/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_commandline
*/
+#include "gmxpre.h"
+
#include "cmdlinemodulemanager.h"
#include <cstdio>
#include <string>
#include <utility>
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/network.h"
-
#include "gromacs/commandline/cmdlinehelpcontext.h"
-#include "gromacs/commandline/cmdlinehelpmodule.h"
#include "gromacs/commandline/cmdlineinit.h"
#include "gromacs/commandline/cmdlinemodule.h"
-#include "gromacs/commandline/cmdlinemodulemanager-impl.h"
#include "gromacs/commandline/cmdlineparser.h"
#include "gromacs/commandline/cmdlineprogramcontext.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
+#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/sysinfo.h"
-// For GMX_BINARY_SUFFIX
-#include "config.h"
+#include "cmdlinehelpmodule.h"
+#include "cmdlinemodulemanager-impl.h"
namespace gmx
{
*/
/*! \brief
- * Implements a CommandLineModuleInterface, given a function with C/C++ main()
+ * Implements a ICommandLineModule, given a function with C/C++ main()
* signature.
*/
-class CMainCommandLineModule : public CommandLineModuleInterface
+class CMainCommandLineModule : public ICommandLineModule
{
public:
//! \copydoc gmx::CommandLineModuleManager::CMainFunction
return shortDescription_;
}
+ virtual void init(CommandLineModuleSettings * /*settings*/)
+ {
+ }
virtual int run(int argc, char *argv[])
{
return mainFunction_(argc, argv);
}
virtual void writeHelp(const CommandLineHelpContext &context) const
{
- char *argv[2];
- int argc = 1;
- // TODO: The constness should not be cast away.
- argv[0] = const_cast<char *>(name_);
- argv[1] = NULL;
- GlobalCommandLineHelpContext global(context);
- mainFunction_(argc, argv);
+ writeCommandLineHelpCMain(context, name_, mainFunction_);
}
private:
const char *name_;
const char *shortDescription_;
CMainFunction mainFunction_;
-
};
+//! \}
+
+} // namespace
+
/********************************************************************
- * CommonOptionsHolder
+ * CommandLineCommonOptionsHolder
*/
-/*! \brief
- * Encapsulates some handling of common options to the wrapper binary.
- */
-class CommonOptionsHolder
+CommandLineCommonOptionsHolder::CommandLineCommonOptionsHolder()
+ : options_(NULL, NULL), bHelp_(false), bHidden_(false),
+ bQuiet_(false), bVersion_(false), bCopyright_(true),
+ niceLevel_(19), bNiceSet_(false), bBackup_(true), bFpexcept_(false),
+ debugLevel_(0)
{
- public:
- CommonOptionsHolder()
- : options_(NULL, NULL), bHelp_(false), bHidden_(false),
- bQuiet_(false), bVersion_(false), bCopyright_(true)
- {
- binaryInfoSettings_.copyright(true);
- }
-
- //! Initializes the common options.
- void initOptions()
- {
- options_.addOption(BooleanOption("h").store(&bHelp_)
- .description("Print help and quit"));
- options_.addOption(BooleanOption("hidden").store(&bHidden_)
- .hidden()
- .description("Show hidden options in help"));
- options_.addOption(BooleanOption("quiet").store(&bQuiet_)
- .description("Do not print common startup info or quotes"));
- options_.addOption(BooleanOption("version").store(&bVersion_)
- .description("Print extended version information and quit"));
- options_.addOption(BooleanOption("copyright").store(&bCopyright_)
- .description("Print copyright information on startup"));
- }
-
- /*! \brief
- * Finishes option parsing.
- *
- * \returns `false` if the wrapper binary should quit without executing
- * any module.
- */
- bool finishOptions()
- {
- options_.finish();
- binaryInfoSettings_.extendedInfo(bVersion_);
- // The latter condition suppresses the copyright with
- // -quiet -version.
- binaryInfoSettings_.copyright(bCopyright_ && !bQuiet_);
- return !bVersion_;
- }
-
- //! Returns the internal Options object.
- Options *options() { return &options_; }
- //! Returns the settings for printing startup information.
- const BinaryInformationSettings &binaryInfoSettings() const
- {
- return binaryInfoSettings_;
- }
-
- /*! \brief
- * Returns `true` if common options are set such that the wrapper
- * binary should quit, without running the actual module.
- */
- bool shouldIgnoreActualModule() const
- {
- return bHelp_ || bVersion_;
- }
- //! Returns whether common options specify showing help.
- bool shouldShowHelp() const { return bHelp_; }
- //! Returns whether common options specify showing hidden options in help.
- bool shouldShowHidden() const { return bHidden_; }
- //! Returns whether common options specify quiet execution.
- bool shouldBeQuiet() const
- {
- return bQuiet_ && !bVersion_;
- }
+ binaryInfoSettings_.copyright(true);
+}
- //! Returns the file to which startup information should be printed.
- FILE *startupInfoFile() const { return (bVersion_ ? stdout : stderr); }
+CommandLineCommonOptionsHolder::~CommandLineCommonOptionsHolder()
+{
+}
- private:
- Options options_;
- //! Settings for what to write in the startup header.
- BinaryInformationSettings binaryInfoSettings_;
- bool bHelp_;
- bool bHidden_;
- bool bQuiet_;
- bool bVersion_;
- bool bCopyright_;
-};
+void CommandLineCommonOptionsHolder::initOptions()
+{
+ options_.addOption(BooleanOption("h").store(&bHelp_)
+ .description("Print help and quit"));
+ options_.addOption(BooleanOption("hidden").store(&bHidden_)
+ .hidden()
+ .description("Show hidden options in help"));
+ options_.addOption(BooleanOption("quiet").store(&bQuiet_)
+ .description("Do not print common startup info or quotes"));
+ options_.addOption(BooleanOption("version").store(&bVersion_)
+ .description("Print extended version information and quit"));
+ options_.addOption(BooleanOption("copyright").store(&bCopyright_)
+ .description("Print copyright information on startup"));
+ options_.addOption(IntegerOption("nice").store(&niceLevel_).storeIsSet(&bNiceSet_)
+ .description("Set the nicelevel (default depends on command)"));
+ options_.addOption(BooleanOption("backup").store(&bBackup_)
+ .description("Write backups if output files exist"));
+ options_.addOption(BooleanOption("fpexcept").store(&bFpexcept_)
+ .hidden().description("Enable floating-point exceptions"));
+ options_.addOption(IntegerOption("debug").store(&debugLevel_)
+ .hidden().defaultValueIfSet(1)
+ .description("Write file with debug information, "
+ "1: short (default), 2: also x and f"));
+}
-//! \}
+bool CommandLineCommonOptionsHolder::finishOptions()
+{
+ options_.finish();
+ binaryInfoSettings_.extendedInfo(bVersion_);
+ // The latter condition suppresses the copyright with
+ // -quiet -version.
+ binaryInfoSettings_.copyright(bCopyright_ && !bQuiet_);
+ return !bVersion_;
+}
-} // namespace
+void CommandLineCommonOptionsHolder::adjustFromSettings(
+ const CommandLineModuleSettings &settings)
+{
+ if (!bNiceSet_)
+ {
+ niceLevel_ = settings.defaultNiceLevel();
+ }
+}
/********************************************************************
* CommandLineModuleManager::Impl
*/
CommandLineModuleMap::const_iterator
findModuleByName(const std::string &name) const;
- /*! \brief
- * Finds a module that the name of the binary.
- *
- * \param[in] invokedName Name by which the program was invoked.
- * \throws std::bad_alloc if out of memory.
- * \returns Iterator to the found module, or
- * \c modules_.end() if not found.
- *
- * Checks whether the program is invoked through a symlink whose name
- * is different from \a binaryName_, and if so, checks
- * if a module name matches the name of the symlink.
- *
- * Note that the \p invokedName parameter is currently not necessary
- * (as the program context object is also available and provides this
- * value), but it clarifies the control flow.
- */
- CommandLineModuleMap::const_iterator
- findModuleFromBinaryName(const char *invokedName) const;
/*! \brief
* Processes command-line options for the wrapper binary.
* options). Also finds the module that should be run and the
* arguments that should be passed to it.
*/
- CommandLineModuleInterface *
- processCommonOptions(CommonOptionsHolder *optionsHolder,
+ ICommandLineModule *
+ processCommonOptions(CommandLineCommonOptionsHolder *optionsHolder,
int *argc, char ***argv);
/*! \brief
*/
CommandLineHelpModule *helpModule_;
//! If non-NULL, run this module in single-module mode.
- CommandLineModuleInterface *singleModule_;
+ ICommandLineModule *singleModule_;
//! Stores the value set with setQuiet().
bool bQuiet_;
helpModule_(NULL), singleModule_(NULL),
bQuiet_(false)
{
+ GMX_RELEASE_ASSERT(binaryName_.find('-') == std::string::npos,
+ "Help export does not currently work with binary names with dashes");
}
void CommandLineModuleManager::Impl::addModule(CommandLineModulePointer module)
HelpTopicPointer helpTopic(helpModule_->createModuleHelpTopic(*module));
modules_.insert(std::make_pair(std::string(module->name()),
move(module)));
- helpModule_->addTopic(move(helpTopic));
+ helpModule_->addTopic(move(helpTopic), false);
}
void CommandLineModuleManager::Impl::ensureHelpModuleExists()
return modules_.find(name);
}
-CommandLineModuleMap::const_iterator
-CommandLineModuleManager::Impl::findModuleFromBinaryName(
- const char *invokedName) const
-{
- std::string moduleName = invokedName;
-#ifdef GMX_BINARY_SUFFIX
- moduleName = stripSuffixIfPresent(moduleName, GMX_BINARY_SUFFIX);
-#endif
- if (moduleName == binaryName_)
- {
- return modules_.end();
- }
- if (startsWith(moduleName, "g_"))
- {
- moduleName.erase(0, 2);
- }
- if (startsWith(moduleName, "gmx"))
- {
- moduleName.erase(0, 3);
- }
- return findModuleByName(moduleName);
-}
-
-CommandLineModuleInterface *
+ICommandLineModule *
CommandLineModuleManager::Impl::processCommonOptions(
- CommonOptionsHolder *optionsHolder, int *argc, char ***argv)
+ CommandLineCommonOptionsHolder *optionsHolder, int *argc, char ***argv)
{
// Check if we are directly invoking a certain module.
- CommandLineModuleInterface *module = singleModule_;
- if (module == NULL)
- {
- // Also check for invokation through named symlinks.
- CommandLineModuleMap::const_iterator moduleIter
- = findModuleFromBinaryName(programContext_.programName());
- if (moduleIter != modules_.end())
- {
- module = moduleIter->second.get();
- }
- }
+ ICommandLineModule *module = singleModule_;
// TODO: It would be nice to propagate at least the -quiet option to
// the modules so that they can also be quiet in response to this.
if (module == helpModule_)
{
helpModule_->setShowHidden(optionsHolder->shouldShowHidden());
- helpModule_->setCommonOptions(optionsHolder->options());
}
return module;
}
impl_->bQuiet_ = bQuiet;
}
-void CommandLineModuleManager::setOutputRedirect(File *output)
+void CommandLineModuleManager::setOutputRedirector(
+ IFileOutputRedirector *output)
{
impl_->ensureHelpModuleExists();
- impl_->helpModule_->setOutputRedirect(output);
+ impl_->helpModule_->setOutputRedirector(output);
}
-void CommandLineModuleManager::setSingleModule(CommandLineModuleInterface *module)
+void CommandLineModuleManager::setSingleModule(ICommandLineModule *module)
{
impl_->singleModule_ = module;
}
void CommandLineModuleManager::addHelpTopic(HelpTopicPointer topic)
{
impl_->ensureHelpModuleExists();
- impl_->helpModule_->addTopic(move(topic));
+ impl_->helpModule_->addTopic(move(topic), true);
}
int CommandLineModuleManager::run(int argc, char *argv[])
{
- CommandLineModuleInterface *module;
- const bool bMaster = (!gmx_mpi_initialized() || gmx_node_rank() == 0);
- bool bQuiet = impl_->bQuiet_ || !bMaster;
- CommonOptionsHolder optionsHolder;
+ ICommandLineModule *module;
+ const bool bMaster = (gmx_node_rank() == 0);
+ bool bQuiet = impl_->bQuiet_ || !bMaster;
+ CommandLineCommonOptionsHolder optionsHolder;
try
{
optionsHolder.initOptions();
{
return 0;
}
- int rc = module->run(argc, argv);
+
+ CommandLineModuleSettings settings;
+ module->init(&settings);
+ optionsHolder.adjustFromSettings(settings);
+
+ gmx_set_max_backup_count(optionsHolder.shouldBackup() ? -1 : 0);
+
+ // Open the debug file.
+ if (optionsHolder.debugLevel() > 0)
+ {
+ std::string filename(impl_->programContext_.programName());
+ if (gmx_node_num() > 1)
+ {
+ filename.append(formatString("%d", gmx_node_rank()));
+ }
+ filename.append(".debug");
+
+ fprintf(stderr, "Will write debug log file: %s\n", filename.c_str());
+ gmx_init_debug(optionsHolder.debugLevel(), filename.c_str());
+ }
+ // Set the nice level unless disabled in the configuration.
+ if (optionsHolder.niceLevel() != 0)
+ {
+ static bool bNiceSet = false; // Only set it once.
+ if (!bNiceSet)
+ {
+ // TODO: Diagnostic if this fails and the user explicitly requested it.
+ gmx_set_nice(optionsHolder.niceLevel());
+ bNiceSet = true;
+ }
+ }
+ if (optionsHolder.enableFPExceptions())
+ {
+ //TODO: currently it is always enabled for mdrun (verlet) and tests.
+ gmx_feenableexcept();
+ }
+
+ int rc = 0;
+ if (!(module == impl_->helpModule_ && !bMaster))
+ {
+ rc = module->run(argc, argv);
+ }
if (!bQuiet)
{
gmx_thanx(stderr);
// static
int CommandLineModuleManager::runAsMainSingleModule(
- int argc, char *argv[], CommandLineModuleInterface *module)
+ int argc, char *argv[], ICommandLineModule *module)
{
CommandLineProgramContext &programContext = gmx::initForCommandLine(&argc, &argv);
try
catch (const std::exception &ex)
{
printFatalErrorMessage(stderr, ex);
- return processExceptionAtExit(ex);
+ return processExceptionAtExitForCommandLine(ex);
}
}
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