From f55f466128b805ebfd85fb839cfb901f497d3dbb Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Wed, 22 Feb 2017 16:52:42 -0600
Subject: [PATCH] Copied VMD cvs versions of imd.C and imd.h and cleaned up
unused variable causing compiler warnings
---
README | 5 +--
src/ComputeForce.cu | 10 +++---
src/GrandBrownTown.cu | 15 +++++----
src/imd.c | 74 ++++++++++++++++++++++++++++---------------
src/imd.h | 48 +++++++++++-----------------
5 files changed, 80 insertions(+), 72 deletions(-)
diff --git a/README b/README
index 935089f..3abef46 100644
--- a/README
+++ b/README
@@ -111,9 +111,6 @@ Terrance Howard
particles further than the pairlist distance move to within the
cutoff
-* Failed assertions deliver messages that don't describe where the
- failure occured
-
-- Bugs --
* An issue with memory management causes some invalid memory to be
@@ -124,6 +121,6 @@ Terrance Howard
* A large amount of GPU memory for pairlists is allocated statically,
which may cause out-of-memory crashes in older hardware
-* If the number of pairs in the sytem exceeds the length of the array
+* If the number of pairs in the system exceeds the length of the array
allocated for pairlists, the non-bonded kernel will try to access
forbidden regions of memory, causing a crash
diff --git a/src/ComputeForce.cu b/src/ComputeForce.cu
index 77b439a..54a6ca2 100644
--- a/src/ComputeForce.cu
+++ b/src/ComputeForce.cu
@@ -405,12 +405,10 @@ bool ComputeForce::addDihedralPotential(String fileName, int ind, Dihedral dihed
void ComputeForce::decompose() {
gpuErrchk( cudaProfilerStart() );
+
// Reset the cell decomposition.
- bool newDecomp = false;
if (decomp_d)
cudaFree(decomp_d);
- else
- newDecomp = true;
decomp.decompose_d(pos_d, num);
decomp_d = decomp.copyToCUDA();
@@ -426,15 +424,15 @@ void ComputeForce::decompose() {
// initializePairlistArrays
int nCells = decomp.nCells.x * decomp.nCells.y * decomp.nCells.z;
- int blocksPerCell = 10;
+ // int blocksPerCell = 10;
/* cuMemGetInfo(&free,&total); */
/* printf("Free memory: %zu / %zu\n", free, total); */
- const int NUMTHREADS = 128;
+ // const int NUMTHREADS = 128;
//const size_t nBlocks = (num * numReplicas) / NUM_THREADS + 1;
- const size_t nBlocks = nCells*blocksPerCell;
+ // const size_t nBlocks = nCells*blocksPerCell;
/* clearPairlists<<< 1, 32 >>>(pos, num, numReplicas, sys_d, decomp_d); */
/* gpuErrchk(cudaDeviceSynchronize()); */
diff --git a/src/GrandBrownTown.cu b/src/GrandBrownTown.cu
index eedfdc1..9584117 100644
--- a/src/GrandBrownTown.cu
+++ b/src/GrandBrownTown.cu
@@ -413,7 +413,7 @@ void GrandBrownTown::run() {
for (long int s = 1; s < steps; s++) {
// Compute the internal forces. Only calculate the energy when we are about to output.
bool get_energy = ((s % outputEnergyPeriod) == 0);
- float energy = 0.0f;
+ // float energy = 0.0f;
// Set the timer
wkf_timer_start(cputimer);
@@ -439,10 +439,11 @@ void GrandBrownTown::run() {
//MLog: added Bond* bondList to the list of passed in variables.
/*energy = internal->computeTabulated(forceInternal_d, pos_d, type_d, bonds_d, bondMap_d, excludes_d, excludeMap_d, angles_d, dihedrals_d, get_energy);*/
- energy = internal -> computeTabulated(get_energy);
+ // energy = internal -> computeTabulated(get_energy);
+ internal -> computeTabulated(get_energy);
break;
default: // [ N^2 ] interactions, no cutoff | decompositions
- energy = internal->computeTabulatedFull(get_energy);
+ internal->computeTabulatedFull(get_energy);
break;
}
@@ -458,19 +459,19 @@ void GrandBrownTown::run() {
internal->decompose();
RBC.updateParticleLists( internal->getPos_d() );
}
- energy = internal->compute(get_energy);
+ internal->compute(get_energy);
break;
case 1: // Do not use cutoff
- energy = internal->computeFull(get_energy);
+ internal->computeFull(get_energy);
break;
case 2: // Compute only softcore forces.
- energy = internal->computeSoftcoreFull(get_energy);
+ internal->computeSoftcoreFull(get_energy);
break;
case 3: // Compute only electrostatic forces.
- energy = internal->computeElecFull(get_energy);
+ internal->computeElecFull(get_energy);
break;
}
}
diff --git a/src/imd.c b/src/imd.c
index 0097a98..779ef57 100644
--- a/src/imd.c
+++ b/src/imd.c
@@ -1,11 +1,34 @@
-
-
+/***************************************************************************
+ *cr
+ *cr (C) Copyright 1995-2016 The Board of Trustees of the
+ *cr University of Illinois
+ *cr All Rights Reserved
+ *cr
+ ***************************************************************************/
+
+/***************************************************************************
+ * RCS INFORMATION:
+ *
+ * $RCSfile: imd.C,v $
+ * $Author: johns $ $Locker: $ $State: Exp $
+ * $Revision: 1.19 $ $Date: 2016/11/28 03:05:07 $
+ *
+ ***************************************************************************
+ * DESCRIPTION:
+ * Lowest level interactive MD communication routines.
+ *
+ * LICENSE:
+ * UIUC Open Source License
+ * http://www.ks.uiuc.edu/Research/vmd/plugins/pluginlicense.html
+ *
+ ***************************************************************************/
#include "imd.h"
#include "vmdsock.h"
#include <string.h>
#include <errno.h>
#include <stdlib.h>
+/// IMD communication protocol message header structure
typedef struct {
int32 type;
int32 length;
@@ -14,20 +37,16 @@ typedef struct {
#define HEADERSIZE 8
#define IMDVERSION 2
-static void swap4(char *data, int ndata) {
- int i;
- char *dataptr;
- char b0, b1;
-
- dataptr = data;
- for (i=0; i<ndata; i+=4) {
- b0 = dataptr[0];
- b1 = dataptr[1];
- dataptr[0] = dataptr[3];
- dataptr[1] = dataptr[2];
- dataptr[2] = b1;
- dataptr[3] = b0;
- dataptr += 4;
+/* Only works with aligned 4-byte quantities, will cause a bus error */
+/* on some platforms if used on unaligned data. */
+void swap4_aligned(void *v, long ndata) {
+ int *data = (int *) v;
+ long i;
+ int *N;
+ for (i=0; i<ndata; i++) {
+ N = data + i;
+ *N=(((*N>>24)&0xff) | ((*N&0xff)<<24) |
+ ((*N>>8)&0xff00) | ((*N&0xff00)<<8));
}
}
@@ -40,6 +59,7 @@ static int32 imd_htonl(int32 h) {
return n;
}
+/// structure used to perform byte swapping operations
typedef struct {
unsigned int highest : 8;
unsigned int high : 8;
@@ -50,7 +70,8 @@ typedef struct {
static int32 imd_ntohl(int32 n) {
int32 h = 0;
netint net;
- net = *((netint *)&n);
+
+ memcpy((void *)&net,(void *)&n, sizeof(n));
h |= net.highest << 24 | net.high << 16 | net.low << 8 | net.lowest;
return h;
}
@@ -144,11 +165,11 @@ int imd_trate(void *s, int32 rate) {
/* Data methods */
int imd_send_mdcomm(void *s,int32 n,const int32 *indices,const float *forces) {
int rc;
- int32 size = HEADERSIZE+16*n;
+ int32 size = HEADERSIZE+16L*n;
char *buf = (char *) malloc(sizeof(char) * size);
fill_header((IMDheader *)buf, IMD_MDCOMM, n);
- memcpy(buf+HEADERSIZE, indices, 4*n);
- memcpy(buf+HEADERSIZE+4*n, forces, 12*n);
+ memcpy(buf+HEADERSIZE, indices, 4L*n);
+ memcpy(buf+HEADERSIZE+4*n, forces, 12L*n);
rc = (imd_writen(s, buf, size) != size);
free(buf);
return rc;
@@ -167,10 +188,10 @@ int imd_send_energies(void *s, const IMDEnergies *energies) {
int imd_send_fcoords(void *s, int32 n, const float *coords) {
int rc;
- int32 size = HEADERSIZE+12*n;
+ int32 size = HEADERSIZE+12L*n;
char *buf = (char *) malloc(sizeof(char) * size);
fill_header((IMDheader *)buf, IMD_FCOORDS, n);
- memcpy(buf+HEADERSIZE, coords, 12*n);
+ memcpy(buf+HEADERSIZE, coords, 12L*n);
rc = (imd_writen(s, buf, size) != size);
free(buf);
return rc;
@@ -211,7 +232,8 @@ int imd_recv_handshake(void *s) {
if (!imd_go(s)) return 0;
return -1;
}
- swap4((char *)&buf, 4);
+
+ swap4_aligned(&buf, 1);
if (buf == IMDVERSION) {
if (!imd_go(s)) return 1;
}
@@ -221,8 +243,8 @@ int imd_recv_handshake(void *s) {
}
int imd_recv_mdcomm(void *s, int32 n, int32 *indices, float *forces) {
- if (imd_readn(s, (char *)indices, 4*n) != 4*n) return 1;
- if (imd_readn(s, (char *)forces, 12*n) != 12*n) return 1;
+ if (imd_readn(s, (char *)indices, 4L*n) != 4L*n) return 1;
+ if (imd_readn(s, (char *)forces, 12L*n) != 12L*n) return 1;
return 0;
}
@@ -232,6 +254,6 @@ int imd_recv_energies(void *s, IMDEnergies *energies) {
}
int imd_recv_fcoords(void *s, int32 n, float *coords) {
- return (imd_readn(s, (char *)coords, 12*n) != 12*n);
+ return (imd_readn(s, (char *)coords, 12L*n) != 12L*n);
}
diff --git a/src/imd.h b/src/imd.h
index 6d722aa..3414cdf 100644
--- a/src/imd.h
+++ b/src/imd.h
@@ -1,6 +1,6 @@
/***************************************************************************
*cr
- *cr (C) Copyright 1995-2003 The Board of Trustees of the
+ *cr (C) Copyright 1995-2016 The Board of Trustees of the
*cr University of Illinois
*cr All Rights Reserved
*cr
@@ -11,7 +11,11 @@
*
* $RCSfile: imd.h,v $
* $Author: johns $ $Locker: $ $State: Exp $
- * $Revision: 1.1 $ $Date: 2003/09/12 18:30:46 $
+ * $Revision: 1.22 $ $Date: 2016/11/28 03:05:07 $
+ *
+ * LICENSE:
+ * UIUC Open Source License
+ * http://www.ks.uiuc.edu/Research/vmd/plugins/pluginlicense.html
*
***************************************************************************/
@@ -26,6 +30,7 @@ typedef int int32;
typedef short int32;
#endif
+
typedef enum IMDType_t {
IMD_DISCONNECT, /**< close IMD connection, leaving sim running */
IMD_ENERGIES, /**< energy data block */
@@ -37,7 +42,8 @@ typedef enum IMDType_t {
IMD_PAUSE, /**< pause the running simulation */
IMD_TRATE, /**< set IMD update transmission rate */
IMD_IOERROR /**< indicate an I/O error */
-} IMDType;
+} IMDType; /**< IMD command message type enumerations */
+
typedef struct {
int32 tstep; /**< integer timestep index */
@@ -50,7 +56,8 @@ typedef struct {
float Eangle; /**< Angle energy, Kcal/mol */
float Edihe; /**< Dihedral energy, Kcal/mol */
float Eimpr; /**< Improper energy, Kcal/mol */
-} IMDEnergies; /**< */
+} IMDEnergies; /**< IMD simulation energy report structure */
+
/* Send control messages - these consist of a header with no subsequent data */
extern int imd_disconnect(void *); /**< leave sim running but close IMD */
@@ -60,21 +67,14 @@ extern int imd_handshake(void *); /**< check endianness, version compat */
extern int imd_trate(void *, int32); /**< set IMD update transmission rate */
/* Send data update messages */
-/**
- * Send MDComm compatible forces
- * Forces are in Kcal/mol/angstrom
- */
+
+/** Send MDComm compatible forces, units are Kcal/mol/angstrom */
extern int imd_send_mdcomm(void *, int32, const int32 *, const float *);
-/**
- * Send energies
- */
+/** Send energies */
extern int imd_send_energies(void *, const IMDEnergies *);
-/**
- * Send atom forces and coordinates
- * Forces are in Kcal/mol/angstrom
- */
+/** Send atom forces and coordinates, units are Kcal/mol/angstrom */
extern int imd_send_fcoords(void *, int32, const float *);
/**
@@ -84,26 +84,16 @@ extern int imd_send_fcoords(void *, int32, const float *);
*/
extern int imd_recv_handshake(void *);
-/**
- * Receive header and data
- */
+/** Receive header and data */
extern IMDType imd_recv_header(void *, int32 *);
-/**
- * Receive MDComm-style forces
- * Forces are in Kcal/mol/angstrom
- */
+/** Receive MDComm-style forces, units are Kcal/mol/angstrom */
extern int imd_recv_mdcomm(void *, int32, int32 *, float *);
-/**
- * Receive energies
- */
+/** Receive energies */
extern int imd_recv_energies(void *, IMDEnergies *);
-/**
- * Receive atom coordinates and forces
- * Forces are in Kcal/mol/angstrom
- */
+/** Receive atom coordinates and forces, units are Kcal/mol/angstrom */
extern int imd_recv_fcoords(void *, int32, float *);
#endif
--
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