% /*@@ % @file Infrastructure.tex % @date 27 Jan 1999 % @author Tom Goodale, Gabrielle Allen, Gerd Lanferman, Thomas Radke % @desc % Infrastructure thorn writer's guide for the Cactus User's Guide % @enddesc % @version $Header$ % @@*/ \renewcommand{\thepage}{\Alph{part}\arabic{page}} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \chapter{Infrastructure Thorns} \label{chap:infrastructure} \begin{itemize} \item{} Concepts and terminology (Overloading and registration of functions) \item{} The cGH structure --- what it is and how to use it \item{} Extending the cGH structure \item{} Querying group and variable information \item{} Providing an I/O layer \item{} Providing a communication layer \item{} Providing a reduction operator \item{} Providing an interpolation operator \item{} Overloadable functions \end{itemize} \section{Concepts and Terminology} \label{chap:cote} \subsection{Overloading and Registration} The flesh defines a core API which guarantees the presence of a set of functions. Although the flesh guarantees the presence of these functions, they can be provided by thorns. Thorns do this by either the \textit{overloading} or the \textit{registration} of functions. \subsubsection{Overloading} Some functions can only be provided by one thorn. The first thorn to \textit{overload} this function succeeds, and any later attempt to overload the function fails. For each overloadable function, there is a function with a name something like {\tt CCTK\_Overload...} which is passed the function pointer. \subsubsection{Registration} Some functions may be provided by several thorns. The thorns \textit{register} their function with the flesh, and when the flesh-provided function is called, the flesh calls all the registered functions. \subsection{GH Extensions} A GH extension is a way to associate data with each cGH. This data should be data that is required to be associated with a particular GH by a thorn. Each GH extension is given a unique handle. \subsection{I/O Methods} An I/O method is a distinct way to output data. Each I/O method has a unique name, and the flesh-provided I/O functions operate on all registered I/O methods. \section{GH Extensions} A GH extension is created by calling {\tt CCTK\_RegisterGHExtension}, with the name of the extension. This returns a unique handle that identifies the extension. (This handle can be retrieved at any time by a call to {\tt CCTK\_GHExtensionHandle}.) Associated with a GH extension are three functions \begin{Lentry} \item[{\tt SetupGH}] this is used to actually create the data structure holding the extension. It is called when a new cGH is created. \item[{\tt InitGH}] this is used to initialise the extension. It is called after the scheduler has been initialised on the cGH. \item[{\tt ScheduleTraverseGH}] this is called whenever the schedule tree is due to be traversed on the GH. It should initialise the data on the cGH and the call {\tt CCTK\_ScheduleTraverse} to traverse the schedule tree. \end{Lentry} \section{Overloadable and Registerable Functions in Main} \begin{tabular}{|l|l|} \hline {\bf Function} & {\bf Default} \\ \hline {\t CCTK\_Initialise} &\\ \hline {\t CCTK\_Evolve} &\\ \hline {\t CCTK\_Shutdown} &\\ \hline \end{tabular} \section{Overloadable and Registerable Functions in Comm} \begin{tabular}{|l|l|} \hline {\bf Function} & {\bf Default} \\ \hline {\t CCTK\_SyncGroup} &\\ \hline {\t CCTK\_SyncGroupsByDirI} &\\ \hline {\t CCTK\_EnableGroupStorage} &\\ \hline {\t CCTK\_DisableGroupStorage} &\\ \hline {\t CCTK\_EnableGroupComm} &\\ \hline {\t CCTK\_DisableGroupComm} &\\ \hline {\t CCTK\_Barrier} &\\ \hline {\t CCTK\_Reduce} &\\ \hline {\t CCTK\_Interp} &\\ \hline {\t CCTK\_ParallelInit} &\\ \hline \end{tabular} \section{Overloadable and Registerable Functions in I/O} \begin{tabular}{|l|l|} \hline {\bf Function} & {\bf Default} \\ \hline {\t CCTK\_OutputGH} & \\ \hline {\t CCTK\_OutputVarAsByMethod} & \\ \hline \end{tabular} \section{Drivers} The flesh does not know about memory allocation for grid variables, about how to communicate data when synchronisation is called for, or about multiple patches or adaptive mesh refinement. All this is the job of a driver. This chapter describes how to add a driver to your code. \subsection{Anatomy} A driver consists of a Startup routine which creates a GH extension, registers its associated functions, and overloads the communication functions. It may optionally register interpolation, reduction, and I/O methods. A driver may also overload the default Initialisation and Evolution routines, although a simple unigrid evolver is supplied in the flesh. \subsection{Startup} A driver consists of a GH extension, and the following overloaded functions. \begin{enumerate} \item{} {\tt CCTK\_EnableGroupStorage} \item{} {\tt CCTK\_DisableGroupStorage} \item{} {\tt CCTK\_ArrayGroupSizeB} \item{} {\tt CCTK\_QueryGroupStorageB} \item{} {\tt CCTK\_SyncGroup} \item{} {\tt CCTK\_SyncGroupsByDirI} \item{} {\tt CCTK\_EnableGroupComm} \item{} {\tt CCTK\_DisableGroupComm} \item{} {\tt CCTK\_Barrier} \item{} {\tt CCTK\_OverloadParallelInit} \item{} {\tt CCTK\_OverloadExit} \item{} {\tt CCTK\_OverloadAbort} \item{} {\tt CCTK\_OverloadMyProc} \item{} {\tt CCTK\_OverloadnProcs} \end{enumerate} The overloadable function {\tt CCTK\_SyncGroup} is deprecated, a driver should instead provide a routine to overload the more general function {\tt CCTK\_SyncGroupsByDirI}. \subsection{The GH Extension} The GH extension is where the driver stores all its grid-dependent information. This is stuff like any data associated with a grid variable (e.g.\ storage and communication state), how many grids if it is AMR, ... It is very difficult to describe in general, but one simple example might be \begin{verbatim} struct SimpleExtension { /* The data associated with each variable */ /* data[var][timelevel][ijk] */ void ***data } ; \end{verbatim} with a {\tt SetupGH} routine like \begin{verbatim} struct SimpleExtension *SimpleSetupGH(tFleshConfig *config, int conv_level, cGH *GH) { struct SimpleExtension *extension; extension = NULL; if(conv_level < max_conv_level) { /* Create the extension */ extension = malloc(sizeof(struct SimpleExtension)); /* Allocate data for all the variables */ extension->data = malloc(num_vars*sizeof(void**)); for(var = 0 ; var < num_vars; var++) { /* Allocate the memory for the time levels */ extension->data[var] = malloc(num_var_time_levels*sizeof(void *)); for(time_level = 0; time_level < num_var_time_level; time_level++) { /* Initialise the data to NULL */ extension->data[var][time_level] = NULL; } } } return extension; } \end{verbatim} Basically, what this example is doing is preparing a data array for use. The function can query the flesh for information on every variable. Note that scalars should always have memory actually assigned to them. An {\tt InitGH} function isn't strictly necessary, and in this case, it could just be a dummy function. The {\tt ScheduleTraverseGH} function needs to fill out the cGH data, and then call {\tt CCTK\_ScheduleTraverse} to have the functions scheduled at that point executed on the grid \begin{verbatim} int SimpleScheduleTraverseGH(cGH *GH, const char *where) { int retcode; int var; int gtype; int ntimelevels; int level; int idir; extension = (struct SimpleExtension *)GH->extensions[SimpleExtension]; for (idir=0;idircctk_dim;idir++) { GH->cctk_levfac[idir] = 1; GH->cctk_nghostzones[idir] = extension->nghostzones[idir]; GH->cctk_lsh[idir] = extension->lnsize[idir]; GH->cctk_gsh[idir] = extension->nsize[idir]; GH->cctk_bbox[2*idir] = extension->lb[extension->myproc][idir] == 0; GH->cctk_bbox[2*idir+1] = extension->ub[extension->myproc][idir] == extension->nsize[idir]-1; GH->cctk_lbnd[idir] = extension->lb[extension->myproc][idir]; GH->cctk_ubnd[idir] = extension->ub[extension->myproc][idir]; } for(var = 0; var < extension->nvariables; var++) { gtype = CCTK_GroupTypeFromVarI(var); ntimelevels = CCTK_MaxTimeLevelsVI(var); for(level = 0; level < ntimelevels; level++) { switch(gtype) { case CCTK_SCALAR : GH->data[var][level] = extension->variables[var][level]; break; case CCTK_GF : GH->data[var][level] = ((pGF ***)(extension->variables))[var][level]->data; break; case CCTK_ARRAY : GH->data[var][level] = ((pGA ***)(extension->variables))[var][level]->data; break; default: CCTK_WARN(CCTK_WARN_ALERT,"Unknown group type in SimpleScheduleTraverse"); } } } retcode = CCTK_ScheduleTraverse(where, GH, NULL); return retcode; } \end{verbatim} The third argument to {\tt CCTK\_ScheduleTraverse} is actually a function which will be called by the scheduler when it wants to call a function scheduled by a thorn. This function is given some information about the function to call, and is an alternative place where the cGH can be setup. This function is optional, but a simple implementation might be \begin{verbatim} int SimpleCallFunction(void *function, cFunctionData *fdata, void *data) { void (*standardfunc)(void *); int (*noargsfunc)(void); switch(fdata->type) { case FunctionNoArgs: noargsfunc = (int (*)(void))function; noargsfunc(); break; case FunctionStandard: switch(fdata->language) { case LangC: standardfunc = (void (*)(void *))function; standardfunc(data); break; case LangFortran: fdata->FortranCaller(data, function); break; default : CCTK_WARN(CCTK_WARN_ALERT, "Unknown language."); } break; default : CCTK_WARN(CCTK_WARN_ALERT, "Unknown function type."); } /* Return 0, meaning didn't synchronise */ return 0; } \end{verbatim} The return code of the function signifies whether or not the function synchronised the groups in this functions synchronisation list of not. The flesh will synchronise them if the function returns false. Providing this function is probably the easiest way to do multi-patch or AMR drivers. \subsection{Memory Functions} These consist of \begin{enumerate} \item{} {\tt CCTK\_EnableGroupStorage} \item{} {\tt CCTK\_DisableGroupStorage} \item{} {\tt CCTK\_QueryGroupStorageB} \item{} {\tt CCTK\_ArrayGroupSizeB} \end{enumerate} \subsubsection{En/Disable Group Storage} These are responsible for switching the memory for all variables in a group on or off. They should return the former state, e.g.\ if the group already has storage assigned, they should return 1. In our simple example above, the enabling routine would look something like \begin{verbatim} int SimpleEnableGroupStorage(cGH *GH, const char *groupname) { extension = (struct SimpleExtension *)GH->extensions[SimpleExtension]; if(extension->data[first][0][0] == NULL) { for(var = first; var <= last; var++) { allocate memory for all time levels; } retcode = 0; } else { retcode = 1; } return retcode; } \end{verbatim} The disable function is basically the reverse of the enable one. The {\tt QueryGroupStorage} function basically returns true or false if there is storage for the group, and the {\tt ArrayGroupSize} returns the size of the grid function or array group in a particular direction. \subsubsection{En/Disable Group Comm} These are the communication analogues to the storage functions. Basically, they flag that communication is to be done on that group or not, and may initialise data structures for the communication. \section{I/O Methods} \label{chap:io_methods} % The flesh by itself does not provide output for grid variables or other data. Instead, it provides a mechanism for thorns to register their own routines as I/O methods, and to invoke these I/O methods by either the flesh scheduler or by other thorn routines. This chapter explains how to implement your own I/O methods and register them with the flesh. % \subsection{I/O Method Registration} % All I/O methods have to be registered with the flesh before they can be used. The flesh I/O registration API provides a routine {\t CCTK\_RegisterIOMethod()} to create a handle for a new I/O method which is identified by its name (this name must be unique for all I/O methods). With such a handle, a thorn can then register a set of functions (using the {\t CCTK\_RegisterIOMethod*()} routines from the flesh) for doing periodic, triggered, and/or unconditional output. The following example shows how a thorn would register an I/O method, {\tt SimpleIO}, with routines to provide all these different types of output. % \begin{verbatim} void SimpleIO_Startup (void) { int handle = CCTK_RegisterIOMethod ("SimpleIO"); if (handle >= 0) { CCTK_RegisterIOMethodOutputGH (handle, SimpleIO_OutputGH); CCTK_RegisterIOMethodTimeToOutput (handle, SimpleIO_TimeToOutput); CCTK_RegisterIOMethodTriggerOutput (handle, SimpleIO_TriggerOutput); CCTK_RegisterIOMethodOutputVarAs (handle, SimpleIO_OutputVarAs); } } \end{verbatim} % % \subsection{Periodic Output of Grid Variables} % The flesh scheduler will automatically call {\t CCTK\_OutputGH()} at every iteration after the {\tt CCTK\_ANALYSIS} time bin. This function loops over all I/O methods and calls their routines registered as {\t OutputGH()} (see also Section \ref{subsec:schedule_ccl}). % \begin{alltt} int SimpleIO_OutputGH (const cGH *\var{GH}); \end{alltt} % The {\t OutputGH()} routine itself should loop over all variables living on the \texttt{GH} grid hierarchy, and do all necessary output if requested (this is usually determined by I/O parameter settings). As its return code, it should pass back the number of variables which were output at the current iteration, or zero if no output was done by this I/O method. % % \subsection{Triggered Output of Grid Variables} % Besides the periodic output at every so many iterations using {\t OutputGH()}, analysis and output of grid variables can also be done via triggers. For this, a {\t TimeToOutput()} routine is registered with an I/O method. This routine will be called by the flesh scheduler at every iteration before {\tt CCTK\_ANALYSIS} with the triggering variable(s) as defined in the schedule block for all {\tt CCTK\_ANALYSIS} routines (see Section \ref{scheduling:schedule_block}). If the {\t TimeToOutput()} routine decides that it is now time to do output, the flesh scheduler will invoke the corresponding analysis routine and also request output of the triggering variable(s) using {\t TriggerOutput()}. % \begin{alltt} int SimpleIO_TimeToOutput (const cGH *\var{GH}, int \var{varindex}); int SimpleIO_TriggerOutput (const cGH *\var{GH}, int \var{varindex}); \end{alltt} % Both routines get passed the index of a possible triggering grid variable. {\t TimeToOutput()} should return a non-zero value if analysis and output for \texttt{\var{varindex}} should take place at the current iteration, and zero otherwise. {\t TriggerOutput()} should return zero for successful output of variable \texttt{\var{varindex}}, and a negative value in case of an error. % % \subsection{Unconditional Output of Grid Variables} An I/O method's {\t OutputVarAs()} routine is supposed to do output for a specific grid variable if ever possible. It will be invoked by the flesh I/O API routines {\t CCTK\_OutputVar*()} for unconditional, non-triggered output of grid variables (see also Section \ref{sec:io}). A function registered as an \texttt{OutputVarAs()} routine has the following prototype: % \begin{alltt} int SimpleIO_OutputVarAs (const cGH *\var{GH}, const char *\var{varname}, const char *\var{alias}); \end{alltt} % The variable to output, \texttt{\var{varname}}, is given by its full name. The full name may have appended an optional I/O options string enclosed in curly braces (with no space between the full name and the opening curly brace). In addition to that, an \texttt{\var{alias}} string can be passed which then serves the purpose of constructing a unique name for the output file. The {\t OutputVarAs()} routine should return zero if output for \texttt{\var{varname}} was done successfully, or a negative error code otherwise. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Checkpointing/Recovery Methods} \label{chap:cp_recovery_methods} Like for I/O methods, checkpointing/recovery functionality must be implemented by thorns. The flesh only provides specific time bins at which the scheduler will call thorns' routines, in order to perform checkpointing and/or recovery. This chapter explains how to implement checkpointing and recovery methods in your thorn. For further information, see the documentation for thorn \texttt{CactusBase/IOUtil}. \subsection{Checkpointing Invocation} Thorns register their checkpointing routines at {\t CCTK\_CPINITIAL} and/or {\t CCTK\_CHECKPOINT} and/or {\t CCTK\_TERMINATE}. These time bins are scheduled right after all initial data has been set up, after every evolution timestep, and after the last time step of a simulation, respectively. (See Section \ref{subsec:schedule_ccl} for a description of all timebins). Depending on parameter settings, the checkpoint routines decide whether to write an initial data checkpoint, and when to write an evolution checkpoint. Each checkpoint routine should save all information to persistent storage, which is necessary to restart the simulation at a later time from exactly the same state. Such information would include % \begin{itemize} \item the current settings of all parameters \item the contents of all grid variables which have global storage assigned and are not tagged with {\tt checkpoint="no"} (see also Section \ref{subsec:Appendix.interface-variables} on page \pageref{subsec:Appendix.interface-variables} for a list of possible tags)\\ Note that grid variables should be synced before writing them to disk. \item other relevant information such as the current iteration number and physical time, the number of processors, etc. \end{itemize} \subsection{Recovery Invocation} Recovering from a checkpoint is a two-phase operation for which the flesh provides distinct timebins for recovery routines to be scheduled at: % \begin{Lentry} \item[{\t CCTK\_RECOVER\_PARAMETERS}] This time bin is executed before {\t CCTK\_STARTUP}, in which the parameter file is parsed. From these parameter settings, the recovery routines should decide whether recovery was requested, and if so, restore all parameters from the checkpoint file and overwrite those which aren't steerable.\\ The flesh loops over all registered recovery routines to find out whether recovery was requested. Each recovery routine should, therefore, return a positive integer value for successful parameter recovery (causing a shortcut of the loop over all registered recovery routines), zero for no recovery, or a negative value to flag an error.\\ If recovery was requested, but no routine could successfully recover parameters, the flesh will abort the run with an error message. If no routine recovered any parameters, i.e. if all parameter recovery routines returned zero, then this indicates that this run is not a recovery run.\\ If parameter recovery was performed successfully, the scheduler will set the {\tt recovered} flag which---in combination with the setting of the {\tt Cactus::recovery\_mode} parameter---decides whether any thorn routine scheduled for {\t CCTK\_INITIAL} and {\t CCTK\_POSTINITIAL} will be called. The default is to not execute these initial time bins during recovery, because the initial data will be set up from the checkpoint file during the following {\t CCTK\_RECOVER\_VARIABLES} time bin. \item[{\t CCTK\_RECOVER\_VARIABLES}] Recovery routines scheduled for this time bin are responsible for restoring the contents of all grid variables with storage assigned from the checkpoint.\\ Depending on the setting of {\tt Cactus::recovery\_mode}, they should also decide how to treat errors in recovering individual grid variables. Strict recovery (which is the default) requires all variables to be restored successfully (and will stop the code if not), whereas a relaxed mode could, e.g. allow for grid variables, which are not found in the checkpoint file, to be gracefully ignored during recovery. \end{Lentry} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Clocks for Timing} \label{chap:clocks} To add a Cactus clock, you need to write several functions to provide the timer functionality (see Section \ref{sec:timers}), and then register these functions with the flesh as a named clock. The function pointers are placed in function pointer fields of a \texttt{cClockFuncs} structure. The fields of this structure are are: \begin{Lentry} \item[{\t create}] {\t void *(*create)(int)} \item[{\t destroy}] {\t void (*destroy)(int, void *)} \item[{\t start}] {\t void (*start)(int, void *)} \item[{\t stop}] {\t void (*stop)(int, void *)} \item[{\t reset}] {\t void (*reset)(int, void *)} \item[{\t get}] {\t void (*get)(int, void *, cTimerVal *)} \item[{\t set}] {\t void (*set)(int, void *, cTimerVal *)} \item[{\t n\_vals}] {\t int} \end{Lentry} The first \texttt{int} argument of the functions may be used in any way you see fit. The \texttt{n\_vals} field holds the number of elements in the \texttt{vals} array field of the \texttt{cTimerVal} structure used by your timer (usually 1). The return value of the \texttt{create} function will be a pointer to a new structure representing your clock. The second \texttt{void*} argument of all the other functions will be the pointer returned from the \texttt{create} function. The \texttt{get} and \texttt{set} functions should write to and read from (respectively) a structure pointed to by the \texttt{cTimerVal*} argument: \begin{verbatim} typedef enum {val_none, val_int, val_long, val_double} cTimerValType; typedef struct { cTimerValType type; const char *heading; const char *units; union { int i; long int l; double d; } val; double seconds; double resolution; } cTimerVal; \end{verbatim} The \texttt{heading} field is the name of the clock, the \texttt{units} field holds a string describing the type held in the \texttt{val} field, and the \texttt{seconds} field is the time elapsed in seconds. The \texttt{resolution} field is the smallest non-zero difference in values of two calls to the timer, in seconds. For example, it could reflect that the clock saves the time value internally as an integer value representing milliseconds. To name and register the clock with the flesh, call the function \begin{alltt} CCTK_ClockRegister( "\var{my_clock_name}", &\var{clock_func} ). \end{alltt} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \end{cactuspart}