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 gromacs (5.0.1-1) unstable; urgency=medium
* New upstream release. * New upstream release.
......
...@@ -4,7 +4,7 @@ Priority: extra ...@@ -4,7 +4,7 @@ Priority: extra
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org> Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Nicholas Breen <nbreen@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 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/ Homepage: http://www.gromacs.org/
Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/ Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/
Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/gromacs/ Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/gromacs/
......
This diff is collapsed.
...@@ -3,10 +3,10 @@ Origin: vendor ...@@ -3,10 +3,10 @@ Origin: vendor
Last-Update: 2014-06-12 Last-Update: 2014-06-12
--- ---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ 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-5.0.2.orig/src/contrib/mkice.c
+++ gromacs-5.0.1/src/contrib/mkice.c +++ gromacs-5.0.2/src/contrib/mkice.c
@@ -494,7 +494,7 @@ int main(int argc,char *argv[]) @@ -494,7 +494,7 @@ int main(int argc,char *argv[])
"If an input file is given it is interpreted as a series of oxygen", "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.", "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 ...@@ -16,11 +16,11 @@ Index: gromacs-5.0.1/src/contrib/mkice.c
"build water clusters based on oxygen coordinates only." "build water clusters based on oxygen coordinates only."
}; };
static int nx=1,ny=1,nz=1; 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-5.0.2.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 +++ gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -200,7 +200,7 @@ void @@ -201,7 +201,7 @@ void
{{ {{
if (ic->ljpme_comb_rule == eljpmeLB) if (ic->ljpme_comb_rule == eljpmeLB)
{{ {{
...@@ -29,11 +29,11 @@ Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator ...@@ -29,11 +29,11 @@ Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator
}} }}
vdwkt = vdwktLJEWALDCOMBGEOM; 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-5.0.2.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 +++ gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -335,7 +335,7 @@ nbnxn_kernel_simd_2xnn(nbnxn_pairlist_se @@ -336,7 +336,7 @@ nbnxn_kernel_simd_2xnn(nbnxn_pairlist_se
{ {
if (ic->ljpme_comb_rule == eljpmeLB) 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 ...@@ -42,11 +42,11 @@ Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd
} }
vdwkt = vdwktLJEWALDCOMBGEOM; 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-5.0.2.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 +++ gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -334,7 +334,7 @@ nbnxn_kernel_simd_4xn(nbnxn_pairlist_set @@ -335,7 +335,7 @@ nbnxn_kernel_simd_4xn(nbnxn_pairlist_set
{ {
if (ic->ljpme_comb_rule == eljpmeLB) 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_ ...@@ -55,10 +55,10 @@ Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_
} }
vdwkt = vdwktLJEWALDCOMBGEOM; 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-5.0.2.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0.1/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[]) @@ -386,8 +386,8 @@ int gmx_mdrun(int argc, char *argv[])
"the [TT]mdrun[tt] process that is the parent of the others.", "the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]", "[PAR]",
...@@ -70,10 +70,10 @@ Index: gromacs-5.0.1/src/programs/mdrun/mdrun.cpp ...@@ -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", "[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
"IMD remote can be turned on by [TT]-imdpull[tt].", "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", "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-5.0.2.orig/docs/man/man1/gmx-mdrun.1
+++ gromacs-5.0.1/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 @@ -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. 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 ...@@ -51,11 +51,14 @@ endif
endif endif
# Include "gpu" in DEB_BUILD_OPTIONS to build GPU-accelerated binaries as well. # 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. # This build option is not always well tested, please send comments.
# You must have OpenMM development headers (not packaged) and "nvidia-cuda-dev" # You must have the pacakges "nvidia-cuda-toolkit" and "nvidia-cuda-dev"
# installed! # 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))) ifneq (,$(findstring gpu,$(DEB_BUILD_OPTIONS)))
COMMON_CONFIG_PARAMS += -DGMX_GPU=ON GPU_CONFIG_PARAMS += -DGMX_GPU=ON
endif endif
MPICH_CONFIG_PARAMS = \ MPICH_CONFIG_PARAMS = \
...@@ -80,15 +83,15 @@ endif ...@@ -80,15 +83,15 @@ endif
configure: configure-stamp configure: configure-stamp
configure-stamp: configure-stamp:
dh_testdir 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/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 \ (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 \ (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") $(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))) 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 \ (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 \ (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") $(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
endif endif
......
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