[gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/

[Christoph Junghans]

commit:     7bd36f7c9752fe04b58fdb1956bbcb3421711c22
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 12 20:49:33 2012 +0000
Commit:     Christoph Junghans <kleiner_otti <AT> gmx <DOT> de>
CommitDate: Sun Feb 12 20:49:33 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7bd36f7c

sci-chemistry/gromacs: clean up

(Portage version: 2.2.0_alpha86/git/Linux i686, unsigned Manifest commit)

---
 sci-chemistry/gromacs/ChangeLog               |    3 +
 sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |   52 +++---------------------
 2 files changed, 10 insertions(+), 45 deletions(-)

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index 77af425..c508a38 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   12 Feb 2012; Christoph Junghans <ottxor@g.o> gromacs-4.6.9999.ebuild:
+  sci-chemistry/gromacs: clean up
+
+  12 Feb 2012; Christoph Junghans <ottxor@g.o> gromacs-4.6.9999.ebuild:
   fixed threads and mpi
 
   05 Feb 2012; Christoph Junghans <ottxor@g.o> gromacs-4.6.9999.ebuild:

diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
index 0bd4bf3..9ecb639 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild
@@ -53,6 +53,10 @@ RDEPEND="${CDEPEND}
 
 RESTRICT="test"
 
+pkg_pretend() {
+	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+}
+
 pkg_setup() {
 	use fkernels && fortran-2_pkg_setup
 }
@@ -61,13 +65,6 @@ src_prepare() {
 	#add user patches from /etc/portage/patches/sci-chemistry/gromacs
 	epatch_user
 
-	if use mpi && use threads; then
-		elog "mdrun uses only threads OR mpi, and gromacs favours the"
-		elog "use of mpi over threads, so a mpi-version of mdrun will"
-		elog "be compiled. If you want to run mdrun on shared memory"
-		elog "machines only, you can safely disable mpi"
-	fi
-
 	GMX_DIRS=""
 	use single-precision && GMX_DIRS+=" float"
 	use double-precision && GMX_DIRS+=" double"
@@ -83,21 +80,6 @@ src_prepare() {
 
 src_configure() {
 	local mycmakeargs_pre=( )
-	#from gromacs configure
-	if use fftw; then
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftw3")
-	else
-		mycmakeargs_pre+=("-DGMX_FFT_LIBRARY=fftpack")
-		ewarn "WARNING: The built-in FFTPACK routines are slow."
-		ewarn "Are you sure you don\'t want to use FFTW?"
-		ewarn "It is free and much faster..."
-	fi
-
-	if [[ $(gcc-version) == "4.1" ]]; then
-		eerror "gcc 4.1 is not supported by gromacs"
-		eerror "please run test suite"
-		die
-	fi
 
 	#note for gentoo-PREFIX on apple: use --enable-apple-64bit
 
@@ -107,27 +89,6 @@ src_configure() {
 		ewarn "I hope, you know what are you doing..."
 	fi
 
-	if use double-precision ; then
-		#from gromacs manual
-		elog
-		elog "For most simulations single precision is accurate enough. In some"
-		elog "cases double precision is required to get reasonable results:"
-		elog
-		elog "-normal mode analysis, for the conjugate gradient or l-bfgs minimization"
-		elog " and the calculation and diagonalization of the Hessian "
-		elog "-calculation of the constraint force between two large groups of	atoms"
-		elog "-energy conservation: this can only be done without temperature coupling and"
-		elog " without cutoffs"
-		elog
-	fi
-
-	if use mpi ; then
-		elog "You have enabled mpi, only mdrun will make use of mpi, that is why"
-		elog "we configure/compile gromacs twice (with and without mpi) and only"
-		elog "install mdrun with mpi support. In addtion you will get libgmx and"
-		elog "libmd with and without mpi support."
-	fi
-
 	#go from slowest to fasterest acceleration
 	local acce="none"
 	use fkernels && acce="fortran"
@@ -136,11 +97,11 @@ src_configure() {
 	use sse2 && acce="sse"
 
 	mycmakeargs_pre+=(
+		-DGMX_FFT_LIBRARY=$(usex fftw fftw3 fftwpack)
 		$(cmake-utils_use X GMX_X11)
 		$(cmake-utils_use blas GMX_EXTERNAL_BLAS)
 		$(cmake-utils_use gsl GMX_GSL)
 		$(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
-		$(cmake-utils_use threads GMX_THREAD_MPI)
 		$(cmake-utils_use openmp GMX_OPENMP)
 		$(cmake-utils_use xml GMX_XML)
 		-DGMX_DEFAULT_SUFFIX=off
@@ -158,11 +119,12 @@ src_configure() {
 		local p
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
+			$(cmake-utils_use threads GMX_THREAD_MPI)
 			-DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
 		use mpi || continue
 		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=ON
+		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF -DGMX_MPI=ON
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" )
 		CMAKE_BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
 	done