[nwchem] Initial import (#984605).
Marcin Dulak
marcindulak at fedoraproject.org
Thu Feb 6 19:53:44 UTC 2014
commit 810ac3cd988155dc0effb4062be12d042339f186
Author: marcindulak <Marcin.Dulak at gmail.com>
Date: Thu Feb 6 20:54:08 2014 +0100
Initial import (#984605).
.gitignore | 1 +
nwchem.spec | 483 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
sources | 1 +
3 files changed, 485 insertions(+), 0 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index e69de29..d424b58 100644
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+/Nwchem-6.3.revision2-src.2013-10-17.tar.gz
diff --git a/nwchem.spec b/nwchem.spec
new file mode 100644
index 0000000..0d84865
--- /dev/null
+++ b/nwchem.spec
@@ -0,0 +1,483 @@
+%global upstream_name Nwchem
+
+%{?!major_version: %global major_version 6.3}
+%{?!minor_version: %global minor_version 2}
+%{?!posttag: %global posttag 2013-10-17}
+
+%ifarch %ix86 %arm
+%global make64_to_32 0
+%global NWCHEM_TARGET LINUX
+%endif
+%ifarch x86_64
+%global make64_to_32 1
+%global NWCHEM_TARGET LINUX64
+# nwchem by default assumes that python is installed
+# under lib on a 64 bit machine
+%{?!USE_PYTHON64: %global USE_PYTHON64 1}
+%endif
+
+# Global Arrays (part of Nwchem source) is FTBFS on ARM
+# https://bugzilla.redhat.com/show_bug.cgi?id=964424
+ExcludeArch: %arm
+
+%if 0%{?el6}
+%global mpich mpich2
+%global mpich_load %_mpich2_load
+%global mpich_unload %_mpich2_unload
+%else
+%global mpich mpich
+%global mpich_load %_mpich_load
+%global mpich_unload %_mpich_unload
+%endif
+
+# static (a) or shared (so) libpython.*
+%global PYTHONLIBTYPE so
+
+%if 0%{?fedora} >= 21
+%global BLASOPT -L%{_libdir}/atlas -lsatlas
+%else
+%global BLASOPT -L%{_libdir}/atlas -lf77blas -lcblas -latlas
+%endif
+
+Name: nwchem
+Version: %{major_version}.%{minor_version}
+Release: 6%{?dist}
+Summary: Delivering High-Performance Computational Chemistry to Science
+
+License: ECL 2.0
+URL: http://www.nwchem-sw.org/
+# Nwchem changes naming convention of tarballs very often!
+Source0: http://www.nwchem-sw.org/images/%{upstream_name}-%{major_version}.revision%{minor_version}-src.%{posttag}.tar.gz
+
+# https://fedoraproject.org/wiki/Packaging:Guidelines#Compiler_flags
+# One needs to patch gfortran/gcc makefiles in order to use
+# $RPM_OPT_FLAGS (= %%optflags), but an attempt resulted in broken
+# executables http://koji.fedoraproject.org/koji/taskinfo?taskID=6429073
+# even after removing the -Werror=format-security flag
+# https://bugzilla.redhat.com/show_bug.cgi?id=1037075
+
+
+%global PKG_TOP ${RPM_BUILD_DIR}/%{name}-%{major_version}.revision%{minor_version}-src.%{posttag}
+
+BuildRequires: time
+
+BuildRequires: python2-devel
+
+BuildRequires: gcc-gfortran
+
+BuildRequires: atlas-devel
+
+%if 0%{?fedora} || 0%{?rhel} >= 7
+BuildRequires: fdupes
+%endif
+
+BuildRequires: libsysfs-devel
+BuildRequires: ncurses-devel
+BuildRequires: perl
+BuildRequires: readline-devel
+BuildRequires: tcsh
+BuildRequires: zlib-devel
+
+BuildRequires: openssh-clients
+
+Requires: openssh-clients
+Requires: %{name}-common = %{version}-%{release}
+
+
+%global nwchem_desc_base \
+NWChem aims to provide its users with computational chemistry tools that are\
+scalable both in their ability to treat large scientific computational\
+chemistry problems efficiently, and in their use of available parallel\
+computing resources from high-performance parallel supercomputers to\
+conventional workstation clusters.
+
+%global nwchem_desc_cite \
+Please cite the following reference when\
+publishing results obtained with NWChem:\
+M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P. Straatsma,\
+H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus, W.A. de Jong,\
+"NWChem: a comprehensive and scalable open-source solution for\
+large scale molecular simulations" Comput. Phys. Commun. 181, 1477 (2010)
+
+
+%description
+%{nwchem_desc_base}
+%{nwchem_desc_cite}
+
+
+%package openmpi
+Summary: %{upstream_name} - openmpi version
+BuildRequires: openmpi-devel
+Requires: openmpi
+Requires: %{name}-common = %{version}-%{release}
+
+%description openmpi
+%{nwchem_desc_base}
+%{nwchem_desc_cite}
+
+This package contains the openmpi version.
+
+
+%package %{mpich}
+Summary: %{upstream_name} - %{mpich} version
+BuildRequires: %{mpich}-devel
+Requires: %{mpich}
+Requires: %{name}-common = %{version}-%{release}
+
+%description %{mpich}
+%{nwchem_desc_base}
+%{nwchem_desc_cite}
+
+This package contains the %{mpich} version.
+
+
+%package common
+Summary: %{upstream_name} - common files
+BuildArch: noarch
+
+%description common
+%{nwchem_desc_base}
+%{nwchem_desc_cite}
+
+This package contains the data files.
+
+
+%prep
+%setup -q -n %{name}-%{major_version}.revision%{minor_version}-src.%{posttag}
+
+
+%build
+# base settings
+echo "# see http://www.nwchem-sw.org/index.php/Compiling_NWChem" > settings.sh
+echo export NWCHEM_TOP=%{PKG_TOP} >> settings.sh
+echo export NWCHEM_TARGET=%{NWCHEM_TARGET} >> settings.sh
+#
+echo export CC=gcc >> settings.sh
+echo export FC=gfortran >> settings.sh
+#
+echo export LARGE_FILES=TRUE >> settings.sh
+echo export USE_NOFSCHECK=TRUE >> settings.sh
+#
+echo export PYTHONHOME=/usr >> settings.sh
+echo export PYTHONVERSION=%{python_version} >> settings.sh
+echo export PYTHONLIBTYPE=%{PYTHONLIBTYPE} >> settings.sh
+%if 0%{?USE_PYTHON64}
+echo export USE_PYTHON64=y >> settings.sh
+%endif
+echo export HAS_BLAS=yes >> settings.sh
+echo export BLASOPT="'%{BLASOPT}'" >> settings.sh
+echo export MAKE='%{__make}' >> settings.sh
+echo '$MAKE nwchem_config NWCHEM_MODULES="all python" 2>&1 | tee ../make_nwchem_config.log' > make.sh
+%if 0%{?make64_to_32}
+echo '$MAKE 64_to_32 2>&1 | tee ../make_64_to_32.log' >> make.sh
+echo 'export MAKEOPTS="USE_64TO32=y"' >> make.sh
+%else
+echo 'export MAKEOPTS=""' >> make.sh
+%endif
+# final make (log of ~200MB, don't write it)
+echo '$MAKE ${MAKEOPTS} 2>&1' >> make.sh # | tee ../make.log' >> make.sh
+
+# Have to do off-root builds to be able to build many versions at once
+mv src src.orig
+
+# To avoid replicated code define a macro
+%global dobuild() \
+cd src; \
+cp -p ../settings.sh ../compile$MPI_SUFFIX.sh; \
+echo export LD_LIBRARY_PATH=$MPI_LIB >> ../compile$MPI_SUFFIX.sh; \
+echo export USE_MPI=y >> ../compile$MPI_SUFFIX.sh; \
+echo export USE_MPIF=y >> ../compile$MPI_SUFFIX.sh; \
+echo export USE_MPIF4=y >> ../compile$MPI_SUFFIX.sh; \
+echo export MPIEXEC=$MPI_BIN/mpiexec >> ../compile$MPI_SUFFIX.sh; \
+echo export MPI_LIB=$MPI_LIB >> ../compile$MPI_SUFFIX.sh; \
+echo export MPI_INCLUDE=$MPI_INCLUDE >> ../compile$MPI_SUFFIX.sh; \
+if [ "$MPI_SUFFIX" == "_openmpi" ] && [ -r "$MPI_LIB/libmpi_f90.so" ]; then echo export LIBMPI="'-lmpi -lmpi_f90 -lmpi_f77'" >> ../compile$MPI_SUFFIX.sh; fi; \
+if [ "$MPI_SUFFIX" == "_openmpi" ] && [ -r "$MPI_LIB/libmpi_usempi.so" ]; then echo export LIBMPI="'-lmpi -lmpi_usempi -lmpi_mpifh'" >> ../compile$MPI_SUFFIX.sh; fi; \
+if [ "$MPI_SUFFIX" == "_mpich2" ]; then echo export LIBMPI='-lmpich' >> ../compile$MPI_SUFFIX.sh; fi; \
+if [ "$MPI_SUFFIX" == "_mpich" ]; then echo export LIBMPI='-lmpich' >> ../compile$MPI_SUFFIX.sh; fi; \
+cat ../make.sh >> ../compile$MPI_SUFFIX.sh; \
+%{__sed} -i "s|.log|$MPI_SUFFIX.log|g" ../compile$MPI_SUFFIX.sh; \
+cat ../compile$MPI_SUFFIX.sh; \
+sh ../compile$MPI_SUFFIX.sh; \
+mv ../bin/%{NWCHEM_TARGET}/%{name} ../bin/%{NWCHEM_TARGET}/%{name}$MPI_SUFFIX; \
+NWCHEM_TARGET=%{NWCHEM_TARGET} NWCHEM_TOP=%{PKG_TOP} %{__make} clean; \
+cd ..
+
+# build serial version
+export MPI_SUFFIX=_serial
+cp -rp src.orig src
+cd src
+cp -p ../settings.sh ../compile$MPI_SUFFIX.sh
+echo export ARMCI_NETWORK=SOCKETS >> ../compile$MPI_SUFFIX.sh
+# without TCGSSH armci configure fails!
+echo export TCGSSH=ssh >> ../compile$MPI_SUFFIX.sh
+cat ../make.sh >> ../compile$MPI_SUFFIX.sh
+%{__sed} -i "s|.log|$MPI_SUFFIX.log|g" ../compile$MPI_SUFFIX.sh; \
+cat ../compile$MPI_SUFFIX.sh
+sh ../compile$MPI_SUFFIX.sh
+mv ../bin/%{NWCHEM_TARGET}/%{name} ../bin/%{NWCHEM_TARGET}/%{name}$MPI_SUFFIX; \
+NWCHEM_TARGET=%{NWCHEM_TARGET} NWCHEM_TOP=%{PKG_TOP} %{__make} clean; \
+cd ..
+rm -rf src
+
+# build openmpi version
+cp -rp src.orig src
+%{_openmpi_load}
+%dobuild
+%{_openmpi_unload}
+rm -rf src
+
+cp -rp src.orig src
+# build mpich version
+%{mpich_load}
+%dobuild
+%{mpich_unload}
+# leave last src build for debuginfo
+
+rm -f make.sh settings.sh
+
+cat <<EOF > %{PKG_TOP}/%{name}.sh
+# NOTE: This is an automatically-generated file! (generated by the
+# %%{name} RPM). Any changes made here will be lost if the RPM is
+# uninstalled or upgraded.
+
+# must end with slash!
+PA=%{_datadir}/%{name}/libraries/
+
+case \$NWCHEM_BASIS_LIBRARY in
+ *\${PA}*);;
+ *?*) NWCHEM_BASIS_LIBRARY=\${PA}:\${NWCHEM_BASIS_LIBRARY};;
+ *) NWCHEM_BASIS_LIBRARY=\${PA};;
+esac
+export NWCHEM_BASIS_LIBRARY
+
+# must end with slash!
+PA=%{_datadir}/%{name}/libraryps/
+
+case \$NWCHEM_NWPW_LIBRARY in
+ *\${PA}*);;
+ *?*) NWCHEM_NWPW_LIBRARY=\${PA}:\${NWCHEM_NWPW_LIBRARY};;
+ *) NWCHEM_NWPW_LIBRARY=\${PA};;
+esac
+export NWCHEM_NWPW_LIBRARY
+
+EOF
+
+cat <<EOF > %{PKG_TOP}/%{name}.csh
+# NOTE: This is an automatically-generated file! (generated by the
+# %%{name} RPM). Any changes made here will be lost if the RPM is
+# uninstalled or upgraded.
+
+# must end with slash!
+set PA=%{_datadir}/%{name}/libraries/
+
+if (\$?NWCHEM_BASIS_LIBRARY) then
+ if ("\$NWCHEM_BASIS_LIBRARY" !~ *\${PA}*) then
+ setenv NWCHEM_BASIS_LIBRARY \${PA}:\${NWCHEM_BASIS_LIBRARY}
+ endif
+else
+ setenv NWCHEM_BASIS_LIBRARY \${PA}
+endif
+
+unset PA
+
+# must end with slash!
+set PA=%{_datadir}/%{name}/libraryps/
+
+if (\$?NWCHEM_NWPW_LIBRARY) then
+ if ("\$NWCHEM_NWPW_LIBRARY" !~ *\${PA}*) then
+ setenv NWCHEM_NWPW_LIBRARY \${PA}:\${NWCHEM_NWPW_LIBRARY}
+ endif
+else
+ setenv NWCHEM_NWPW_LIBRARY \${PA}
+endif
+
+unset PA
+EOF
+
+# create /etc/nwchemrc
+cat <<EOF > %{PKG_TOP}/nwchemrc
+# NOTE: This is an automatically-generated file! (generated by the
+# %%{name} RPM). Any changes made here will be lost if the RPM is
+# uninstalled or upgraded.
+
+# data directory names must end with slash!
+NWCHEM_BASIS_LIBRARY %{_datadir}/%{name}/libraries/
+NWCHEM_NWPW_LIBRARY %{_datadir}/%{name}/libraryps/
+FFIELD amber
+AMBER_1 %{_datadir}/%{name}/amber_s/
+AMBER_2 %{_datadir}/%{name}/amber_q/
+AMBER_3 %{_datadir}/%{name}/amber_x/
+AMBER_4 %{_datadir}/%{name}/amber_u/
+SPCE %{_datadir}/%{name}/solvents/spce.rst
+CHARMM_s %{_datadir}/%{name}/charmm_s/
+CHARMM_x %{_datadir}/%{name}/charmm_x/
+EOF
+
+
+%install
+mkdir -p $RPM_BUILD_ROOT%{_sysconfdir}
+
+# *.bak files not allowed by rpmlint
+for file in `find %{PKG_TOP} -name "*.bak"`; do
+ rm -f ${file}
+done
+
+# To avoid replicated code define a macro
+%global doinstall() \
+mkdir -p $RPM_BUILD_ROOT/$MPI_BIN; \
+install -p -m 755 %{PKG_TOP}/bin/%{NWCHEM_TARGET}/%{name}$MPI_SUFFIX $RPM_BUILD_ROOT/$MPI_BIN
+
+# install serial version
+mkdir -p $RPM_BUILD_ROOT%{_bindir}
+install -p -m 755 %{PKG_TOP}/bin/%{NWCHEM_TARGET}/%{name}_serial $RPM_BUILD_ROOT%{_bindir}/%{name}
+
+# install openmpi version
+%{_openmpi_load}
+%doinstall
+%{_openmpi_unload}
+
+# install mpich version
+%{mpich_load}
+%doinstall
+%{mpich_unload}
+
+mkdir -p $RPM_BUILD_ROOT%{_datadir}/%{name}
+
+cp -rp %{PKG_TOP}/src/data/* $RPM_BUILD_ROOT%{_datadir}/%{name}
+cp -rp %{PKG_TOP}/src/basis/libraries $RPM_BUILD_ROOT%{_datadir}/%{name}
+cp -rp %{PKG_TOP}/src/nwpw/libraryps $RPM_BUILD_ROOT%{_datadir}/%{name}
+rm -f $RPM_BUILD_ROOT%{_datadir}/%{name}/libraryps/{*MakeFile,*.fh,*.F,dependencies,include_stamp}
+
+# env scripts
+install -p -m 444 %{PKG_TOP}/*.*sh $RPM_BUILD_ROOT%{_datadir}/%{name}
+# /etc/nwchemrc not working globally anymore?
+install -p -m 444 %{PKG_TOP}/nwchemrc $RPM_BUILD_ROOT%{_datadir}/%{name}
+mkdir -p $RPM_BUILD_ROOT%{_sysconfdir}/profile.d
+install -p -m 444 %{PKG_TOP}/%{name}*.*sh $RPM_BUILD_ROOT%{_sysconfdir}/profile.d
+
+# To avoid: "Found '/tmp/rpmbuild/build/' in installed files; aborting"
+for file in `find %{PKG_TOP} -name "*.log"`; do
+ %{__sed} -i "s|$RPM_BUILD_ROOT||g" ${file}
+done
+for file in `find %{PKG_TOP} -name "*.sh"`; do
+ %{__sed} -i "s|$RPM_BUILD_ROOT||g" ${file}
+done
+
+%if 0%{?fedora} || 0%{?rhel} >= 7
+%fdupes -s $RPM_BUILD_ROOT
+%endif
+
+
+%check
+export NWCHEM_TOP=%{PKG_TOP}
+export NWCHEM_TARGET=%{NWCHEM_TARGET}
+# data directory names must end with slash!
+export NWCHEM_BASIS_LIBRARY=$RPM_BUILD_ROOT%{_datadir}/%{name}/libraries/
+export NWCHEM_NWPW_LIBRARY=$RPM_BUILD_ROOT%{_datadir}/%{name}/libraryps/
+
+mv QA QA.orig
+
+# cosmo_h2o_dft hangs on i386? MD Feb 8 2012
+# h2o-response hangs on i386? MD Jul 31 2013
+
+# To avoid replicated code define a macro
+%global docheck() \
+cp -rp QA.orig QA; \
+cd QA; \
+export LD_LIBRARY_PATH=${MPI_LIB}; \
+export PATH=${MPI_BIN}:${PATH}; \
+export MPIRUN_PATH=${MPI_BIN}/mpiexec; \
+export NWCHEM_EXECUTABLE=$NWCHEM_TOP/bin/$NWCHEM_TARGET/nwchem$MPI_SUFFIX; \
+%{__sed} -i '/cosmo_h2o_dft/d' doafewqmtests.mpi; \
+%{__sed} -i '/h2o-response/d' doafewqmtests.mpi; \
+time ./doafewqmtests.mpi %{NPROC} 2>&1 | tee ../doafewqmtests.mpi.%{NPROC}$MPI_SUFFIX.log; \
+mv testoutputs ../testoutputs.doafewqmtests.mpi.%{NPROC}$MPI_SUFFIX.log; \
+cd ..; \
+rm -rf QA
+
+%global NPROC 0
+# check serial version
+MPI_SUFFIX=_serial %docheck
+
+%global NPROC %(cat /proc/cpuinfo | grep processor | wc -l)
+# check openmpi version
+%{_openmpi_load}
+%docheck
+%{_openmpi_unload}
+
+# this will fail for mpich2 on el6 - mpd would need to be started ...
+# check mpich version
+%{mpich_load}
+%docheck
+%{mpich_unload}
+
+# restore QA
+mv QA.orig QA
+
+
+%files
+%{_bindir}/%{name}
+
+
+%files common
+%doc LICENSE*
+%{_datadir}/%{name}
+%config(noreplace) %{_sysconfdir}/profile.d/%{name}*.*sh
+
+
+%files openmpi
+%{_libdir}/openmpi%{?_opt_cc_suffix}/bin/%{name}_openmpi
+
+
+%files %{mpich}
+%{_libdir}/%{mpich}%{?_opt_cc_suffix}/bin/%{name}_%{mpich}
+
+
+%changelog
+* Sun Jan 26 2014 Marcin Dulak <Marcin.Dulak at gmail.com> 6.3.2-6
+- common is noarch
+- LICENSE* in common
+- %%config(noreplace) %%{_sysconfdir}/profile.d/* + more explicit glob
+- shorten %%description and %%summary
+- use serial atlas (-lsatlas)
+
+* Sat Jan 25 2014 Marcin Dulak <Marcin.Dulak at gmail.com> 6.3.2-5
+- ExcludeArch: %%arm
+
+* Fri Jan 24 2014 Marcin Dulak <Marcin.Dulak at gmail.com> 6.3.2-4
+- the idea of %%optflags dropped, resulting executables were broken
+
+* Tue Jan 14 2014 Marcin Dulak <Marcin.Dulak at gmail.com> 6.3.2-3
+- https://bugzilla.redhat.com/show_bug.cgi?id=984605#c12: timestamps
+
+* Wed Nov 6 2013 Marcin Dulak <Marcin.Dulak at gmail.com> 6.3.2-2
+- update version
+- explicitly set ARMCI_NETWORK=SOCKETS for serial build
+- dependency on openssh-clients for serial build
+- use tatlas on Fedora >= 21
+- basis are now under src/basis/libraries
+
+* Wed Jul 10 2013 Marcin Dulak <Marcin.Dulak at gmail.com> 6.3.1-2
+- conform to http://fedoraproject.org/wiki/Packaging:MPI#Packaging_of_MPI_software
+
+* Wed Jul 10 2013 Marcin Dulak <Marcin.Dulak at gmail.com> 6.3.1-1
+- adopted for Fedora and EPEL
+- split into the main and data package
+
+* Mon Aug 13 2012 Marcin Dulak <Marcin.Dulak at fysik.dtu.dk> 6.1.1-1
+- restructured for build.opensuse.org and Fedora based on nwchem.spec
+
+* Sat Feb 4 2012 Marcin Dulak <Marcin.Dulak at gmail.com> 6.1-1
+- USE_NOFSCHECK set to True
+- src/data/* installed under %%{prefix}/share/%%{prgname}/data
+- contrib/python/Gnuplot.py excluded
+- scalapack build on Fedora (for some reason libscalapack.a not found on build.opensuse.org)
+- {doc,web} directories not in source anymore
+
+* Wed Dec 21 2011 Marcin Dulak <Marcin.Dulak at gmail.com> 6.1.pre6-1
+- allow pre releases to be built
+- fixed ga-5-0 configure problems on EL5 and openSUSE 11.3-12.1
+
+* Mon Oct 31 2011 Marcin Dulak <Marcin.Dulak at gmail.com> 6.0-1
+- initial version
diff --git a/sources b/sources
index e69de29..6a9c94f 100644
--- a/sources
+++ b/sources
@@ -0,0 +1 @@
+f961c1e5ee46fbc8718cf7b1b59bafa9 Nwchem-6.3.revision2-src.2013-10-17.tar.gz
More information about the scm-commits
mailing list