Commit 252e4b48 authored by Nicholas Breen's avatar Nicholas Breen

New upstream relese; update GPU rules

parent 4ec466ee
gromacs (5.0.2-1) unstable; urgency=medium
* New upstream release.
* Update Standards-Version to 3.9.6, no changes required.
* Update rules to build GPU-accelerated packages, with thanks to
Steffen Möller.
-- Nicholas Breen <nbreen@debian.org> Sun, 05 Oct 2014 10:29:34 -0700
gromacs (5.0.1-1) unstable; urgency=medium
* New upstream release.
......
......@@ -4,7 +4,7 @@ Priority: extra
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Nicholas Breen <nbreen@debian.org>
Build-Depends: debhelper (>= 7.0.0), libfftw3-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.2.4-5) [alpha amd64 arm64 armel armhf hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el sparc sparc64], libx11-dev, zlib1g-dev, libgsl0-dev, libxml2-dev, libblas-dev, liblapack-dev, libboost-dev, cmake
Standards-Version: 3.9.5
Standards-Version: 3.9.6
Homepage: http://www.gromacs.org/
Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/
Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/gromacs/
......
This diff is collapsed.
......@@ -3,10 +3,10 @@ Origin: vendor
Last-Update: 2014-06-12
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-5.0.1/src/contrib/mkice.c
Index: gromacs-5.0.2/src/contrib/mkice.c
===================================================================
--- gromacs-5.0.1.orig/src/contrib/mkice.c
+++ gromacs-5.0.1/src/contrib/mkice.c
--- gromacs-5.0.2.orig/src/contrib/mkice.c
+++ gromacs-5.0.2/src/contrib/mkice.c
@@ -494,7 +494,7 @@ int main(int argc,char *argv[])
"If an input file is given it is interpreted as a series of oxygen",
"coordinates the distance between which can be scaled by the odist flag.",
......@@ -16,11 +16,11 @@ Index: gromacs-5.0.1/src/contrib/mkice.c
"build water clusters based on oxygen coordinates only."
};
static int nx=1,ny=1,nz=1;
Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
Index: gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
===================================================================
--- gromacs-5.0.1.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -200,7 +200,7 @@ void
--- gromacs-5.0.2.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -201,7 +201,7 @@ void
{{
if (ic->ljpme_comb_rule == eljpmeLB)
{{
......@@ -29,11 +29,11 @@ Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator
}}
vdwkt = vdwktLJEWALDCOMBGEOM;
}}
Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
Index: gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
===================================================================
--- gromacs-5.0.1.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -335,7 +335,7 @@ nbnxn_kernel_simd_2xnn(nbnxn_pairlist_se
--- gromacs-5.0.2.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -336,7 +336,7 @@ nbnxn_kernel_simd_2xnn(nbnxn_pairlist_se
{
if (ic->ljpme_comb_rule == eljpmeLB)
{
......@@ -42,11 +42,11 @@ Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
Index: gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
===================================================================
--- gromacs-5.0.1.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -334,7 +334,7 @@ nbnxn_kernel_simd_4xn(nbnxn_pairlist_set
--- gromacs-5.0.2.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -335,7 +335,7 @@ nbnxn_kernel_simd_4xn(nbnxn_pairlist_set
{
if (ic->ljpme_comb_rule == eljpmeLB)
{
......@@ -55,10 +55,10 @@ Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0.1/src/programs/mdrun/mdrun.cpp
Index: gromacs-5.0.2/src/programs/mdrun/mdrun.cpp
===================================================================
--- gromacs-5.0.1.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0.1/src/programs/mdrun/mdrun.cpp
--- gromacs-5.0.2.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0.2/src/programs/mdrun/mdrun.cpp
@@ -386,8 +386,8 @@ int gmx_mdrun(int argc, char *argv[])
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
......@@ -70,10 +70,10 @@ Index: gromacs-5.0.1/src/programs/mdrun/mdrun.cpp
"[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
"IMD remote can be turned on by [TT]-imdpull[tt].",
"The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
Index: gromacs-5.0.1/docs/man/man1/gmx-mdrun.1
Index: gromacs-5.0.2/docs/man/man1/gmx-mdrun.1
===================================================================
--- gromacs-5.0.1.orig/docs/man/man1/gmx-mdrun.1
+++ gromacs-5.0.1/docs/man/man1/gmx-mdrun.1
--- gromacs-5.0.2.orig/docs/man/man1/gmx-mdrun.1
+++ gromacs-5.0.2/docs/man/man1/gmx-mdrun.1
@@ -101,7 +101,7 @@ With option \fB\-maxh\fR a simulation is
When \fBmdrun\fR receives a TERM signal, it will set nsteps to the current step plus one. When \fBmdrun\fR receives an INT signal (e.g. when ctrl+C is pressed), it will stop after the next neighbor search step (with nstlist=0 at the next step). In both cases all the usual output will be written to file. When running with MPI, a signal to one of the \fBmdrun\fR ranks is sufficient, this signal should not be sent to mpirun or the \fBmdrun\fR process that is the parent of the others.
......
......@@ -51,11 +51,14 @@ endif
endif
# Include "gpu" in DEB_BUILD_OPTIONS to build GPU-accelerated binaries as well.
# See INSTALL-GPU. This build option is not tested, please send comments.
# You must have OpenMM development headers (not packaged) and "nvidia-cuda-dev"
# installed!
# This build option is not always well tested, please send comments.
# You must have the pacakges "nvidia-cuda-toolkit" and "nvidia-cuda-dev"
# installed. Those are not official build dependencies to keep the package in
# Debian main!
# Further details at http://www.gromacs.org/GPU_acceleration
GPU_CONFIG_PARAMS =
ifneq (,$(findstring gpu,$(DEB_BUILD_OPTIONS)))
COMMON_CONFIG_PARAMS += -DGMX_GPU=ON
GPU_CONFIG_PARAMS += -DGMX_GPU=ON
endif
MPICH_CONFIG_PARAMS = \
......@@ -80,15 +83,15 @@ endif
configure: configure-stamp
configure-stamp:
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake $(COMMON_CONFIG_PARAMS) -DGMX_MPI=OFF -DBUILD_SHARED_LIBS=TRUE)
(mkdir -p build/basic; cd build/basic; cmake $(COMMON_CONFIG_PARAMS) $(GPU_CONFIG_PARAMS) -DGMX_MPI=OFF -DBUILD_SHARED_LIBS=TRUE)
(mkdir -p build/basic-dp; cd build/basic-dp; cmake $(COMMON_CONFIG_PARAMS) -DGMX_MPI=OFF -DBUILD_SHARED_LIBS=TRUE -DGMX_DOUBLE=ON)
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpic++.mpich cmake \
$(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
$(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS) $(GPU_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpic++.mpich cmake \
$(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS) -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpic++.openmpi cmake \
$(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
$(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) $(GPU_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpic++.openmpi cmake \
$(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
endif
......
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