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37 /* This file is completely threadsafe - keep it that way! */
38 #include "gromacs/commandline/pargs.h"
52 #include "thread_mpi/threads.h"
54 #include "gromacs/commandline/cmdlinehelpcontext.h"
55 #include "gromacs/commandline/cmdlinehelpwriter.h"
56 #include "gromacs/commandline/cmdlineparser.h"
57 #include "gromacs/fileio/timecontrol.h"
58 #include "gromacs/options/basicoptions.h"
59 #include "gromacs/options/filenameoption.h"
60 #include "gromacs/options/filenameoptionmanager.h"
61 #include "gromacs/options/options.h"
62 #include "gromacs/options/timeunitmanager.h"
63 #include "gromacs/utility/arrayref.h"
64 #include "gromacs/utility/basenetwork.h"
65 #include "gromacs/utility/common.h"
66 #include "gromacs/utility/cstringutil.h"
67 #include "gromacs/utility/exceptions.h"
68 #include "gromacs/utility/fatalerror.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 int nenum(const char *const enumc[])
82 /* we *can* compare pointers directly here! */
83 while (enumc[i] && enumc[0] != enumc[i])
91 int opt2parg_int(const char *option, int nparg, t_pargs pa[])
95 for (i = 0; (i < nparg); i++)
97 if (strcmp(pa[i].option, option) == 0)
103 gmx_fatal(FARGS, "No integer option %s in pargs", option);
108 gmx_bool opt2parg_bool(const char *option, int nparg, t_pargs pa[])
112 for (i = 0; (i < nparg); i++)
114 if (strcmp(pa[i].option, option) == 0)
120 gmx_fatal(FARGS, "No boolean option %s in pargs", option);
125 real opt2parg_real(const char *option, int nparg, t_pargs pa[])
129 for (i = 0; (i < nparg); i++)
131 if (strcmp(pa[i].option, option) == 0)
137 gmx_fatal(FARGS, "No real option %s in pargs", option);
142 const char *opt2parg_str(const char *option, int nparg, t_pargs pa[])
146 for (i = 0; (i < nparg); i++)
148 if (strcmp(pa[i].option, option) == 0)
154 gmx_fatal(FARGS, "No string option %s in pargs", option);
159 gmx_bool opt2parg_bSet(const char *option, int nparg, t_pargs pa[])
163 for (i = 0; (i < nparg); i++)
165 if (strcmp(pa[i].option, option) == 0)
171 gmx_fatal(FARGS, "No such option %s in pargs", option);
173 return FALSE; /* Too make some compilers happy */
176 const char *opt2parg_enum(const char *option, int nparg, t_pargs pa[])
180 for (i = 0; (i < nparg); i++)
182 if (strcmp(pa[i].option, option) == 0)
188 gmx_fatal(FARGS, "No such option %s in pargs", option);
193 /********************************************************************
194 * parse_common_args()
204 * Returns the index of the default xvg format.
206 * \ingroup module_commandline
208 int getDefaultXvgFormat(gmx::ConstArrayRef<const char *> xvgFormats)
210 const char *const select = getenv("GMX_VIEW_XVG");
213 ConstArrayRef<const char *>::const_iterator i =
214 std::find(xvgFormats.begin(), xvgFormats.end(), std::string(select));
215 if (i != xvgFormats.end())
217 return i - xvgFormats.begin();
224 /* The default is the first option */
229 * Conversion helper between t_pargs/t_filenm and Options.
231 * This class holds the necessary mapping between the old C structures and
232 * the new C++ options to allow copying values back after parsing for cases
233 * where the C++ options do not directly provide the type of value required for
236 * \ingroup module_commandline
242 * Initializes the adapter to convert from a specified command line.
244 * The command line is required, because t_pargs wants to return
245 * strings by reference to the original command line.
246 * OptionsAdapter creates a copy of the `argv` array (but not the
247 * strings) to make this possible, even if the parser removes
248 * options it has recognized.
250 OptionsAdapter(int argc, const char *const argv[])
251 : argv_(argv, argv + argc)
256 * Converts a t_filenm option into an Options option.
258 * \param options Options object to add the new option to.
259 * \param fnm t_filenm option to convert.
261 void filenmToOptions(Options *options, t_filenm *fnm);
263 * Converts a t_pargs option into an Options option.
265 * \param options Options object to add the new option to.
266 * \param pa t_pargs option to convert.
268 void pargsToOptions(Options *options, t_pargs *pa);
271 * Copies values back from options to t_pargs/t_filenm.
273 void copyValues(bool bReadNode);
278 //! Creates a conversion helper for a given `t_filenm` struct.
279 explicit FileNameData(t_filenm *fnm) : fnm(fnm), optionInfo(NULL)
283 //! t_filenm structure to receive the final values.
285 //! Option info object for the created FileNameOption.
286 FileNameOptionInfo *optionInfo;
287 //! Value storage for the created FileNameOption.
288 std::vector<std::string> values;
290 struct ProgramArgData
292 //! Creates a conversion helper for a given `t_pargs` struct.
293 explicit ProgramArgData(t_pargs *pa)
294 : pa(pa), optionInfo(NULL), enumIndex(0), boolValue(false)
298 //! t_pargs structure to receive the final values.
300 //! Option info object for the created option.
301 OptionInfo *optionInfo;
302 //! Value storage for a non-enum StringOption (unused for other types).
303 std::string stringValue;
304 //! Value storage for an enum option (unused for other types).
306 //! Value storage for a BooleanOption (unused for other types).
310 std::vector<const char *> argv_;
311 // These are lists instead of vectors to avoid relocating existing
312 // objects in case the container is reallocated (the Options object
313 // contains pointes to members of the objects, which would get
315 std::list<FileNameData> fileNameOptions_;
316 std::list<ProgramArgData> programArgs_;
318 GMX_DISALLOW_COPY_AND_ASSIGN(OptionsAdapter);
321 void OptionsAdapter::filenmToOptions(Options *options, t_filenm *fnm)
323 if (fnm->opt == NULL)
325 // Existing code may use opt2fn() instead of ftp2fn() for
326 // options that use the default option name, so we need to
327 // keep the old behavior instead of fixing opt2fn().
328 // TODO: Check that this is not the case, remove this, and make
329 // opt2*() work even if fnm->opt is NULL for some options.
330 fnm->opt = ftp2defopt(fnm->ftp);
332 const bool bRead = ((fnm->flag & ffREAD) != 0);
333 const bool bWrite = ((fnm->flag & ffWRITE) != 0);
334 const bool bOptional = ((fnm->flag & ffOPT) != 0);
335 const bool bLibrary = ((fnm->flag & ffLIB) != 0);
336 const bool bMultiple = ((fnm->flag & ffMULT) != 0);
337 const char *const name = &fnm->opt[1];
338 const char * defName = fnm->fn;
341 defName = ftp2defnm(fnm->ftp);
343 fileNameOptions_.push_back(FileNameData(fnm));
344 FileNameData &data = fileNameOptions_.back();
345 data.optionInfo = options->addOption(
346 FileNameOption(name).storeVector(&data.values)
347 .defaultBasename(defName).legacyType(fnm->ftp)
348 .legacyOptionalBehavior()
349 .readWriteFlags(bRead, bWrite).required(!bOptional)
350 .libraryFile(bLibrary).multiValue(bMultiple)
351 .description(ftp2desc(fnm->ftp)));
354 void OptionsAdapter::pargsToOptions(Options *options, t_pargs *pa)
356 const bool bHidden = startsWith(pa->desc, "HIDDEN");
357 const char *const name = &pa->option[1];
358 const char *const desc = (bHidden ? &pa->desc[6] : pa->desc);
359 programArgs_.push_back(ProgramArgData(pa));
360 ProgramArgData &data = programArgs_.back();
364 data.optionInfo = options->addOption(
365 IntegerOption(name).store(pa->u.i)
366 .description(desc).hidden(bHidden));
369 data.optionInfo = options->addOption(
370 Int64Option(name).store(pa->u.is)
371 .description(desc).hidden(bHidden));
374 data.optionInfo = options->addOption(
375 RealOption(name).store(pa->u.r)
376 .description(desc).hidden(bHidden));
379 data.optionInfo = options->addOption(
380 RealOption(name).store(pa->u.r).timeValue()
381 .description(desc).hidden(bHidden));
385 const char *const defValue = (*pa->u.c != NULL ? *pa->u.c : "");
386 data.optionInfo = options->addOption(
387 StringOption(name).store(&data.stringValue)
388 .defaultValue(defValue)
389 .description(desc).hidden(bHidden));
393 data.optionInfo = options->addOption(
394 BooleanOption(name).store(&data.boolValue)
395 .defaultValue(*pa->u.b)
396 .description(desc).hidden(bHidden));
399 data.optionInfo = options->addOption(
400 RealOption(name).store(*pa->u.rv).vector()
401 .description(desc).hidden(bHidden));
405 const int defaultIndex = (pa->u.c[0] != NULL ? nenum(pa->u.c) - 1 : 0);
406 data.optionInfo = options->addOption(
407 StringOption(name).storeEnumIndex(&data.enumIndex)
408 .defaultEnumIndex(defaultIndex)
409 .enumValueFromNullTerminatedArray(pa->u.c + 1)
410 .description(desc).hidden(bHidden));
414 GMX_THROW(NotImplementedError("Argument type not implemented"));
417 void OptionsAdapter::copyValues(bool bReadNode)
419 std::list<FileNameData>::const_iterator file;
420 for (file = fileNameOptions_.begin(); file != fileNameOptions_.end(); ++file)
422 if (!bReadNode && (file->fnm->flag & ffREAD))
426 if (file->optionInfo->isSet())
428 file->fnm->flag |= ffSET;
430 file->fnm->nfiles = file->values.size();
431 snew(file->fnm->fns, file->fnm->nfiles);
432 for (int i = 0; i < file->fnm->nfiles; ++i)
434 file->fnm->fns[i] = gmx_strdup(file->values[i].c_str());
437 std::list<ProgramArgData>::const_iterator arg;
438 for (arg = programArgs_.begin(); arg != programArgs_.end(); ++arg)
440 arg->pa->bSet = arg->optionInfo->isSet();
441 switch (arg->pa->type)
447 std::vector<const char *>::const_iterator pos =
448 std::find(argv_.begin(), argv_.end(), arg->stringValue);
449 GMX_RELEASE_ASSERT(pos != argv_.end(),
450 "String argument got a value not in argv");
451 *arg->pa->u.c = *pos;
456 *arg->pa->u.b = arg->boolValue;
459 *arg->pa->u.c = arg->pa->u.c[arg->enumIndex + 1];
462 // For other types, there is nothing type-specific to do.
472 gmx_bool parse_common_args(int *argc, char *argv[], unsigned long Flags,
473 int nfile, t_filenm fnm[], int npargs, t_pargs *pa,
474 int ndesc, const char **desc,
475 int nbugs, const char **bugs,
478 /* This array should match the order of the enum in oenv.h */
479 const char *const xvg_formats[] = { "xmgrace", "xmgr", "none" };
481 // Handle the flags argument, which is a bit field
482 // The FF macro returns whether or not the bit is set
483 #define FF(arg) ((Flags & arg) == arg)
488 double tbegin = 0.0, tend = 0.0, tdelta = 0.0;
491 gmx::TimeUnitManager timeUnitManager;
492 gmx::OptionsAdapter adapter(*argc, argv);
493 gmx::Options options(NULL, NULL);
494 gmx::FileNameOptionManager fileOptManager;
496 fileOptManager.disableInputOptionChecking(
497 FF(PCA_NOT_READ_NODE) || FF(PCA_DISABLE_INPUT_FILE_CHECKING));
498 options.addManager(&fileOptManager);
499 options.setDescription(gmx::ConstArrayRef<const char *>(desc, ndesc));
502 gmx::IntegerOption("nice").store(&nicelevel)
503 .defaultValue(FF(PCA_BE_NICE) ? 19 : 0)
504 .description("Set the nicelevel"));
506 if (FF(PCA_CAN_SET_DEFFNM))
508 fileOptManager.addDefaultFileNameOption(&options, "deffnm");
510 if (FF(PCA_CAN_BEGIN))
513 gmx::DoubleOption("b").store(&tbegin).timeValue()
514 .description("First frame (%t) to read from trajectory"));
519 gmx::DoubleOption("e").store(&tend).timeValue()
520 .description("Last frame (%t) to read from trajectory"));
525 gmx::DoubleOption("dt").store(&tdelta).timeValue()
526 .description("Only use frame when t MOD dt = first time (%t)"));
528 if (FF(PCA_TIME_UNIT))
530 timeUnitManager.setTimeUnitFromEnvironment();
531 timeUnitManager.addTimeUnitOption(&options, "tu");
533 if (FF(PCA_CAN_VIEW))
536 gmx::BooleanOption("w").store(&bView)
537 .description("View output [TT].xvg[tt], [TT].xpm[tt], "
538 "[TT].eps[tt] and [TT].pdb[tt] files"));
542 for (int i = 0; i < nfile; i++)
544 bXvgr = bXvgr || (fnm[i].ftp == efXVG);
546 xvgFormat = gmx::getDefaultXvgFormat(xvg_formats);
550 gmx::StringOption("xvg").enumValue(xvg_formats)
551 .storeEnumIndex(&xvgFormat)
552 .description("xvg plot formatting"));
555 /* Now append the program specific arguments */
556 for (int i = 0; i < nfile; i++)
558 adapter.filenmToOptions(&options, &fnm[i]);
560 for (int i = 0; i < npargs; i++)
562 adapter.pargsToOptions(&options, &pa[i]);
565 const gmx::CommandLineHelpContext *context =
566 gmx::GlobalCommandLineHelpContext::get();
569 GMX_RELEASE_ASSERT(gmx_node_rank() == 0,
570 "Help output should be handled higher up and "
571 "only get called only on the master rank");
572 gmx::CommandLineHelpWriter(options)
573 .setShowDescriptions(true)
574 .setTimeUnitString(timeUnitManager.timeUnitAsString())
575 .setKnownIssues(gmx::ConstArrayRef<const char *>(bugs, nbugs))
576 .writeHelp(*context);
580 /* Now parse all the command-line options */
581 gmx::CommandLineParser(&options).skipUnknown(FF(PCA_NOEXIT_ON_ARGS))
585 /* set program name, command line, and default values for output options */
586 output_env_init(oenv, gmx::getProgramContext(),
587 (time_unit_t)(timeUnitManager.timeUnit() + 1), bView,
588 (xvg_format_t)(xvgFormat + 1), 0);
590 /* Set the nice level */
593 /* The some system, e.g. the catamount kernel on cray xt3 do not have nice(2). */
596 static gmx_bool nice_set = FALSE; /* only set it once */
597 static tMPI_Thread_mutex_t init_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
598 tMPI_Thread_mutex_lock(&init_mutex);
601 if (nice(nicelevel) == -1)
603 /* Do nothing, but use the return value to avoid warnings. */
607 tMPI_Thread_mutex_unlock(&init_mutex);
612 timeUnitManager.scaleTimeOptions(&options);
614 /* Extract Time info from arguments */
615 // TODO: Use OptionInfo objects instead of string constants
616 if (FF(PCA_CAN_BEGIN) && options.isSet("b"))
618 setTimeValue(TBEGIN, tbegin);
620 if (FF(PCA_CAN_END) && options.isSet("e"))
622 setTimeValue(TEND, tend);
624 if (FF(PCA_CAN_DT) && options.isSet("dt"))
626 setTimeValue(TDELTA, tdelta);
629 adapter.copyValues(!FF(PCA_NOT_READ_NODE));
633 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;