|
|
7e46d68 |
# Copyright (c) 2013, 2014, 2015 Dave Love, Liverpool University
|
|
|
55b18ca |
# The licence for this file is as for the package itself.
|
|
|
55b18ca |
|
|
|
cdc1de9 |
# fixme: look at shipping example/benchmark data (~ 40MB total)
|
|
|
55b18ca |
|
|
|
cdc1de9 |
# Allow -march=native if you want to rebuild
|
|
|
55b18ca |
%bcond_with native
|
|
|
55b18ca |
|
|
|
8c10471 |
%if 0%{?el6}
|
|
|
8c10471 |
%ifarch ppc64
|
|
|
8c10471 |
%bcond_with mpich
|
|
|
8c10471 |
%else
|
|
|
8c10471 |
%bcond_without mpich
|
|
|
8c10471 |
%endif
|
|
|
8c10471 |
%else
|
|
|
8c10471 |
%bcond_without mpich
|
|
|
8c10471 |
%endif
|
|
|
8c10471 |
|
|
|
55b18ca |
Name: dl_poly
|
|
|
cdc1de9 |
Version: 1.10
|
|
|
f2a8b4a |
Release: 2%{?dist}
|
|
|
55b18ca |
Summary: General purpose classical molecular dynamics (MD) simulation
|
|
|
55b18ca |
License: BSD
|
|
|
cdc1de9 |
URL: http://www.ccp5.ac.uk/DL_POLY_C/
|
|
|
55b18ca |
# NB, the numbers in this URL change when it's updated, but the version doesn't
|
|
|
cdc1de9 |
Source0: http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/574/8924/dl_class_1.10.tar.gz
|
|
|
55b18ca |
Source1: dl_poly-makefile
|
|
|
55b18ca |
Source2: dl_poly.desktop
|
|
|
cdc1de9 |
# Change executable
|
|
|
55b18ca |
Patch2: dl_poly-javaexec.patch
|
|
|
b39e9ea |
BuildRequires: gcc-gfortran java-devel openmpi-devel desktop-file-utils
|
|
|
8c10471 |
%if %{with mpich}
|
|
|
8c10471 |
BuildRequires: mpich-devel
|
|
|
8c10471 |
%endif
|
|
|
55b18ca |
Requires: %{name}-common = %{version}-%{release}
|
|
|
55b18ca |
|
|
|
55b18ca |
%global base_description \
|
|
|
55b18ca |
DL_POLY Classic is a general purpose molecular dynamics simulation\
|
|
|
55b18ca |
package developed at Daresbury Laboratory by W. Smith, T.R. Forester\
|
|
|
55b18ca |
and I.T. Todorov. It is based on the package DL_POLY_2, which was\
|
|
|
55b18ca |
originally developed by the Computational Chemistry Group, (CCG) at\
|
|
|
55b18ca |
Daresbury Laboratory under the auspices of the Engineering and\
|
|
|
55b18ca |
Physical Sciences Research Council (EPSRC) for (CCP5), the EPSRC's\
|
|
|
55b18ca |
Collaborative Computational Project for the Computer Simulation of\
|
|
|
55b18ca |
Condensed Phases.\
|
|
|
55b18ca |
\
|
|
|
cdc1de9 |
DL_POLY Classic achieves parallelisation using the Replicated Data strategy\
|
|
|
55b18ca |
which is suitable for homogeneous, distributed-memory, parallel\
|
|
|
55b18ca |
computers. The code is useful for simulations of up to 30,000 atoms\
|
|
|
55b18ca |
with good parallel performance on up to 100 processors, though in some\
|
|
|
55b18ca |
circumstances it can exceed or fail to reach these limits.\
|
|
|
55b18ca |
\
|
|
|
55b18ca |
Reference: I.T. Todorov, W. Smith, K. Trachenko & M.T. Dove,\
|
|
|
55b18ca |
Journal of Materials Chemistry, (2006) 16, 1911-1918
|
|
|
55b18ca |
|
|
|
55b18ca |
%description
|
|
|
55b18ca |
%{base_description}
|
|
|
55b18ca |
|
|
|
55b18ca |
%package common
|
|
|
55b18ca |
Summary: General purpose classical molecular dynamics (MD) simulation - common files
|
|
|
55b18ca |
BuildArch: noarch
|
|
|
55b18ca |
|
|
|
55b18ca |
%description common
|
|
|
55b18ca |
Common files for %name.
|
|
|
55b18ca |
This package contains, principally the "utility" source and data files.
|
|
|
55b18ca |
|
|
|
55b18ca |
%package doc
|
|
|
55b18ca |
Summary: Documentation for %name and %{name}-gui
|
|
|
55b18ca |
BuildArch: noarch
|
|
|
55b18ca |
|
|
|
55b18ca |
%description doc
|
|
|
55b18ca |
Documentation for %{name} and %{name}-gui.
|
|
|
55b18ca |
|
|
|
55b18ca |
%package openmpi
|
|
|
55b18ca |
Summary: General purpose classical molecular dynamics (MD) simulation - openmpi version
|
|
|
55b18ca |
Requires: openmpi%{_isa}, %{name}-common = %{version}-%{release}
|
|
|
55b18ca |
|
|
|
55b18ca |
%description openmpi
|
|
|
55b18ca |
%{base_description}
|
|
|
55b18ca |
|
|
|
55b18ca |
This is a parallel version using openmpi.
|
|
|
55b18ca |
|
|
|
8c10471 |
%if %{with mpich}
|
|
|
55b18ca |
%package mpich
|
|
|
55b18ca |
Summary: General purpose classical molecular dynamics (MD) simulation - mpich version
|
|
|
55b18ca |
Requires: mpich%{_isa}, %{name}-common = %{version}-%{release}
|
|
|
55b18ca |
|
|
|
55b18ca |
%description mpich
|
|
|
55b18ca |
%{base_description}
|
|
|
55b18ca |
|
|
|
55b18ca |
This is a parallel version using mpich.
|
|
|
8c10471 |
%endif
|
|
|
55b18ca |
|
|
|
55b18ca |
%package gui
|
|
|
55b18ca |
Summary: GUI for %name
|
|
|
580adaf |
Requires: java, jpackage-utils
|
|
|
55b18ca |
BuildArch: noarch
|
|
|
55b18ca |
|
|
|
55b18ca |
%description gui
|
|
|
55b18ca |
This package provides the Java-based graphical user interface for %name.
|
|
|
55b18ca |
|
|
|
55b18ca |
%prep
|
|
|
cdc1de9 |
%setup -q -n dl_class_1.10
|
|
|
55b18ca |
rm java/GUI.jar
|
|
|
55b18ca |
cp %{SOURCE1} source/Makefile
|
|
|
55b18ca |
|
|
|
55b18ca |
%patch2 -p1
|
|
|
55b18ca |
|
|
|
55b18ca |
%build
|
|
|
cdc1de9 |
# Serial version no longer builds. Reported to Bill Smith, but no fix
|
|
|
cdc1de9 |
# forthcoming.
|
|
|
55b18ca |
%if %{with native}
|
|
|
55b18ca |
%global native NATIVE=-march=native
|
|
|
55b18ca |
%else
|
|
|
55b18ca |
%global native NATIVE=
|
|
|
55b18ca |
%endif
|
|
|
cdc1de9 |
echo %{build_cflags}
|
|
|
cdc1de9 |
# Parallel make fails. Extra opt flags are from the original.
|
|
|
55b18ca |
%global dobuild \
|
|
|
55b18ca |
mkdir $MPI_COMPILER;\
|
|
|
cdc1de9 |
%make_build -j1 build PAR=1 %native; \
|
|
|
55b18ca |
mv ../execute/DLPOLY.X $MPI_COMPILER/%{name}$MPI_SUFFIX
|
|
|
55b18ca |
|
|
|
55b18ca |
cd source
|
|
|
55b18ca |
|
|
|
55b18ca |
%{_openmpi_load}
|
|
|
55b18ca |
%{dobuild}
|
|
|
55b18ca |
%{_openmpi_unload}
|
|
|
cdc1de9 |
rm basic_comms.o merge_tools.o pass_tools.o
|
|
|
cdc1de9 |
make clean
|
|
|
8c10471 |
%if %{with mpich}
|
|
|
55b18ca |
%{_mpich_load}
|
|
|
55b18ca |
%{dobuild}
|
|
|
55b18ca |
%{_mpich_unload}
|
|
|
8c10471 |
%endif
|
|
|
55b18ca |
|
|
|
55b18ca |
cd ../java
|
|
|
55b18ca |
sh build
|
|
|
55b18ca |
cat <<+ >%{name}_gui
|
|
|
55b18ca |
#!/bin/sh
|
|
|
55b18ca |
exec java -jar %{_javadir}/DL_POLY_GUI.jar
|
|
|
55b18ca |
+
|
|
|
55b18ca |
cd ..
|
|
|
55b18ca |
cat <<+ >README.running
|
|
|
55b18ca |
Use the environment modules command
|
|
|
55b18ca |
module load <mpi>-%{_arch}
|
|
|
55b18ca |
to put the %{name}_<mpi> parallel executable on your path,
|
|
|
55b18ca |
where <mpi> may be openmpi or mpich. In a batch job You may
|
|
|
55b18ca |
need to source /etc/profile.d/modules.sh or /etc/profile.d/modules.csh
|
|
|
55b18ca |
first.
|
|
|
55b18ca |
+
|
|
|
55b18ca |
|
|
|
55b18ca |
%install
|
|
|
55b18ca |
mkdir -p $RPM_BUILD_ROOT%{_javadir} $RPM_BUILD_ROOT%_datadir/%name
|
|
|
55b18ca |
mkdir -p $RPM_BUILD_ROOT%{_bindir}
|
|
|
55b18ca |
mkdir -p $RPM_BUILD_ROOT/%{_libdir}/openmpi/bin
|
|
|
55b18ca |
install source/openmpi*/%{name}_* $RPM_BUILD_ROOT%{_libdir}/openmpi/bin
|
|
|
8c10471 |
%if %{with mpich}
|
|
|
8c10471 |
mkdir -p $RPM_BUILD_ROOT/%{_libdir}/mpich/bin
|
|
|
55b18ca |
install source/mpich*/%{name}_* $RPM_BUILD_ROOT%{_libdir}/mpich/bin
|
|
|
8c10471 |
%endif
|
|
|
55b18ca |
cp data/README README.data
|
|
|
55b18ca |
chmod 644 utility/dl2xyz
|
|
|
55b18ca |
cp -a utility $RPM_BUILD_ROOT%{_datadir}/%{name}
|
|
|
7e46d68 |
install -m 644 java/GUI.jar $RPM_BUILD_ROOT%{_javadir}/DL_POLY_GUI.jar
|
|
|
55b18ca |
install -m 755 java/%{name}_gui $RPM_BUILD_ROOT%{_bindir}
|
|
|
55b18ca |
chmod 644 LICENCE.pdf manual/JavaGUI.pdf
|
|
|
55b18ca |
desktop-file-install --dir=${RPM_BUILD_ROOT}%{_datadir}/applications %{SOURCE2}
|
|
|
55b18ca |
|
|
|
cdc1de9 |
|
|
|
55b18ca |
%check
|
|
|
cdc1de9 |
# Would depend on shipping at least some data files, per fixme above
|
|
|
55b18ca |
|
|
|
55b18ca |
|
|
|
55b18ca |
%files common
|
|
|
cdc1de9 |
%license LICENCE.pdf
|
|
|
cdc1de9 |
%doc README.data README
|
|
|
55b18ca |
%{_datadir}/%{name}
|
|
|
55b18ca |
|
|
|
55b18ca |
%files doc
|
|
|
cdc1de9 |
%license LICENCE.pdf
|
|
|
55b18ca |
%doc manual/USRMAN.pdf manual/JavaGUI.pdf
|
|
|
55b18ca |
|
|
|
55b18ca |
%files gui
|
|
|
cdc1de9 |
%license LICENCE.pdf
|
|
|
55b18ca |
%{_javadir}/DL_POLY_GUI.jar
|
|
|
55b18ca |
%{_bindir}/%{name}_gui
|
|
|
cdc1de9 |
%doc README
|
|
|
55b18ca |
%{_datadir}/applications/*
|
|
|
55b18ca |
|
|
|
55b18ca |
%files openmpi
|
|
|
55b18ca |
%{_libdir}/openmpi/bin/*
|
|
|
55b18ca |
|
|
|
8c10471 |
%if %{with mpich}
|
|
|
55b18ca |
%files mpich
|
|
|
55b18ca |
%{_libdir}/mpich/bin/*
|
|
|
8c10471 |
%endif
|
|
|
8c10471 |
|
|
|
55b18ca |
|
|
|
55b18ca |
%changelog
|
|
|
f2a8b4a |
* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.10-2
|
|
|
f2a8b4a |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
|
|
|
f2a8b4a |
|
|
|
cdc1de9 |
* Mon Oct 29 2018 Dave Love <loveshack@fedoraproject.org> - 1.10-1
|
|
|
cdc1de9 |
- New version
|
|
|
cdc1de9 |
- Drop serial version, which no longer builds
|
|
|
cdc1de9 |
- Fix homepaage
|
|
|
cdc1de9 |
- Drop java patch
|
|
|
cdc1de9 |
- Improve optimization flags
|
|
|
cdc1de9 |
|
|
|
4d0e8d6 |
* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.20140324-22
|
|
|
4d0e8d6 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
|
|
|
4d0e8d6 |
|
|
|
380e939 |
* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.20140324-21
|
|
|
380e939 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
|
|
|
380e939 |
|
|
|
d412947 |
* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.20140324-20
|
|
|
d412947 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
|
|
|
d412947 |
|
|
|
ac69ddd |
* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.20140324-19
|
|
|
ac69ddd |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
|
|
|
ac69ddd |
|
|
|
f64cdff |
* Sun Feb 05 2017 Kalev Lember <klember@redhat.com> - 1.9.20140324-18
|
|
|
f64cdff |
- Rebuilt for libgfortran soname bump
|
|
|
f64cdff |
|
|
Orion Poplawski |
65a9bab |
* Fri Oct 21 2016 Orion Poplawski <orion@cora.nwra.com> - 1.9.20140324-17
|
|
Orion Poplawski |
65a9bab |
- Rebuild for openmpi 2.0
|
|
Orion Poplawski |
65a9bab |
|
|
|
315f4f1 |
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.9.20140324-16
|
|
|
315f4f1 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
|
|
|
315f4f1 |
|
|
Orion Poplawski |
ecafedc |
* Tue Sep 15 2015 Orion Poplawski <orion@cora.nwra.com> - 1.9.20140324-15
|
|
Orion Poplawski |
ecafedc |
- Rebuild for openmpi 1.10.0
|
|
Orion Poplawski |
ecafedc |
|
|
|
e28a259 |
* Sat Aug 15 2015 Zbigniew Jędrzejewski-Szmek <zbyszek@in.waw.pl> - 1.9.20140324-14
|
|
|
e28a259 |
- Rebuild for MPI provides
|
|
|
e28a259 |
|
|
|
d649be8 |
* Mon Jul 27 2015 Sandro Mani <manisandro@gmail.com> - 1.9.20140324-13
|
|
|
d649be8 |
- Rebuild for RPM MPI Requires Provides Change
|
|
|
d649be8 |
|
|
|
e26a6a9 |
* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.9.20140324-12
|
|
|
e26a6a9 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
|
|
|
e26a6a9 |
|
|
Dave Love |
ac24b79 |
* Wed Mar 18 2015 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-11
|
|
Dave Love |
ac24b79 |
- Rebuild for mpich change
|
|
Dave Love |
ac24b79 |
|
|
|
580adaf |
* Sun Feb 22 2015 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-10
|
|
|
580adaf |
- Drop java minimum version (for ppc64 el6)
|
|
|
580adaf |
|
|
|
7e46d68 |
* Fri Feb 20 2015 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-9
|
|
|
7e46d68 |
- Specify permissions for installed .jar
|
|
|
7e46d68 |
|
|
|
8c10471 |
* Thu Feb 19 2015 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-8
|
|
|
8c10471 |
- Conditionalize out mpich on ppc64 el6
|
|
|
8c10471 |
|
|
|
55b18ca |
* Wed Feb 11 2015 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-7
|
|
|
55b18ca |
- Remove _isa on -common and java requires
|
|
|
55b18ca |
|
|
|
55b18ca |
* Tue Feb 10 2015 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-6
|
|
|
55b18ca |
- Add _isa suffix to requires
|
|
|
55b18ca |
- Use %%global, not %%define
|
|
|
55b18ca |
|
|
|
55b18ca |
* Fri Feb 6 2015 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-5
|
|
|
55b18ca |
From review:
|
|
|
55b18ca |
- Remove bundled .jar
|
|
|
55b18ca |
- Change buildroot to the preferred form
|
|
|
55b18ca |
- Add desktop file
|
|
|
55b18ca |
- Zap %%defattr
|
|
|
55b18ca |
- Use %%optflags (sigh)
|
|
|
55b18ca |
|
|
|
55b18ca |
* Thu Dec 11 2014 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-4
|
|
|
55b18ca |
- Drop EPEL5 for now
|
|
|
55b18ca |
|
|
|
55b18ca |
* Fri Nov 21 2014 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-3
|
|
|
55b18ca |
- Adjust for mpich3 on EPEL6
|
|
|
55b18ca |
|
|
|
55b18ca |
* Sun Jul 27 2014 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-2
|
|
|
55b18ca |
- Add doc package
|
|
|
55b18ca |
- Add jpackage-utils dependency for gui
|
|
|
55b18ca |
- Remove Group tags
|
|
|
55b18ca |
|
|
|
55b18ca |
* Thu Jun 5 2014 Dave Love <d.love@liverpool.ac.uk> - 1.9.20140324-1
|
|
|
55b18ca |
- Build serial and mpich packages as well as openmpi, for Fedora
|
|
|
55b18ca |
- Make common and gui packages
|
|
|
55b18ca |
- Use updated tarball (which has the same version number)
|
|
|
55b18ca |
|
|
|
55b18ca |
* Fri Oct 11 2013 Dave Love <d.love@liverpool.ac.uk> - 1.9-1
|
|
|
55b18ca |
- Initial packaging
|