Commit 612d3aec authored by Nicholas Breen's avatar Nicholas Breen

Preliminary work for 5.1:

  * New upstream release.  This release completes the transition to "gmx"
    as the sole binary to replace all the former g_* commands, and the
    compatibility symlinks have been removed.
  * Some package reshuffling: gromacs-dev becomes libgromacs-dev, and the
    shared library gets split out into libgromacs0.  (Closes: #797744)
  * Remove gromacs-dev.preinst, only needed for upgrades from well before
    the version in squeeze.
parent b780feda
gromacs (5.1-1) UNRELEASED; urgency=medium
* New upstream release. This release completes the transition to "gmx"
as the sole binary to replace all the former g_* commands, and the
compatibility symlinks have been removed.
* Some package reshuffling: gromacs-dev becomes libgromacs-dev, and the
shared library gets split out into libgromacs0. (Closes: #797744)
* Remove gromacs-dev.preinst, only needed for upgrades from well before
the version in squeeze.
-- Nicholas Breen <nbreen@debian.org> Sat, 26 Sep 2015 15:07:40 -0700
gromacs (5.0.6-1) unstable; urgency=medium
* New upstream release.
......
......@@ -47,12 +47,31 @@ Description: GROMACS molecular dynamics sim, data and documentation
This package contains architecture-independent topology and force field
data, documentation, man pages, and example files.
Package: gromacs-dev
Package: libgromacs0
Architecture: any
Section: libs
Breaks: gromacs (<< 5.1-1~)
Description:
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
the Newtonian equations of motion for systems with hundreds to millions of
particles.
.
It is primarily designed for biochemical molecules like proteins and lipids
that have a lot of complicated bonded interactions, but since GROMACS is
extremely fast at calculating the nonbonded interactions (that usually
dominate simulations) many groups are also using it for research on non-
biological systems, e.g. polymers.
.
This package contains the shared library, libgromacs.
Package: libgromacs-dev
Architecture: any
Section: devel
Depends: ${shlibs:Depends}, gromacs (= ${binary:Version}), fftw3-dev, ${misc:Depends}
Depends: ${shlibs:Depends}, libgromacs0 (= ${binary:Version}), fftw3-dev, ${misc:Depends}
Recommends: gromacs-data
Suggests: gromacs-mpich (= ${binary:Version}) | gromacs-openmpi (= ${binary:Version}) [alpha amd64 arm64 armel armhf hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el sparc sparc64], libmpich-dev, libx11-dev, zlib1g-dev
Replaces: gromacs-dev (<< 5.1-1~)
Breaks: gromacs-dev (<< 5.1-1~)
Description: GROMACS molecular dynamics sim, development kit
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
the Newtonian equations of motion for systems with hundreds to millions of
......@@ -68,6 +87,13 @@ Description: GROMACS molecular dynamics sim, development kit
purposes, plus sample Makefiles. Development components for MPI-enabled
GROMACS builds also require their respective packages.
Package: gromacs-dev
Architecture: any
Section: metapackages
Depends: libgromacs-dev
This is a metapackage to bring in the replacement package libgromacs-dev.
It can safely be removed after that installation.
Package: gromacs-mpich
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, mpich
......
#!/bin/sh
# preinst script for gromacs-dev
#
# see: dh_installdeb(1)
set -e
# summary of how this script can be called:
# * <new-preinst> `install'
# * <new-preinst> `install' <old-version>
# * <new-preinst> `upgrade' <old-version>
# * <old-preinst> `abort-upgrade' <new-version>
# for details, see http://www.debian.org/doc/debian-policy/ or
# the debian-policy package
case "$1" in
upgrade)
# versions prior to 3.3.3~pre1-1 shipped /usr/share/doc/gromacs-dev as a
# symlink; this must be removed before installing newer versions that
# ship it as a directory instead.
if [ -L /usr/share/doc/gromacs-dev ] ; then
rm -f /usr/share/doc/gromacs-dev
fi
;;
install|abort-upgrade)
;;
*)
echo "preinst called with unknown argument \`$1'" >&2
exit 1
;;
esac
# dh_installdeb will replace this with shell code automatically
# generated by other debhelper scripts.
#DEBHELPER#
exit 0
......@@ -4,22 +4,23 @@ Description: Install only a single copyright file
Author: Nicholas Breen
Origin: vendor
Forwarded: not-needed
Last-Update: 2013-05-15
Last-Update: 2015-09-26
---
Index: gromacs-5.0.6/CMakeLists.txt
Index: gromacs-5.1/CMakeLists.txt
===================================================================
--- gromacs-5.0.6.orig/CMakeLists.txt
+++ gromacs-5.0.6/CMakeLists.txt
@@ -144,7 +144,7 @@ set(CPACK_PACKAGE_VENDOR "gromacs.org")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
# Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
-set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
--- gromacs-5.1.orig/CMakeLists.txt
+++ gromacs-5.1/CMakeLists.txt
@@ -89,6 +89,9 @@ set(build_types_with_explicit_flags RELE
set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
+# Debian specific, see debian/patches/copyright-file.patch
+set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/debian/copyright")
set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
@@ -921,7 +921,7 @@ endif()
+
# Set a default valgrind suppression file.
# This unfortunately needs to duplicate information from CTest to work as
# expected...
@@ -844,7 +847,7 @@ endif()
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
......@@ -27,4 +28,4 @@ Index: gromacs-5.0.6/CMakeLists.txt
+install(FILES DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
if(GMX_EXTERNAL_BOOST)
include_directories(${Boost_INCLUDE_DIRS})
include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
This diff is collapsed.
readme.patch
copyright-file.patch
manpage_hyphenation.patch
# manpage_hyphenation.patch
spelling.patch
......@@ -3,11 +3,11 @@ Origin: vendor
Last-Update: 2014-06-12
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-5.0.6/src/contrib/mkice.c
Index: gromacs-5.1/src/contrib/mkice.c
===================================================================
--- gromacs-5.0.6.orig/src/contrib/mkice.c
+++ gromacs-5.0.6/src/contrib/mkice.c
@@ -494,7 +494,7 @@ int main(int argc,char *argv[])
--- gromacs-5.1.orig/src/contrib/mkice.c
+++ gromacs-5.1/src/contrib/mkice.c
@@ -493,7 +493,7 @@ 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.",
"The program then adds hydrogens to the oxygens in random orientation",
......@@ -16,11 +16,11 @@ Index: gromacs-5.0.6/src/contrib/mkice.c
"build water clusters based on oxygen coordinates only."
};
static int nx=1,ny=1,nz=1;
Index: gromacs-5.0.6/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
Index: gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
===================================================================
--- gromacs-5.0.6.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.0.6/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -201,7 +201,7 @@ void
--- gromacs-5.1.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -202,7 +202,7 @@ void
{{
if (ic->ljpme_comb_rule == eljpmeLB)
{{
......@@ -29,11 +29,11 @@ Index: gromacs-5.0.6/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator
}}
vdwkt = vdwktLJEWALDCOMBGEOM;
}}
Index: gromacs-5.0.6/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
Index: gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
===================================================================
--- gromacs-5.0.6.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.0.6/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -336,7 +336,7 @@ nbnxn_kernel_simd_2xnn(nbnxn_pairlist_se
--- gromacs-5.1.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -338,7 +338,7 @@ nbnxn_kernel_simd_2xnn(nbnxn_pairlist_se
{
if (ic->ljpme_comb_rule == eljpmeLB)
{
......@@ -42,11 +42,11 @@ Index: gromacs-5.0.6/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0.6/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
Index: gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
===================================================================
--- gromacs-5.0.6.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.0.6/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -335,7 +335,7 @@ nbnxn_kernel_simd_4xn(nbnxn_pairlist_set
--- gromacs-5.1.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -337,7 +337,7 @@ nbnxn_kernel_simd_4xn(nbnxn_pairlist_set
{
if (ic->ljpme_comb_rule == eljpmeLB)
{
......@@ -55,11 +55,11 @@ Index: gromacs-5.0.6/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0.6/src/programs/mdrun/mdrun.cpp
Index: gromacs-5.1/src/programs/mdrun/mdrun.cpp
===================================================================
--- gromacs-5.0.6.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0.6/src/programs/mdrun/mdrun.cpp
@@ -386,8 +386,8 @@ int gmx_mdrun(int argc, char *argv[])
--- gromacs-5.1.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.1/src/programs/mdrun/mdrun.cpp
@@ -214,8 +214,8 @@ int gmx_mdrun(int argc, char *argv[])
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"Interactive molecular dynamics (IMD) can be activated by using at least one",
......@@ -70,24 +70,11 @@ Index: gromacs-5.0.6/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-5.0.6/docs/man/man1/gmx-mdrun.1
Index: gromacs-5.1/src/gromacs/gmxana/gmx_wham.cpp
===================================================================
--- gromacs-5.0.6.orig/docs/man/man1/gmx-mdrun.1
+++ gromacs-5.0.6/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.
-Interactive molecular dynamics (IMD) can be activated by using at least one of the three IMD switches: The \fB\-imdterm\fR switch allows to terminate the simulation from the molecular viewer (e.g. VMD). With \fB\-imdwait\fR, \fBmdrun\fR pauses whenever no IMD client is connected. Pulling from the IMD remote can be turned on by \fB\-imdpull\fR. The port \fBmdrun\fR listens to can be altered by \fB\-imdport\fR.The file pointed to by \fB\-if\fR contains atom indices and forces if IMD pulling is used.
+Interactive molecular dynamics (IMD) can be activated by using at least one of the three IMD switches: The \fB\-imdterm\fR switch allows one to terminate the simulation from the molecular viewer (e.g. VMD). With \fB\-imdwait\fR, \fBmdrun\fR pauses whenever no IMD client is connected. Pulling from the IMD remote can be turned on by \fB\-imdpull\fR. The port \fBmdrun\fR listens to can be altered by \fB\-imdport\fR.The file pointed to by \fB\-if\fR contains atom indices and forces if IMD pulling is used.
When \fBmdrun\fR is started with MPI, it does not run niced by default.
Index: gromacs-5.0.6/src/gromacs/gmxana/gmx_wham.cpp
===================================================================
--- gromacs-5.0.6.orig/src/gromacs/gmxana/gmx_wham.cpp
+++ gromacs-5.0.6/src/gromacs/gmxana/gmx_wham.cpp
@@ -3306,7 +3306,7 @@ int gmx_wham(int argc, char *argv[])
--- gromacs-5.1.orig/src/gromacs/gmxana/gmx_wham.cpp
+++ gromacs-5.1/src/gromacs/gmxana/gmx_wham.cpp
@@ -3427,7 +3427,7 @@ int gmx_wham(int argc, char *argv[])
{ "-ac-trestart", FALSE, etREAL, {&opt.acTrestart},
"When computing autocorrelation functions, restart computing every .. (ps)"},
{ "-acred", FALSE, etBOOL, {&opt.bAllowReduceIact},
......@@ -96,24 +83,3 @@ Index: gromacs-5.0.6/src/gromacs/gmxana/gmx_wham.cpp
"during smoothing"},
{ "-nBootstrap", FALSE, etINT, {&opt.nBootStrap},
"nr of bootstraps to estimate statistical uncertainty (e.g., 200)" },
Index: gromacs-5.0.6/docs/man/man1/gmx-dos.1
===================================================================
--- gromacs-5.0.6.orig/docs/man/man1/gmx-dos.1
+++ gromacs-5.0.6/docs/man/man1/gmx-dos.1
@@ -12,7 +12,15 @@ gmx dos [\-f [<.trr/.cpt/...>]] [\-s [<.
[\-beginfit <real>] [\-endfit <real>]
.SH DESCRIPTION
-\fBgmx dos\fR computes the Density of States from a simulations. In order for this to be meaningful the velocities must be saved in the trajecotry with sufficiently high frequency such as to cover all vibrations. For flexible systems that would be around a few fs between saving. Properties based on the DoS are printed on the standard output.Note that the density of states is calculated from the mass\-weighted autocorrelation, and by default only from the square of the real component rather than absolute value. This means the shape can differ substantially from the plain vibrational power spectrum you can calculate with gmx velacc.
+\fBgmx dos\fR computes the Density of States from a simulation. In order for
+this to be meaningful the velocities must be saved in the trajectory with
+sufficiently high frequency such as to cover all vibrations. For flexible
+systems, that would be around a few fs between saving. Properties based on the
+DoS are printed on the standard output. Note that the density of states is
+calculated from the mass\-weighted autocorrelation, and by default only from
+the square of the real component rather than absolute value. This means the
+shape can differ substantially from the plain vibrational power spectrum you
+can calculate with \fBgmx velacc\fR.
.SH OPTIONS
Options to specify input and output files:
......@@ -141,7 +141,7 @@ clean:
install: build install-basic install-mpich install-openmpi
dh_testdir
dh_testroot
dh_prep -pgromacs-data -pgromacs-dev
dh_prep -pgromacs-data -plibgromacs-dev
dh_installdirs -pgromacs-data
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/top \
......@@ -157,21 +157,24 @@ install: build install-basic install-mpich install-openmpi
$(CURDIR)/debian/gromacs-data/usr/share/gromacs/shell-specific
chmod 644 $(CURDIR)/debian/gromacs-data/usr/share/gromacs/shell-specific/*
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/gromacs-data/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/gromacs-dev/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs-dev/html
# this name is also give in documentation
dh_link -pgromacs-data usr/share/doc/gromacs-data/copyright usr/share/doc/gromacs-data/COPYING
# rename a pair of Perl scripts to drop the .pl extension (Policy 10.4)
mv $(CURDIR)/debian/gromacs/usr/bin/demux.pl $(CURDIR)/debian/gromacs/usr/bin/demux
mv $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx.pl $(CURDIR)/debian/gromacs/usr/bin/xplor2gmx
dh_installdirs -pgromacs-dev
mv $(CURDIR)/debian/gromacs/usr/include $(CURDIR)/debian/gromacs-dev/usr/include
mkdir -p $(CURDIR)/debian/libgromacs0/usr/lib/$(DEB_HOST_MULTIARCH)
dh_install -plibgromacs0
dh_installdirs -plibgromacs-dev
mv $(CURDIR)/debian/gromacs/usr/include $(CURDIR)/debian/libgromacs-dev/usr/include
# catch normal libraries plus all applicable MPI variants
mkdir -p $(CURDIR)/debian/gromacs-dev/usr/lib/$(DEB_HOST_MULTIARCH)
mkdir -p $(CURDIR)/debian/libgromacs-dev/usr/lib/$(DEB_HOST_MULTIARCH)
mv $(CURDIR)/debian/gromacs/usr/lib/$(DEB_HOST_MULTIARCH)/*.so \
$(CURDIR)/debian/gromacs/usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
$(CURDIR)/debian/gromacs-dev/usr/lib/$(DEB_HOST_MULTIARCH)/
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/template $(CURDIR)/debian/gromacs-dev/usr/share/gromacs/template
$(CURDIR)/debian/libgromacs-dev/usr/lib/$(DEB_HOST_MULTIARCH)/
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/template $(CURDIR)/debian/libgromacs-dev/usr/share/gromacs/template
# remaining documentation catch-all
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/* $(CURDIR)/debian/gromacs-data/usr/share/doc/gromacs
-rmdir $(CURDIR)/debian/gromacs/usr/share/gromacs
......
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