From 3f689ab1e88538a41e502b25315eecdb91fc4d5a Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Wed, 26 Jul 2017 11:16:06 -0400
Subject: [PATCH] PG-PuReMD: fix compilation issues with GCC.
---
PG-PuReMD/configure.ac | 6 +++---
PG-PuReMD/src/ffield.c | 38 ++++++++++++++++++------------------
PG-PuReMD/src/ffield.h | 2 +-
PG-PuReMD/src/forces.c | 2 +-
PG-PuReMD/src/parallelreax.c | 5 +++++
PG-PuReMD/src/reax_types.h | 3 ++-
6 files changed, 31 insertions(+), 25 deletions(-)
diff --git a/PG-PuReMD/configure.ac b/PG-PuReMD/configure.ac
index a9eba5fa..6e9f3fb5 100644
--- a/PG-PuReMD/configure.ac
+++ b/PG-PuReMD/configure.ac
@@ -68,10 +68,10 @@ CFLAGS="$CFLAGS"
AC_CHECK_DECL([OPEN_MPI], [mpi_vendor="OpenMPI"],
[], [#include "mpi.h"])
# MPICH v2
-AC_CHECK_DECL([MPICH2], [mpi_vendor="MPICH"],
+AC_CHECK_DECL([MPICH2], [mpi_vendor="MPICH2"],
[], [#include "mpi.h"])
# MPICH v3
-AC_CHECK_DECL([MPICH_VERSION], [mpi_vendor="MPICH"],
+AC_CHECK_DECL([MPICH_VERSION], [mpi_vendor="MPICH3"],
[], [#include "mpi.h"])
CC="$sav_CC"
CFLAGS="$sav_CFLAGS"
@@ -86,7 +86,7 @@ then
AC_MSG_NOTICE([OpenMPI found])
AC_MSG_NOTICE([MPI_CFLAGS=$MPI_CFLAGS])
AC_MSG_NOTICE([MPI_LIBS=$MPI_LIBS])
-elif test "$mpi_vendor" = "MPICH"
+elif test "$mpi_vendor" = "MPICH2" || test "$mpi_vendor" = "MPICH3"
then
# build MPI_CFLAGS
tmp=`$MPICC -compile-info | awk '{$1=""; print $0 }'`
diff --git a/PG-PuReMD/src/ffield.c b/PG-PuReMD/src/ffield.c
index d985339b..7252674c 100644
--- a/PG-PuReMD/src/ffield.c
+++ b/PG-PuReMD/src/ffield.c
@@ -30,7 +30,7 @@
#endif
-char Read_Force_Field( char *ffield_file, reax_interaction *reax,
+int Read_Force_Field( char *ffield_file, reax_interaction *reax,
control_params *control )
{
FILE *fp;
@@ -45,7 +45,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
/* open force field file */
if ( (fp = fopen( ffield_file, "r" ) ) == NULL )
{
- fprintf( stderr, "error opening the force filed file! terminating...\n" );
+ fprintf( stderr, "[ERROR] cannot open force filed file! terminating...\n" );
MPI_Abort( MPI_COMM_WORLD, FILE_NOT_FOUND );
}
@@ -68,7 +68,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
if ( n < 1 )
{
fprintf( stderr, "[WARNING] number of globals in ffield file is 0!\n" );
- return 1;
+ return SUCCESS;
}
reax->gp.n_global = n;
@@ -233,7 +233,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
{
if ( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3 )
{
- fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n"
+ fprintf( stderr, "[WARNING] inconsistent vdWaals-parameters\n"
"Force field parameters for element %s\n"
"indicate inner wall+shielding, but earlier\n"
"atoms indicate different vdWaals-method.\n"
@@ -255,12 +255,12 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
{
if ( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 2 )
{
- fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" );
- fprintf( stderr, "Force field parameters for element %s\n", reax->sbp[i].name );
- fprintf( stderr, "indicate inner wall without shielding, but earlier\n" );
- fprintf( stderr, "atoms indicate different vdWaals-method.\n" );
- fprintf( stderr, "This may cause division-by-zero errors.\n" );
- fprintf( stderr, "Keeping vdWaals-setting for earlier atoms.\n" );
+ fprintf( stderr, "[WARNING] inconsistent vdWaals-parameters\n" );
+ fprintf( stderr, " [INFO] Force field parameters for element %s\n", reax->sbp[i].name );
+ fprintf( stderr, " [INFO] indicate inner wall without shielding, but earlier\n" );
+ fprintf( stderr, " [INFO] atoms indicate different vdWaals-method.\n" );
+ fprintf( stderr, " [INFO] This may cause division-by-zero errors.\n" );
+ fprintf( stderr, " [INFO] Keeping vdWaals-setting for earlier atoms.\n" );
}
else
{
@@ -279,12 +279,12 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
if ( reax->sbp[i].gamma_w > 0.5 )
{
if ( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 1 )
- fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \
- "Force field parameters for element %s\n" \
- "indicate shielding without inner wall, but earlier\n" \
- "atoms indicate different vdWaals-method.\n" \
- "This may cause division-by-zero errors.\n" \
- "Keeping vdWaals-setting for earlier atoms.\n",
+ fprintf( stderr, "[WARNING] inconsistent vdWaals-parameters\n" \
+ " [INFO] Force field parameters for element %s\n" \
+ " [INFO] indicate shielding without inner wall, but earlier\n" \
+ " [INFO] atoms indicate different vdWaals-method.\n" \
+ " [INFO] This may cause division-by-zero errors.\n" \
+ " [INFO] Keeping vdWaals-setting for earlier atoms.\n",
reax->sbp[i].name );
else
{
@@ -297,8 +297,8 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
}
else
{
- fprintf( stderr, "Error: inconsistent vdWaals-parameters\n"\
- "No shielding or inner-wall set for element %s\n",
+ fprintf( stderr, "[ERROR] inconsistent vdWaals-parameters\n"\
+ " [INFO] No shielding or inner-wall set for element %s\n",
reax->sbp[i].name );
MPI_Abort( MPI_COMM_WORLD, INVALID_INPUT );
}
@@ -315,7 +315,7 @@ char Read_Force_Field( char *ffield_file, reax_interaction *reax,
if ( reax->sbp[i].mass < 21 &&
reax->sbp[i].valency_val != reax->sbp[i].valency_boc )
{
- fprintf( stderr, "Warning: changed valency_val to valency_boc for %s\n",
+ fprintf( stderr, "[WARNING] changed valency_val to valency_boc for atom type %s\n",
reax->sbp[i].name );
reax->sbp[i].valency_val = reax->sbp[i].valency_boc;
}
diff --git a/PG-PuReMD/src/ffield.h b/PG-PuReMD/src/ffield.h
index 313c3e67..5cca5e9d 100644
--- a/PG-PuReMD/src/ffield.h
+++ b/PG-PuReMD/src/ffield.h
@@ -29,7 +29,7 @@
extern "C" {
#endif
-char Read_Force_Field( char*, reax_interaction*, control_params* );
+int Read_Force_Field( char*, reax_interaction*, control_params* );
#ifdef __cplusplus
}
diff --git a/PG-PuReMD/src/forces.c b/PG-PuReMD/src/forces.c
index f210c3b4..d3e295cf 100644
--- a/PG-PuReMD/src/forces.c
+++ b/PG-PuReMD/src/forces.c
@@ -1655,7 +1655,7 @@ void Estimate_Storages( reax_system *system, control_params *control,
*Htop = (int)(MAX( *Htop * SAFE_ZONE, MIN_CAP * MIN_CM_ENTRIES ));
// Set max sparse entries, needed for first iteration of validate_list
- system->max_sparse_entries = *Htop * SAFE_ZONE;
+ system->total_cm_entries = *Htop * SAFE_ZONE;
for ( i = 0; i < system->n; ++i )
{
diff --git a/PG-PuReMD/src/parallelreax.c b/PG-PuReMD/src/parallelreax.c
index 304bb1f6..cc5f9d3d 100644
--- a/PG-PuReMD/src/parallelreax.c
+++ b/PG-PuReMD/src/parallelreax.c
@@ -42,9 +42,12 @@
#ifdef HAVE_CUDA
#include "cuda/cuda_copy.h"
#include "cuda/cuda_environment.h"
+ #include "cuda/cuda_forces.h"
+ #include "cuda/cuda_init_md.h"
#include "cuda/cuda_neighbors.h"
#include "cuda/cuda_post_evolve.h"
#include "cuda/cuda_reset_tools.h"
+ #include "cuda/cuda_system_props.h"
#include "cuda/cuda_utils.h"
#include "cuda/cuda_validation.h"
#endif
@@ -173,7 +176,9 @@ int main( int argc, char* argv[] )
mpi_datatypes *mpi_data;
int i, ret, retries;
real t_start = 0, t_elapsed;
+#if defined(DEBUG)
real t_begin, t_end;
+#endif
if ( argc != 4 )
{
diff --git a/PG-PuReMD/src/reax_types.h b/PG-PuReMD/src/reax_types.h
index d683df1c..c0bac402 100644
--- a/PG-PuReMD/src/reax_types.h
+++ b/PG-PuReMD/src/reax_types.h
@@ -198,11 +198,12 @@
#endif
/**************** RESOURCE CONSTANTS **********************/
+/* 20 MB */
+#define HOST_SCRATCH_SIZE (1024 * 1024 * 20)
#ifdef HAVE_CUDA
/* 20 MB */
#define DEVICE_SCRATCH_SIZE (1024 * 1024 * 20)
/* 20 MB */
-#define HOST_SCRATCH_SIZE (1024 * 1024 * 20)
#define RES_SCRATCH 0x90
/* BLOCK SIZES for kernels */
--
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