From ef7ebd0f7e7679002cb1be33430ce5a768902413 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Fri, 21 Sep 2018 17:40:21 +0200
Subject: [PATCH] Updated patch to GMX 2018.3
---
...cs-2018.1.config => gromacs-2018.3.config} | 0
.../src/gromacs/CMakeLists.txt | 20 ++---
.../src/gromacs/CMakeLists.txt.preplumed | 20 ++---
.../src/gromacs/mdlib/force.cpp | 0
.../src/gromacs/mdlib/force.cpp.preplumed | 0
.../src/gromacs/mdlib/minimize.cpp | 73 ++++++++++++++-----
.../src/gromacs/mdlib/minimize.cpp.preplumed | 73 ++++++++++++++-----
.../src/programs/mdrun/md.cpp | 0
.../src/programs/mdrun/md.cpp.preplumed | 0
.../src/programs/mdrun/mdrun.cpp | 0
.../src/programs/mdrun/mdrun.cpp.preplumed | 0
.../src/programs/mdrun/repl_ex.cpp | 0
.../src/programs/mdrun/repl_ex.cpp.preplumed | 0
.../src/programs/mdrun/repl_ex.h | 0
.../src/programs/mdrun/repl_ex.h.preplumed | 0
.../src/programs/mdrun/runner.cpp | 2 +-
.../src/programs/mdrun/runner.cpp.preplumed | 2 +-
.../src/programs/mdrun/runner.h | 0
.../src/programs/mdrun/runner.h.preplumed | 0
19 files changed, 132 insertions(+), 58 deletions(-)
rename patches/{gromacs-2018.1.config => gromacs-2018.3.config} (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/gromacs/CMakeLists.txt (92%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/gromacs/CMakeLists.txt.preplumed (92%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/gromacs/mdlib/force.cpp (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/gromacs/mdlib/force.cpp.preplumed (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/gromacs/mdlib/minimize.cpp (97%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/gromacs/mdlib/minimize.cpp.preplumed (97%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/md.cpp (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/md.cpp.preplumed (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/mdrun.cpp (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/mdrun.cpp.preplumed (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/repl_ex.cpp (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/repl_ex.cpp.preplumed (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/repl_ex.h (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/repl_ex.h.preplumed (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/runner.cpp (99%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/runner.cpp.preplumed (99%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/runner.h (100%)
rename patches/{gromacs-2018.1.diff => gromacs-2018.3.diff}/src/programs/mdrun/runner.h.preplumed (100%)
diff --git a/patches/gromacs-2018.1.config b/patches/gromacs-2018.3.config
similarity index 100%
rename from patches/gromacs-2018.1.config
rename to patches/gromacs-2018.3.config
diff --git a/patches/gromacs-2018.1.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-2018.3.diff/src/gromacs/CMakeLists.txt
similarity index 92%
rename from patches/gromacs-2018.1.diff/src/gromacs/CMakeLists.txt
rename to patches/gromacs-2018.3.diff/src/gromacs/CMakeLists.txt
index 41d5aa5a8..0e0d82c68 100644
--- a/patches/gromacs-2018.1.diff/src/gromacs/CMakeLists.txt
+++ b/patches/gromacs-2018.3.diff/src/gromacs/CMakeLists.txt
@@ -1,7 +1,7 @@
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
@@ -63,7 +63,7 @@ function (gmx_install_headers)
if (NOT GMX_BUILD_MDRUN_ONLY)
file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
install(FILES ${ARGN}
- DESTINATION "${INCL_INSTALL_DIR}/${_dest}"
+ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/${_dest}"
COMPONENT development)
endif()
_gmx_add_files_to_property(GMX_INSTALLED_HEADERS ${ARGN})
@@ -194,8 +194,10 @@ if (HAS_NO_UNUSED)
endif()
set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
-if(SIMD_AVX_512_CXX_SUPPORTED)
- # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file
+if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
+ # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
+ # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
+ # with the SIMD_AVX_512_CXX_FLAGS flags.
set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
endif()
@@ -227,9 +229,9 @@ gmx_write_installed_header_list()
if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
install(TARGETS libgromacs
EXPORT libgromacs
- LIBRARY DESTINATION ${LIB_INSTALL_DIR}
- RUNTIME DESTINATION ${BIN_INSTALL_DIR}
- ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
COMPONENT libraries)
endif()
@@ -248,7 +250,7 @@ if (INSTALL_CUDART_LIB) #can be set manual by user
#install also name-links (linker uses those)
file(GLOB CUDA_LIBS ${CUDA_LIB}*)
install(FILES ${CUDA_LIBS} DESTINATION
- ${LIB_INSTALL_DIR} COMPONENT libraries)
+ ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
endif()
endforeach()
else()
@@ -260,7 +262,7 @@ if(GMX_USE_OPENCL)
set(OPENCL_KERNELS ${MDLIB_OPENCL_KERNELS})
install(FILES ${OPENCL_KERNELS} DESTINATION
- ${OCL_INSTALL_DIR} COMPONENT libraries)
+ ${GMX_INSTALL_OCLDIR} COMPONENT libraries)
endif()
if (BUILD_TESTING)
diff --git a/patches/gromacs-2018.1.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-2018.3.diff/src/gromacs/CMakeLists.txt.preplumed
similarity index 92%
rename from patches/gromacs-2018.1.diff/src/gromacs/CMakeLists.txt.preplumed
rename to patches/gromacs-2018.3.diff/src/gromacs/CMakeLists.txt.preplumed
index a88015302..2be059308 100644
--- a/patches/gromacs-2018.1.diff/src/gromacs/CMakeLists.txt.preplumed
+++ b/patches/gromacs-2018.3.diff/src/gromacs/CMakeLists.txt.preplumed
@@ -1,7 +1,7 @@
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
@@ -61,7 +61,7 @@ function (gmx_install_headers)
if (NOT GMX_BUILD_MDRUN_ONLY)
file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
install(FILES ${ARGN}
- DESTINATION "${INCL_INSTALL_DIR}/${_dest}"
+ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/${_dest}"
COMPONENT development)
endif()
_gmx_add_files_to_property(GMX_INSTALLED_HEADERS ${ARGN})
@@ -192,8 +192,10 @@ if (HAS_NO_UNUSED)
endif()
set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
-if(SIMD_AVX_512_CXX_SUPPORTED)
- # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file
+if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
+ # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
+ # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
+ # with the SIMD_AVX_512_CXX_FLAGS flags.
set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
endif()
@@ -224,9 +226,9 @@ gmx_write_installed_header_list()
if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
install(TARGETS libgromacs
EXPORT libgromacs
- LIBRARY DESTINATION ${LIB_INSTALL_DIR}
- RUNTIME DESTINATION ${BIN_INSTALL_DIR}
- ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
COMPONENT libraries)
endif()
@@ -245,7 +247,7 @@ if (INSTALL_CUDART_LIB) #can be set manual by user
#install also name-links (linker uses those)
file(GLOB CUDA_LIBS ${CUDA_LIB}*)
install(FILES ${CUDA_LIBS} DESTINATION
- ${LIB_INSTALL_DIR} COMPONENT libraries)
+ ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
endif()
endforeach()
else()
@@ -257,7 +259,7 @@ if(GMX_USE_OPENCL)
set(OPENCL_KERNELS ${MDLIB_OPENCL_KERNELS})
install(FILES ${OPENCL_KERNELS} DESTINATION
- ${OCL_INSTALL_DIR} COMPONENT libraries)
+ ${GMX_INSTALL_OCLDIR} COMPONENT libraries)
endif()
if (BUILD_TESTING)
diff --git a/patches/gromacs-2018.1.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-2018.3.diff/src/gromacs/mdlib/force.cpp
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/gromacs/mdlib/force.cpp
rename to patches/gromacs-2018.3.diff/src/gromacs/mdlib/force.cpp
diff --git a/patches/gromacs-2018.1.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-2018.3.diff/src/gromacs/mdlib/force.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/gromacs/mdlib/force.cpp.preplumed
rename to patches/gromacs-2018.3.diff/src/gromacs/mdlib/force.cpp.preplumed
diff --git a/patches/gromacs-2018.1.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-2018.3.diff/src/gromacs/mdlib/minimize.cpp
similarity index 97%
rename from patches/gromacs-2018.1.diff/src/gromacs/mdlib/minimize.cpp
rename to patches/gromacs-2018.3.diff/src/gromacs/mdlib/minimize.cpp
index 8fcef5673..a268949cb 100644
--- a/patches/gromacs-2018.1.diff/src/gromacs/mdlib/minimize.cpp
+++ b/patches/gromacs-2018.3.diff/src/gromacs/mdlib/minimize.cpp
@@ -3,7 +3,7 @@
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
@@ -577,27 +577,36 @@ static void write_em_traj(FILE *fplog, t_commrec *cr,
&state->s, state_global, observablesHistory,
state->f);
- if (confout != nullptr && MASTER(cr))
+ if (confout != nullptr)
{
- GMX_RELEASE_ASSERT(bX, "The code below assumes that (with domain decomposition), x is collected to state_global in the call above.");
- /* With domain decomposition the call above collected the state->s.x
- * into state_global->x. Without DD we copy the local state pointer.
- */
- if (!DOMAINDECOMP(cr))
+ if (DOMAINDECOMP(cr))
+ {
+ /* If bX=true, x was collected to state_global in the call above */
+ if (!bX)
+ {
+ gmx::ArrayRef<gmx::RVec> globalXRef = MASTER(cr) ? gmx::makeArrayRef(state_global->x) : gmx::EmptyArrayRef();
+ dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
+ }
+ }
+ else
{
+ /* Copy the local state pointer */
state_global = &state->s;
}
- if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
+ if (MASTER(cr))
{
- /* Make molecules whole only for confout writing */
- do_pbc_mtop(fplog, ir->ePBC, state->s.box, top_global,
- as_rvec_array(state_global->x.data()));
- }
+ if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
+ {
+ /* Make molecules whole only for confout writing */
+ do_pbc_mtop(fplog, ir->ePBC, state->s.box, top_global,
+ as_rvec_array(state_global->x.data()));
+ }
- write_sto_conf_mtop(confout,
- *top_global->name, top_global,
- as_rvec_array(state_global->x.data()), nullptr, ir->ePBC, state->s.box);
+ write_sto_conf_mtop(confout,
+ *top_global->name, top_global,
+ as_rvec_array(state_global->x.data()), nullptr, ir->ePBC, state->s.box);
+ }
}
}
@@ -724,6 +733,17 @@ static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
nullptr, nullptr, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
+ if (cr->nnodes > 1)
+ {
+ /* This global reduction will affect performance at high
+ * parallelization, but we can not really avoid it.
+ * But usually EM is not run at high parallelization.
+ */
+ int reductionBuffer = !validStep;
+ gmx_sumi(1, &reductionBuffer, cr);
+ validStep = (reductionBuffer == 0);
+ }
+
// We should move this check to the different minimizers
if (!validStep && ir->eI != eiSteep)
{
@@ -1106,8 +1126,20 @@ double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
step = 0;
- // Ensure the extra per-atom state array gets allocated
- state_global->flags |= (1<<estCGP);
+ if (MASTER(cr))
+ {
+ // In CG, the state is extended with a search direction
+ state_global->flags |= (1<<estCGP);
+
+ // Ensure the extra per-atom state array gets allocated
+ state_change_natoms(state_global, state_global->natoms);
+
+ // Initialize the search direction to zero
+ for (RVec &cg_p : state_global->cg_p)
+ {
+ cg_p = { 0, 0, 0 };
+ }
+ }
/* Create 4 states on the stack and extract pointers that we will swap */
em_state_t s0 {}, s1 {}, s2 {}, s3 {};
@@ -1270,7 +1302,7 @@ double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
gmx_sumd(1, &minstep, cr);
}
- minstep = GMX_REAL_EPS/sqrt(minstep/(3*state_global->natoms));
+ minstep = GMX_REAL_EPS/sqrt(minstep/(3*top_global->natoms));
if (stepsize < minstep)
{
@@ -1603,7 +1635,7 @@ double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
}
/* Send energies and positions to the IMD client if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle) && MASTER(cr))
+ if (MASTER(cr) && do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle))
{
IMD_send_positions(inputrec->imd);
}
@@ -1665,6 +1697,9 @@ double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
* However, we should only do it if we did NOT already write this step
* above (which we did if do_x or do_f was true).
*/
+ /* Note that with 0 < nstfout != nstxout we can end up with two frames
+ * in the trajectory with the same step number.
+ */
do_x = !do_per_step(step, inputrec->nstxout);
do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout));
diff --git a/patches/gromacs-2018.1.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-2018.3.diff/src/gromacs/mdlib/minimize.cpp.preplumed
similarity index 97%
rename from patches/gromacs-2018.1.diff/src/gromacs/mdlib/minimize.cpp.preplumed
rename to patches/gromacs-2018.3.diff/src/gromacs/mdlib/minimize.cpp.preplumed
index a27575016..d06da48c4 100644
--- a/patches/gromacs-2018.1.diff/src/gromacs/mdlib/minimize.cpp.preplumed
+++ b/patches/gromacs-2018.3.diff/src/gromacs/mdlib/minimize.cpp.preplumed
@@ -3,7 +3,7 @@
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
@@ -533,27 +533,36 @@ static void write_em_traj(FILE *fplog, t_commrec *cr,
&state->s, state_global, observablesHistory,
state->f);
- if (confout != nullptr && MASTER(cr))
+ if (confout != nullptr)
{
- GMX_RELEASE_ASSERT(bX, "The code below assumes that (with domain decomposition), x is collected to state_global in the call above.");
- /* With domain decomposition the call above collected the state->s.x
- * into state_global->x. Without DD we copy the local state pointer.
- */
- if (!DOMAINDECOMP(cr))
+ if (DOMAINDECOMP(cr))
+ {
+ /* If bX=true, x was collected to state_global in the call above */
+ if (!bX)
+ {
+ gmx::ArrayRef<gmx::RVec> globalXRef = MASTER(cr) ? gmx::makeArrayRef(state_global->x) : gmx::EmptyArrayRef();
+ dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
+ }
+ }
+ else
{
+ /* Copy the local state pointer */
state_global = &state->s;
}
- if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
+ if (MASTER(cr))
{
- /* Make molecules whole only for confout writing */
- do_pbc_mtop(fplog, ir->ePBC, state->s.box, top_global,
- as_rvec_array(state_global->x.data()));
- }
+ if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
+ {
+ /* Make molecules whole only for confout writing */
+ do_pbc_mtop(fplog, ir->ePBC, state->s.box, top_global,
+ as_rvec_array(state_global->x.data()));
+ }
- write_sto_conf_mtop(confout,
- *top_global->name, top_global,
- as_rvec_array(state_global->x.data()), nullptr, ir->ePBC, state->s.box);
+ write_sto_conf_mtop(confout,
+ *top_global->name, top_global,
+ as_rvec_array(state_global->x.data()), nullptr, ir->ePBC, state->s.box);
+ }
}
}
@@ -680,6 +689,17 @@ static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
nullptr, nullptr, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
+ if (cr->nnodes > 1)
+ {
+ /* This global reduction will affect performance at high
+ * parallelization, but we can not really avoid it.
+ * But usually EM is not run at high parallelization.
+ */
+ int reductionBuffer = !validStep;
+ gmx_sumi(1, &reductionBuffer, cr);
+ validStep = (reductionBuffer == 0);
+ }
+
// We should move this check to the different minimizers
if (!validStep && ir->eI != eiSteep)
{
@@ -1032,8 +1052,20 @@ double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
step = 0;
- // Ensure the extra per-atom state array gets allocated
- state_global->flags |= (1<<estCGP);
+ if (MASTER(cr))
+ {
+ // In CG, the state is extended with a search direction
+ state_global->flags |= (1<<estCGP);
+
+ // Ensure the extra per-atom state array gets allocated
+ state_change_natoms(state_global, state_global->natoms);
+
+ // Initialize the search direction to zero
+ for (RVec &cg_p : state_global->cg_p)
+ {
+ cg_p = { 0, 0, 0 };
+ }
+ }
/* Create 4 states on the stack and extract pointers that we will swap */
em_state_t s0 {}, s1 {}, s2 {}, s3 {};
@@ -1196,7 +1228,7 @@ double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
gmx_sumd(1, &minstep, cr);
}
- minstep = GMX_REAL_EPS/sqrt(minstep/(3*state_global->natoms));
+ minstep = GMX_REAL_EPS/sqrt(minstep/(3*top_global->natoms));
if (stepsize < minstep)
{
@@ -1529,7 +1561,7 @@ double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
}
/* Send energies and positions to the IMD client if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle) && MASTER(cr))
+ if (MASTER(cr) && do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle))
{
IMD_send_positions(inputrec->imd);
}
@@ -1591,6 +1623,9 @@ double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
* However, we should only do it if we did NOT already write this step
* above (which we did if do_x or do_f was true).
*/
+ /* Note that with 0 < nstfout != nstxout we can end up with two frames
+ * in the trajectory with the same step number.
+ */
do_x = !do_per_step(step, inputrec->nstxout);
do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout));
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2018.3.diff/src/programs/mdrun/md.cpp
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/md.cpp
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/md.cpp
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-2018.3.diff/src/programs/mdrun/md.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/md.cpp.preplumed
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/md.cpp.preplumed
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-2018.3.diff/src/programs/mdrun/mdrun.cpp
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/mdrun.cpp
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/mdrun.cpp
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-2018.3.diff/src/programs/mdrun/mdrun.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/mdrun.cpp.preplumed
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/mdrun.cpp.preplumed
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2018.3.diff/src/programs/mdrun/repl_ex.cpp
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/repl_ex.cpp
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/repl_ex.cpp
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/repl_ex.cpp.preplumed b/patches/gromacs-2018.3.diff/src/programs/mdrun/repl_ex.cpp.preplumed
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/repl_ex.cpp.preplumed
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/repl_ex.cpp.preplumed
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/repl_ex.h b/patches/gromacs-2018.3.diff/src/programs/mdrun/repl_ex.h
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/repl_ex.h
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/repl_ex.h
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/repl_ex.h.preplumed b/patches/gromacs-2018.3.diff/src/programs/mdrun/repl_ex.h.preplumed
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/repl_ex.h.preplumed
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/repl_ex.h.preplumed
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-2018.3.diff/src/programs/mdrun/runner.cpp
similarity index 99%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/runner.cpp
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/runner.cpp
index 983d71938..4dfff857a 100644
--- a/patches/gromacs-2018.1.diff/src/programs/mdrun/runner.cpp
+++ b/patches/gromacs-2018.3.diff/src/programs/mdrun/runner.cpp
@@ -572,7 +572,7 @@ int Mdrunner::mdrunner()
}
/* Check and update the hardware options for internal consistency */
- check_and_update_hw_opt_1(&hw_opt, cr, domdecOptions.numPmeRanks);
+ check_and_update_hw_opt_1(mdlog, &hw_opt, cr, domdecOptions.numPmeRanks);
/* Early check for externally set process affinity. */
gmx_check_thread_affinity_set(mdlog, cr,
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-2018.3.diff/src/programs/mdrun/runner.cpp.preplumed
similarity index 99%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/runner.cpp.preplumed
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/runner.cpp.preplumed
index ea058f65c..917ada568 100644
--- a/patches/gromacs-2018.1.diff/src/programs/mdrun/runner.cpp.preplumed
+++ b/patches/gromacs-2018.3.diff/src/programs/mdrun/runner.cpp.preplumed
@@ -566,7 +566,7 @@ int Mdrunner::mdrunner()
}
/* Check and update the hardware options for internal consistency */
- check_and_update_hw_opt_1(&hw_opt, cr, domdecOptions.numPmeRanks);
+ check_and_update_hw_opt_1(mdlog, &hw_opt, cr, domdecOptions.numPmeRanks);
/* Early check for externally set process affinity. */
gmx_check_thread_affinity_set(mdlog, cr,
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/runner.h b/patches/gromacs-2018.3.diff/src/programs/mdrun/runner.h
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/runner.h
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/runner.h
diff --git a/patches/gromacs-2018.1.diff/src/programs/mdrun/runner.h.preplumed b/patches/gromacs-2018.3.diff/src/programs/mdrun/runner.h.preplumed
similarity index 100%
rename from patches/gromacs-2018.1.diff/src/programs/mdrun/runner.h.preplumed
rename to patches/gromacs-2018.3.diff/src/programs/mdrun/runner.h.preplumed
--
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