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37 /* This file is completely threadsafe - keep it that way! */
38 #include "gromacs/commandline/pargs.h"
53 #include "thread_mpi/threads.h"
55 #include "gromacs/legacyheaders/gmx_fatal.h"
56 #include "gromacs/legacyheaders/macros.h"
57 #include "gromacs/legacyheaders/network.h"
59 #include "gromacs/commandline/cmdlinehelpcontext.h"
60 #include "gromacs/commandline/cmdlinehelpwriter.h"
61 #include "gromacs/commandline/shellcompletions.h"
62 #include "gromacs/fileio/timecontrol.h"
63 #include "gromacs/options/basicoptions.h"
64 #include "gromacs/options/filenameoption.h"
65 #include "gromacs/options/options.h"
66 #include "gromacs/utility/arrayref.h"
67 #include "gromacs/utility/cstringutil.h"
68 #include "gromacs/utility/exceptions.h"
69 #include "gromacs/utility/gmxassert.h"
70 #include "gromacs/utility/programcontext.h"
71 #include "gromacs/utility/smalloc.h"
72 #include "gromacs/utility/stringutil.h"
74 /* The source code in this file should be thread-safe.
75 Please keep it that way. */
77 static void usage(const char *type, const char *arg)
79 GMX_ASSERT(arg != NULL, "NULL command-line argument should not occur");
80 gmx_fatal(FARGS, "Expected %s argument for option %s\n", type, arg);
83 /* Scan an int for argument argv[*i] from argument at argv[*i + 1].
84 * eg: -p 32. argv[*i] is only used for error reporting.
85 * If there is no value, or the conversion is not successful, the
86 * routine exits with an error, otherwise it returns the value found.
87 * *i is incremented once.
89 static int iscan(int argc, char *argv[], int *i)
91 const char *const arg = argv[*i];
94 usage("an integer", arg);
96 const char *const value = argv[++(*i)];
98 int var = std::strtol(value, &endptr, 10);
99 if (*value == '\0' || *endptr != '\0')
101 usage("an integer", arg);
106 /* Same as above, but for large integer values */
107 static gmx_int64_t istepscan(int argc, char *argv[], int *i)
109 const char *const arg = argv[*i];
112 usage("an integer", arg);
114 const char *const value = argv[++(*i)];
116 gmx_int64_t var = str_to_int64_t(value, &endptr);
117 if (*value == '\0' || *endptr != '\0')
119 usage("an integer", arg);
124 /* Routine similar to the above, but working on doubles. */
125 static double dscan(int argc, char *argv[], int *i)
127 const char *const arg = argv[*i];
130 usage("a real", arg);
132 const char *const value = argv[++(*i)];
134 double var = std::strtod(value, &endptr);
135 if (*value == '\0' || *endptr != '\0')
137 usage("a real", arg);
142 /* Routine similar to the above, but working on strings. The pointer
143 * returned is a pointer to the argv field.
145 static char *sscan(int argc, char *argv[], int *i)
149 if ( (argv[(*i)+1][0] == '-') && (argc > (*i)+2) &&
150 (argv[(*i)+2][0] != '-') )
152 fprintf(stderr, "Possible missing string argument for option %s\n\n",
158 usage("a string", argv[*i]);
164 static gmx_bool is_hidden(t_pargs *pa)
166 return (strstr(pa->desc, "HIDDEN") != NULL);
169 int nenum(const char *const enumc[])
174 /* we *can* compare pointers directly here! */
175 while (enumc[i] && enumc[0] != enumc[i])
183 /* Read a number of arguments from the command line.
184 * For etINT, etREAL and etCHAR an extra argument is read (when present)
185 * for etBOOL the gmx_boolean option is changed to the negate value
187 static void get_pargs(int *argc, char *argv[], int nparg, t_pargs pa[])
194 snew(bKeep, *argc+1);
198 for (i = 1; (i < *argc); i++)
201 for (j = 0; (j < nparg); j++)
203 if (pa[j].type == etBOOL)
205 sprintf(buf, "-no%s", pa[j].option+1);
206 if (strcmp(pa[j].option, argv[i]) == 0)
212 else if (strcmp(buf, argv[i]) == 0)
219 else if (strcmp(pa[j].option, argv[i]) == 0)
223 fprintf(stderr, "Setting option %s more than once!\n",
231 *pa[j].u.i = iscan(*argc, argv, &i);
234 *pa[j].u.is = istepscan(*argc, argv, &i);
238 *pa[j].u.r = dscan(*argc, argv, &i);
241 *(pa[j].u.c) = sscan(*argc, argv, &i);
245 ptr = sscan(*argc, argv, &i);
246 for (k = 1; (pa[j].u.c[k] != NULL); k++)
248 /* only check ptr against beginning of
250 if (gmx_strncasecmp(ptr, pa[j].u.c[k], strlen(ptr)) == 0)
252 if ( ( match == -1 ) ||
253 ( strlen(pa[j].u.c[k]) <
254 strlen(pa[j].u.c[match]) ) )
262 pa[j].u.c[0] = pa[j].u.c[match];
266 gmx_fatal(FARGS, "Invalid argument %s for option %s",
271 (*pa[j].u.rv)[0] = dscan(*argc, argv, &i);
272 if ( (i+1 == *argc) ||
273 ( (argv[i+1][0] == '-') &&
274 !isdigit(argv[i+1][1]) ) )
283 (*pa[j].u.rv)[1] = dscan(*argc, argv, &i);
284 if ( (i+1 == *argc) ||
285 ( (argv[i+1][0] == '-') &&
286 !isdigit(argv[i+1][1]) ) )
289 "%s: vector must have 1 or 3 real parameters",
293 (*pa[j].u.rv)[2] = dscan(*argc, argv, &i);
297 gmx_fatal(FARGS, "Invalid type %d in pargs", pa[j].type);
299 /* i may be incremented, so set it to not keep */
305 /* Remove used entries */
306 for (i = j = 0; (i <= *argc); i++)
317 int opt2parg_int(const char *option, int nparg, t_pargs pa[])
321 for (i = 0; (i < nparg); i++)
323 if (strcmp(pa[i].option, option) == 0)
329 gmx_fatal(FARGS, "No integer option %s in pargs", option);
334 gmx_bool opt2parg_bool(const char *option, int nparg, t_pargs pa[])
338 for (i = 0; (i < nparg); i++)
340 if (strcmp(pa[i].option, option) == 0)
346 gmx_fatal(FARGS, "No boolean option %s in pargs", option);
351 real opt2parg_real(const char *option, int nparg, t_pargs pa[])
355 for (i = 0; (i < nparg); i++)
357 if (strcmp(pa[i].option, option) == 0)
363 gmx_fatal(FARGS, "No real option %s in pargs", option);
368 const char *opt2parg_str(const char *option, int nparg, t_pargs pa[])
372 for (i = 0; (i < nparg); i++)
374 if (strcmp(pa[i].option, option) == 0)
380 gmx_fatal(FARGS, "No string option %s in pargs", option);
385 gmx_bool opt2parg_bSet(const char *option, int nparg, t_pargs pa[])
389 for (i = 0; (i < nparg); i++)
391 if (strcmp(pa[i].option, option) == 0)
397 gmx_fatal(FARGS, "No such option %s in pargs", option);
399 return FALSE; /* Too make some compilers happy */
402 const char *opt2parg_enum(const char *option, int nparg, t_pargs pa[])
406 for (i = 0; (i < nparg); i++)
408 if (strcmp(pa[i].option, option) == 0)
414 gmx_fatal(FARGS, "No such option %s in pargs", option);
419 /********************************************************************
420 * parse_common_args()
423 static void set_default_time_unit(const char *time_list[], gmx_bool bCanTime)
426 const char *select = NULL;
430 select = getenv("GMXTIMEUNIT");
434 while (time_list[i] && strcmp(time_list[i], select) != 0)
440 if (!bCanTime || select == NULL ||
441 time_list[i] == NULL || strcmp(time_list[i], select) != 0)
443 /* Set it to the default: ps */
445 while (time_list[i] && strcmp(time_list[i], "ps") != 0)
451 time_list[0] = time_list[i];
454 static void set_default_xvg_format(const char *xvg_list[])
459 select = getenv("GMX_VIEW_XVG");
462 /* The default is the first option */
463 xvg_list[0] = xvg_list[1];
468 while (xvg_list[i] && strcmp(xvg_list[i], select) != 0)
472 if (xvg_list[i] != NULL)
474 xvg_list[0] = xvg_list[i];
478 xvg_list[0] = xvg_list[exvgNONE];
483 static int add_parg(int npargs, t_pargs *pa, t_pargs *pa_add)
485 memcpy(&(pa[npargs]), pa_add, sizeof(*pa_add));
497 * Converts a t_filenm option into an Options option.
499 * \param options Options object to add the new option to.
500 * \param[in] fnm t_filenm option to convert.
502 * \ingroup module_commandline
504 void filenmToOptions(Options *options, const t_filenm *fnm)
506 const bool bRead = ((fnm->flag & ffREAD) != 0);
507 const bool bWrite = ((fnm->flag & ffWRITE) != 0);
508 const bool bOptional = ((fnm->flag & ffOPT) != 0);
509 const bool bLibrary = ((fnm->flag & ffLIB) != 0);
510 const bool bMultiple = ((fnm->flag & ffMULT) != 0);
511 const char *const name = &fnm->opt[1];
512 const char * defName = fnm->fn;
515 defName = ftp2defnm(fnm->ftp);
517 // Since we are not (yet) using this for actual parsing, we don't need to
520 FileNameOption(name).defaultBasename(defName).legacyType(fnm->ftp)
521 .readWriteFlags(bRead, bWrite).required(!bOptional)
522 .libraryFile(bLibrary).multiValue(bMultiple)
523 .description(ftp2desc(fnm->ftp)));
527 * Converts a t_pargs option into an Options option.
529 * \param options Options object to add the new option to.
530 * \param[in] pa t_pargs option to convert.
532 * \ingroup module_commandline
534 void pargsToOptions(Options *options, t_pargs *pa)
536 const bool bHidden = is_hidden(pa);
537 const char *const name = &pa->option[1];
538 const char *const desc = (bHidden ? &pa->desc[6] : pa->desc);
539 // Since we are not (yet) using this for actual parsing, we can take some
540 // shortcuts and not set any storage where there is no direct
541 // correspondence in the types.
546 IntegerOption(name).store(pa->u.i)
547 .description(desc).hidden(bHidden));
551 Int64Option(name).store(pa->u.is)
552 .description(desc).hidden(bHidden));
556 RealOption(name).store(pa->u.r)
557 .description(desc).hidden(bHidden));
561 RealOption(name).store(pa->u.r).timeValue()
562 .description(desc).hidden(bHidden));
566 const char *const defValue = (*pa->u.c != NULL ? *pa->u.c : "");
568 StringOption(name).defaultValue(defValue)
569 .description(desc).hidden(bHidden));
574 BooleanOption(name).defaultValue(*pa->u.b)
575 .description(desc).hidden(bHidden));
579 RealOption(name).store(*pa->u.rv).vector()
580 .description(desc).hidden(bHidden));
584 StringOption(name).defaultEnumIndex(nenum(pa->u.c) - 1)
585 .enumValueFromNullTerminatedArray(pa->u.c + 1)
586 .description(desc).hidden(bHidden));
589 GMX_THROW(NotImplementedError("Argument type not implemented"));
596 gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
597 int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
598 int ndesc, const char **desc,
599 int nbugs, const char **bugs,
602 /* This array should match the order of the enum in oenv.h */
603 const char *xvg_format[] = { NULL, "xmgrace", "xmgr", "none", NULL };
604 /* This array should match the order of the enum in oenv.h */
605 const char *time_units[] = {
606 NULL, "fs", "ps", "ns", "us", "ms", "s",
609 int nicelevel = 0, debug_level = 0;
611 real tbegin = 0, tend = 0, tdelta = 0;
612 gmx_bool bView = FALSE;
614 t_pargs *all_pa = NULL;
617 "-nice", FALSE, etINT, {&nicelevel},
620 t_pargs deffnm_pa = {
621 "-deffnm", FALSE, etSTR, {&deffnm},
622 "Set the default filename for all file options"
625 "-b", FALSE, etTIME, {&tbegin},
626 "First frame (%t) to read from trajectory"
629 "-e", FALSE, etTIME, {&tend},
630 "Last frame (%t) to read from trajectory"
633 "-dt", FALSE, etTIME, {&tdelta},
634 "Only use frame when t MOD dt = first time (%t)"
637 "-w", FALSE, etBOOL, {&bView},
638 "View output [TT].xvg[tt], [TT].xpm[tt], [TT].eps[tt] and [TT].pdb[tt] files"
641 "-xvg", FALSE, etENUM, {xvg_format},
642 "xvg plot formatting"
645 "-tu", FALSE, etENUM, {time_units},
648 /* Maximum number of extra arguments */
652 { "-debug", FALSE, etINT, {&debug_level},
653 "HIDDENWrite file with debug information, 1: short, 2: also x and f" },
655 #define NPCA_PA asize(pca_pa)
657 int i, j, k, npall, max_pa;
659 // Handle the flags argument, which is a bit field
660 // The FF macro returns whether or not the bit is set
661 #define FF(arg) ((Flags & arg) == arg)
663 /* Check for double arguments */
664 for (i = 1; (i < *argc); i++)
666 if (argv[i] && (strlen(argv[i]) > 1) && (!std::isdigit(argv[i][1])))
668 for (j = i+1; (j < *argc); j++)
670 if ( (argv[i][0] == '-') && (argv[j][0] == '-') &&
671 (strcmp(argv[i], argv[j]) == 0) )
673 if (FF(PCA_NOEXIT_ON_ARGS))
675 fprintf(stderr, "Double command line argument %s\n",
680 gmx_fatal(FARGS, "Double command line argument %s\n",
689 /* Check ALL the flags ... */
690 max_pa = NPCA_PA + EXTRA_PA + npargs+1;
691 snew(all_pa, max_pa);
693 for (i = npall = 0; (i < static_cast<int>(NPCA_PA)); i++)
695 npall = add_parg(npall, all_pa, &(pca_pa[i]));
702 npall = add_parg(npall, all_pa, &nice_pa);
704 if (FF(PCA_CAN_SET_DEFFNM))
706 npall = add_parg(npall, all_pa, &deffnm_pa);
708 if (FF(PCA_CAN_BEGIN))
710 npall = add_parg(npall, all_pa, &begin_pa);
714 npall = add_parg(npall, all_pa, &end_pa);
718 npall = add_parg(npall, all_pa, &dt_pa);
720 if (FF(PCA_TIME_UNIT))
722 npall = add_parg(npall, all_pa, &time_pa);
724 if (FF(PCA_CAN_VIEW))
726 npall = add_parg(npall, all_pa, &view_pa);
730 for (i = 0; (i < nfile); i++)
732 bXvgr = bXvgr || (fnm[i].ftp == efXVG);
736 npall = add_parg(npall, all_pa, &xvg_pa);
739 /* Now append the program specific arguments */
740 for (i = 0; (i < npargs); i++)
742 npall = add_parg(npall, all_pa, &(pa[i]));
745 /* set etENUM options to default */
746 for (i = 0; (i < npall); i++)
748 if (all_pa[i].type == etENUM)
750 all_pa[i].u.c[0] = all_pa[i].u.c[1];
753 set_default_time_unit(time_units, FF(PCA_TIME_UNIT));
754 set_default_xvg_format(xvg_format);
756 /* Now parse all the command-line options */
757 get_pargs(argc, argv, npall, all_pa);
759 /* set program name, command line, and default values for output options */
760 output_env_init(oenv, gmx::getProgramContext(), (time_unit_t)nenum(time_units), bView,
761 (xvg_format_t)nenum(xvg_format), 0, debug_level);
763 /* Parse the file args */
764 parse_file_args(argc, argv, nfile, fnm, deffnm, !FF(PCA_NOT_READ_NODE));
766 /* Open the debug file */
771 if (gmx_mpi_initialized())
773 sprintf(buf, "%s%d.debug", output_env_get_short_program_name(*oenv),
778 sprintf(buf, "%s.debug", output_env_get_short_program_name(*oenv));
781 init_debug(debug_level, buf);
782 fprintf(stderr, "Opening debug file %s (src code file %s, line %d)\n",
783 buf, __FILE__, __LINE__);
786 /* Now copy the results back... */
787 for (i = 0, k = npall-npargs; (i < npargs); i++, k++)
789 memcpy(&(pa[i]), &(all_pa[k]), (size_t)sizeof(pa[i]));
795 const gmx::CommandLineHelpContext *context =
796 gmx::GlobalCommandLineHelpContext::get();
797 bExit = (context != NULL);
798 if (context != NULL && !(FF(PCA_QUIET)))
800 gmx::Options options(NULL, NULL);
801 options.setDescription(gmx::ConstArrayRef<const char *>(desc, ndesc));
802 for (i = 0; i < nfile; i++)
804 gmx::filenmToOptions(&options, &fnm[i]);
806 for (i = 0; i < npall; i++)
808 gmx::pargsToOptions(&options, &all_pa[i]);
810 gmx::CommandLineHelpWriter(options)
811 .setShowDescriptions(true)
812 .setTimeUnitString(output_env_get_time_unit(*oenv))
813 .setKnownIssues(gmx::ConstArrayRef<const char *>(bugs, nbugs))
814 .writeHelp(*context);
817 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
819 /* Set the nice level */
822 /* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
823 if (nicelevel != 0 && !bExit)
825 static gmx_bool nice_set = FALSE; /* only set it once */
826 static tMPI_Thread_mutex_t init_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
827 tMPI_Thread_mutex_lock(&init_mutex);
830 if (nice(nicelevel) == -1)
832 /* Do nothing, but use the return value to avoid warnings. */
836 tMPI_Thread_mutex_unlock(&init_mutex);
841 /* convert time options, must be done after printing! */
843 for (i = 0; i < npall; i++)
845 if (all_pa[i].type == etTIME && all_pa[i].bSet)
847 *all_pa[i].u.r *= output_env_get_time_invfactor(*oenv);
851 /* Extract Time info from arguments */
852 if (FF(PCA_CAN_BEGIN) && opt2parg_bSet("-b", npall, all_pa))
854 setTimeValue(TBEGIN, opt2parg_real("-b", npall, all_pa));
857 if (FF(PCA_CAN_END) && opt2parg_bSet("-e", npall, all_pa))
859 setTimeValue(TEND, opt2parg_real("-e", npall, all_pa));
862 if (FF(PCA_CAN_DT) && opt2parg_bSet("-dt", npall, all_pa))
864 setTimeValue(TDELTA, opt2parg_real("-dt", npall, all_pa));
870 if (!FF(PCA_NOEXIT_ON_ARGS))