %(pkg-config --variable=completionsdir bash-completion)
 %if "%{compdir}" == ""
 %define compdir "/etc/bash_completion.d"
@@ -238,24 +219,20 @@ This package single and double precision binaries and libraries.
%prep
 %setup -q %{?SOURCE2:-a 2} -n gromacs-%{version}%{?_rc}
-%patch0 -p1
-%patch1 -p1
-%patch2 -p1
-%patch3 -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
 # test, see: https://redmine.gromacs.org/issues/2389
 rm -r src/external/{fftpack,tng_io,lmfit}
+# increase timeout of tests
 sed -i 's/set(_timeout [0-9]*)/set(_timeout 9000)/' src/testutils/TestMacros.cmake
%build
 # Default options, used for all compilations
 %global defopts \\
  -DBUILD_TESTING:BOOL=ON \\
- -DCMAKE_SKIP_RPATH:BOOL=ON \\
- -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON \\
+ -DCMAKE_SKIP_INSTALL_RPATH=ON \\
  -DGMX_BLAS_USER=%{blaslib} \\
  -DGMX_BUILD_UNITTESTS:BOOL=ON \\
  -DGMX_EXTERNAL_LMFIT:BOOL=ON \\
@@ -264,11 +241,14 @@ sed -i 's/set(_timeout [0-9]*)/set(_timeout 9000)/' src/testutils/TestMacros.cma
  -DGMX_EXTERNAL_TINYXML2:BOOL=OFF \\
  -DGMX_LAPACK_USER=%{blaslib} \\
  -DGMX_USE_RDTSCP=OFF \\
+ -DGMX_INSTALL_LEGACY_API=ON \\
+ -DGMX_DSSP_PROGRAM_PATH=/usr/bin/dssp \\
+ -DGMX_VERSION_STRING_OF_FORK='Fedora%{fedora}' \\
  -DGMX_SIMD=%{simd}
%if %{with_opencl}
 # OpenCL is available for single precision only
-%global single -DGMX_GPU:BOOL=ON -DGMX_USE_OPENCL:BOOL=ON
+%global single -DGMX_GPU=OpenCL
 %endif
 %global double -DGMX_DOUBLE:BOOL=ON
 %global mpi -DGMX_BUILD_MDRUN_ONLY:BOOL=ON -DGMX_MPI:BOOL=ON -DGMX_THREAD_MPI:BOOL=OFF -DGMX_DEFAULT_SUFFIX:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF
@@ -283,9 +263,7 @@ for p in '' _d ; do
     test -z "${mpi}" && cp -al ../regressiontests* tests/ # use with -DREGRESSIONTEST_PATH=${PWD}/tests below
     %{cmake3} %{defopts} \
       $(test -n "${mpi}" && echo %{mpi} -DGMX_BINARY_SUFFIX=${MPI_SUFFIX}${p} -DGMX_LIBS_SUFFIX=${MPI_SUFFIX}${p} -DCMAKE_INSTALL_BINDIR=${MPI_BIN} || echo -DGMX_X11=ON) \
-%ifnarch i686 %arm ppc64le # regressiontest are not support on 32-bit archs: http://redmine.gromacs.org/issues/2584#note-35, ppc64le: https://redmine.gromacs.org/issues/2734
       $(test -z "${mpi}" && echo "-DREGRESSIONTEST_PATH=${PWD}/tests") \
-%endif
       $(test -n "$p" && echo %{double} || echo %{?single})
     %cmake_build
     popd
@@ -333,17 +311,11 @@ rm ./%{_bindir}/gmx-completion.bash ./%{_libdir}/*mpi*/bin/gmx-completion-*mpi*.
 . /etc/profile.d/modules.sh
 for p in '' _d ; do
   for mpi in '' mpich openmpi ; do
-    # https://bugzilla.redhat.com/show_bug.cgi?id=1512229 (retested 16. Feb 2018)
-%ifarch s390x armv7hl
-    test "${mpi}"  = "openmpi" && continue
-%endif
-    old_LD_LIBRARY_PATH="${LD_LIBRARY_PATH}"
     test -n "${mpi}" && module load mpi/${mpi}-%{_arch}
-    test -n "${mpi}" && xLD_LIBRARY_PATH=$LD_LIBRARY_PATH:%{buildroot}${MPI_LIB} || xLD_LIBRARY_PATH=%{buildroot}%{_libdir}
     pushd ${mpi:-serial}${p}
-    export LD_LIBRARY_PATH="${xLD_LIBRARY_PATH}"
+    [[ ${mpi} = openmpi ]] && export OMPI_MCA_rmaps_base_oversubscribe=1
     %cmake_build --target check
-    export LD_LIBRARY_PATH="${old_LD_LIBRARY_PATH}"
+    [[ ${mpi} = openmpi ]] && unset OMPI_MCA_rmaps_base_oversubscribe
     popd
     test -n "${mpi}" && module unload mpi/${mpi}-%{_arch}
   done
@@ -373,13 +345,20 @@ done
%files libs
 %{_libdir}/libgromacs*.so.*
+%{_libdir}/libgmxapi*.so.*
+%{_libdir}/libnblib*.so.*
%files devel
 %{_includedir}/%{name}
+%{_includedir}/gmxapi
+%{_includedir}/nblib
 %{_libdir}/libgromacs*.so
+%{_libdir}/libgmxapi*.so
+%{_libdir}/libnblib*.so
 %{_libdir}/pkgconfig/libgromacs*.pc
 %{_datadir}/%{name}/template
 %{_datadir}/cmake/gromacs*
+%{_datadir}/cmake/gmxapi*
%files openmpi
 %{_libdir}/openmpi/bin/mdrun_openmpi*
@@ -388,6 +367,9 @@ done
 %{_libdir}/mpich/bin/mdrun_mpich*
%changelog
+* Sat Jan 29 2022 Christoph Junghans junghans@votca.org - 2021.5-1
+- Version bump to v2021.5 (bug #1787785)
+
 * Thu Jan 20 2022 Fedora Release Engineering releng@fedoraproject.org - 2019.6-11
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
diff --git a/sources b/sources
index c3a5f6d..01978a2 100644
--- a/sources
+++ b/sources
@@ -1,3 +1,3 @@
-SHA512 (gromacs-2019.6.tar.gz) = 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
-SHA512 (manual-2019.6.pdf) = dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
-SHA512 (regressiontests-2019.6.tar.gz) = eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
+SHA512 (gromacs-2021.5.tar.gz) = 56c1b312fc8e52ec6f86e445d2fa2d07107c461b35d4dc8cdf95580f05fd8e6c5fd671d0e72b2b9e74e3232bc8c41db496fe4bcaf2b9a3ae3c2cfa93489a31c5
+SHA512 (manual-2021.5.pdf) = 7635108c935e4953d722df6a16ee43edf97eef7e49f047218728f68f61f8f185192ff1d8b13a573b643b040955af211355a7b560c8a894c858d7f71249d41296
+SHA512 (regressiontests-2021.5.tar.gz) = 3605d04b2602339fb7d33e2776da2ada337ca58a3802472d47f490d4e8dd04249a950bf34608a498eedebf69f344c0311bac8f7fcb58ce0ebbb6d608ee39aa2e
commit 74b8096dd055d0ffa4b2b410eba949988c4c4070
Author: Fedora Release Engineering releng@fedoraproject.org
Date:   Thu Jan 20 11:48:43 2022 +0000
- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
Signed-off-by: Fedora Release Engineering releng@fedoraproject.org
diff --git a/gromacs.spec b/gromacs.spec
index f38c5aa..9beceec 100644
--- a/gromacs.spec
+++ b/gromacs.spec
@@ -37,7 +37,7 @@
Name:		gromacs
 Version:	2019.6
-Release:	10%{?dist}
+Release:	11%{?dist}
 Summary:	Fast, Free and Flexible Molecular Dynamics
 License:	GPLv2+
 URL:		http://www.gromacs.org
@@ -388,6 +388,9 @@ done
 %{_libdir}/mpich/bin/mdrun_mpich*
%changelog
+* Thu Jan 20 2022 Fedora Release Engineering releng@fedoraproject.org - 2019.6-11
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
+
 * Thu Jul 22 2021 Fedora Release Engineering releng@fedoraproject.org - 2019.6-10
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild

    