libsilo-dev 4.10.2-6+b3 / usr / include / pmpio.h

/*
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#ifndef PMPIO_H
#define PMPIO_H

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Introduction 
 *
 * Description:
 * This header file defines the Poor Main's Parallel I/O support interface.
 * To use it, include pmpio.h /after/ mpi.h in your application.
 *
 * PMPIO makes it *very*simple* to take an existing application that writes
 * a file per processor and add the ability to vary the number of files
 * the application writes to from 1 (e.g. serial I/O) to one for each
 * processor and anything in between.
 *
 * I/O libraries like serial HDF5 and Silo can be used very effectively
 * in parallel without having to resort to writing a file per processor.
 * PMPIO impliments a simple approach to using serial I/O libraries
 * effectively in parallel by having the application decompose the set of
 * processors into /N/ groups and write a file per group. At any one moment,
 * only one processor from each group has a file open for writing. Hence,
 * the I/O is serial /within/ a group. However, because a processor in each
 * of the /N/ groups is writing to its own file, simultaneously, the I/O is
 * parallel /across/ groups.
 *
 * The number of files, /N/, can be chosen wholly
 * independently of the total number of processors permitting the application
 * to tune /N/ to the underlying filesystem. For example, a parallel
 * application running on 2,000 processors and writing to a filesystem that
 * supports 8 parallel I/O channels could select /N=8/ and achieve nearly
 * optimum I/O performance and create only 8 files.
 *
 * This is a simple and effective I/O strategy that has been used by codes
 * like Ale3d and SAMRAI for many years. PMPIO impliments some basic
 * functions to help take an existing application that generates a file per
 * processor and modify it to generate a file per group of processors.
 *
 * In order for the strategy implemented here to work, some functionality
 * must be available in the I/O library being used to read/write the data.
 * The I/O library needs to support the following
 * A) Random access to named data objects
 * B) Separate name spaces within a file (e.g. like unix directories)
 * C) Variable sized I/O requests for same data objects from different
 *    processors
 *
 * A large number of I/O libraries and/or file formats support these
 * features including HDF5, Silo, PDB (Portable Database),
 * HDF4, Boxlib. There are probably numerous others. Some noteable I/O
 * libraries and/or file formats that do not support these features are
 * netCDF and VTK.
 *
 * The pmpio.h header file contains three key routines to facilitate
 * using a basic serial I/O library in the fashion of
 * 'Poor Man's Parallel I/O'. Pseudocode pattern of its use is below...
 *
 *        PMPIO_baton_t *bat = PMPIO_Init(MPI_COMM_WORLD,...)
 *        fileHandle = (<fileHandleType> *) PMPIO_WaitForBaton(bat, a, b)
 *        .
 *        do this processor's work on the file
 *        .
 *        PMPIO_HandOffBaton(fileHandle,...)
 *            
 * All processors call all of these methods. PMPIO_Init() returns immediately.
 * PMPIO_WaitForBaton() returns immediatly only on the /first/ processor in
 * each group sharing a file. All other processors wait to recieve a baton
 * from the previous processor. When a processor finishes its work on the file
 * and reaches the PMPIO_HandOffBaton(), that call returns immediately and it
 * also passes the baton to the next processor in the group. In turn, that
 * processor then returns from the PMPIO_WaitForBaton() call it is waiting.
 * This process continues with each processor in a group handing off a baton
 * to the next processor.
 *-----------------------------------------------------------------------------
 */

#include <stdlib.h>

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Initialization 
 * Purpose:     I/O Modes
 * Description:
 * Used to indicate if PMPIO is being used to write data or
 * read it 
 *-----------------------------------------------------------------------------
 */
typedef enum {
    PMPIO_READ=0x1,
    PMPIO_WRITE=0x3
} PMPIO_iomode_t;

struct _PMPIO_baton_t;

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Create Callback
 * Description:
 * Defines the create file callback interface. When used for
 * writing, the create file callback should 1) create a file, 2) create a
 * namespace in the file for the first processor of the group to write to
 * and 3) set the file to that namespace. The create file call back is
 * never called during reading. 
 *
 *     typedef void * (*PMPIO_CreateFileCallBack)(
 *         const char *fname,  name of the file to create
 *         const char *nsname, name of the namespace in the file to create
 *         void *udata         optional, user data passed by PMPIO
 *     );
 *-----------------------------------------------------------------------------
 */
typedef void * (*PMPIO_CreateFileCallBack)(const char *fname, const char *nsname,
                                           void *udata);

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Open Callback
 * Description:
 * Defines the open file callback interface. When used for
 * writing, the open file callback should 1) open a file, 2) create a
 * namespace in the file for the current processor of the group to write
 * to and 3) set the file to that namespace. When used for  reading,
 * the open file callback should 1) open a file and 2) set the file
 * to the namespace the current processor should read from.
 *
 *     typedef void * (*PMPIO_OpenFileCallBack)(
 *         const char *fname,     name of the file to open
 *         const char *nsname,    name of the namespace to create (write)
 *                                or set (read)
 *         PMPIO_iomode_t iomode, indicates if read or write
 *         void *udata            optional user data passed by PMPIO
 *     );
 *-----------------------------------------------------------------------------
 */
typedef void * (*PMPIO_OpenFileCallBack)(const char *fname, const char *nsname,
                                         PMPIO_iomode_t iomode, void *udata);

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Close Callback
 * Description:
 * Defines the close file callback interface. This should close the file.
 *
 *     typedef void  (*PMPIO_CloseFileCallBack)(
 *         void *file,   pointer to the file object to close
 *         void *udata   optional user data passed by PMPIO
 *     );
 *-----------------------------------------------------------------------------
 */
typedef void  (*PMPIO_CloseFileCallBack)(void *file, void *udata);

typedef struct _PMPIO_baton_t
{
    PMPIO_iomode_t ioMode;
    int commSize;
    int rankInComm;
    int numGroups;
    int groupSize;
    int numGroupsWithExtraProc;
    int commSplit;
    int groupRank;
    int rankInGroup;
    int procBeforeMe;
    int procAfterMe;
    int mpiVal;
    int mpiTag;
    MPI_Comm mpiComm;
    PMPIO_CreateFileCallBack createCb;
    PMPIO_OpenFileCallBack openCb;
    PMPIO_CloseFileCallBack closeCb;
    void *userData;

} PMPIO_baton_t;

#define PMPIO_BATON_OK  0 
#define PMPIO_BATON_ERR 1

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Initialization 
 * Purpose:     Initialize a PMPIO baton
 * Description:
 * Initializes PMPIO to write a specified number of files. If the
 * specified number of files is one (1), the result will effectively be serial
 * I/O. If the number of files is equal to the number of processors, the result
 * will be file per processor. It is best to choose a number of files that does
 * not exceed the total number of available I/O channels. On large parallel
 * systems, this number can typically be between 8 and 64.
 * 
 * Given the MPI communicator, and the desired number of files, this function
 * will divide all processors in the communicator into a number of groups.
 * If the number of groups does not equally divide the number of processors,
 * some groups will contain an extra processor.
 * Each group of processors will write to its own file.
 *
 * PMPIO_Init() makes no MPI calls other than obtaining the size of the MPI
 * communicator and the rank of the calling processor.
 *
 * A call to PMPIO_Init() should be followed by a call to PMPIO_WaitForBaton,
 * followed by a call to PMPIO_HandOffBaton and finally by a call to
 * PMPIO_Finish(). A call to PMPIO_Init() returns a /baton/, a pointer to
 * a PMPIO_baton_t, that is /active/ until PMPIO_Finish() is called.
 *
 * Multiple calls to PMPIO_Init() can be made within a single execution. In
 * fact, as long as the mpiTag used in baton-passing messages is unique
 * across all /active/batons/, calls can be interleaved between /active/
 * batons.
 *
 * All processors should call this function with identical arguments otherwise
 * behavior is undefined. The call returns immediatly on all processors.
 *-----------------------------------------------------------------------------
 */
static PMPIO_baton_t *
PMPIO_Init(
    int numFiles,                       /* The number of files to be created */
    PMPIO_iomode_t ioMode,              /* Indicates whether this is for writing a file or for reading a file.
                                           Specify either PMPIO_READ or PMPIO_WRITE. Note, read and write
                                           at the same time is not supported. */
    MPI_Comm mpiComm,                   /* The MPI communicator PMPIO should use */
    int mpiTag,                         /* The message tag PMPIO should use for its baton-pass messages. */
    PMPIO_CreateFileCallBack createCb,  /* The create file callback. In the case of PMPIO_WRITE, this
                                           callback should 1) create a file, 2) create a namespace in
                                           the file for the first processor of the group to write to and
                                           3) set the file to that namespace. In the
                                           case of PMPIO_READ, this callback is never called. */
    PMPIO_OpenFileCallBack openCb,      /* The open file callback. In the case of PMPIO_WRITE, this callback 
                                           should 1) open the file, 2) create a namespace in the file for the
                                           current processor to write to and 3) set the file to that namespace.
                                           In the case of PMPIO_READ, this callback should 1) open the file
                                           and 2) set the file to the namespace for the current processor to
                                           read from. */
    PMPIO_CloseFileCallBack closeCb,    /* The close file callback. This method should close the file. */
    void *userData                      /* Optional, user-specified data that PMPIO passes into the callbacks.
                                           Pass 0 if you have no need for this. */
                                          
    )
{
    int numGroups = numFiles;
    int commSize, rankInComm;
    int groupSize, numGroupsWithExtraProc, commSplit,
        groupRank, rankInGroup, procBeforeMe, procAfterMe;
    PMPIO_baton_t *ret = 0;

    procBeforeMe = -1;
    procAfterMe = -1;

    MPI_Comm_size(mpiComm, &commSize);
    MPI_Comm_rank(mpiComm, &rankInComm);

    groupSize              = commSize / numGroups;
    numGroupsWithExtraProc = commSize % numGroups;
    commSplit = numGroupsWithExtraProc * (groupSize + 1);

    if (rankInComm < commSplit)
    {
        groupRank = rankInComm / (groupSize + 1);
        rankInGroup = rankInComm % (groupSize + 1);
        if (rankInGroup < groupSize)
            procAfterMe = rankInComm + 1;
    }
    else
    {
        groupRank = numGroupsWithExtraProc + (rankInComm - commSplit) / groupSize; 
        rankInGroup = (rankInComm - commSplit) % groupSize;
        if (rankInGroup < groupSize - 1)
            procAfterMe = rankInComm + 1;
    }
    if (rankInGroup > 0)
        procBeforeMe = rankInComm - 1;

    if (createCb == 0 || openCb == 0 || closeCb == 0)
        return 0;

    ret = (PMPIO_baton_t *) malloc(sizeof(PMPIO_baton_t));
    ret->ioMode = ioMode;
    ret->commSize = commSize;
    ret->rankInComm = rankInComm;
    ret->numGroups = numGroups;
    ret->groupSize = groupSize;
    ret->numGroupsWithExtraProc = numGroupsWithExtraProc;
    ret->commSplit = commSplit;
    ret->groupRank = groupRank;
    ret->rankInGroup = rankInGroup;
    ret->procBeforeMe = procBeforeMe;
    ret->procAfterMe = procAfterMe;
    ret->mpiVal = PMPIO_BATON_OK;
    ret->mpiTag = mpiTag;
    ret->mpiComm = mpiComm;
    ret->createCb = createCb;
    ret->openCb = openCb;
    ret->closeCb = closeCb;
    ret->userData = userData;

    return ret;
}

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Initialization 
 * Purpose:     Finish use of an active baton 
 * Description:
 * Finishes the use of an active PMPIO baton and deallocates any storage.
 *-----------------------------------------------------------------------------
 */
static void
PMPIO_Finish(
    PMPIO_baton_t *bat
)
{
    free(bat);
}

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Baton Passing 
 * Purpose:     Wait for a PMPIO baton
 * Description:
 * Causes the calling processor to wait until it is handed a 
 * baton. This call will return immediately *only* for the /first/ processor
 * in each group. All other processors in a group will block, waiting to get
 * the baton from their predecessor. To give up the baton, a processor must
 * call PMPIO_HandOffBaton().
 *-----------------------------------------------------------------------------
 */
static void *
PMPIO_WaitForBaton(
    PMPIO_baton_t *Bat,         /* The PMPIO baton obtained from a PMPIO_Init() call. */
    const char *fname,          /* The name of the file this processor will open. */
    const char *nsname          /* The name of the namespace in the file this processor will work on. */
)
{
    if (Bat->procBeforeMe != -1)
    {
        MPI_Status mpi_stat;
        int baton;
        int mpi_err =
            MPI_Recv(&baton, 1, MPI_INT, Bat->procBeforeMe,
                Bat->mpiTag, Bat->mpiComm, &mpi_stat);
        if (mpi_err == MPI_SUCCESS && baton != PMPIO_BATON_ERR)
        {
            return Bat->openCb(fname, nsname, Bat->ioMode, Bat->userData);
        }
        else
        {
            Bat->mpiVal = PMPIO_BATON_ERR;
            return 0;
        }
    }
    else
    {
        if (Bat->ioMode == PMPIO_WRITE)
            return Bat->createCb(fname, nsname, Bat->userData);
        else
            return Bat->openCb(fname, nsname, Bat->ioMode, Bat->userData);
    }
}

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Baton Passing 
 * Purpose:     Wait for a PMPIO baton
 * Description:
 * Causes the calling processor to hand off its baton to the next processor. 
 * This call returns immediately.
 *-----------------------------------------------------------------------------
 */
static void
PMPIO_HandOffBaton(
    const PMPIO_baton_t *Bat,   /* The PMPIO baton obtained from a PMPIO_Init() call. */
    void *file                  /* A void pointer to the file object obtained
                                   from a PMPIO_WaitForBaton() call. */
)
{
    Bat->closeCb(file, Bat->userData);
    if (Bat->procAfterMe != -1)
    {
        int baton = Bat->mpiVal;
        MPI_Ssend(&baton, 1, MPI_INT, Bat->procAfterMe,
            Bat->mpiTag, Bat->mpiComm);
    }
}

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Ranking 
 * Purpose:     Return 'group rank' of a given processor in the communicator 
 * Description:
 * Given a processor's rank in the communicator used to initialize PMPIO, 
 * determine the 'group rank' of the processor (e.g. which group) indexed
 * from zero.
 *-----------------------------------------------------------------------------
 */
static int
PMPIO_GroupRank(const PMPIO_baton_t *Bat, int rankInComm)
{
    int retval;

    if (rankInComm < Bat->commSplit)
    {
        retval = rankInComm / (Bat->groupSize + 1);
    }
    else
    {
        retval = Bat->numGroupsWithExtraProc +
                 (rankInComm - Bat->commSplit) / Bat->groupSize; 
    }

    return retval;
}

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Ranking 
 * Purpose:     Return 'rank in group' of a given processor in the communicator 
 * Description:
 * Given a processor's rank in the communicator used to initialize PMPIO, 
 * determine the 'rank in grouop' of the processor (e.g. which processor in the
 * group) indexed from zero.
 *-----------------------------------------------------------------------------
 */
static int
PMPIO_RankInGroup(const PMPIO_baton_t *Bat, int rankInComm)
{
    int retval;

    if (rankInComm < Bat->commSplit)
    {
        retval = rankInComm % (Bat->groupSize + 1);
    }
    else
    {
        retval = (rankInComm - Bat->commSplit) % Bat->groupSize;
    }

    return retval;
}

/* Define this Default PMPIO functions only if we have silo.h. We use existence
of 'DB_HDF5' as indication that silo.h is present. */
#ifdef DB_HDF5X
/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Callbacks
 * Purpose:     Impliment the create callback
 *
 * Description: The caller can specify which Silo driver to use by passing
 * a void pointer to the driver specification as the userData argument. If
 * that pointer is NULL or the value to which it points is not a known
 * driver type (DB_HDF5 or DB_PDB), it is set to DB_PDB driver as that is
 * guarenteed to exist in any Silo implmentation.
 *-----------------------------------------------------------------------------
 */
static void *
PMPIO_DefaultCreate(const char *fname, const char *nsname, void *userData)
{
    DBfile *siloFile;
    int driver = userData ? *((int*) userData) : DB_PDB;
    if (driver != DB_PDB && driver != DB_HDF5)
        driver = DB_PDB;
    siloFile = DBCreate(fname, DB_CLOBBER, DB_LOCAL, "PMPIO_DefaultCreate", driver);
    if (siloFile)
    {
        DBMkDir(siloFile, nsname);
        DBSetDir(siloFile, nsname);
    }
    return (void *) siloFile;
}

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Callbacks
 * Purpose:     Impliment the open callback
 *-----------------------------------------------------------------------------
 */
static void *
PMPIO_DefaultOpen(const char *fname, const char *nsname, PMPIO_iomode_t ioMode, void *userData)
{
    DBfile *siloFile = DBOpen(fname, DB_UNKNOWN,
        ioMode == PMPIO_WRITE ? DB_APPEND : DB_READ);
    if (siloFile)
    {
        if (ioMode == PMPIO_WRITE)
            DBMkDir(siloFile, nsname);
        DBSetDir(siloFile, nsname);
    }
    return (void *) siloFile;
}

/*-----------------------------------------------------------------------------
 * Audience:    Public
 * Chapter:     Callbacks
 * Purpose:     Impliment the close callback
 *-----------------------------------------------------------------------------
 */
static void
PMPIO_DefaultClose(void *file, void *userData)
{
    DBfile *siloFile = (DBfile *) file;
    if (siloFile)
        DBClose(siloFile);
}
#endif

#endif