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4 * This source code is part of
8 * GROningen MAchine for Chemical Simulations
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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34 * GROningen Mixture of Alchemy and Childrens' Stories
54 #include "gmx_fatal.h"
57 #include "mtop_util.h"
61 #include "thread_mpi.h"
66 #include <sys/schedctl.h>
67 #include <sys/sysmp.h>
70 /* The source code in this file should be thread-safe.
71 Please keep it that way. */
73 /******************************************************************
75 * T R A J E C T O R Y S T U F F
77 ******************************************************************/
79 /* inherently globally shared names: */
80 static const char *program_name=NULL;
81 static char *cmd_line=NULL;
84 /* For now, some things here are simply not re-entrant, so
85 we have to actively lock them. */
86 static tMPI_Thread_mutex_t init_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
90 /****************************************************************
92 * E X P O R T E D F U N C T I O N S
94 ****************************************************************/
97 /* progam names, etc. */
99 const char *ShortProgram(void)
103 tMPI_Thread_mutex_lock(&init_mutex);
107 tMPI_Thread_mutex_unlock(&init_mutex);
109 if ((pr=strrchr(ret,DIR_SEPARATOR)) != NULL)
111 /* Strip away the libtool prefix if it's still there. */
112 if(strlen(ret) > 3 && !strncmp(ret, "lt-", 3))
117 const char *Program(void)
121 tMPI_Thread_mutex_lock(&init_mutex);
125 tMPI_Thread_mutex_unlock(&init_mutex);
130 const char *command_line(void)
134 tMPI_Thread_mutex_lock(&init_mutex);
138 tMPI_Thread_mutex_unlock(&init_mutex);
143 void set_program_name(const char *argvzero)
146 tMPI_Thread_mutex_lock(&init_mutex);
148 /* When you run a dynamically linked program before installing
149 * it, libtool uses wrapper scripts and prefixes the name with "lt-".
150 * Until libtool is fixed to set argv[0] right, rip away the prefix:
152 if (program_name == NULL)
154 if(strlen(argvzero)>3 && !strncmp(argvzero,"lt-",3))
155 program_name=strdup(argvzero+3);
157 program_name=strdup(argvzero);
159 if (program_name == NULL)
160 program_name="GROMACS";
162 tMPI_Thread_mutex_unlock(&init_mutex);
167 void set_command_line(int argc, char *argv[])
173 tMPI_Thread_mutex_lock(&init_mutex);
177 cmdlength = strlen(argv[0]);
178 for (i=1; i<argc; i++)
180 cmdlength += strlen(argv[i]);
183 /* Fill the cmdline string */
184 snew(cmd_line,cmdlength+argc+1);
185 for (i=0; i<argc; i++)
187 strcat(cmd_line,argv[i]);
188 strcat(cmd_line," ");
192 tMPI_Thread_mutex_unlock(&init_mutex);
197 /* utility functions */
199 bool bRmod_fd(double a, double b, double c, bool bDouble)
204 tol = 2*(bDouble ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS);
206 iq = (a - b + tol*a)/c;
208 if (fabs(a - b - c*iq) <= tol*fabs(a))
214 int check_times2(real t,real t0,real tp, real tpp, bool bDouble)
220 /* since t is float, we can not use double precision for bRmod */
224 if (t-tp>0 && tp-tpp>0)
225 margin = 0.1*min(t-tp,tp-tpp);
230 if ((!bTimeSet(TBEGIN) || (t >= rTimeValue(TBEGIN))) &&
231 (!bTimeSet(TEND) || (t <= rTimeValue(TEND)))) {
232 if (bTimeSet(TDELTA) && !bRmod_fd(t,t0,rTimeValue(TDELTA),bDouble))
237 else if (bTimeSet(TEND) && (t >= rTimeValue(TEND)))
240 fprintf(debug,"t=%g, t0=%g, b=%g, e=%g, dt=%g: r=%d\n",
241 t,t0,rTimeValue(TBEGIN),rTimeValue(TEND),rTimeValue(TDELTA),r);
245 int check_times(real t)
247 return check_times2(t,t,t,t,FALSE);
253 static void set_default_time_unit(const char *time_list[], bool bCanTime)
260 select = getenv("GMXTIMEUNIT");
264 while(time_list[i] && strcmp(time_list[i], select) != 0)
270 if (!bCanTime || select == NULL || strcmp(time_list[i], select) != 0)
272 /* Set it to the default: ps */
274 while(time_list[i] && strcmp(time_list[i], "ps") != 0)
280 time_list[0] = time_list[i];
284 static void set_default_xvg_format(const char *xvg_list[])
287 const char *select,*tmp;
289 select = getenv("GMX_VIEW_XVG");
292 /* The default is the first option */
293 xvg_list[0] = xvg_list[1];
298 while (xvg_list[i] && strcmp(xvg_list[i], select) != 0)
302 if (xvg_list[i] != NULL)
304 xvg_list[0] = xvg_list[i];
308 xvg_list[0] = xvg_list[exvgNONE];
314 /***** T O P O L O G Y S T U F F ******/
316 t_topology *read_top(const char *fn,int *ePBC)
322 epbc = read_tpx_top(fn,NULL,NULL,&natoms,NULL,NULL,NULL,top);
329 /*************************************************************
331 * P A R S I N G S T U F F
333 *************************************************************/
335 static void usage(const char *type,const char *arg)
338 gmx_fatal(FARGS,"Expected %s argument for option %s\n",type,arg);
341 int iscan(int argc,char *argv[],int *i)
346 if (!sscanf(argv[++(*i)],"%d",&var))
347 usage("an integer",argv[(*i)-1]);
349 usage("an integer",argv[*i]);
354 gmx_large_int_t istepscan(int argc,char *argv[],int *i)
359 if (!sscanf(argv[++(*i)],gmx_large_int_pfmt,&var))
360 usage("an integer",argv[(*i)-1]);
362 usage("an integer",argv[*i]);
367 double dscan(int argc,char *argv[],int *i)
372 if (!sscanf(argv[++(*i)],"%lf",&var))
373 usage("a real",argv[(*i)-1]);
375 usage("a real",argv[*i]);
380 char *sscan(int argc,char *argv[],int *i)
384 if ( (argv[(*i)+1][0]=='-') && (argc > (*i)+2) &&
385 (argv[(*i)+2][0]!='-') )
387 fprintf(stderr,"Possible missing string argument for option %s\n\n",
392 usage("a string",argv[*i]);
397 int nenum(const char *const enumc[])
402 /* we *can* compare pointers directly here! */
403 while(enumc[i] && enumc[0]!=enumc[i])
409 static void pdesc(char *desc)
414 if ((int)strlen(ptr) < 70)
415 fprintf(stderr,"\t%s\n",ptr);
417 for(nptr=ptr+70; (nptr != ptr) && (!isspace(*nptr)); nptr--)
420 fprintf(stderr,"\t%s\n",ptr);
424 fprintf(stderr,"\t%s\n",ptr);
430 static FILE *man_file(const output_env_t oenv,const char *mantp)
434 const char *pr = output_env_get_short_program_name(oenv);
436 if (strcmp(mantp,"ascii") != 0)
437 sprintf(buf,"%s.%s",pr,mantp);
439 sprintf(buf,"%s.txt",pr);
440 fp = gmx_fio_fopen(buf,"w");
445 static int add_parg(int npargs,t_pargs *pa,t_pargs *pa_add)
447 memcpy(&(pa[npargs]),pa_add,sizeof(*pa_add));
452 static char *mk_desc(t_pargs *pa, const char *time_unit_str)
454 char *newdesc=NULL,*ndesc=NULL,*nptr=NULL;
458 /* First compute length for description */
459 len = strlen(pa->desc)+1;
460 if ((ptr = strstr(pa->desc,"HIDDEN")) != NULL)
462 if (pa->type == etENUM) {
464 for(k=1; (pa->u.c[k] != NULL); k++) {
465 len += strlen(pa->u.c[k])+12;
470 /* add label for hidden options */
472 sprintf(newdesc,"[hidden] %s",ptr+6);
474 strcpy(newdesc,pa->desc);
476 /* change '%t' into time_unit */
477 #define TUNITLABEL "%t"
478 #define NTUNIT strlen(TUNITLABEL)
479 if (pa->type == etTIME)
480 while( (nptr=strstr(newdesc,TUNITLABEL)) != NULL ) {
483 len+=strlen(time_unit_str)-NTUNIT;
485 strcpy(ndesc,newdesc);
486 strcat(ndesc,time_unit_str);
495 /* Add extra comment for enumerateds */
496 if (pa->type == etENUM) {
497 strcat(newdesc,": ");
498 for(k=1; (pa->u.c[k] != NULL); k++) {
499 strcat(newdesc,"[TT]");
500 strcat(newdesc,pa->u.c[k]);
501 strcat(newdesc,"[tt]");
502 /* Print a comma everywhere but at the last one */
503 if (pa->u.c[k+1] != NULL) {
504 if (pa->u.c[k+2] == NULL)
505 strcat(newdesc," or ");
507 strcat(newdesc,", ");
515 void parse_common_args(int *argc,char *argv[],unsigned long Flags,
516 int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
517 int ndesc,const char **desc,
518 int nbugs,const char **bugs,
521 bool bHelp=FALSE,bHidden=FALSE,bQuiet=FALSE,bVersion=FALSE;
522 const char *manstr[] = { NULL, "no", "html", "tex", "nroff", "ascii",
523 "completion", "py", "xml", "wiki", NULL };
524 /* This array should match the order of the enum in oenv.h */
525 const char *xvg_format[] = { NULL, "xmgrace", "xmgr", "none", NULL };
526 /* This array should match the order of the enum in oenv.h */
527 const char *time_units[] = { NULL, "fs", "ps", "ns", "us", "ms", "s",
529 int nicelevel=0,mantp=0,npri=0,debug_level=0,verbose_level=0;
531 real tbegin=0,tend=0,tdelta=0;
534 t_pargs *all_pa=NULL;
536 t_pargs npri_pa = { "-npri", FALSE, etINT, {&npri},
537 "HIDDEN Set non blocking priority (try 128)" };
538 t_pargs nice_pa = { "-nice", FALSE, etINT, {&nicelevel},
539 "Set the nicelevel" };
540 t_pargs deffnm_pa = { "-deffnm", FALSE, etSTR, {&deffnm},
541 "Set the default filename for all file options" };
542 t_pargs begin_pa = { "-b", FALSE, etTIME, {&tbegin},
543 "First frame (%t) to read from trajectory" };
544 t_pargs end_pa = { "-e", FALSE, etTIME, {&tend},
545 "Last frame (%t) to read from trajectory" };
546 t_pargs dt_pa = { "-dt", FALSE, etTIME, {&tdelta},
547 "Only use frame when t MOD dt = first time (%t)" };
548 t_pargs view_pa = { "-w", FALSE, etBOOL, {&bView},
549 "View output xvg, xpm, eps and pdb files" };
550 t_pargs xvg_pa = { "-xvg", FALSE, etENUM, {xvg_format},
551 "xvg plot formatting" };
552 t_pargs time_pa = { "-tu", FALSE, etENUM, {time_units},
554 /* Maximum number of extra arguments */
558 { "-h", FALSE, etBOOL, {&bHelp},
559 "Print help info and quit" },
560 { "-version", FALSE, etBOOL, {&bVersion},
561 "Print version info and quit" },
562 { "-verb", FALSE, etINT, {&verbose_level},
563 "HIDDENLevel of verbosity for this program" },
564 { "-hidden", FALSE, etBOOL, {&bHidden},
565 "HIDDENPrint hidden options" },
566 { "-quiet",FALSE, etBOOL, {&bQuiet},
567 "HIDDENDo not print help info" },
568 { "-man", FALSE, etENUM, {manstr},
569 "HIDDENWrite manual and quit" },
570 { "-debug",FALSE, etINT, {&debug_level},
571 "HIDDENWrite file with debug information, 1: short, 2: also x and f" },
573 #define NPCA_PA asize(pca_pa)
575 bool bPrint,bExit,bXvgr;
576 int i,j,k,npall,max_pa,cmdlength;
580 #define FF(arg) ((Flags & arg)==arg)
584 cmdlength = strlen(argv[0]);
585 /* Check for double arguments */
586 for (i=1; (i<*argc); i++)
588 cmdlength += strlen(argv[i]);
589 if (argv[i] && (strlen(argv[i]) > 1) && (!isdigit(argv[i][1])))
591 for (j=i+1; (j<*argc); j++)
593 if ( (argv[i][0]=='-') && (argv[j][0]=='-') &&
594 (strcmp(argv[i],argv[j])==0) )
596 if (FF(PCA_NOEXIT_ON_ARGS))
597 fprintf(stderr,"Double command line argument %s\n",
600 gmx_fatal(FARGS,"Double command line argument %s\n",
607 set_program_name(argv[0]);
608 set_command_line(*argc, argv);
610 /* Handle the flags argument, which is a bit field
611 * The FF macro returns whether or not the bit is set
613 bPrint = !FF(PCA_SILENT);
615 /* Check ALL the flags ... */
616 max_pa = NPCA_PA + EXTRA_PA + npargs+1;
619 for(i=npall=0; (i<NPCA_PA); i++)
620 npall = add_parg(npall,all_pa,&(pca_pa[i]));
623 envstr = getenv("GMXNPRIALL");
625 npri=strtol(envstr,NULL,10);
626 if (FF(PCA_BE_NICE)) {
627 envstr = getenv("GMXNPRI");
629 npri=strtol(envstr,NULL,10);
631 npall = add_parg(npall,all_pa,&npri_pa);
636 npall = add_parg(npall,all_pa,&nice_pa);
638 if (FF(PCA_CAN_SET_DEFFNM))
639 npall = add_parg(npall,all_pa,&deffnm_pa);
640 if (FF(PCA_CAN_BEGIN))
641 npall = add_parg(npall,all_pa,&begin_pa);
643 npall = add_parg(npall,all_pa,&end_pa);
646 npall = add_parg(npall,all_pa,&dt_pa);
648 if (FF(PCA_TIME_UNIT)) {
649 npall = add_parg(npall,all_pa,&time_pa);
651 if (FF(PCA_CAN_VIEW))
652 npall = add_parg(npall,all_pa,&view_pa);
655 for(i=0; (i<nfile); i++)
657 bXvgr = bXvgr || (fnm[i].ftp == efXVG);
661 npall = add_parg(npall,all_pa,&xvg_pa);
664 /* Now append the program specific arguments */
665 for(i=0; (i<npargs); i++)
666 npall = add_parg(npall,all_pa,&(pa[i]));
668 /* set etENUM options to default */
669 for(i=0; (i<npall); i++)
671 if (all_pa[i].type==etENUM)
673 all_pa[i].u.c[0]=all_pa[i].u.c[1];
676 set_default_time_unit(time_units,FF(PCA_TIME_UNIT));
677 set_default_xvg_format(xvg_format);
679 /* Now parse all the command-line options */
680 get_pargs(argc,argv,npall,all_pa,FF(PCA_KEEP_ARGS));
682 /* set program name, command line, and default values for output options */
683 output_env_init(*oenv, *argc, argv, (time_unit_t)nenum(time_units), bView,
684 (xvg_format_t)nenum(xvg_format), verbose_level, debug_level);
687 printf("Program: %s\n",output_env_get_program_name(*oenv));
688 gmx_print_version_info(stdout);
692 if (FF(PCA_CAN_SET_DEFFNM) && (deffnm!=NULL))
693 set_default_file_name(deffnm);
695 /* Parse the file args */
696 parse_file_args(argc,argv,nfile,fnm,FF(PCA_KEEP_ARGS),!FF(PCA_NOT_READ_NODE));
698 /* Open the debug file */
699 if (debug_level > 0) {
702 if (gmx_mpi_initialized())
703 sprintf(buf,"%s%d.debug",output_env_get_short_program_name(*oenv),
706 sprintf(buf,"%s.debug",output_env_get_short_program_name(*oenv));
708 init_debug(debug_level,buf);
709 fprintf(stderr,"Opening debug file %s (src code file %s, line %d)\n",
710 buf,__FILE__,__LINE__);
713 /* Now copy the results back... */
714 for(i=0,k=npall-npargs; (i<npargs); i++,k++)
715 memcpy(&(pa[i]),&(all_pa[k]),(size_t)sizeof(pa[i]));
718 for(i=0; (i<npall); i++)
719 all_pa[i].desc = mk_desc(&(all_pa[i]), output_env_get_time_unit(*oenv));
721 bExit = bHelp || (strcmp(manstr[0],"no") != 0);
723 #if (defined __sgi && USE_SGI_FPE)
727 /* Set the nice level */
729 if (npri != 0 && !bExit) {
730 schedctl(MPTS_RTPRI,0,npri);
737 /* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
738 if (nicelevel != 0 && !bExit)
741 static bool nice_set=FALSE; /* only set it once */
742 tMPI_Thread_mutex_lock(&init_mutex);
746 i=nice(nicelevel); /* assign ret value to avoid warnings */
750 tMPI_Thread_mutex_unlock(&init_mutex);
756 /* Update oenv for parsed command line options settings. */
757 (*oenv)->xvg_format = (xvg_format_t)nenum(xvg_format);
758 (*oenv)->time_unit = (time_unit_t)nenum(time_units);
760 if (!(FF(PCA_QUIET) || bQuiet )) {
762 write_man(stderr,"help",output_env_get_program_name(*oenv),
763 ndesc,desc,nfile, fnm,npall,all_pa, nbugs,bugs,bHidden);
765 pr_fns(stderr,nfile,fnm);
766 print_pargs(stderr,npall,all_pa,FALSE);
770 if (strcmp(manstr[0],"no") != 0) {
771 if(!strcmp(manstr[0],"completion")) {
772 /* one file each for csh, bash and zsh if we do completions */
773 fp=man_file(*oenv,"completion-zsh");
775 write_man(fp,"completion-zsh",output_env_get_program_name(*oenv),
776 ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
778 fp=man_file(*oenv,"completion-bash");
779 write_man(fp,"completion-bash",output_env_get_program_name(*oenv),
780 ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
782 fp=man_file(*oenv,"completion-csh");
783 write_man(fp,"completion-csh",output_env_get_program_name(*oenv),
784 ndesc,desc,nfile, fnm, npall,all_pa,nbugs,bugs,bHidden);
787 fp=man_file(*oenv,manstr[0]);
788 write_man(fp,manstr[0],output_env_get_program_name(*oenv),
789 ndesc,desc,nfile,fnm, npall, all_pa,nbugs,bugs,bHidden);
794 /* convert time options, must be done after printing! */
796 for(i=0; i<npall; i++) {
797 if ((all_pa[i].type == etTIME) && (*all_pa[i].u.r >= 0)) {
798 *all_pa[i].u.r *= output_env_get_time_invfactor(*oenv);
802 /* Extract Time info from arguments */
803 if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b",npall,all_pa))
804 setTimeValue(TBEGIN,opt2parg_real("-b",npall,all_pa));
806 if (FF(PCA_CAN_END) && opt2parg_bSet("-e",npall,all_pa))
807 setTimeValue(TEND,opt2parg_real("-e",npall,all_pa));
809 if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt",npall,all_pa))
810 setTimeValue(TDELTA,opt2parg_real("-dt",npall,all_pa));
813 for (i = 0; i < npall; ++i)
814 sfree((void *)all_pa[i].desc);
817 if (!FF(PCA_NOEXIT_ON_ARGS)) {
823 if (gmx_parallel_env_initialized())
824 /*gmx_abort(gmx_node_rank(),gmx_node_num(),0);*/