BitcoinGUI::BitcoinGUI(const NetworkStyle *networkStyle, QWidget *parent) :
QMainWindow(parent),
clientModel(0),
walletFrame(0),
unitDisplayControl(0),
labelEncryptionIcon(0),
labelConnectionsIcon(0),
labelBlocksIcon(0),
progressBarLabel(0),
progressBar(0),
progressDialog(0),
appMenuBar(0),
overviewAction(0),
historyAction(0),
quitAction(0),
sendCoinsAction(0),
usedSendingAddressesAction(0),
usedReceivingAddressesAction(0),
signMessageAction(0),
verifyMessageAction(0),
aboutAction(0),
receiveCoinsAction(0),
optionsAction(0),
toggleHideAction(0),
encryptWalletAction(0),
backupWalletAction(0),
changePassphraseAction(0),
aboutQtAction(0),
openRPCConsoleAction(0),
openAction(0),
showHelpMessageAction(0),
trayIcon(0),
trayIconMenu(0),
notificator(0),
rpcConsole(0),
prevBlocks(0),
spinnerFrame(0)
{
/* Open CSS when configured */
this->setStyleSheet(GUIUtil::loadStyleSheet());
GUIUtil::restoreWindowGeometry("nWindow", QSize(850, 550), this);
QString windowTitle = tr("DarkNet Core") + " - ";
#ifdef ENABLE_WALLET
/* if compiled with wallet support, -disablewallet can still disable the wallet */
enableWallet = !GetBoolArg("-disablewallet", false);
#else
enableWallet = false;
#endif // ENABLE_WALLET
if(enableWallet)
{
windowTitle += tr("Wallet");
} else {
windowTitle += tr("Node");
}
QString userWindowTitle = QString::fromStdString(GetArg("-windowtitle", ""));
if(!userWindowTitle.isEmpty()) windowTitle += " - " + userWindowTitle;
windowTitle += " " + networkStyle->getTitleAddText();
#ifndef Q_OS_MAC
QApplication::setWindowIcon(networkStyle->getAppIcon());
setWindowIcon(networkStyle->getAppIcon());
#else
MacDockIconHandler::instance()->setIcon(networkStyle->getAppIcon());
#endif
setWindowTitle(windowTitle);
#if defined(Q_OS_MAC) && QT_VERSION < 0x050000
// This property is not implemented in Qt 5. Setting it has no effect.
// A replacement API (QtMacUnifiedToolBar) is available in QtMacExtras.
setUnifiedTitleAndToolBarOnMac(true);
#endif
rpcConsole = new RPCConsole(enableWallet ? this : 0);
#ifdef ENABLE_WALLET
if(enableWallet)
{
/** Create wallet frame*/
walletFrame = new WalletFrame(this);
} else
#endif // ENABLE_WALLET
{
/* When compiled without wallet or -disablewallet is provided,
* the central widget is the rpc console.
*/
setCentralWidget(rpcConsole);
}
// Accept D&D of URIs
setAcceptDrops(true);
// Create actions for the toolbar, menu bar and tray/dock icon
// Needs walletFrame to be initialized
createActions(networkStyle);
// Create application menu bar
createMenuBar();
// Create the toolbars
createToolBars();
// Create system tray icon and notification
createTrayIcon(networkStyle);
// Create status bar
statusBar();
// Status bar notification icons
QFrame *frameBlocks = new QFrame();
frameBlocks->setContentsMargins(0,0,0,0);
frameBlocks->setSizePolicy(QSizePolicy::Fixed, QSizePolicy::Preferred);
QHBoxLayout *frameBlocksLayout = new QHBoxLayout(frameBlocks);
frameBlocksLayout->setContentsMargins(3,0,3,0);
frameBlocksLayout->setSpacing(3);
unitDisplayControl = new UnitDisplayStatusBarControl();
labelEncryptionIcon = new QLabel();
labelConnectionsIcon = new QPushButton();
labelConnectionsIcon->setFlat(true); // Make the button look like a label, but clickable
labelConnectionsIcon->setStyleSheet(".QPushButton { background-color: rgba(255, 255, 255, 0);}");
labelConnectionsIcon->setMaximumSize(STATUSBAR_ICONSIZE, STATUSBAR_ICONSIZE);
labelBlocksIcon = new QLabel();
if(enableWallet)
{
frameBlocksLayout->addStretch();
frameBlocksLayout->addWidget(unitDisplayControl);
frameBlocksLayout->addStretch();
frameBlocksLayout->addWidget(labelEncryptionIcon);
}
frameBlocksLayout->addStretch();
frameBlocksLayout->addWidget(labelConnectionsIcon);
frameBlocksLayout->addStretch();
frameBlocksLayout->addWidget(labelBlocksIcon);
frameBlocksLayout->addStretch();
// Progress bar and label for blocks download
progressBarLabel = new QLabel();
progressBarLabel->setVisible(true);
progressBar = new GUIUtil::ProgressBar();
progressBar->setAlignment(Qt::AlignCenter);
progressBar->setVisible(true);
// Override style sheet for progress bar for styles that have a segmented progress bar,
// as they make the text unreadable (workaround for issue #1071)
// See https://qt-project.org/doc/qt-4.8/gallery.html
QString curStyle = QApplication::style()->metaObject()->className();
if(curStyle == "QWindowsStyle" || curStyle == "QWindowsXPStyle")
{
progressBar->setStyleSheet("QProgressBar { background-color: #F8F8F8; border: 1px solid grey; border-radius: 7px; padding: 1px; text-align: center; } QProgressBar::chunk { background: QLinearGradient(x1: 0, y1: 0, x2: 1, y2: 0, stop: 0 #00CCFF, stop: 1 #33CCFF); border-radius: 7px; margin: 0px; }");
}
statusBar()->addWidget(progressBarLabel);
statusBar()->addWidget(progressBar);
statusBar()->addPermanentWidget(frameBlocks);
// Jump directly to tabs in RPC-console
connect(openInfoAction, SIGNAL(triggered()), rpcConsole, SLOT(showInfo()));
connect(openRPCConsoleAction, SIGNAL(triggered()), rpcConsole, SLOT(showConsole()));
connect(openNetworkAction, SIGNAL(triggered()), rpcConsole, SLOT(showNetwork()));
connect(openPeersAction, SIGNAL(triggered()), rpcConsole, SLOT(showPeers()));
connect(openRepairAction, SIGNAL(triggered()), rpcConsole, SLOT(showRepair()));
connect(openConfEditorAction, SIGNAL(triggered()), rpcConsole, SLOT(showConfEditor()));
connect(showBackupsAction, SIGNAL(triggered()), rpcConsole, SLOT(showBackups()));
connect(labelConnectionsIcon, SIGNAL(clicked()), rpcConsole, SLOT(showPeers()));
// Get restart command-line parameters and handle restart
connect(rpcConsole, SIGNAL(handleRestart(QStringList)), this, SLOT(handleRestart(QStringList)));
// prevents an open debug window from becoming stuck/unusable on client shutdown
connect(quitAction, SIGNAL(triggered()), rpcConsole, SLOT(hide()));
// Install event filter to be able to catch status tip events (QEvent::StatusTip)
this->installEventFilter(this);
// Initially wallet actions should be disabled
setWalletActionsEnabled(false);
// Subscribe to notifications from core
subscribeToCoreSignals();
}
//! Implements C-style main function for mdrun
int gmx_mdrun(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] is the main computational chemistry engine",
"within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
"but it can also perform Stochastic Dynamics, Energy Minimization,",
"test particle insertion or (re)calculation of energies.",
"Normal mode analysis is another option. In this case [TT]mdrun[tt]",
"builds a Hessian matrix from single conformation.",
"For usual Normal Modes-like calculations, make sure that",
"the structure provided is properly energy-minimized.",
"The generated matrix can be diagonalized by [gmx-nmeig].[PAR]",
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over ranks if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
"The option [TT]-dhdl[tt] is only used when free energy calculation is",
"turned on.[PAR]",
"Running mdrun efficiently in parallel is a complex topic topic,",
"many aspects of which are covered in the online User Guide. You",
"should look there for practical advice on using many of the options",
"available in mdrun.[PAR]",
"ED (essential dynamics) sampling and/or additional flooding potentials",
"are switched on by using the [TT]-ei[tt] flag followed by an [REF].edi[ref]",
"file. The [REF].edi[ref] file can be produced with the [TT]make_edi[tt] tool",
"or by using options in the essdyn menu of the WHAT IF program.",
"[TT]mdrun[tt] produces a [REF].xvg[ref] output file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
"[REF].mdp[ref] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
"a formatted table with potential functions. The file is read from",
"either the current directory or from the [TT]GMXLIB[tt] directory.",
"A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
"for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
"normal Coulomb.",
"When pair interactions are present, a separate table for pair interaction",
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
"For each different tabulated interaction type used, a table file name must",
"be given. For the topology to work, a file name given here must match a",
"character sequence before the file extension. That sequence is: an underscore,",
"then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals,",
"and finally the matching table number index used in the topology.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [REF].mdp[ref] file.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability.",
"[PAR]",
"The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
"a protein into a membrane. This module requires a number of settings",
"that are provided in a data file that is the argument of this option.",
"For more details in membrane embedding, see the documentation in the",
"user guide. The options [TT]-mn[tt] and [TT]-mp[tt] are used to provide",
"the index and topology files used for the embedding.",
"[PAR]",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"forces of atoms with a force larger than a certain value will",
"be printed to stderr. It will also terminate the run when non-finite",
"forces are present.",
"[PAR]",
"Checkpoints containing the complete state of the system are written",
"at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
"unless option [TT]-cpt[tt] is set to -1.",
"The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
"make sure that a recent state of the system is always available,",
"even when the simulation is terminated while writing a checkpoint.",
"With [TT]-cpnum[tt] all checkpoint files are kept and appended",
"with the step number.",
"A simulation can be continued by reading the full state from file",
"with option [TT]-cpi[tt]. This option is intelligent in the way that",
"if no checkpoint file is found, GROMACS just assumes a normal run and",
"starts from the first step of the [REF].tpr[ref] file. By default the output",
"will be appending to the existing output files. The checkpoint file",
"contains checksums of all output files, such that you will never",
"loose data when some output files are modified, corrupt or removed.",
"There are three scenarios with [TT]-cpi[tt]:[PAR]",
"[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
"[TT]*[tt] all files are present with names and checksums matching those stored",
"in the checkpoint file: files are appended[PAR]",
"[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
"With [TT]-noappend[tt] new output files are opened and the simulation",
"part number is added to all output file names.",
"Note that in all cases the checkpoint file itself is not renamed",
"and will be overwritten, unless its name does not match",
"the [TT]-cpo[tt] option.",
"[PAR]",
"With checkpointing the output is appended to previously written",
"output files, unless [TT]-noappend[tt] is used or none of the previous",
"output files are present (except for the checkpoint file).",
"The integrity of the files to be appended is verified using checksums",
"which are stored in the checkpoint file. This ensures that output can",
"not be mixed up or corrupted due to file appending. When only some",
"of the previous output files are present, a fatal error is generated",
"and no old output files are modified and no new output files are opened.",
"The result with appending will be the same as from a single run.",
"The contents will be binary identical, unless you use a different number",
"of ranks or dynamic load balancing or the FFT library uses optimizations",
"through timing.",
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
"exceeds [TT]-maxh[tt]\\*0.99 hours. This option is particularly useful in",
"combination with setting [TT]nsteps[tt] to -1 either in the mdp or using the",
"similarly named command line option. This results in an infinite run,",
"terminated only when the time limit set by [TT]-maxh[tt] is reached (if any)"
"or upon receiving a signal."
"[PAR]",
"When [TT]mdrun[tt] receives a TERM signal, it will stop as soon as",
"checkpoint file can be written, i.e. after the next global communication step.",
"When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
"pressed), it will stop at the next neighbor search step or at the",
"second global communication step, whichever happens later.",
"In both cases all the usual output will be written to file.",
"When running with MPI, a signal to one of the [TT]mdrun[tt] ranks",
"is sufficient, this signal should not be sent to mpirun or",
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"Interactive molecular dynamics (IMD) can be activated by using at least one",
"of the three IMD switches: The [TT]-imdterm[tt] switch allows one to terminate",
"the simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
"[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
"IMD remote can be turned on by [TT]-imdpull[tt].",
"The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
"file pointed to by [TT]-if[tt] contains atom indices and forces if IMD",
"pulling is used."
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
};
t_commrec *cr;
t_filenm fnm[] = {
{ efTPR, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efCOMPRESSED, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD | ffALLOW_MISSING },
{ efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-dhdl", "dhdl", ffOPTWR },
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
{ efXVG, "-tableb", "table", ffOPTRDMULT },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
{ efXVG, "-eo", "edsam", ffOPTWR },
{ efXVG, "-devout", "deviatie", ffOPTWR },
{ efXVG, "-runav", "runaver", ffOPTWR },
{ efXVG, "-px", "pullx", ffOPTWR },
{ efXVG, "-pf", "pullf", ffOPTWR },
{ efXVG, "-ro", "rotation", ffOPTWR },
{ efLOG, "-ra", "rotangles", ffOPTWR },
{ efLOG, "-rs", "rotslabs", ffOPTWR },
{ efLOG, "-rt", "rottorque", ffOPTWR },
{ efMTX, "-mtx", "nm", ffOPTWR },
{ efRND, "-multidir", NULL, ffOPTRDMULT},
{ efDAT, "-membed", "membed", ffOPTRD },
{ efTOP, "-mp", "membed", ffOPTRD },
{ efNDX, "-mn", "membed", ffOPTRD },
{ efXVG, "-if", "imdforces", ffOPTWR },
{ efXVG, "-swap", "swapions", ffOPTWR }
};
const int NFILE = asize(fnm);
/* Command line options ! */
gmx_bool bDDBondCheck = TRUE;
gmx_bool bDDBondComm = TRUE;
gmx_bool bTunePME = TRUE;
gmx_bool bVerbose = FALSE;
gmx_bool bRerunVSite = FALSE;
gmx_bool bConfout = TRUE;
gmx_bool bReproducible = FALSE;
gmx_bool bIMDwait = FALSE;
gmx_bool bIMDterm = FALSE;
gmx_bool bIMDpull = FALSE;
int npme = -1;
int nstlist = 0;
int nmultisim = 0;
int nstglobalcomm = -1;
int repl_ex_nst = 0;
int repl_ex_seed = -1;
int repl_ex_nex = 0;
int nstepout = 100;
int resetstep = -1;
gmx_int64_t nsteps = -2; /* the value -2 means that the mdp option will be used */
int imdport = 8888; /* can be almost anything, 8888 is easy to remember */
rvec realddxyz = {0, 0, 0};
const char *ddrank_opt[ddrankorderNR+1] =
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
const char *thread_aff_opt[threadaffNR+1] =
{ NULL, "auto", "on", "off", NULL };
const char *nbpu_opt[] =
{ NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
real cpt_period = 15.0, max_hours = -1;
gmx_bool bTryToAppendFiles = TRUE;
gmx_bool bKeepAndNumCPT = FALSE;
gmx_bool bResetCountersHalfWay = FALSE;
gmx_output_env_t *oenv = NULL;
/* Non transparent initialization of a complex gmx_hw_opt_t struct.
* But unfortunately we are not allowed to call a function here,
* since declarations follow below.
*/
gmx_hw_opt_t hw_opt = {
0, 0, 0, 0, threadaffSEL, 0, 0,
{ NULL, FALSE, 0, NULL }
};
t_pargs pa[] = {
{ "-dd", FALSE, etRVEC, {&realddxyz},
"Domain decomposition grid, 0 is optimize" },
{ "-ddorder", FALSE, etENUM, {ddrank_opt},
"DD rank order" },
{ "-npme", FALSE, etINT, {&npme},
"Number of separate ranks to be used for PME, -1 is guess" },
{ "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
"Total number of threads to start (0 is guess)" },
{ "-ntmpi", FALSE, etINT, {&hw_opt.nthreads_tmpi},
"Number of thread-MPI threads to start (0 is guess)" },
{ "-ntomp", FALSE, etINT, {&hw_opt.nthreads_omp},
"Number of OpenMP threads per MPI rank to start (0 is guess)" },
{ "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
"Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
{ "-pin", FALSE, etENUM, {thread_aff_opt},
"Whether mdrun should try to set thread affinities" },
{ "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
"The lowest logical core number to which mdrun should pin the first thread" },
{ "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
"Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
{ "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},
"List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping" },
{ "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
"Check for all bonded interactions with DD" },
{ "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
"HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
{ "-rdd", FALSE, etREAL, {&rdd},
"The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
{ "-rcon", FALSE, etREAL, {&rconstr},
"Maximum distance for P-LINCS (nm), 0 is estimate" },
{ "-dlb", FALSE, etENUM, {dddlb_opt},
"Dynamic load balancing (with DD)" },
{ "-dds", FALSE, etREAL, {&dlb_scale},
"Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to "
"provide a margin in which dynamic load balancing can act while preserving the minimum cell size." },
{ "-ddcsx", FALSE, etSTR, {&ddcsx},
"HIDDENA string containing a vector of the relative sizes in the x "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-ddcsy", FALSE, etSTR, {&ddcsy},
"HIDDENA string containing a vector of the relative sizes in the y "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-ddcsz", FALSE, etSTR, {&ddcsz},
"HIDDENA string containing a vector of the relative sizes in the z "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-gcom", FALSE, etINT, {&nstglobalcomm},
"Global communication frequency" },
{ "-nb", FALSE, etENUM, {&nbpu_opt},
"Calculate non-bonded interactions on" },
{ "-nstlist", FALSE, etINT, {&nstlist},
"Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
{ "-tunepme", FALSE, etBOOL, {&bTunePME},
"Optimize PME load between PP/PME ranks or GPU/CPU" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
{ "-reprod", FALSE, etBOOL, {&bReproducible},
"Try to avoid optimizations that affect binary reproducibility" },
{ "-cpt", FALSE, etREAL, {&cpt_period},
"Checkpoint interval (minutes)" },
{ "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
"Keep and number checkpoint files" },
{ "-append", FALSE, etBOOL, {&bTryToAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-nsteps", FALSE, etINT64, {&nsteps},
"Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
{ "-maxh", FALSE, etREAL, {&max_hours},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT, {&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
"Attempt replica exchange periodically with this period (steps)" },
{ "-nex", FALSE, etINT, {&repl_ex_nex},
"Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-imdport", FALSE, etINT, {&imdport},
"HIDDENIMD listening port" },
{ "-imdwait", FALSE, etBOOL, {&bIMDwait},
"HIDDENPause the simulation while no IMD client is connected" },
{ "-imdterm", FALSE, etBOOL, {&bIMDterm},
"HIDDENAllow termination of the simulation from IMD client" },
{ "-imdpull", FALSE, etBOOL, {&bIMDpull},
"HIDDENAllow pulling in the simulation from IMD client" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
"HIDDENFrequency of writing the remaining wall clock time for the run" },
{ "-resetstep", FALSE, etINT, {&resetstep},
"HIDDENReset cycle counters after these many time steps" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
};
unsigned long Flags;
ivec ddxyz;
int dd_rank_order;
gmx_bool bDoAppendFiles, bStartFromCpt;
FILE *fplog;
int rc;
char **multidir = NULL;
cr = init_commrec();
unsigned long PCA_Flags = PCA_CAN_SET_DEFFNM;
// With -multi or -multidir, the file names are going to get processed
// further (or the working directory changed), so we can't check for their
// existence during parsing. It isn't useful to do any completion based on
// file system contents, either.
if (is_multisim_option_set(argc, argv))
{
PCA_Flags |= PCA_DISABLE_INPUT_FILE_CHECKING;
}
/* Comment this in to do fexist calls only on master
* works not with rerun or tables at the moment
* also comment out the version of init_forcerec in md.c
* with NULL instead of opt2fn
*/
/*
if (!MASTER(cr))
{
PCA_Flags |= PCA_NOT_READ_NODE;
}
*/
if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv))
{
sfree(cr);
return 0;
}
dd_rank_order = nenum(ddrank_opt);
hw_opt.thread_affinity = nenum(thread_aff_opt);
/* now check the -multi and -multidir option */
if (opt2bSet("-multidir", NFILE, fnm))
{
if (nmultisim > 0)
{
gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
}
nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
}
if (repl_ex_nst != 0 && nmultisim < 2)
{
gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
}
if (repl_ex_nex < 0)
{
gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
}
if (nmultisim >= 1)
{
#if !GMX_THREAD_MPI
init_multisystem(cr, nmultisim, multidir, NFILE, fnm);
#else
gmx_fatal(FARGS, "mdrun -multi or -multidir are not supported with the thread-MPI library. "
"Please compile GROMACS with a proper external MPI library.");
#endif
}
if (!opt2bSet("-cpi", NFILE, fnm))
{
// If we are not starting from a checkpoint we never allow files to be appended
// to, since that has caused a ton of strange behaviour and bugs in the past.
if (opt2parg_bSet("-append", asize(pa), pa))
{
// If the user explicitly used the -append option, explain that it is not possible.
gmx_fatal(FARGS, "GROMACS can only append to files when restarting from a checkpoint.");
}
else
{
// If the user did not say anything explicit, just disable appending.
bTryToAppendFiles = FALSE;
}
}
handleRestart(cr, bTryToAppendFiles, NFILE, fnm, &bDoAppendFiles, &bStartFromCpt);
Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (bStartFromCpt ? MD_STARTFROMCPT : 0);
Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
Flags = Flags | (opt2parg_bSet("-ntomp", asize(pa), pa) ? MD_NTOMPSET : 0);
Flags = Flags | (bIMDwait ? MD_IMDWAIT : 0);
Flags = Flags | (bIMDterm ? MD_IMDTERM : 0);
Flags = Flags | (bIMDpull ? MD_IMDPULL : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
if (MASTER(cr) && !bDoAppendFiles)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
Flags & MD_APPENDFILES, &fplog);
}
else
{
fplog = NULL;
}
ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
rc = gmx::mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose,
nstglobalcomm, ddxyz, dd_rank_order, npme, rdd, rconstr,
dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
nbpu_opt[0], nstlist,
nsteps, nstepout, resetstep,
nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
pforce, cpt_period, max_hours, imdport, Flags);
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
if (MASTER(cr) && !bDoAppendFiles)
{
gmx_log_close(fplog);
}
return rc;
}
