Commit e67fad43 authored by Nicholas Breen's avatar Nicholas Breen

Rebasing for 5.0.1

parent 4c368a5c
Description: Remove architecture check from Random123 library
Random123 upstream has only tested the code on i386, amd64, and powerpc
architectures. It probably works on others, and disabling this check
allows us to run the unit tests to verify that.
Bug: http://redmine.gromacs.org/issues/1545
Last-Update: 2014-07-02
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-5.0/src/external/Random123-1.08/include/Random123/features/gccfeatures.h
===================================================================
--- gromacs-5.0.orig/src/external/Random123-1.08/include/Random123/features/gccfeatures.h
+++ gromacs-5.0/src/external/Random123-1.08/include/Random123/features/gccfeatures.h
@@ -34,15 +34,15 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE
#define R123_GNUC_VERSION (__GNUC__*10000 + __GNUC_MINOR__*100 + __GNUC_PATCHLEVEL__)
-#if !defined(__x86_64__) && !defined(__i386__) && !defined(__powerpc__)
+/* #if !defined(__x86_64__) && !defined(__i386__) && !defined(__powerpc__)
# error "This code has only been tested on x86 and powerpc platforms."
#include <including_a_nonexistent_file_will_stop_some_compilers_from_continuing_with_a_hopeless_task>
-{ /* maybe an unbalanced brace will terminate the compilation */
+{ */ /* maybe an unbalanced brace will terminate the compilation */
/* Feel free to try the Random123 library on other architectures by changing
the conditions that reach this error, but you should consider it a
porting exercise and expect to encounter bugs and deficiencies.
Please let the authors know of any successes (or failures). */
-#endif
+/* #endif */
#ifdef __powerpc__
#include <ppu_intrinsics.h>
......@@ -6,20 +6,20 @@ Origin: vendor
Forwarded: not-needed
Last-Update: 2013-05-15
---
Index: gromacs-5.0/CMakeLists.txt
Index: gromacs-5.0.1/CMakeLists.txt
===================================================================
--- gromacs-5.0.orig/CMakeLists.txt
+++ gromacs-5.0/CMakeLists.txt
@@ -138,7 +138,7 @@ set(CPACK_PACKAGE_VENDOR "gromacs.org")
--- gromacs-5.0.1.orig/CMakeLists.txt
+++ gromacs-5.0.1/CMakeLists.txt
@@ -141,7 +141,7 @@ 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")
+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$;\\\\.git/;\\\\.gitignore$")
set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
@@ -839,7 +839,7 @@ endif()
@@ -897,7 +897,7 @@ endif()
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
......
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -2,10 +2,10 @@ Description: Edit README to explain that this is not an official upstream build
Origin: vendor
Author: Nicholas Breen <nbreen@debian.org>
Index: gromacs-5.0/README
Index: gromacs-5.0.1/README
===================================================================
--- gromacs-5.0.orig/README
+++ gromacs-5.0/README
--- gromacs-5.0.1.orig/README
+++ gromacs-5.0.1/README
@@ -1,5 +1,5 @@
- Welcome to the official version of GROMACS!
......
11_readme.patch
12_copyright-file.patch
20_random123_platforms.patch
31_manpage_hyphenation.patch
32_spelling.patch
readme.patch
copyright-file.patch
manpage_hyphenation.patch
spelling.patch
......@@ -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/src/contrib/mkice.c
Index: gromacs-5.0.1/src/contrib/mkice.c
===================================================================
--- gromacs-5.0.orig/src/contrib/mkice.c
+++ gromacs-5.0/src/contrib/mkice.c
--- gromacs-5.0.1.orig/src/contrib/mkice.c
+++ gromacs-5.0.1/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.",
......@@ -16,10 +16,10 @@ Index: gromacs-5.0/src/contrib/mkice.c
"build water clusters based on oxygen coordinates only."
};
static int nx=1,ny=1,nz=1;
Index: gromacs-5.0/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
===================================================================
--- gromacs-5.0.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.0/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
{{
if (ic->ljpme_comb_rule == eljpmeLB)
......@@ -29,10 +29,10 @@ Index: gromacs-5.0/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/n
}}
vdwkt = vdwktLJEWALDCOMBGEOM;
}}
Index: gromacs-5.0/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
===================================================================
--- gromacs-5.0.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.0/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
{
if (ic->ljpme_comb_rule == eljpmeLB)
......@@ -42,10 +42,10 @@ Index: gromacs-5.0/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
Index: gromacs-5.0.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
===================================================================
--- gromacs-5.0.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.0/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
{
if (ic->ljpme_comb_rule == eljpmeLB)
......@@ -55,10 +55,10 @@ Index: gromacs-5.0/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4x
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0/src/programs/mdrun/mdrun.cpp
Index: gromacs-5.0.1/src/programs/mdrun/mdrun.cpp
===================================================================
--- gromacs-5.0.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0/src/programs/mdrun/mdrun.cpp
--- gromacs-5.0.1.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0.1/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/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/share/man/man1/gmx-mdrun.1
Index: gromacs-5.0.1/docs/man/man1/gmx-mdrun.1
===================================================================
--- gromacs-5.0.orig/share/man/man1/gmx-mdrun.1
+++ gromacs-5.0/share/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
@@ -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.
......
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