void InitPriority(void) {
/* set process priority high */
if (schedctl (NDPRI,getpid(), NDPHIMIN) < 0)
perror ("schedctl NDPNORMMIN");
/* lock memory to avoid paging */
plock(PROCLOCK);
/* schedctl requires set user id root, so we need to return to regular
user id to avoid security problems */
setuid(getuid());
}
static void
sit_and_spin(int child_index)
{
long *my_counter_ptr;
/* only use C stuff if we are not WIN32 unless and until we */
/* switch from CreateThread to _beginthread. raj 1/96 */
#ifndef WIN32
/* we are the child. we could decide to exec some separate */
/* program, but that doesn't really seem worthwhile - raj 4/95 */
if (debug > 1) {
fprintf(where,
"Looper child %d is born, pid %d\n",
child_index,
getpid());
fflush(where);
}
#endif /* WIN32 */
/* reset our base pointer to be at the appropriate offset */
my_counter_ptr = (long *) ((char *)lib_base_pointer +
(netlib_get_page_size() *
PAGES_PER_CHILD * child_index));
/* in the event we are running on an MP system, it would */
/* probably be good to bind the soaker processes to specific */
/* processors. I *think* this is the most reasonable thing to */
/* do, and would be closes to simulating the information we get */
/* on HP-UX with pstat. I could put all the system-specific code */
/* here, but will "abstract it into another routine to keep this */
/* area more readable. I'll probably do the same thine with the */
/* "low pri code" raj 10/95 */
/* NOTE. I do *NOT* think it would be appropriate for the actual */
/* test processes to be bound to a particular processor - that */
/* is something that should be left up to the operating system. */
bind_to_processor(child_index);
for (*my_counter_ptr = 0L;
;
(*my_counter_ptr)++) {
if (!(*lib_base_pointer % 1)) {
/* every once and again, make sure that our process priority is */
/* nice and low. also, by making system calls, it may be easier */
/* for us to be pre-empted by something that needs to do useful */
/* work - like the thread of execution actually sending and */
/* receiving data across the network :) */
#ifdef _AIX
int pid,prio;
prio = PRIORITY;
pid = getpid();
/* if you are not root, this call will return EPERM - why one */
/* cannot change one's own priority to lower value is beyond */
/* me. raj 2/26/96 */
setpri(pid, prio);
#else /* _AIX */
#ifdef __sgi
int pid,prio;
prio = PRIORITY;
pid = getpid();
schedctl(NDPRI, pid, prio);
sginap(0);
#else /* __sgi */
#ifdef WIN32
SetThreadPriority(GetCurrentThread(),THREAD_PRIORITY_IDLE);
#else /* WIN32 */
#if defined(__sun) && defined(__SVR4)
#include <sys/types.h>
#include <sys/priocntl.h>
#include <sys/rtpriocntl.h>
#include <sys/tspriocntl.h>
/* I would *really* like to know how to use priocntl to make the */
/* priority low for this looper process. however, either my mind */
/* is addled, or the manpage in section two for priocntl is not */
/* terribly helpful - for one, it has no examples :( so, if you */
/* can help, I'd love to hear from you. in the meantime, we will */
/* rely on nice(39). raj 2/26/96 */
nice(39);
#else /* __sun && __SVR4 */
nice(39);
#endif /* __sun && _SVR4 */
#endif /* WIN32 */
#endif /* __sgi */
#endif /* _AIX */
}
}
}
void parse_common_args(int *argc,char *argv[],unsigned long Flags,
int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
int ndesc,char **desc,int nbugs,char **bugs)
{
static bool bHelp=FALSE,bHidden=FALSE,bQuiet=FALSE;
static char *manstr[] = { NULL, "no", "html", "tex", "nroff", "ascii", "completion", NULL };
static char *not_nicestr[] = { NULL, "0", "4", "10", "19", NULL };
static char *nicestr[] = { NULL, "19", "10", "4", "0", NULL };
static char *not_npristr[] = { NULL, "0", "128", "100", "200", "250", NULL };
static char *npristr[] = { NULL, "128", "250", "200", "100", "0", NULL };
static int nicelevel=0,mantp=0,npri=0;
static bool bGUI=FALSE,bDebug=FALSE;
static char *deffnm=NULL;
FILE *fp;
bool bPrint,bExit;
int i,j,k,npall;
char *ptr,*newdesc;
char *envstr;
t_pargs *all_pa=NULL;
t_pargs motif_pa = { "-X", FALSE, etBOOL, {&bGUI},
"Use dialog box GUI to edit command line options" };
t_pargs npri_paX = { "-npri", FALSE, etENUM, {not_npristr},
"Set non blocking priority" };
t_pargs npri_pa = { "-npri", FALSE, etINT, {&npri},
"HIDDEN Set non blocking priority (try 128)" };
t_pargs nice_paX = { "-nice", FALSE, etENUM, {not_nicestr},
"Set the nicelevel" };
t_pargs nice_pa = { "-nice", FALSE, etINT, {&nicelevel},
"Set the nicelevel" };
t_pargs deffnm_pa = { "-deffnm", FALSE, etSTR, {&deffnm},
"Set the default filename for all file options" };
t_pargs begin_pa = { "-b", FALSE, etTIME, {&tbegin},
"First frame (%t) to read from trajectory" };
t_pargs end_pa = { "-e", FALSE, etTIME, {&tend},
"Last frame (%t) to read from trajectory" };
t_pargs dt_pa = { "-dt", FALSE, etTIME, {&tdelta},
"Only use frame when t MOD dt = first time (%t)" };
t_pargs view_pa = { "-w", FALSE, etBOOL, {&bView},
"View output xvg, xpm, eps and pdb files" };
t_pargs time_pa = { "-tu", FALSE, etENUM, {timestr},
"Time unit" };
t_pargs pca_pa[] = {
{ "-h", FALSE, etBOOL, {&bHelp},
"Print help info and quit" },
{ "-hidden", FALSE, etBOOL, {&bHidden},
"HIDDENPrint hidden options" },
{ "-quiet",FALSE, etBOOL, {&bQuiet},
"HIDDENDo not print help info" },
{ "-man", FALSE, etENUM, {manstr},
"HIDDENWrite manual and quit" },
{ "-debug",FALSE, etBOOL, {&bDebug},
"HIDDENWrite file with debug information" },
};
#define NPCA_PA asize(pca_pa)
debug_gmx();
if (debug) {
fprintf(debug,"PID=%d, argc = %d\n",gmx_node_id(),*argc);
for(i=0; (i<*argc); i++)
fprintf(debug,"PID=%d, argv[%d] = %s\n",gmx_node_id(),i,argv[i]);
}
/* Check for double arguments */
for (i=1; (i<*argc); i++) {
if (argv[i] && (strlen(argv[i]) > 1) && (!isdigit(argv[i][1]))) {
for (j=i+1; (j<*argc); j++) {
if ( (argv[i][0]=='-') && (argv[j][0]=='-') &&
(strcmp(argv[i],argv[j])==0) ) {
if (FF(PCA_NOEXIT_ON_ARGS))
fprintf(stderr,"Double command line argument %s\n",argv[i]);
else
fatal_error(0,"Double command line argument %s\n",argv[i]);
}
}
}
}
debug_gmx();
/* Handle the flags argument, which is a bit field
* The FF macro returns whether or not the bit is set
*/
uFlags = Flags;
bPrint = !FF(PCA_SILENT);
/* Check whether we should have GUI or not */
#ifdef HAVE_MOTIF
bGUI = (getenv("GMXMOTIF") != NULL);
for(i=1; (i<*argc); i++) {
if (strcmp(argv[i],"-X") == 0)
bGUI = TRUE;
else if (strcmp(argv[i],"-noX") == 0)
bGUI = FALSE;
}
if (bGUI)
bQuiet = TRUE;
#else
bGUI = FALSE;
#endif
set_program_name(argv[0]);
/* Check ALL the flags ... */
snew(all_pa,NPCA_PA+npargs);
for(i=npall=0; (i<NPCA_PA); i++)
npall = add_parg(npall,&(all_pa),&(pca_pa[i]));
/* Motif options */
npall = add_parg(npall,&(all_pa),&motif_pa);
#if (defined __sgi && !defined SPEC_CPU)
envstr = getenv("GMXNPRIALL");
if (envstr)
npri=atoi(envstr);
if (FF(PCA_BE_NICE)) {
envstr = getenv("GMXNPRI");
if (envstr)
npri=atoi(envstr);
}
if (bGUI) {
if (npri)
npri_paX.u.c = npristr;
npall = add_parg(npall,&(all_pa),&npri_paX);
}
else
npall = add_parg(npall,&(all_pa),&npri_pa);
#endif
if (bGUI) {
/* Automatic nice or scheduling options */
if (FF(PCA_BE_NICE))
nice_paX.u.c = nicestr;
npall = add_parg(npall,&(all_pa),&nice_paX);
}
else {
if (FF(PCA_BE_NICE))
nicelevel=19;
npall = add_parg(npall,&(all_pa),&nice_pa);
}
if (FF(PCA_CAN_SET_DEFFNM))
npall = add_parg(npall,&(all_pa),&deffnm_pa);
if (FF(PCA_CAN_BEGIN))
npall = add_parg(npall,&(all_pa),&begin_pa);
if (FF(PCA_CAN_END))
npall = add_parg(npall,&(all_pa),&end_pa);
if (FF(PCA_CAN_DT))
npall = add_parg(npall,&(all_pa),&dt_pa);
#ifndef SPEC_CPU
if (FF(PCA_TIME_UNIT)) {
envstr = getenv("GMXTIMEUNIT");
if ( envstr == NULL )
envstr="ps";
set_default_time_unit(envstr);
npall = add_parg(npall,&(all_pa),&time_pa);
} else
#endif
set_default_time_unit("ps");
if (FF(PCA_CAN_VIEW))
npall = add_parg(npall,&(all_pa),&view_pa);
/* Now append the program specific arguments */
for(i=0; (i<npargs); i++)
npall = add_parg(npall,&(all_pa),&(pa[i]));
/* set etENUM options to default */
for(i=0; (i<npall); i++)
if (all_pa[i].type==etENUM)
all_pa[i].u.c[0]=all_pa[i].u.c[1];
/* Now parse all the command-line options */
get_pargs(argc,argv,npall,all_pa,FF(PCA_KEEP_ARGS));
if (FF(PCA_CAN_SET_DEFFNM) && (deffnm!=NULL))
set_default_file_name(deffnm);
/* Parse the file args */
parse_file_args(argc,argv,nfile,fnm,FF(PCA_KEEP_ARGS));
/* Open the debug file */
if (bDebug) {
char buf[256];
if (gmx_node_num() > 1)
sprintf(buf,"%s%d.log",ShortProgram(),gmx_node_id());
else
sprintf(buf,"%s.log",ShortProgram());
init_debug(buf);
fprintf(debug,"%s (this file) opened in file %s, line %d\n",
buf,__FILE__,__LINE__);
}
/* Now we have parsed the command line arguments. If the user wants it
* we can now plop up a GUI dialog box to edit options.
*/
if (bGUI) {
#ifdef HAVE_MOTIF
gmx_gui(argc,argv,nfile,fnm,npall,all_pa,ndesc,desc,nbugs,bugs);
#else
fatal_error(0,"GROMACS compiled without MOTIF support - can't use X interface");
#endif
}
/* Now copy the results back... */
for(i=0,k=npall-npargs; (i<npargs); i++,k++)
memcpy(&(pa[i]),&(all_pa[k]),(size_t)sizeof(pa[i]));
for(i=0; (i<npall); i++)
all_pa[i].desc = mk_desc(&(all_pa[i]), time_unit() );
bExit = bHelp || (strcmp(manstr[0],"no") != 0);
#if (defined __sgi && USE_SGI_FPE)
doexceptions();
#endif
/* Set the nice level */
#ifdef __sgi
if (bGUI)
if (npri)
sscanf(npristr[0],"%d",&npri);
else
sscanf(not_npristr[0],"%d",&npri);
if (npri != 0 && !bExit) {
(void) schedctl(MPTS_RTPRI,0,npri);
}
else
#endif
#ifdef HAVE_UNISTD_H
if (bGUI) {
if (FF(PCA_BE_NICE))
sscanf(nicestr[0],"%d",&nicelevel);
else
sscanf(not_nicestr[0],"%d",&nicelevel);
}
if (nicelevel != 0 && !bExit)
nice(nicelevel);
#endif
if (!(FF(PCA_QUIET) || bQuiet )) {
if (bHelp)
write_man(stderr,"help",program,ndesc,desc,nfile,fnm,npall,all_pa,
nbugs,bugs,bHidden);
else if (bPrint) {
pr_fns(stderr,nfile,fnm);
print_pargs(stderr,npall,all_pa);
}
}
if (strcmp(manstr[0],"no") != 0) {
if(!strcmp(manstr[0],"completion")) {
/* one file each for csh, bash and zsh if we do completions */
fp=man_file(program,"completion-zsh");
write_man(fp,"completion-zsh",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
fclose(fp);
fp=man_file(program,"completion-bash");
write_man(fp,"completion-bash",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
fclose(fp);
fp=man_file(program,"completion-csh");
write_man(fp,"completion-csh",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
fclose(fp);
} else {
fp=man_file(program,manstr[0]);
write_man(fp,manstr[0],program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
fclose(fp);
}
}
/* convert time options, must be done after printing! */
init_time_factor();
for(i=0; i<npall; i++) {
if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0)) {
*all_pa[i].u.r /= timefactor;
}
}
/* clear memory */
for(i=0; i<npall; i++)
sfree(all_pa[i].desc);
sfree(all_pa);
if (!FF(PCA_NOEXIT_ON_ARGS)) {
if (*argc > 1) {
for(i=1; (i<*argc); i++)
fprintf(stderr,"Unknown argument: %s\n",argv[i]);
fatal_error(0,"Program %s halted",Program());
}
}
if (bExit) {
#ifdef USE_MPI
if (gmx_parallel)
gmx_abort(gmx_node_id(),gmx_node_num(),0);
#endif
exit(0);
}
}
void parse_common_args(int *argc,char *argv[],unsigned long Flags,
int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
int ndesc,char **desc,int nbugs,char **bugs)
{
static bool bHelp=FALSE,bHidden=FALSE,bQuiet=FALSE;
static char *manstr[] = { NULL, "no", "html", "tex", "nroff", "ascii", "completion", "py", "xml", "wiki", NULL };
static int nicelevel=0,mantp=0,npri=0,debug_level=0;
static char *deffnm=NULL;
static real tbegin=0,tend=0,tdelta=0;
t_pargs *all_pa=NULL;
t_pargs npri_pa = { "-npri", FALSE, etINT, {&npri},
"HIDDEN Set non blocking priority (try 128)" };
t_pargs nice_pa = { "-nice", FALSE, etINT, {&nicelevel},
"Set the nicelevel" };
t_pargs deffnm_pa = { "-deffnm", FALSE, etSTR, {&deffnm},
"Set the default filename for all file options" };
t_pargs begin_pa = { "-b", FALSE, etTIME, {&tbegin},
"First frame (%t) to read from trajectory" };
t_pargs end_pa = { "-e", FALSE, etTIME, {&tend},
"Last frame (%t) to read from trajectory" };
t_pargs dt_pa = { "-dt", FALSE, etTIME, {&tdelta},
"Only use frame when t MOD dt = first time (%t)" };
t_pargs view_pa = { "-w", FALSE, etBOOL, {&bView},
"View output xvg, xpm, eps and pdb files" };
t_pargs code_pa = { "-xvgr", FALSE, etBOOL, {&bXvgrCodes},
"Add specific codes (legends etc.) in the output xvg files for the xmgrace program" };
t_pargs time_pa = { "-tu", FALSE, etENUM, {timestr},
"Time unit" };
/* Maximum number of extra arguments */
#define EXTRA_PA 16
t_pargs pca_pa[] = {
{ "-h", FALSE, etBOOL, {&bHelp},
"Print help info and quit" },
{ "-hidden", FALSE, etBOOL, {&bHidden},
"HIDDENPrint hidden options" },
{ "-quiet",FALSE, etBOOL, {&bQuiet},
"HIDDENDo not print help info" },
{ "-man", FALSE, etENUM, {manstr},
"HIDDENWrite manual and quit" },
{ "-debug",FALSE, etINT, {&debug_level},
"HIDDENWrite file with debug information, 1: short, 2: also x and f" },
};
#define NPCA_PA asize(pca_pa)
FILE *fp;
bool bPrint,bExit,bXvgr;
int i,j,k,npall,max_pa,cmdlength;
char *ptr,*newdesc;
char *envstr;
#define FF(arg) ((Flags & arg)==arg)
cmdlength = strlen(argv[0]);
/* Check for double arguments */
for (i=1; (i<*argc); i++) {
cmdlength += strlen(argv[i]);
if (argv[i] && (strlen(argv[i]) > 1) && (!isdigit(argv[i][1]))) {
for (j=i+1; (j<*argc); j++) {
if ( (argv[i][0]=='-') && (argv[j][0]=='-') &&
(strcmp(argv[i],argv[j])==0) ) {
if (FF(PCA_NOEXIT_ON_ARGS))
fprintf(stderr,"Double command line argument %s\n",argv[i]);
else
gmx_fatal(FARGS,"Double command line argument %s\n",argv[i]);
}
}
}
}
debug_gmx();
/* Fill the cmdline string */
snew(cmdline,cmdlength+*argc+1);
for (i=0; (i<*argc); i++) {
strcat(cmdline,argv[i]);
strcat(cmdline," ");
}
/* Handle the flags argument, which is a bit field
* The FF macro returns whether or not the bit is set
*/
bPrint = !FF(PCA_SILENT);
set_program_name(argv[0]);
/* Check ALL the flags ... */
max_pa = NPCA_PA + EXTRA_PA + npargs;
snew(all_pa,max_pa);
for(i=npall=0; (i<NPCA_PA); i++)
npall = add_parg(npall,all_pa,&(pca_pa[i]));
#ifdef __sgi
envstr = getenv("GMXNPRIALL");
if (envstr)
npri=atoi(envstr);
if (FF(PCA_BE_NICE)) {
envstr = getenv("GMXNPRI");
if (envstr)
npri=atoi(envstr);
}
npall = add_parg(npall,all_pa,&npri_pa);
#endif
if (FF(PCA_BE_NICE))
nicelevel=19;
npall = add_parg(npall,all_pa,&nice_pa);
if (FF(PCA_CAN_SET_DEFFNM))
npall = add_parg(npall,all_pa,&deffnm_pa);
if (FF(PCA_CAN_BEGIN))
npall = add_parg(npall,all_pa,&begin_pa);
if (FF(PCA_CAN_END))
npall = add_parg(npall,all_pa,&end_pa);
if (FF(PCA_CAN_DT))
npall = add_parg(npall,all_pa,&dt_pa);
if (FF(PCA_TIME_UNIT)) {
envstr = getenv("GMXTIMEUNIT");
if ( envstr == NULL )
envstr="ps";
set_default_time_unit(envstr);
npall = add_parg(npall,all_pa,&time_pa);
} else
set_default_time_unit("ps");
if (FF(PCA_CAN_VIEW))
npall = add_parg(npall,all_pa,&view_pa);
bXvgr = FALSE;
for(i=0; (i<nfile); i++)
bXvgr = bXvgr || (fnm[i].ftp == efXVG);
if (bXvgr)
npall = add_parg(npall,all_pa,&code_pa);
/* Now append the program specific arguments */
for(i=0; (i<npargs); i++)
npall = add_parg(npall,all_pa,&(pa[i]));
/* set etENUM options to default */
for(i=0; (i<npall); i++)
if (all_pa[i].type==etENUM)
all_pa[i].u.c[0]=all_pa[i].u.c[1];
/* Now parse all the command-line options */
get_pargs(argc,argv,npall,all_pa,FF(PCA_KEEP_ARGS));
if (FF(PCA_CAN_SET_DEFFNM) && (deffnm!=NULL))
set_default_file_name(deffnm);
/* Parse the file args */
parse_file_args(argc,argv,nfile,fnm,FF(PCA_KEEP_ARGS));
/* Open the debug file */
if (debug_level > 0) {
char buf[256];
if (gmx_mpi_initialized())
sprintf(buf,"%s%d.log",ShortProgram(),gmx_node_rank());
else
sprintf(buf,"%s.log",ShortProgram());
init_debug(debug_level,buf);
fprintf(stderr,"Opening debug file %s (src code file %s, line %d)\n",
buf,__FILE__,__LINE__);
}
/* Now copy the results back... */
for(i=0,k=npall-npargs; (i<npargs); i++,k++)
memcpy(&(pa[i]),&(all_pa[k]),(size_t)sizeof(pa[i]));
for(i=0; (i<npall); i++)
all_pa[i].desc = mk_desc(&(all_pa[i]), time_unit() );
bExit = bHelp || (strcmp(manstr[0],"no") != 0);
#if (defined __sgi && USE_SGI_FPE)
doexceptions();
#endif
/* Set the nice level */
#ifdef __sgi
if (npri != 0 && !bExit) {
schedctl(MPTS_RTPRI,0,npri);
}
#endif
#ifdef HAVE_UNISTD_H
#ifndef GMX_NO_NICE
/* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
if (nicelevel != 0 && !bExit)
i=nice(nicelevel); /* assign ret value to avoid warnings */
#endif
#endif
if (!(FF(PCA_QUIET) || bQuiet )) {
if (bHelp)
write_man(stderr,"help",program,ndesc,desc,nfile,fnm,npall,all_pa,
nbugs,bugs,bHidden);
else if (bPrint) {
pr_fns(stderr,nfile,fnm);
print_pargs(stderr,npall,all_pa,FALSE);
}
}
if (strcmp(manstr[0],"no") != 0) {
if(!strcmp(manstr[0],"completion")) {
/* one file each for csh, bash and zsh if we do completions */
fp=man_file(program,"completion-zsh");
write_man(fp,"completion-zsh",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
fp=man_file(program,"completion-bash");
write_man(fp,"completion-bash",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
fp=man_file(program,"completion-csh");
write_man(fp,"completion-csh",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
} else {
fp=man_file(program,manstr[0]);
write_man(fp,manstr[0],program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
}
}
/* convert time options, must be done after printing! */
init_time_factor();
for(i=0; i<npall; i++) {
if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0)) {
*all_pa[i].u.r *= timeinvfac;
}
}
/* Extract Time info from arguments */
if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b",npall,all_pa))
setTimeValue(TBEGIN,opt2parg_real("-b",npall,all_pa));
if (FF(PCA_CAN_END) && opt2parg_bSet("-e",npall,all_pa))
setTimeValue(TEND,opt2parg_real("-e",npall,all_pa));
if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt",npall,all_pa))
setTimeValue(TDELTA,opt2parg_real("-dt",npall,all_pa));
/* clear memory */
sfree(all_pa);
if (!FF(PCA_NOEXIT_ON_ARGS)) {
if (*argc > 1) {
gmx_cmd(argv[1]);
}
}
if (bExit) {
if (gmx_parallel_env)
gmx_abort(gmx_node_rank(),gmx_node_num(),0);
else
exit(0);
}
#undef FF
}
void parse_common_args(int *argc,char *argv[],unsigned long Flags,
int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
int ndesc,const char **desc,
int nbugs,const char **bugs,
output_env_t *oenv)
{
gmx_bool bHelp=FALSE,bHidden=FALSE,bQuiet=FALSE,bVersion=FALSE;
const char *manstr[] = { NULL, "no", "html", "tex", "nroff", "ascii",
"completion", "py", "xml", "wiki", NULL };
/* This array should match the order of the enum in oenv.h */
const char *xvg_format[] = { NULL, "xmgrace", "xmgr", "none", NULL };
/* This array should match the order of the enum in oenv.h */
const char *time_units[] = { NULL, "fs", "ps", "ns", "us", "ms", "s",
NULL };
int nicelevel=0,mantp=0,npri=0,debug_level=0,verbose_level=0;
char *deffnm=NULL;
real tbegin=0,tend=0,tdelta=0;
gmx_bool bView=FALSE;
t_pargs *all_pa=NULL;
t_pargs npri_pa = { "-npri", FALSE, etINT, {&npri},
"HIDDEN Set non blocking priority (try 128)" };
t_pargs nice_pa = { "-nice", FALSE, etINT, {&nicelevel},
"Set the nicelevel" };
t_pargs deffnm_pa = { "-deffnm", FALSE, etSTR, {&deffnm},
"Set the default filename for all file options" };
t_pargs begin_pa = { "-b", FALSE, etTIME, {&tbegin},
"First frame (%t) to read from trajectory" };
t_pargs end_pa = { "-e", FALSE, etTIME, {&tend},
"Last frame (%t) to read from trajectory" };
t_pargs dt_pa = { "-dt", FALSE, etTIME, {&tdelta},
"Only use frame when t MOD dt = first time (%t)" };
t_pargs view_pa = { "-w", FALSE, etBOOL, {&bView},
"View output xvg, xpm, eps and pdb files" };
t_pargs xvg_pa = { "-xvg", FALSE, etENUM, {xvg_format},
"xvg plot formatting" };
t_pargs time_pa = { "-tu", FALSE, etENUM, {time_units},
"Time unit" };
/* Maximum number of extra arguments */
#define EXTRA_PA 16
t_pargs pca_pa[] = {
{ "-h", FALSE, etBOOL, {&bHelp},
"Print help info and quit" },
{ "-version", FALSE, etBOOL, {&bVersion},
"Print version info and quit" },
{ "-verb", FALSE, etINT, {&verbose_level},
"HIDDENLevel of verbosity for this program" },
{ "-hidden", FALSE, etBOOL, {&bHidden},
"HIDDENPrint hidden options" },
{ "-quiet",FALSE, etBOOL, {&bQuiet},
"HIDDENDo not print help info" },
{ "-man", FALSE, etENUM, {manstr},
"HIDDENWrite manual and quit" },
{ "-debug",FALSE, etINT, {&debug_level},
"HIDDENWrite file with debug information, 1: short, 2: also x and f" },
};
#define NPCA_PA asize(pca_pa)
FILE *fp;
gmx_bool bPrint,bExit,bXvgr;
int i,j,k,npall,max_pa,cmdlength;
char *ptr,*newdesc;
const char *envstr;
#define FF(arg) ((Flags & arg)==arg)
snew(*oenv, 1);
cmdlength = strlen(argv[0]);
/* Check for double arguments */
for (i=1; (i<*argc); i++)
{
cmdlength += strlen(argv[i]);
if (argv[i] && (strlen(argv[i]) > 1) && (!isdigit(argv[i][1])))
{
for (j=i+1; (j<*argc); j++)
{
if ( (argv[i][0]=='-') && (argv[j][0]=='-') &&
(strcmp(argv[i],argv[j])==0) )
{
if (FF(PCA_NOEXIT_ON_ARGS))
fprintf(stderr,"Double command line argument %s\n",
argv[i]);
else
gmx_fatal(FARGS,"Double command line argument %s\n",
argv[i]);
}
}
}
}
debug_gmx();
set_program_name(argv[0]);
set_command_line(*argc, argv);
/* Handle the flags argument, which is a bit field
* The FF macro returns whether or not the bit is set
*/
bPrint = !FF(PCA_SILENT);
/* Check ALL the flags ... */
max_pa = NPCA_PA + EXTRA_PA + npargs+1;
snew(all_pa,max_pa);
for(i=npall=0; (i<NPCA_PA); i++)
npall = add_parg(npall,all_pa,&(pca_pa[i]));
#ifdef __sgi
envstr = getenv("GMXNPRIALL");
if (envstr)
npri=strtol(envstr,NULL,10);
if (FF(PCA_BE_NICE)) {
envstr = getenv("GMXNPRI");
if (envstr)
npri=strtol(envstr,NULL,10);
}
npall = add_parg(npall,all_pa,&npri_pa);
#endif
if (FF(PCA_BE_NICE))
nicelevel=19;
npall = add_parg(npall,all_pa,&nice_pa);
if (FF(PCA_CAN_SET_DEFFNM))
npall = add_parg(npall,all_pa,&deffnm_pa);
if (FF(PCA_CAN_BEGIN))
npall = add_parg(npall,all_pa,&begin_pa);
if (FF(PCA_CAN_END))
npall = add_parg(npall,all_pa,&end_pa);
if (FF(PCA_CAN_DT))
{
npall = add_parg(npall,all_pa,&dt_pa);
}
if (FF(PCA_TIME_UNIT)) {
npall = add_parg(npall,all_pa,&time_pa);
}
if (FF(PCA_CAN_VIEW))
npall = add_parg(npall,all_pa,&view_pa);
bXvgr = FALSE;
for(i=0; (i<nfile); i++)
{
bXvgr = bXvgr || (fnm[i].ftp == efXVG);
}
if (bXvgr)
{
npall = add_parg(npall,all_pa,&xvg_pa);
}
/* Now append the program specific arguments */
for(i=0; (i<npargs); i++)
npall = add_parg(npall,all_pa,&(pa[i]));
/* set etENUM options to default */
for(i=0; (i<npall); i++)
{
if (all_pa[i].type==etENUM)
{
all_pa[i].u.c[0]=all_pa[i].u.c[1];
}
}
set_default_time_unit(time_units,FF(PCA_TIME_UNIT));
set_default_xvg_format(xvg_format);
/* Now parse all the command-line options */
get_pargs(argc,argv,npall,all_pa,FF(PCA_KEEP_ARGS));
/* set program name, command line, and default values for output options */
output_env_init(*oenv, *argc, argv, (time_unit_t)nenum(time_units), bView,
(xvg_format_t)nenum(xvg_format), verbose_level, debug_level);
if (bVersion) {
printf("Program: %s\n",output_env_get_program_name(*oenv));
gmx_print_version_info(stdout);
exit(0);
}
if (FF(PCA_CAN_SET_DEFFNM) && (deffnm!=NULL))
set_default_file_name(deffnm);
/* Parse the file args */
parse_file_args(argc,argv,nfile,fnm,FF(PCA_KEEP_ARGS),!FF(PCA_NOT_READ_NODE));
/* Open the debug file */
if (debug_level > 0) {
char buf[256];
if (gmx_mpi_initialized())
sprintf(buf,"%s%d.debug",output_env_get_short_program_name(*oenv),
gmx_node_rank());
else
sprintf(buf,"%s.debug",output_env_get_short_program_name(*oenv));
init_debug(debug_level,buf);
fprintf(stderr,"Opening debug file %s (src code file %s, line %d)\n",
buf,__FILE__,__LINE__);
}
/* Now copy the results back... */
for(i=0,k=npall-npargs; (i<npargs); i++,k++)
memcpy(&(pa[i]),&(all_pa[k]),(size_t)sizeof(pa[i]));
for(i=0; (i<npall); i++)
all_pa[i].desc = mk_desc(&(all_pa[i]), output_env_get_time_unit(*oenv));
bExit = bHelp || (strcmp(manstr[0],"no") != 0);
#if (defined __sgi && USE_SGI_FPE)
doexceptions();
#endif
/* Set the nice level */
#ifdef __sgi
if (npri != 0 && !bExit) {
schedctl(MPTS_RTPRI,0,npri);
}
#endif
#ifdef HAVE_UNISTD_H
#ifndef GMX_NO_NICE
/* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
if (nicelevel != 0 && !bExit)
{
#ifdef GMX_THREADS
static gmx_bool nice_set=FALSE; /* only set it once */
tMPI_Thread_mutex_lock(&init_mutex);
if (!nice_set)
{
#endif
i=nice(nicelevel); /* assign ret value to avoid warnings */
#ifdef GMX_THREADS
nice_set=TRUE;
}
tMPI_Thread_mutex_unlock(&init_mutex);
#endif
}
#endif
#endif
/* Update oenv for parsed command line options settings. */
(*oenv)->xvg_format = (xvg_format_t)nenum(xvg_format);
(*oenv)->time_unit = (time_unit_t)nenum(time_units);
if (!(FF(PCA_QUIET) || bQuiet )) {
if (bHelp)
write_man(stderr,"help",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm,npall,all_pa, nbugs,bugs,bHidden);
else if (bPrint) {
pr_fns(stderr,nfile,fnm);
print_pargs(stderr,npall,all_pa,FALSE);
}
}
if (strcmp(manstr[0],"no") != 0) {
if(!strcmp(manstr[0],"completion")) {
/* one file each for csh, bash and zsh if we do completions */
fp=man_file(*oenv,"completion-zsh");
write_man(fp,"completion-zsh",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
fp=man_file(*oenv,"completion-bash");
write_man(fp,"completion-bash",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
fp=man_file(*oenv,"completion-csh");
write_man(fp,"completion-csh",output_env_get_program_name(*oenv),
ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
} else {
fp=man_file(*oenv,manstr[0]);
write_man(fp,manstr[0],output_env_get_program_name(*oenv),
ndesc,desc,nfile,fnm, npall, all_pa,nbugs,bugs,bHidden);
gmx_fio_fclose(fp);
}
}
/* convert time options, must be done after printing! */
for(i=0; i<npall; i++) {
if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0)) {
*all_pa[i].u.r *= output_env_get_time_invfactor(*oenv);
}
}
/* Extract Time info from arguments */
if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b",npall,all_pa))
setTimeValue(TBEGIN,opt2parg_real("-b",npall,all_pa));
if (FF(PCA_CAN_END) && opt2parg_bSet("-e",npall,all_pa))
setTimeValue(TEND,opt2parg_real("-e",npall,all_pa));
if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt",npall,all_pa))
setTimeValue(TDELTA,opt2parg_real("-dt",npall,all_pa));
/* clear memory */
for (i = 0; i < npall; ++i)
sfree((void *)all_pa[i].desc);
sfree(all_pa);
if (!FF(PCA_NOEXIT_ON_ARGS)) {
if (*argc > 1) {
gmx_cmd(argv[1]);
}
}
if (bExit) {
if (gmx_parallel_env_initialized())
/*gmx_abort(gmx_node_rank(),gmx_node_num(),0);*/
gmx_finalize();
exit(0);
}
#undef FF
}