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37 /* This file is completely threadsafe - keep it that way! */
38 #include "gromacs/commandline/pargs.h"
55 #include <sys/schedctl.h>
56 #include <sys/sysmp.h>
59 #include "gromacs/legacyheaders/gmx_fatal.h"
60 #include "gromacs/legacyheaders/macros.h"
61 #include "gromacs/legacyheaders/network.h"
62 #include "gromacs/legacyheaders/smalloc.h"
63 #include "gromacs/legacyheaders/string2.h"
64 #include "gromacs/legacyheaders/thread_mpi/threads.h"
66 #include "gromacs/commandline/cmdlinehelpcontext.h"
67 #include "gromacs/commandline/cmdlinehelpwriter.h"
68 #include "gromacs/commandline/shellcompletions.h"
69 #include "gromacs/fileio/timecontrol.h"
70 #include "gromacs/options/basicoptions.h"
71 #include "gromacs/options/filenameoption.h"
72 #include "gromacs/options/options.h"
73 #include "gromacs/utility/arrayref.h"
74 #include "gromacs/utility/exceptions.h"
75 #include "gromacs/utility/gmxassert.h"
76 #include "gromacs/utility/stringutil.h"
78 /* The source code in this file should be thread-safe.
79 Please keep it that way. */
81 static void usage(const char *type, const char *arg)
83 GMX_ASSERT(arg != NULL, "NULL command-line argument should not occur");
84 gmx_fatal(FARGS, "Expected %s argument for option %s\n", type, arg);
87 /* Scan an int for argument argv[*i] from argument at argv[*i + 1].
88 * eg: -p 32. argv[*i] is only used for error reporting.
89 * If there is no value, or the conversion is not successful, the
90 * routine exits with an error, otherwise it returns the value found.
91 * *i is incremented once.
93 static int iscan(int argc, char *argv[], int *i)
95 const char *const arg = argv[*i];
98 usage("an integer", arg);
100 const char *const value = argv[++(*i)];
102 int var = std::strtol(value, &endptr, 10);
103 if (*value == '\0' || *endptr != '\0')
105 usage("an integer", arg);
110 /* Same as above, but for large integer values */
111 static gmx_int64_t istepscan(int argc, char *argv[], int *i)
113 const char *const arg = argv[*i];
116 usage("an integer", arg);
118 const char *const value = argv[++(*i)];
120 gmx_int64_t var = str_to_int64_t(value, &endptr);
121 if (*value == '\0' || *endptr != '\0')
123 usage("an integer", arg);
128 /* Routine similar to the above, but working on doubles. */
129 static double dscan(int argc, char *argv[], int *i)
131 const char *const arg = argv[*i];
134 usage("a real", arg);
136 const char *const value = argv[++(*i)];
138 double var = std::strtod(value, &endptr);
139 if (*value == '\0' || *endptr != '\0')
141 usage("a real", arg);
146 /* Routine similar to the above, but working on strings. The pointer
147 * returned is a pointer to the argv field.
149 static char *sscan(int argc, char *argv[], int *i)
153 if ( (argv[(*i)+1][0] == '-') && (argc > (*i)+2) &&
154 (argv[(*i)+2][0] != '-') )
156 fprintf(stderr, "Possible missing string argument for option %s\n\n",
162 usage("a string", argv[*i]);
168 gmx_bool is_hidden(t_pargs *pa)
170 return (strstr(pa->desc, "HIDDEN") != NULL);
173 int nenum(const char *const enumc[])
178 /* we *can* compare pointers directly here! */
179 while (enumc[i] && enumc[0] != enumc[i])
187 /* Read a number of arguments from the command line.
188 * For etINT, etREAL and etCHAR an extra argument is read (when present)
189 * for etBOOL the gmx_boolean option is changed to the negate value
191 static void get_pargs(int *argc, char *argv[], int nparg, t_pargs pa[])
198 snew(bKeep, *argc+1);
202 for (i = 1; (i < *argc); i++)
205 for (j = 0; (j < nparg); j++)
207 if (pa[j].type == etBOOL)
209 sprintf(buf, "-no%s", pa[j].option+1);
210 if (strcmp(pa[j].option, argv[i]) == 0)
216 else if (strcmp(buf, argv[i]) == 0)
223 else if (strcmp(pa[j].option, argv[i]) == 0)
227 fprintf(stderr, "Setting option %s more than once!\n",
235 *pa[j].u.i = iscan(*argc, argv, &i);
238 *pa[j].u.is = istepscan(*argc, argv, &i);
242 *pa[j].u.r = dscan(*argc, argv, &i);
245 *(pa[j].u.c) = sscan(*argc, argv, &i);
249 ptr = sscan(*argc, argv, &i);
250 for (k = 1; (pa[j].u.c[k] != NULL); k++)
252 /* only check ptr against beginning of
254 if (gmx_strncasecmp(ptr, pa[j].u.c[k], strlen(ptr)) == 0)
256 if ( ( match == -1 ) ||
257 ( strlen(pa[j].u.c[k]) <
258 strlen(pa[j].u.c[match]) ) )
266 pa[j].u.c[0] = pa[j].u.c[match];
270 gmx_fatal(FARGS, "Invalid argument %s for option %s",
275 (*pa[j].u.rv)[0] = dscan(*argc, argv, &i);
276 if ( (i+1 == *argc) ||
277 ( (argv[i+1][0] == '-') &&
278 !isdigit(argv[i+1][1]) ) )
287 (*pa[j].u.rv)[1] = dscan(*argc, argv, &i);
288 if ( (i+1 == *argc) ||
289 ( (argv[i+1][0] == '-') &&
290 !isdigit(argv[i+1][1]) ) )
293 "%s: vector must have 1 or 3 real parameters",
297 (*pa[j].u.rv)[2] = dscan(*argc, argv, &i);
301 gmx_fatal(FARGS, "Invalid type %d in pargs", pa[j].type);
303 /* i may be incremented, so set it to not keep */
309 /* Remove used entries */
310 for (i = j = 0; (i <= *argc); i++)
321 int opt2parg_int(const char *option, int nparg, t_pargs pa[])
325 for (i = 0; (i < nparg); i++)
327 if (strcmp(pa[i].option, option) == 0)
333 gmx_fatal(FARGS, "No integer option %s in pargs", option);
338 gmx_bool opt2parg_gmx_bool(const char *option, int nparg, t_pargs pa[])
342 for (i = 0; (i < nparg); i++)
344 if (strcmp(pa[i].option, option) == 0)
350 gmx_fatal(FARGS, "No boolean option %s in pargs", option);
355 real opt2parg_real(const char *option, int nparg, t_pargs pa[])
359 for (i = 0; (i < nparg); i++)
361 if (strcmp(pa[i].option, option) == 0)
367 gmx_fatal(FARGS, "No real option %s in pargs", option);
372 const char *opt2parg_str(const char *option, int nparg, t_pargs pa[])
376 for (i = 0; (i < nparg); i++)
378 if (strcmp(pa[i].option, option) == 0)
384 gmx_fatal(FARGS, "No string option %s in pargs", option);
389 gmx_bool opt2parg_bSet(const char *option, int nparg, t_pargs pa[])
393 for (i = 0; (i < nparg); i++)
395 if (strcmp(pa[i].option, option) == 0)
401 gmx_fatal(FARGS, "No such option %s in pargs", option);
403 return FALSE; /* Too make some compilers happy */
406 const char *opt2parg_enum(const char *option, int nparg, t_pargs pa[])
410 for (i = 0; (i < nparg); i++)
412 if (strcmp(pa[i].option, option) == 0)
418 gmx_fatal(FARGS, "No such option %s in pargs", option);
423 /********************************************************************
424 * parse_common_args()
427 static void set_default_time_unit(const char *time_list[], gmx_bool bCanTime)
430 const char *select = NULL;
434 select = getenv("GMXTIMEUNIT");
438 while (time_list[i] && strcmp(time_list[i], select) != 0)
444 if (!bCanTime || select == NULL ||
445 time_list[i] == NULL || strcmp(time_list[i], select) != 0)
447 /* Set it to the default: ps */
449 while (time_list[i] && strcmp(time_list[i], "ps") != 0)
455 time_list[0] = time_list[i];
458 static void set_default_xvg_format(const char *xvg_list[])
463 select = getenv("GMX_VIEW_XVG");
466 /* The default is the first option */
467 xvg_list[0] = xvg_list[1];
472 while (xvg_list[i] && strcmp(xvg_list[i], select) != 0)
476 if (xvg_list[i] != NULL)
478 xvg_list[0] = xvg_list[i];
482 xvg_list[0] = xvg_list[exvgNONE];
487 static int add_parg(int npargs, t_pargs *pa, t_pargs *pa_add)
489 memcpy(&(pa[npargs]), pa_add, sizeof(*pa_add));
501 * Converts a t_filenm option into an Options option.
503 * \param options Options object to add the new option to.
504 * \param[in] fnm t_filenm option to convert.
506 * \ingroup module_commandline
508 void filenmToOptions(Options *options, const t_filenm *fnm)
510 const bool bRead = ((fnm->flag & ffREAD) != 0);
511 const bool bWrite = ((fnm->flag & ffWRITE) != 0);
512 const bool bOptional = ((fnm->flag & ffOPT) != 0);
513 const bool bLibrary = ((fnm->flag & ffLIB) != 0);
514 const bool bMultiple = ((fnm->flag & ffMULT) != 0);
515 const char *const name = &fnm->opt[1];
516 const char * defName = fnm->fn;
519 defName = ftp2defnm(fnm->ftp);
521 // Since we are not (yet) using this for actual parsing, we don't need to
524 FileNameOption(name).defaultBasename(defName).legacyType(fnm->ftp)
525 .readWriteFlags(bRead, bWrite).required(!bOptional)
526 .libraryFile(bLibrary).multiValue(bMultiple)
527 .description(ftp2desc(fnm->ftp)));
531 * Converts a t_pargs option into an Options option.
533 * \param options Options object to add the new option to.
534 * \param[in] pa t_pargs option to convert.
536 * \ingroup module_commandline
538 void pargsToOptions(Options *options, t_pargs *pa)
540 const bool bHidden = is_hidden(pa);
541 const char *const name = &pa->option[1];
542 const char *const desc = (bHidden ? &pa->desc[6] : pa->desc);
543 // Since we are not (yet) using this for actual parsing, we can take some
544 // shortcuts and not set any storage where there is no direct
545 // correspondence in the types.
550 IntegerOption(name).store(pa->u.i)
551 .description(desc).hidden(bHidden));
555 Int64Option(name).store(pa->u.is)
556 .description(desc).hidden(bHidden));
560 RealOption(name).store(pa->u.r)
561 .description(desc).hidden(bHidden));
565 RealOption(name).store(pa->u.r).timeValue()
566 .description(desc).hidden(bHidden));
570 const char *const defValue = (*pa->u.c != NULL ? *pa->u.c : "");
572 StringOption(name).defaultValue(defValue)
573 .description(desc).hidden(bHidden));
578 BooleanOption(name).defaultValue(*pa->u.b)
579 .description(desc).hidden(bHidden));
583 RealOption(name).store(*pa->u.rv).vector()
584 .description(desc).hidden(bHidden));
588 StringOption(name).defaultEnumIndex(nenum(pa->u.c) - 1)
589 .enumValueFromNullTerminatedArray(pa->u.c + 1)
590 .description(desc).hidden(bHidden));
593 GMX_THROW(NotImplementedError("Argument type not implemented"));
600 gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
601 int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
602 int ndesc, const char **desc,
603 int nbugs, const char **bugs,
606 /* This array should match the order of the enum in oenv.h */
607 const char *xvg_format[] = { NULL, "xmgrace", "xmgr", "none", NULL };
608 /* This array should match the order of the enum in oenv.h */
609 const char *time_units[] = {
610 NULL, "fs", "ps", "ns", "us", "ms", "s",
613 int nicelevel = 0, debug_level = 0;
615 real tbegin = 0, tend = 0, tdelta = 0;
616 gmx_bool bView = FALSE;
618 t_pargs *all_pa = NULL;
623 "-npri", FALSE, etINT, {&npri},
624 "HIDDEN Set non blocking priority (try 128)"
628 "-nice", FALSE, etINT, {&nicelevel},
631 t_pargs deffnm_pa = {
632 "-deffnm", FALSE, etSTR, {&deffnm},
633 "Set the default filename for all file options"
636 "-b", FALSE, etTIME, {&tbegin},
637 "First frame (%t) to read from trajectory"
640 "-e", FALSE, etTIME, {&tend},
641 "Last frame (%t) to read from trajectory"
644 "-dt", FALSE, etTIME, {&tdelta},
645 "Only use frame when t MOD dt = first time (%t)"
648 "-w", FALSE, etBOOL, {&bView},
649 "View output [TT].xvg[tt], [TT].xpm[tt], [TT].eps[tt] and [TT].pdb[tt] files"
652 "-xvg", FALSE, etENUM, {xvg_format},
653 "xvg plot formatting"
656 "-tu", FALSE, etENUM, {time_units},
659 /* Maximum number of extra arguments */
663 { "-debug", FALSE, etINT, {&debug_level},
664 "HIDDENWrite file with debug information, 1: short, 2: also x and f" },
666 #define NPCA_PA asize(pca_pa)
668 int i, j, k, npall, max_pa;
670 // Handle the flags argument, which is a bit field
671 // The FF macro returns whether or not the bit is set
672 #define FF(arg) ((Flags & arg) == arg)
674 /* Check for double arguments */
675 for (i = 1; (i < *argc); i++)
677 if (argv[i] && (strlen(argv[i]) > 1) && (!std::isdigit(argv[i][1])))
679 for (j = i+1; (j < *argc); j++)
681 if ( (argv[i][0] == '-') && (argv[j][0] == '-') &&
682 (strcmp(argv[i], argv[j]) == 0) )
684 if (FF(PCA_NOEXIT_ON_ARGS))
686 fprintf(stderr, "Double command line argument %s\n",
691 gmx_fatal(FARGS, "Double command line argument %s\n",
700 /* Check ALL the flags ... */
701 max_pa = NPCA_PA + EXTRA_PA + npargs+1;
702 snew(all_pa, max_pa);
704 for (i = npall = 0; (i < static_cast<int>(NPCA_PA)); i++)
706 npall = add_parg(npall, all_pa, &(pca_pa[i]));
710 const char *envstr = getenv("GMXNPRIALL");
713 npri = strtol(envstr, NULL, 10);
717 envstr = getenv("GMXNPRI");
720 npri = strtol(envstr, NULL, 10);
723 npall = add_parg(npall, all_pa, &npri_pa);
730 npall = add_parg(npall, all_pa, &nice_pa);
732 if (FF(PCA_CAN_SET_DEFFNM))
734 npall = add_parg(npall, all_pa, &deffnm_pa);
736 if (FF(PCA_CAN_BEGIN))
738 npall = add_parg(npall, all_pa, &begin_pa);
742 npall = add_parg(npall, all_pa, &end_pa);
746 npall = add_parg(npall, all_pa, &dt_pa);
748 if (FF(PCA_TIME_UNIT))
750 npall = add_parg(npall, all_pa, &time_pa);
752 if (FF(PCA_CAN_VIEW))
754 npall = add_parg(npall, all_pa, &view_pa);
758 for (i = 0; (i < nfile); i++)
760 bXvgr = bXvgr || (fnm[i].ftp == efXVG);
764 npall = add_parg(npall, all_pa, &xvg_pa);
767 /* Now append the program specific arguments */
768 for (i = 0; (i < npargs); i++)
770 npall = add_parg(npall, all_pa, &(pa[i]));
773 /* set etENUM options to default */
774 for (i = 0; (i < npall); i++)
776 if (all_pa[i].type == etENUM)
778 all_pa[i].u.c[0] = all_pa[i].u.c[1];
781 set_default_time_unit(time_units, FF(PCA_TIME_UNIT));
782 set_default_xvg_format(xvg_format);
784 /* Now parse all the command-line options */
785 get_pargs(argc, argv, npall, all_pa);
787 /* set program name, command line, and default values for output options */
788 output_env_init(oenv, *argc, argv, (time_unit_t)nenum(time_units), bView,
789 (xvg_format_t)nenum(xvg_format), 0, debug_level);
791 /* Parse the file args */
792 parse_file_args(argc, argv, nfile, fnm, deffnm, !FF(PCA_NOT_READ_NODE));
794 /* Open the debug file */
799 if (gmx_mpi_initialized())
801 sprintf(buf, "%s%d.debug", output_env_get_short_program_name(*oenv),
806 sprintf(buf, "%s.debug", output_env_get_short_program_name(*oenv));
809 init_debug(debug_level, buf);
810 fprintf(stderr, "Opening debug file %s (src code file %s, line %d)\n",
811 buf, __FILE__, __LINE__);
814 /* Now copy the results back... */
815 for (i = 0, k = npall-npargs; (i < npargs); i++, k++)
817 memcpy(&(pa[i]), &(all_pa[k]), (size_t)sizeof(pa[i]));
820 #if (defined __sgi && USE_SGI_FPE)
827 const gmx::CommandLineHelpContext *context =
828 gmx::GlobalCommandLineHelpContext::get();
829 bExit = (context != NULL);
830 if (context != NULL && !(FF(PCA_QUIET)))
832 gmx::Options options(NULL, NULL);
833 options.setDescription(gmx::ConstArrayRef<const char *>(desc, ndesc));
834 for (i = 0; i < nfile; i++)
836 gmx::filenmToOptions(&options, &fnm[i]);
838 for (i = 0; i < npall; i++)
840 gmx::pargsToOptions(&options, &all_pa[i]);
842 gmx::CommandLineHelpWriter(options)
843 .setShowDescriptions(true)
844 .setTimeUnitString(output_env_get_time_unit(*oenv))
845 .setKnownIssues(gmx::ConstArrayRef<const char *>(bugs, nbugs))
846 .writeHelp(*context);
849 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
851 /* Set the nice level */
853 if (npri != 0 && !bExit)
855 schedctl(MPTS_RTPRI, 0, npri);
861 /* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
862 if (nicelevel != 0 && !bExit)
864 static gmx_bool nice_set = FALSE; /* only set it once */
865 static tMPI_Thread_mutex_t init_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
866 tMPI_Thread_mutex_lock(&init_mutex);
869 if (nice(nicelevel) == -1)
871 /* Do nothing, but use the return value to avoid warnings. */
875 tMPI_Thread_mutex_unlock(&init_mutex);
880 /* convert time options, must be done after printing! */
882 for (i = 0; i < npall; i++)
884 if (all_pa[i].type == etTIME && all_pa[i].bSet)
886 *all_pa[i].u.r *= output_env_get_time_invfactor(*oenv);
890 /* Extract Time info from arguments */
891 if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b", npall, all_pa))
893 setTimeValue(TBEGIN, opt2parg_real("-b", npall, all_pa));
896 if (FF(PCA_CAN_END) && opt2parg_bSet("-e", npall, all_pa))
898 setTimeValue(TEND, opt2parg_real("-e", npall, all_pa));
901 if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt", npall, all_pa))
903 setTimeValue(TDELTA, opt2parg_real("-dt", npall, all_pa));
909 if (!FF(PCA_NOEXIT_ON_ARGS))