int VMDinitialize(int *argc, char ***argv) {
int i;
#if defined VMDMPI
// hack to fix up env vars if necessary
for (i=0; i<(*argc); i++) {
if(!strupcmp((*argv)[i], "-vmddir")) {
if((*argc) > (i + 1)) {
setenv("VMDDIR", (*argv)[++i], 1);
} else {
msgErr << "-vmddir must specify a fully qualified path." << sendmsg;
}
}
}
vmd_mpi_init(argc, argv); // initialize MPI, fix up env vars, etc.
#endif
#if defined(_MSC_VER) && !defined(VMDSEPARATESTARTUP)
win32vmdstart(); // get registry info etc
#endif
#if !defined(VMDNOMACBUNDLE) && defined(__APPLE__)
macosxvmdstart(*argc, *argv); // get env variables etc
#endif
// Tell Tcl where the executable is located
const char *argv0 = vmd_initialize_tcl((*argv)[0]);
#ifdef VMDTCL
// register signal handler
tclhandler = Tcl_AsyncCreate(VMDTclAsyncProc, (ClientData)NULL);
signal(SIGINT, (sighandler_t) VMDTclSigHandler);
#endif
// Let people know who we are.
VMDtitle();
// Tell the user what we think about the hardware we're running on.
// If VMD is compiled for MPI, then we don't print any of the normal
// standalone startup messages and instead we use the special MPI-specific
// node scan startup messages only.
#if !defined(VMDMPI)
#if defined(VMDTHREADS)
int vmdnumcpus = wkf_thread_numprocessors();
msgInfo << "Multithreading available, " << vmdnumcpus <<
((vmdnumcpus > 1) ? " CPUs" : " CPU") << " detected."
<< sendmsg;
#endif
long vmdcorefree = vmd_get_avail_physmem_mb();
if (vmdcorefree >= 0) {
long vmdcorepcnt = vmd_get_avail_physmem_percent();
msgInfo << "Free system memory: " << vmdcorefree
<< "MB (" << vmdcorepcnt << "%)" << sendmsg;
}
#endif
// Read environment variables and command line options.
// Initialize customArgv with just argv0 to avoid problems with
// Tcl extension.
customArgv.append((char *)argv0);
VMDGetOptions(*argc, *argv);
#if (!defined(__APPLE__) && !defined(_MSC_VER)) && (defined(VMDOPENGL) || defined(VMDFLTK))
// If we're using X-windows, we autodetect if the DISPLAY environment
// variable is unset, and automatically switch back to text mode without
// requiring the user to pass the "-dispdev text" command line parameters
if ((which_display == DISPLAY_WIN) && (getenv("DISPLAY") == NULL)) {
which_display = DISPLAY_TEXT;
}
#endif
#if defined(VMDTKCON)
vmdcon_init();
msgInfo << "Using VMD Console redirection interface." << sendmsg;
// we default to a widget mode console, unless text mode is requested.
// we don't have an tcl interpreter registered yet, so it is set to NULL.
// flushing pending messages to the screen, is only in text mode possible.
if ((which_display == DISPLAY_TEXT) || just_print_help) {
vmdcon_use_text(NULL);
vmdcon_purge();
} else {
vmdcon_use_widget(NULL);
}
#endif
#ifdef VMDFLTK
// Do various special FLTK initialization stuff here
if ((which_display != DISPLAY_TEXT)) {
// Cause FLTK to to use 24-bit color for all windows if possible
// This must be done before any FLTK windows are shown for the first time.
if (!Fl::visual(FL_DOUBLE | FL_RGB8)) {
if (!Fl::visual(FL_RGB8)) {
Fl::visual(FL_RGB);
}
}
// Disable the use of the arrow keys for navigating buttons and other
// non-text widgets, we'll try it out and see how it pans out
Fl::visible_focus(0);
// Disable Drag 'n Drop since the only text field in VMD is the
// atomselection input and DND severely gets in the way there.
Fl::dnd_text_ops(0);
}
#endif
// Quit now if the user just wanted a list of command line options.
if (just_print_help) {
vmd_sleep(10); // This is here so that the user can see the message
// before the terminal/shell exits...
return 0;
}
// Set up default allocators; these may be overridden by cave or freevr.
vmd_alloc = malloc; // system malloc() in the default case
vmd_dealloc = free; // system free() in the default case
vmd_realloc = realloc; // system realloc(), set to NULL when not available
// check for a CAVE display
if (DISPLAY_USES_CAVE(which_display)) {
#ifdef VMDCAVE
// allocate shared memory pool used to communicate with child renderers
int megs = 2048;
if (getenv("VMDCAVEMEM") != NULL) {
megs = atoi(getenv("VMDCAVEMEM"));
}
msgInfo << "Attempting to get " << megs <<
"MB of CAVE Shared Memory" << sendmsg;
grab_CAVE_memory(megs);
CAVEConfigure(argc, *argv, NULL); // configure cave walls and memory use
// point VMD shared memory allocators to CAVE routines
vmd_alloc = malloc_from_CAVE_memory;
vmd_dealloc = free_to_CAVE_memory;
vmd_realloc = NULL; // no realloc() functionality is available presently
#else
msgErr << "Not compiled with the CAVE options set." << sendmsg;
which_display = DISPLAY_WIN;
#endif
}
// check for a FreeVR display
if (DISPLAY_USES_FREEVR(which_display)) {
#ifdef VMDFREEVR
int megs = 2048;
if (getenv("VMDFREEVRMEM") != NULL) {
megs = atoi(getenv("VMDFREEVRMEM"));
}
msgInfo << "Attempting to get " << megs <<
"MB of FreeVR Shared Memory" << sendmsg;
grab_FreeVR_memory(megs); // have to do this *before* vrConfigure() if
// we want more than the default shared mem.
vrConfigure(NULL, NULL, NULL); // configure FreeVR walls
// point shared memory allocators to FreeVR routines
vmd_alloc = malloc_from_FreeVR_memory;
vmd_dealloc = free_to_FreeVR_memory;
vmd_realloc = NULL; // no realloc() functionality is available presently
#else
msgErr << "Not compiled with the FREEVR options set." << sendmsg;
which_display = DISPLAY_WIN;
#endif
}
// return custom argc/argv
*argc = customArgv.num();
for (i=0; i<customArgv.num(); i++) {
(*argv)[i] = customArgv[i];
}
return 1; // successful startup
}
static int vmd_gaussdensity_threaded(int natoms, const float *xyzr,
const float *colors,
float *densitymap, float *voltexmap,
const int *numvoxels,
float radscale, float gridspacing,
float isovalue, float gausslim) {
densitythrparms parms;
memset(&parms, 0, sizeof(parms));
parms.natoms = natoms;
parms.radscale = radscale;
parms.gridspacing = gridspacing;
parms.isovalue = isovalue;
parms.gausslim = gausslim;
parms.numvoxels = numvoxels;
parms.xyzr = xyzr;
parms.colors = colors;
int physprocs = wkf_thread_numprocessors();
int maxprocs = physprocs;
// We can productively use only a few cores per socket due to the
// limited memory bandwidth per socket. Also, hyperthreading
// actually hurts performance. These two considerations combined
// with the linear increase in memory use prevent us from using large
// numbers of cores with this simple approach, so if we've got more
// than 8 CPU cores, we'll iteratively cutting the core count in
// half until we're under 8 cores.
while (maxprocs > 8)
maxprocs /= 2;
// Limit the number of CPU cores used so we don't run the
// machine out of memory during surface computation.
// For now we'll set a practical maximum memory use limit to
// 2GB total for all cores.
long volsz = numvoxels[0] * numvoxels[1] * numvoxels[2];
long volmemsz = sizeof(float) * volsz;
long volmemszkb = volmemsz / 1024;
long volmemtexszkb = (volmemszkb + (voltexmap != NULL) ? 3*volmemszkb : 0);
#if defined(ARCH_BLUEWATERS)
while ((volmemtexszkb * maxprocs) > (4 * 1024 * 1024))
maxprocs /= 2;
#else
while ((volmemtexszkb * maxprocs) > (2 * 1024 * 1024))
maxprocs /= 2;
#endif
if (maxprocs < 1)
maxprocs = 1;
// Loop over number of physical processors and try to create
// per-thread volumetric maps for each of them.
parms.thrdensitymaps = (float **) calloc(1,maxprocs * sizeof(float *));
parms.thrvoltexmaps = (float **) calloc(1, maxprocs * sizeof(float *));
// first thread is already ready to go
parms.thrdensitymaps[0] = densitymap;
parms.thrvoltexmaps[0] = voltexmap;
int i;
int numprocs = maxprocs; // ever the optimist
for (i=1; i<maxprocs; i++) {
parms.thrdensitymaps[i] = (float *) calloc(1, volmemsz);
if (parms.thrdensitymaps[i] == NULL) {
numprocs = i;
break;
}
if (voltexmap != NULL) {
parms.thrvoltexmaps[i] = (float *) calloc(1, 3 * volmemsz);
if (parms.thrvoltexmaps[i] == NULL) {
free(parms.thrdensitymaps[i]);
parms.thrdensitymaps[i] = NULL;
numprocs = i;
break;
}
}
}
// launch independent thread calculations
wkf_tasktile_t tile;
tile.start = 0;
tile.end = natoms;
wkf_threadlaunch(numprocs, &parms, densitythread, &tile);
// do a parallel reduction of the resulting density maps
tile.start = 0;
tile.end = volsz;
wkf_threadlaunch(numprocs, &parms, reductionthread, &tile);
// free work area
for (i=1; i<maxprocs; i++) {
if (parms.thrdensitymaps[i] != NULL)
free(parms.thrdensitymaps[i]);
if (parms.thrvoltexmaps[i] != NULL)
free(parms.thrvoltexmaps[i]);
}
free(parms.thrdensitymaps);
free(parms.thrvoltexmaps);
return 0;
}
