Beispiel #1
0
int declare_group ()
{

    adios_set_max_buffer_size (10);

    adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
    adios_select_method (m_adios_group, "MPI", "verbose=2", "");

    adios_define_var (m_adios_group, "NX"
            ,"", adios_integer
            ,0, 0, 0);

    adios_define_var (m_adios_group, "t1"
            ,"", adios_double
            ,"NX", "100", "0");

    adios_define_var (m_adios_group, "NX"
            ,"", adios_integer
            ,0, 0, 0);

    adios_define_var (m_adios_group, "t2"
            ,"", adios_double
            ,"NX", "100", "0");

    return 0;
}
Beispiel #2
0
int declare_group ()
{

    adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 10);

    adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
    adios_select_method (m_adios_group, "MPI", "verbose=2", "");

    adios_define_var (m_adios_group, "NX"
            ,"", adios_integer
            ,0, 0, 0);

    adios_define_var (m_adios_group, "t1"
            ,"", adios_double
            ,"NX", "100", "0");

    adios_define_var (m_adios_group, "NX"
            ,"", adios_integer
            ,0, 0, 0);

    adios_define_var (m_adios_group, "t2"
            ,"", adios_double
            ,"NX", "100", "0");

    return 0;
}
Beispiel #3
0
int main (int argc, char ** argv) 
{
	MPI_Comm    comm = 0; // dummy mpi 

	/* ADIOS variables declarations for matching gwrite_temperature.ch */
	uint64_t  adios_groupsize, adios_totalsize;
	int64_t   g;
	int64_t   f;
	int64_t   Tid, Pid, Vid; // variable IDs
	char dimstr[32];

	sprintf (dimstr, "%d,%d", NX, NY);

	adios_init_noxml (comm);
	adios_set_max_buffer_size (1);

	adios_declare_group (&g, "vars", "", adios_flag_yes);
	adios_select_method (g, "POSIX", "", "");

	Tid = adios_define_var (g, "T" ,"", adios_double, dimstr, dimstr, "0,0");
	adios_set_transform (Tid, "none");
	Pid = adios_define_var (g, "P" ,"", adios_double, dimstr, dimstr, "0,0");
	adios_set_transform (Pid, "none");
	Vid = adios_define_var (g, "V" ,"", adios_double, dimstr, dimstr, "0,0");
	adios_set_transform (Vid, "none");

    adios_read_init_method(ADIOS_READ_METHOD_BP,0,"");
    if (adios_query_is_method_available (ADIOS_QUERY_METHOD_ALACRITY)) {
        adios_set_transform (Tid, "alacrity");
        adios_set_transform (Pid, "alacrity");
        adios_set_transform (Vid, "alacrity");
        printf ("Turned on ALACRITY transformation for array variables\n");
    }

	adios_open (&f, "vars", "vars.bp", "w", comm);
	adios_groupsize = 3*NX*NY*sizeof(double);
	adios_group_size (f, adios_groupsize, &adios_totalsize);
	adios_write (f, "T", T);
	adios_write (f, "P", P);
	adios_write (f, "V", V);
	adios_close (f);

	adios_finalize (0);
	return 0;
}
Beispiel #4
0
int main (int argc, char ** argv) 
{
	int         size, i, block;
	MPI_Comm    comm = 0; // dummy mpi 

	/* ADIOS variables declarations for matching gwrite_temperature.ch */
	uint64_t  adios_groupsize, adios_totalsize;
        int64_t   g;
        int64_t   f;
        char dimstr[32];

	adios_init_noxml (comm);
        adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 1);

        adios_declare_group (&g, "table", "", adios_flag_yes);
        adios_select_method (g, "POSIX1", "", "");

	sprintf (dimstr, "%d,%d", NX, NY);
        adios_define_var (g, "A" ,"", adios_integer, dimstr, dimstr, "0,0");
	sprintf (dimstr, "%d,%d", n_of_elements, Elements_length);
        adios_define_var (g, "Elements" ,"", adios_byte, dimstr, dimstr, "0,0");
	sprintf (dimstr, "%d,%d", NY, Columns_length);
        adios_define_var (g, "Columns" ,"", adios_byte, dimstr, dimstr, "0,0");
   
   
        adios_open (&f, "table", "table.bp", "w", comm);

        adios_groupsize = NX*NY*sizeof(int32_t)           /* size of A */
                        + n_of_elements * Elements_length /* size of Elements */
                        + NY * Columns_length;            /* size of Columns */

        adios_group_size (f, adios_groupsize, &adios_totalsize);
	adios_write (f, "A", A);
	adios_write (f, "Elements", Elements);
	adios_write (f, "Columns", Columns);
        adios_close (f);

	adios_finalize (0);
	return 0;
}
Beispiel #5
0
int output_init(MPI_Comm comm, int bufsizeMB)
{
    char * wmethodname, *wmethodparams;
    MPI_Comm_rank (comm, &rank);
    adios_init_noxml(comm);
    adios_declare_group(&gh,"writer","",adios_flag_yes);
    adios_set_max_buffer_size (bufsizeMB);

    // Select output method
    wmethodname = getenv("ADIOSMETHOD");
    wmethodparams = getenv("ADIOSMETHOD_PARAMS");
    if (!wmethodname)
        wmethodname = DEFAULT_ADIOSMETHOD_NAME;
    if (!wmethodparams)
        wmethodparams = DEFAULT_ADIOSMETHOD_PARAMS;
    adios_select_method (gh, wmethodname, wmethodparams, "");

    groupsize = 0;

    if (!strcmp(wmethodname, "POSIX1")) 
    {
        file_per_process = 1;
        iocomm = MPI_COMM_SELF;
    } 
    else 
    {
        iocomm = comm;
    }

    if (!strcmp(wmethodname, "DATASPACES") ||  
        !strcmp(wmethodname, "DIMES")      || 
        !strcmp(wmethodname, "FLEXPATH")    ) 
    {
        streaming = 1;
    } else {
        streaming = 0;
    }
    return 0;
}
Beispiel #6
0
/**
 * ADIOS init and create group etc.
 * Return: pointer to the ADIOS group structure
 */
SEXP R_create(SEXP R_groupname,
              SEXP R_buffersize,
              SEXP R_comm)
{
    const char *groupname = CHARPT(R_groupname, 0);
    int buffer = asInteger(R_buffersize);
    MPI_Comm comm = MPI_Comm_f2c(INTEGER(R_comm)[0]);

    int64_t m_adios_group;
    
    adios_init_noxml (comm);
    adios_set_max_buffer_size (buffer); // Default buffer size for write is 20. User can change this value

    adios_declare_group (&m_adios_group, groupname, "", adios_flag_yes);
    adios_select_method (m_adios_group, "MPI", "", ""); // Default method is MPI. Let users choose different methods later.

    // Pass group pointer to R
    SEXP R_group = PROTECT(allocVector(REALSXP, 1));
    REAL(R_group)[0] = (double)m_adios_group;
    UNPROTECT(1);

    return R_group;
}
Beispiel #7
0
int main (int argc, char ** argv) 
{
    int err, step ; 
    int do_write = 1;
    int do_read = 1;
    int m = 0;
    char write_method[16];

    MPI_Init (&argc, &argv);
    MPI_Comm_rank (comm, &rank);
    MPI_Comm_size (comm, &size);

    if (argc > 1) { 
        m = strtol (argv[1], NULL, 10);
        if (errno) { printf("Invalid 1st argument %s\n", argv[1]); Usage(); return 1;}
    }
    if (argc > 2) { 
        if (argv[2][0] == 'w' || argv[2][0] == 'W') {
            do_read = 0;
        } else if (argv[2][0] == 'r' || argv[2][0] == 'R') {
            do_write = 0;
        } else {
            printE ("Invalid command line argument %s. Allowed ones:\n"
                    " w: do write only\n"
                    " r: do read only\n", argv[2]);
            MPI_Finalize ();
            return 1;
        }
    }

    if (m==0) {
        read_method = ADIOS_READ_METHOD_BP;
        strcpy(write_method,"MPI");
    } else {
        read_method = ADIOS_READ_METHOD_DATASPACES;
        strcpy(write_method,"DATASPACES");
    }

    
    log ("Writing: %s method=%s\n"
         "Reading: %s method=%d\n", 
        (do_write ? "yes" : "no"), write_method,
        (do_read ? "yes" : "no"), read_method);

    alloc_vars();
    if (do_write) {
        adios_init_noxml (comm);
        adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 10);
    }
    if (do_read) {
        err = adios_read_init_method(read_method, comm, "verbose=2");
        if (err) {
            printE ("%s\n", adios_errmsg());
        }
    }

    
    if (do_write) {
        adios_declare_group (&m_adios_group, "selections", "iter", adios_flag_yes);
        adios_select_method (m_adios_group, write_method, "verbose=2", "");

        define_vars();

        for (step=0; step<NSTEPS; step++) {
            if (!err) {
                set_vars (step);
                err = write_file (step); 
                sleep(1);
            }
        }
        adios_free_group (m_adios_group);
    }

    if (!err && do_read)
        err = read_points (); 

    //if (!err && do_read)
    //    err = read_writerblocks (); 

    if (do_read) {
        adios_read_finalize_method (read_method);
    }
    fini_vars();
    if (do_write) {
        adios_finalize (rank);
    }
    MPI_Finalize ();
    return err;
}
Beispiel #8
0
int main (int argc, char ** argv) 
{
    char        filename [256];
    int         rank, size, i, j;
    int         NX = 100, gb, offset;  //local/global/offset
    double      t[NX];
    int         nblocks = 3;
    MPI_Comm    comm = MPI_COMM_WORLD;
    char g_str[100], o_str[100], l_str[100];
    // attributes (from C variables)
    int someints[5] = {5,4,3,2,1};
    double somedoubles[5] = {5.55555, 4.4444, 3.333, 2.22, 1.1};

    /* ADIOS variables declarations for matching gwrite_temperature.ch */
    uint64_t    adios_groupsize, adios_totalsize;

    MPI_Init (&argc, &argv);
    MPI_Comm_rank (comm, &rank);
    MPI_Comm_size (comm, &size);

    gb = nblocks * NX * size;
    sprintf (g_str, "%d", gb);
    sprintf (l_str, "%d", NX);

    strcpy (filename, "no_xml_write_byid.bp");

    adios_init_noxml (comm);
    adios_set_max_buffer_size (10);

    int64_t       m_adios_group;
    int64_t       m_adios_file;
    int64_t       var_ids[nblocks];

    adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
    adios_select_method (m_adios_group, "MPI", "", "");

    for (i = 0; i < nblocks; i++)
    {
        offset = rank * nblocks * NX + i * NX;
        sprintf (o_str, "%d", offset);
        var_ids[i] = adios_define_var (m_adios_group, "temperature"
                                       ,"", adios_double
                                       ,l_str, g_str, o_str
        );
        adios_set_transform (var_ids[i], "none");

        // This is here just for fun
        uint64_t varsize = adios_expected_var_size(var_ids[i]);
        // adios_expected_var_size() works here because the definition of the variable
        // does not depend on any dimension variable (but defined with numerical dimensions)
        fprintf (stderr, "Temperature block %d is %" PRIu64 " bytes\n", i, varsize);
    }

    // add some attributes
    adios_define_attribute_byvalue (m_adios_group,
                                    "single_string","", adios_string,  1, "A single string attribute");
    char *strings[] = {"X","Yy","ZzZ"};
    adios_define_attribute_byvalue (m_adios_group,
                                    "three_strings","", adios_string_array,  3, strings);
    adios_define_attribute_byvalue (m_adios_group,
                                    "single_int",   "", adios_integer, 1, &someints);
    adios_define_attribute_byvalue (m_adios_group,
                                    "single_double","", adios_double,  1, &somedoubles);
    adios_define_attribute_byvalue (m_adios_group,
                                    "five_ints",    "", adios_integer, 5, &someints);
    adios_define_attribute_byvalue (m_adios_group,
                                    "five_double",  "", adios_double,  5, &somedoubles);



    adios_open (&m_adios_file, "restart", filename, "w", comm);

    adios_groupsize = nblocks * (4 + 4 + 4 + NX * 8);

    adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
    /* now we will write the data for each sub block */
    for (i = 0; i < nblocks; i++)
    {
        offset = rank * nblocks * NX + i * NX;
        for (j = 0; j < NX; j++)
            t[j] = offset + j;

        adios_write_byid(m_adios_file, var_ids[i], t);
    }

    adios_close (m_adios_file);

    MPI_Barrier (comm);

    adios_finalize (rank);

    MPI_Finalize ();
    return 0;
}
Beispiel #9
0
int main (int argc, char ** argv) 
{
    MPI_Comm    comm = MPI_COMM_WORLD;
    int         rank;
    int         ndx, ndy;             // size of array per processor
    double      * data;

    double      *X;                   //X coordinate
    double      *Y;                   //Y coordinate

    // Offsets and sizes
    int         offs_x, offs_y;       //offset in x and y direction
    int         nx_local, ny_local;   //local address
    int         nx_global, ny_global; //global address
    int         posx, posy;           // position index in the array
    int         i,j;

    int64_t     m_adios_group;
    uint64_t    adios_groupsize, adios_totalsize;
    int64_t     adios_handle;

    MPI_Init (&argc, &argv);
    MPI_Comm_rank (comm, &rank);
    MPI_Comm_size (comm, &nproc);

    if (processArgs(argc, argv)) {
        return 1;
    }

    //will work with each core writing ndx = 65, ndy = 129, (65*4,129*3) global
    ndx = 65;
    ndy = 129;

    //2D array with block,block decomposition
    posx = rank%npx;           // 1st dim
    posy = rank/npx;           // 2nd dim
    offs_x = posx * ndx;
    offs_y = posy * ndy;
    nx_local = ndx;
    ny_local = ndy;
    nx_global = npx * ndx;
    ny_global = npy * ndy;

    data = malloc (ndx * ndy * sizeof(double));
    for( i = 0; i < ndx; i++ )
        for( j = 0; j < ndy; j++)
            data[i*ndy + j] = 1.0*rank;

    X = malloc (ndx * ndy * sizeof(double));
    for( i = 0; i < ndx; i++ )
        for( j = 0; j < ndy; j++)
            X[i*ndy + j] = offs_x + posy*ndx + i*ndx/ndx + (double)ndx*j/ndy;

    Y = malloc (ndx * ndy * sizeof(double));
    Y[0] = offs_y;
    for( i = 0; i < ndx; i++ )
        for( j = 0; j < ndy; j++)
            Y[i*ndy + j] = offs_y + ndy*j/ndy;
  
    char * schema_version = "1.1";
    char * dimemsions = "nx_global,ny_global";
 
	adios_init_noxml (comm);
    adios_set_max_buffer_size (50);

    adios_declare_group (&m_adios_group, "structured2d", "", adios_flag_yes);
    adios_select_method (m_adios_group, "MPI", "", "");

    adios_define_var (m_adios_group, "nx_global"
			,"", adios_integer
			,0, 0, 0);
    adios_define_var (m_adios_group, "ny_global"
            ,"", adios_integer
            ,0, 0, 0);
    adios_define_var (m_adios_group, "nproc"
                ,"", adios_integer                
                ,0, 0, 0);
    adios_define_var (m_adios_group, "offs_x"
                ,"", adios_integer
                ,0, 0, 0);
    adios_define_var (m_adios_group, "offs_y"
                ,"", adios_integer
                ,0, 0, 0);
    adios_define_var (m_adios_group, "nx_local"
                ,"", adios_integer
                ,0, 0, 0);
    adios_define_var (m_adios_group, "ny_local"
                ,"", adios_integer
                ,0, 0, 0);
    adios_define_var (m_adios_group, "X"
                    ,"", adios_double
                    ,"nx_local,ny_local", "nx_global,ny_global", "offs_x,offs_y");
    adios_define_var (m_adios_group, "Y"
                    ,"", adios_double
                    ,"nx_local,ny_local", "nx_global,ny_global", "offs_x,offs_y");
    adios_define_var (m_adios_group, "data"
                    ,"", adios_double
                    ,"nx_local,ny_local", "nx_global,ny_global", "offs_x,offs_y");

    adios_define_schema_version (m_adios_group, schema_version);
    adios_define_mesh_structured (dimemsions, "X,Y", "2", m_adios_group, "structuredmesh");
    adios_define_mesh_timevarying ("no", m_adios_group, "structuredmesh");
    adios_define_var_mesh (m_adios_group, "data", "structuredmesh");
    adios_define_var_centering (m_adios_group, "data", "point");

    adios_open (&adios_handle, "structured2d", "structured2d_noxml.bp", "w", comm);

    adios_groupsize = 7*sizeof(int) \
    + 3*sizeof(double) * (nx_local*ny_local);

    adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
    adios_write (adios_handle, "nproc", &nproc);
    adios_write (adios_handle, "nx_global", &nx_global);
    adios_write (adios_handle, "ny_global", &ny_global);
    adios_write (adios_handle, "offs_x", &offs_x);
    adios_write (adios_handle, "offs_y", &offs_y);
    adios_write (adios_handle, "nx_local", &nx_local);
    adios_write (adios_handle, "ny_local", &ny_local);
    adios_write (adios_handle, "X", X);
    adios_write (adios_handle, "Y", Y);
    adios_write (adios_handle, "data", data);

    adios_close (adios_handle);

    MPI_Barrier (comm);

    free (data);
    free (X);
    free (Y);

	adios_finalize (rank);

	MPI_Finalize ();
	return 0;
}
Beispiel #10
0
int main (int argc, char ** argv) 
{
    int err,i,M; 
    int iconnect;

    MPI_Init (&argc, &argv);
    MPI_Comm_rank (wcomm, &wrank);
    MPI_Comm_size (wcomm, &wsize);

    if (argc < 2) { Usage(); return 1; }
    errno = 0;
    M = strtol (argv[1], NULL, 10);
    if (errno || M < 1 || M > wsize) { 
        printE("Invalid 1st argument %s\n", argv[1]); Usage(); return 1;
    }

    iconnect = (wrank >= wsize-M); // connect to server from ranks N-M, N-M+1, ..., N 
    MPI_Comm_split (wcomm, iconnect, wrank+M-wsize, &subcomm);  
    MPI_Comm_rank (subcomm, &subrank);
    MPI_Comm_size (subcomm, &subsize);
    if (iconnect) {
        if (subsize != M) {
            printE ("Something wrong with communicator split: N=%d, M=%d, splitted size=%d\n",
                     wsize, M, subsize);
            return 2;
        }
        log ("connect as subrank %d\n", subrank);
    }

    alloc_vars();
    adios_read_init_method(ADIOS_READ_METHOD_DATASPACES, subcomm, "verbose=4");
    adios_init_noxml (subcomm);
    adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 1);

    if (iconnect) 
    {
        adios_declare_group (&m_adios_group, "connect", "iter", adios_flag_yes);
        adios_select_method (m_adios_group, "DATASPACES", "verbose=4", "");
        adios_define_var (m_adios_group, "ldim1", "", adios_integer, 0, 0, 0);
        adios_define_var (m_adios_group, "gdim1", "", adios_integer, 0, 0, 0);
        adios_define_var (m_adios_group, "offs1", "", adios_integer, 0, 0, 0);
        adios_define_var (m_adios_group, "a1", "", adios_integer, 
                                         "ldim1", "gdim1", "offs1");
    
        for (i=0; i<NSTEPS; i++) {
            if (!err) {
                set_vars (i);
                err = write_file (i); 
            }
        }
    }
    log ("done with work, sync with others...\n");
    MPI_Barrier (wcomm);
    log ("call adios_finalize...\n");
    adios_finalize (wrank);
    log ("call adios_read_finalize_method...\n");
    adios_read_finalize_method (ADIOS_READ_METHOD_DATASPACES);
    fini_vars();
    MPI_Finalize ();
    return err;
}
Beispiel #11
0
int main (int argc, char ** argv) {
    //For varriable definitions:
    //gbounds = global bounds string, lbounds = local bounds string, offs = offset string, tstring = temp string to hold temperary stuff
    char       gbounds[1007], lbounds[1007], offs[1007],tstring[100];
    //size = number of cores,  gidx = adios group index
    int        rank, size, gidx, i, j, k, ii;
    //data = pointer to read-in data
    void       * data = NULL;
    uint64_t   s[] = {0,0,0,0,0,0,0,0,0,0};  //starting offset
    uint64_t   c[] = {1,1,1,1,1,1,1,1,1,1};  //chunk block array
    uint64_t   bytes_read = 0;
    int        element_size;
    int64_t    new_adios_group, m_adios_file;
    uint64_t   var_size;  //portion_bound,
    uint64_t   adios_groupsize, adios_totalsize;
    int        read_buffer;        //possible maximum size you the user would like for each chunk in MB
    int           write_buffer = 1536;  //actual buffer size you use in MB
    int        itime;
    int        WRITEME=1;
    uint64_t   chunk_size;   //chunk size in # of elements
    char      *var_path, *var_name; // full path cut into dir path and name
    MPI_Init(&argc,&argv);
    MPI_Comm_rank(comm,&rank);
    MPI_Comm_size(comm,&size);

    // timing numbers
    // we will time:
    // 0: adios_open, adios_group_size
    // 1: the total time to read in the data
    // 2: times around each write (will only work if we do NOT buffer....
    // 3: the time in the close
    // 4: fopen, fclose
    // 5: total time
    // timers: the total I/O time
    int        timers = 6;
    double     start_time[timers], end_time[timers], total_time[timers];

    if (TIMING==100) {
        for (itime=0;itime<timers;itime++) {
            start_time[itime] = 0;
            end_time[itime] = 0;
            total_time[itime]=0;
        }
        //MPI_Barrier(MPI_COMM_WORLD);
        start_time[5] = MPI_Wtime();
    }

    if(rank==0)
        printf("converting...\n");

    if (argc < 5) {
        if (rank==0) printf("Usage: %s <BP-file> <ADIOS-file> read_buffer(MB) write_buffer(MB) METHOD (LUSTRE_strip_count) (LUSTRE_strip_size) (LUSTRE_block_size)\n", argv[0]);
        return 1;
    }



    if(TIMING==100)
        start_time[4] = MPI_Wtime();
    ADIOS_FILE * f = adios_fopen (argv[1], MPI_COMM_SELF);
    if(TIMING==100){
        end_time[4] = MPI_Wtime();
        total_time[4] = end_time[4]-start_time[4];
    }
    adios_init_noxml(comm); // no xml will be used to write the new adios file
    read_buffer = atoi(argv[3]);
    write_buffer = atoi(argv[4]);
    adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, write_buffer); // allocate MB buffer



    if (f == NULL) {
        printf("rank=%d, file cant be opened\n", rank);
        if (DEBUG) printf ("%s\n", adios_errmsg());
        return -1;
    }


    for (gidx = 0; gidx < f->groups_count; gidx++) {    //group part
        adios_groupsize = 0;
        ADIOS_GROUP * g = adios_gopen (f, f->group_namelist[gidx]);


        if (g == NULL) {
            if (DEBUG) printf ("%s\n", adios_errmsg());
            printf("rank %d: group cannot be opened.\n", rank);
            return -1;
        }
        /* First create all of the groups */
        // now I need to create this group in the file that will be written

        adios_declare_group(&new_adios_group,f->group_namelist[gidx],"",adios_flag_yes);


        if(strcmp(argv[5],"MPI_LUSTRE")!=0)   //see whether or not the user uses MPI_LUSTRE method
            adios_select_method (new_adios_group, argv[5], "", "");  //non-MPI_LUSTRE methods... like MPI, POSIX....
        else{
            char lustre_pars[1000];
            strcpy(lustre_pars, "");
            strcat(lustre_pars, "stripe_count=");
            sprintf(tstring, "%d", atoi(argv[6]));
            strcat(lustre_pars, tstring);
            strcat(lustre_pars, ",stripe_size=");
            sprintf(tstring, "%d", atoi(argv[7]));
            strcat(lustre_pars, tstring);
            strcat(lustre_pars, ",block_size=");
            sprintf(tstring, "%d", atoi(argv[8]));
            strcat(lustre_pars, tstring);

            if(rank==0)
                printf("lustre_pars=%s\n", lustre_pars);

            adios_select_method (new_adios_group, argv[5], lustre_pars, "");  //Use MPI Lustre method

        }



        // variable definition part
        for (i = 0; i < g->vars_count; i++) {
            ADIOS_VARINFO * v = adios_inq_var_byid (g, i);
            getbasename (g->var_namelist[i], &var_path, &var_name);

            if (v->ndim == 0) 
            {   
                // scalars: every process does them the same.
                adios_define_var(new_adios_group,var_name,var_path,v->type,0,0,0);
                getTypeInfo( v->type, &element_size);    //element_size is size per element based on its type
                if (v->type == adios_string) {  //special case when the scalar is string.
                    adios_groupsize += strlen(v->value);
                } else {
                    adios_groupsize += element_size;
                }
            } 
            else 
            { 
                // vector variables
                getTypeInfo( v->type, &element_size);
                var_size=1;
                for (ii=0;ii<v->ndim;ii++) {
                    var_size*=v->dims[ii];
                }
                uint64_t total_size = var_size;  //total_size tells you the total number of elements in the current vector variable
                var_size*=element_size; //var_size tells you the size of the current vector variable in bytess

                //re-initialize the s and c variables
                for(j=0; j<v->ndim; j++){
                    s[j] = 0;
                    c[j] = 1;
                }

                //find the approximate chunk_size you would like to use.
                chunk_size = calcChunkSize(total_size, read_buffer*1024*1024/element_size, size);

                //set the chunk block array with the total size as close to chunk_size as possible
                calcC(chunk_size, v, c);
                strcpy(lbounds,"");
                for(j=0; j<v->ndim; j++){
                    sprintf(tstring, "%" PRId64 ",", c[j]);
                    strcat(lbounds, tstring);
                }
                printf("rank=%d, name=%s, chunk_size1=%" PRId64 " c[]=%s\n",rank,g->var_namelist[i],chunk_size,lbounds);


                chunk_size = 1;
                for(ii=0; ii<v->ndim; ii++)            //reset chunk_size based on the created c. Now the chunk_size is exact.
                    chunk_size *= c[ii];

                //current step points to where the process is in processing the vector. First sets with respect to rank.
                uint64_t current_step = rank*chunk_size;

                //First advance the starting point s by current_step. Of course, you don't do it if the current_step exceeds total_size.
                if(current_step<total_size)
                    rS(v, s, current_step, rank);

                uint64_t elements_defined = 0;  //First, the number of elements you have defined is 0.

                //You (the process) process your part of the vector when your current_step is smaller than the total_size
                while(current_step < total_size)
                {
                    //ts, temporary s, is introduced for the sake of the inner do while loop below. Copy s to ts.
                    uint64_t ts[] = {0,0,0,0,0,0,0,0,0,0};
                    arrCopy(s, ts);

                    //for every outer while iteration, you always have the whole chunk_size remained to process.
                    uint64_t remain_chunk = chunk_size;
                    if(current_step+chunk_size>total_size) //except when you are nearing the end of the vector....
                        remain_chunk = total_size-current_step;

                    //tc, temporary c, is introduced for the sake of the inner do while loop below. Copy s to tc.
                    uint64_t tc[] = {1,1,1,1,1,1,1,1,1,1};
                    arrCopy(c, tc);

                    do{
                        //how much of the remain chunk you wanna process? initially you think you can do all of it....
                        uint64_t used_chunk = remain_chunk;

                        //you feel like you should process the vector with tc block size, but given ts, you might go over bound.
                        uint64_t uc[] = {1,1,1,1,1,1,1,1,1,1};
                        //so you verify it by setting a new legit chunck block uc, and getting a new remain_chunk.
                        remain_chunk = checkBound(v, ts, tc, uc, remain_chunk);

                        //you check whether or not ts+uc goes over the bound. This is just checking to make sure there's no error.
                        //Thereotically, there should be no problem at all.
                        checkOverflow(0, v, ts, uc);


                        //the below code fragment simply calculates gbounds, and sets place holders for lbounds and offs.
                        strcpy(gbounds,"");
                        strcpy(lbounds,"");
                        strcpy(offs,"");

                        for(j=0; j<v->ndim-1; j++){
                            sprintf(tstring, "%d,", (int)v->dims[j]);
                            strcat(gbounds, tstring);
                            //sprintf(tstring, "ldim%d_%s,", j, var_name);
                            sprintf(tstring, "ldim%d,", j);
                            strcat(lbounds, tstring);
                            //sprintf(tstring, "offs%d_%s,", j, var_name);
                            sprintf(tstring, "offs%d,", j);
                            strcat(offs, tstring);
                        }

                        sprintf(tstring, "%d", (int)v->dims[v->ndim-1]);
                        strcat(gbounds, tstring);
                        //sprintf(tstring, "ldim%d_%s", v->ndim-1, var_name);
                        sprintf(tstring, "ldim%d", v->ndim-1);
                        strcat(lbounds, tstring);
                        //sprintf(tstring, "offs%d_%s", v->ndim-1, var_name);
                        sprintf(tstring, "offs%d", v->ndim-1);
                        strcat(offs, tstring);

                        //sprintf(tstring, "%d", v->ndim);
                        for(j=0; j<v->ndim; j++){
                            //sprintf(tstring, "ldim%d_%s", j, var_name);
                            sprintf(tstring, "ldim%d", j);
                            adios_define_var(new_adios_group, tstring, "bp2bp", adios_unsigned_long, 0, 0, 0);
                            //sprintf(tstring, "offs%d_%s", j, var_name);
                            sprintf(tstring, "offs%d", j);
                            adios_define_var(new_adios_group, tstring, "bp2bp", adios_unsigned_long, 0, 0, 0);
                        }

                        adios_define_var(new_adios_group,var_name,var_path,v->type,lbounds,gbounds,offs);


                        if (DEBUG){
                            strcpy(lbounds,"");
                            strcpy(offs,"");
                            for(j=0; j<v->ndim; j++){
                                sprintf(tstring, "%" PRId64 ",", ts[j]);
                                strcat(offs, tstring);
                                sprintf(tstring, "%" PRId64 ",", uc[j]);
                                strcat(lbounds, tstring);
                            }

                            printf("rank=%d, name=%s, gbounds=%s: lbounds=%s: offs=%s \n",rank,g->var_namelist[i],gbounds, lbounds, offs);
                        }

                        used_chunk -= remain_chunk; //you get the actual used_chunk here.
                        elements_defined += used_chunk;
                        if(remain_chunk!=0){
                            rS(v, ts, used_chunk, rank);  //advance ts by used_chunk.
                            for(k=0; k<10; k++)
                                tc[k] = 1;
                            calcC(remain_chunk, v, tc);   //based on the remain_chunk, calculate new tc chunk block remained to process.
                        }

                        adios_groupsize+= used_chunk*element_size+2*v->ndim*8;

                    }while(remain_chunk!=0);

                    current_step += size*chunk_size;  //once a whole chunk_size is processed, advance the current_step in roll-robin manner.

                    if(current_step<total_size){   //advance s in the same way.
                        rS(v, s, size*chunk_size, rank);
                    }
                }

                //beside checkOverflow above, here you check whether or not the total number of elements processed across processes matches
                //the total number of elements in the original vector.
                if(DEBUG){
                    uint64_t* sb = (uint64_t *) malloc(sizeof(uint64_t));
                    uint64_t* rb = (uint64_t *) malloc(sizeof(uint64_t));
                    sb[0] = elements_defined;
                    MPI_Reduce(sb,rb,1,MPI_UNSIGNED_LONG_LONG,MPI_SUM,0, comm);

                    if(rank==0 && rb[0]!=total_size)
                        printf("some array define mismatch. please use debug mode\n");
                    free(sb); free(rb);
                }
            }
            free (var_name);
            free (var_path);
        } // finished declaring all of the variables


        // Now we can define the attributes....
        for (i = 0; i < g->attrs_count; i++) {
            enum ADIOS_DATATYPES atype;
            int  asize;
            void *adata;
            adios_get_attr_byid (g, i, &atype, &asize, &adata);
            // if (DEBUG) printf("attribute name=%s\n",g->attr_namelist[i]);
            adios_define_attribute(new_adios_group,g->attr_namelist[i],"",atype,adata,0);
        }



        /*------------------------------ NOW WE WRITE -------------------------------------------- */
        // Now we have everything declared... now we need to write them out!!!!!!
        if (WRITEME==1) {
            // open up the file for writing....
            if (DEBUG) printf("rank=%d, opening file = %s, with group %s, size=%" PRId64 "\n",rank,argv[2],f->group_namelist[gidx],adios_groupsize);

            if(TIMING==100)
                start_time[0] = MPI_Wtime();

            adios_open(&m_adios_file, f->group_namelist[gidx],argv[2],"w",comm);
            adios_group_size( m_adios_file, adios_groupsize, &adios_totalsize);

            //get both the total adios_totalsize and total adios_groupsize summed across processes.
            uint64_t* sb = (uint64_t *) malloc(sizeof(uint64_t));;
            uint64_t* rb = (uint64_t *) malloc(sizeof(uint64_t));
            sb[0] = adios_groupsize;
            MPI_Reduce(sb,rb,1,MPI_UNSIGNED_LONG_LONG,MPI_SUM,0, comm);

            uint64_t* sb2 = (uint64_t *) malloc(sizeof(uint64_t));;
            uint64_t* rb2 = (uint64_t *) malloc(sizeof(uint64_t));
            sb2[0] = adios_totalsize;
            MPI_Reduce(sb2,rb2,1,MPI_UNSIGNED_LONG_LONG,MPI_SUM,0, comm);
            if(rank==0){
                printf("total adios_totalsize = %" PRId64 "\n", *rb2);
                printf("total adios_groupsize = %" PRId64 "\n", *rb);
            }
            free(sb); free(rb); free(sb2); free(rb2);

            if (TIMING==100) {
                end_time[0] = MPI_Wtime();
                total_time[0]+=end_time[0] - start_time[0];    //variable definition time taken
            }

            // now we have to write out the variables.... since they are all declared now
            // This will be the place we actually write out the data!!!!!!!!
            for (i = 0; i < g->vars_count; i++) {
                ADIOS_VARINFO * v = adios_inq_var_byid (g, i);
                getbasename (g->var_namelist[i], &var_path, &var_name);
                if (v->ndim == 0) 
                {
                    if (DEBUG) {
                        printf ("ADIOS WRITE SCALAR: rank=%d, name=%s value=",
                                rank,g->var_namelist[i]);
                        print_data (v->value, 0, v->type);
                        printf ("\n");
                    }
                    if (TIMING==100) {
                        start_time[2] = MPI_Wtime();
                    }
                    adios_write(m_adios_file,g->var_namelist[i],v->value);
                    if (TIMING==100) {
                        end_time[2] = MPI_Wtime();
                        total_time[2]+=end_time[2] - start_time[2];     //IO write time...
                    }
                } 
                else 
                {
                    for(j=0; j<v->ndim; j++){
                        s[j] = 0;
                        c[j] = 1;
                    }
                    getTypeInfo( v->type, &element_size);

                    uint64_t total_size = 1;
                    for (ii=0;ii<v->ndim;ii++)
                        total_size*=v->dims[ii];

                    chunk_size = calcChunkSize(total_size, read_buffer*1024*1024/element_size, size);
                    calcC(chunk_size, v, c);
                    chunk_size = 1;
                    for(ii=0; ii<v->ndim; ii++)
                        chunk_size *= c[ii];


                    uint64_t current_step = rank*chunk_size;
                    if(current_step<total_size)
                        rS(v, s, current_step, rank);

                    uint64_t elements_written = 0;

                    while(current_step < total_size)
                    {
                        uint64_t ts[] = {0,0,0,0,0,0,0,0,0,0};
                        arrCopy(s, ts);
                        uint64_t remain_chunk = chunk_size;
                        if(current_step+chunk_size>total_size)
                            remain_chunk = total_size-current_step;
                        uint64_t tc[] = {1,1,1,1,1,1,1,1,1,1};
                        arrCopy(c, tc);

                        do{
                            uint64_t uc[] = {1,1,1,1,1,1,1,1,1,1};
                            uint64_t used_chunk = remain_chunk;
                            remain_chunk = checkBound(v, ts, tc, uc, remain_chunk);

                            checkOverflow(1, v, ts, uc);

                            used_chunk -= remain_chunk;
                            elements_written += used_chunk;

                            //allocated space for data read-in
                            data = (void *) malloc(used_chunk*element_size);

                            if (TIMING==100) {
                                start_time[1] = MPI_Wtime();
                            }
                            if(PERFORMANCE_CHECK) printf("rank=%d, read start\n",rank);
                            bytes_read = adios_read_var_byid(g,v->varid,ts,uc,data);
                            if(PERFORMANCE_CHECK) printf("rank=%d, read end\n",rank);
                            if (TIMING==100) {
                                end_time[1] = MPI_Wtime();
                                total_time[1]+=end_time[1] -start_time[1];      //IO read time
                            }

                            if (DEBUG)
                                printf ("ADIOS WRITE: rank=%d, name=%s datasize=%" PRId64 "\n",rank,g->var_namelist[i],bytes_read);


                            if (TIMING==100) {
                                start_time[2] = MPI_Wtime();
                            }
                            if (DEBUG){
                                printf("rank=%d, write ts=",rank);
                                int k;
                                for(k=0; k<v->ndim; k++)
                                    printf("%" PRId64 ",", ts[k]);
                                printf("  uc=");
                                for(k=0; k<v->ndim; k++)
                                    printf("%" PRId64 ",", uc[k]);
                                printf("\n");
                            }

                            //local bounds and offets placeholders are not written out with actual values.
                            if(PERFORMANCE_CHECK) printf("rank=%d, adios write start\n", rank);
                            for(k=0; k<v->ndim; k++){
                                //sprintf(tstring, "ldim%d_%s", k, var_name);
                                sprintf(tstring, "ldim%d", k);
                                if (DEBUG) {
                                    printf ("ADIOS WRITE DIMENSION: rank=%d, name=%s value=",
                                            rank,tstring);
                                    print_data (&uc[k], 0, adios_unsigned_long);
                                    printf ("\n");
                                }
                                adios_write(m_adios_file, tstring, &uc[k]);

                                //sprintf(tstring, "offs%d_%s", k, var_name);
                                sprintf(tstring, "offs%d", k);
                                if (DEBUG) {
                                    printf ("ADIOS WRITE OFFSET: rank=%d, name=%s value=",
                                            rank,tstring);
                                    print_data (&ts[k], 0, adios_unsigned_long);
                                    printf ("\n");
                                }
                                adios_write(m_adios_file, tstring, &ts[k]);
                            }
                            adios_write(m_adios_file,g->var_namelist[i],data);
                            if(PERFORMANCE_CHECK) printf("rank=%d, adios write end\n", rank);


                            if (TIMING==100) {
                                end_time[2] = MPI_Wtime();
                                total_time[2]+=end_time[2] - start_time[2];   //IO write time
                            }

                            free(data);


                            if(remain_chunk!=0){
                                rS(v, ts, used_chunk, rank);
                                for(k=0; k<10; k++)
                                    tc[k] = 1;
                                calcC(remain_chunk, v, tc);
                            }

                        }while(remain_chunk!=0);

                        current_step += size*chunk_size;

                        if(current_step<total_size)
                            rS(v, s, size*chunk_size,rank);
                    }

                    if(DEBUG){
                        uint64_t* sb = (uint64_t *) malloc(sizeof(uint64_t));;
                        uint64_t* rb = (uint64_t *) malloc(sizeof(uint64_t));
                        sb[0] = elements_written;
                        MPI_Reduce(sb,rb,1,MPI_UNSIGNED_LONG_LONG,MPI_SUM,0, comm);
                        if(rank==0 && rb[0]!=total_size)
                            printf("some array read mismatch. please use debug mode\n");
                        free(sb); free(rb);
                    }
                }
                free (var_name);
                free (var_path);
            }// end of the writing of the variable..
            if (TIMING==100) {
                start_time[3] = MPI_Wtime();
            }
            if(PERFORMANCE_CHECK) printf("rank=%d, adios_close start\n", rank);
            adios_close(m_adios_file);
            if(PERFORMANCE_CHECK) printf("rank=%d, adios_close end\n", rank);
            if (TIMING==100) {
                end_time[3] = MPI_Wtime();
                total_time[3]+=end_time[3] - start_time[3];
            }
            adios_gclose(g);
        } //end of WRITEME
    } // end of all of the groups

    if(rank==0)
        printf("conversion done!\n");

    if(TIMING==100)
        start_time[4] = MPI_Wtime();
    adios_fclose(f);
    if(TIMING==100){
        end_time[4] = MPI_Wtime();
        total_time[4] = total_time[4]+end_time[4]-start_time[4];
    }
    adios_finalize(rank);


    // now, we write out the timing data, for each category, we give max, min, avg, std, all in seconds, across all processes.
    if(TIMING==100){

        // 0: adios_open, adios_group_size
        // 1: the total time to read in the data
        // 2: times around each write (will only work if we do NOT buffer....
        // 3: the time in the close
        // 4: fopen, fclose
        // 5: total time
        end_time[5] = MPI_Wtime();
        total_time[5] = end_time[5] - start_time[5];

        double sb[7];
        sb[0] = total_time[1]; sb[1] = total_time[4];   //read_var, fopen+fclose
        sb[2] = sb[0]+sb[1];
        sb[3] = total_time[0]; sb[4] = total_time[2]+total_time[3]; //adios_open+adios_group_size, write+close
        sb[5] = sb[3]+sb[4];
        sb[6] = total_time[5]; //total

        double * rb = NULL;

        if(rank==0)
            rb = (double *)malloc(size*7*sizeof(double));
        //MPI_Barrier(comm);
        MPI_Gather(sb, 7, MPI_DOUBLE, rb, 7, MPI_DOUBLE, 0, comm);

        if(rank==0){
            double read_avg1 = 0;
            double read_avg2 = 0;
            double tread_avg = 0;
            double write_avg1 = 0;
            double write_avg2 = 0;
            double twrite_avg = 0;
            double total_avg = 0;
            for(j=0; j<size; j++){
                read_avg1 += rb[7*j];
                read_avg2 += rb[7*j+1];
                tread_avg += rb[7*j+2];
                write_avg1 += rb[7*j+3];
                write_avg2 += rb[7*j+4];
                twrite_avg += rb[7*j+5];
                total_avg += rb[7*j+6];
            }
            read_avg1 /= size;
            read_avg2 /= size;
            tread_avg /= size;
            write_avg1 /= size;
            write_avg2 /= size;
            twrite_avg /= size;
            total_avg /= size;

            double read1_max = rb[0];
            double read1_min = rb[0];
            double read1_std = rb[0]-read_avg1; read1_std *= read1_std;

            double read2_max = rb[1];
            double read2_min = rb[1];
            double read2_std = rb[1]-read_avg2; read2_std *= read2_std;

            double tread_max = rb[2];
            double tread_min = rb[2];
            double tread_std = rb[2]-tread_avg; tread_std *= tread_std;

            double write1_max = rb[3];
            double write1_min = rb[3];
            double write1_std = rb[3]-write_avg1; write1_std *= write1_std;

            double write2_max = rb[4];
            double write2_min = rb[4];
            double write2_std = rb[4]-write_avg2; write2_std *= write2_std;

            double twrite_max = rb[5];
            double twrite_min = rb[5];
            double twrite_std = rb[5]-twrite_avg; twrite_std *= twrite_std;

            double total_max = rb[6];
            double total_min = rb[6];
            double total_std = rb[6]-total_avg; total_std *= total_std;

            for(j=1; j<size; j++){
                if(rb[7*j]>read1_max)
                    read1_max = rb[7*j];
                else if(rb[7*j]<read1_min)
                    read1_min = rb[7*j];
                double std = rb[7*j]-read_avg1; std *= std;
                read1_std += std;

                if(rb[7*j+1]>read2_max)
                    read2_max = rb[7*j+1];
                else if(rb[7*j+1]<read2_min)
                    read2_min = rb[7*j+1];
                std = rb[7*j+1]-read_avg2; std *= std;
                read2_std += std;

                if(rb[7*j+2]>tread_max)
                    tread_max = rb[7*j+2];
                else if(rb[7*j+2]<tread_min)
                    tread_min = rb[7*j+2];
                std = rb[7*j+2]-tread_avg; std *= std;
                tread_std += std;

                if(rb[7*j+3]>write1_max)
                    write1_max = rb[7*j+3];
                else if(rb[7*j+3]<write1_min)
                    write1_min = rb[7*j+3];
                std = rb[7*j+3]-write_avg1; std *= std;
                write1_std += std;

                if(rb[7*j+4]>write2_max)
                    write2_max = rb[7*j+4];
                else if(rb[7*j+4]<write2_min)
                    write2_min = rb[7*j+4];
                std = rb[7*j+4]-write_avg2; std *= std;
                write2_std += std;

                if(rb[7*j+5]>twrite_max)
                    twrite_max = rb[7*j+5];
                else if(rb[7*j+5]<twrite_min)
                    twrite_min = rb[7*j+5];
                std = rb[7*j+5]-twrite_avg; std *= std;
                twrite_std += std;

                if(rb[7*j+6]>total_max)
                    total_max = rb[7*j+6];
                else if(rb[7*j+6]<total_min)
                    total_min = rb[7*j+6];
                std = rb[7*j+6]-total_avg; std *= std;
                total_std += std;
            }
            read1_std /= size;  read1_std = sqrt(read1_std);
            read2_std /= size;  read2_std = sqrt(read2_std);
            tread_std /= size;    tread_std = sqrt(tread_std);
            write1_std /= size; write1_std = sqrt(write1_std);
            write2_std /= size; write2_std = sqrt(write2_std);
            twrite_std /= size;    twrite_std = sqrt(twrite_std);
            total_std /= size; total_std = sqrt(total_std);

            printf("---type---                       max\tmin\tavg\tstd\n");
            printf("---read_var---                   %lf\t%lf\t%lf\t%lf\n", read1_max, read1_min, read_avg1, read1_std);
            printf("---fopen+fclose---               %lf\t%lf\t%lf\t%lf\n", read2_max, read2_min, read_avg2, read2_std);
            printf("---total_read---                 %lf\t%lf\t%lf\t%lf\n", tread_max, tread_min, tread_avg, tread_std);
            printf("---adios_open+adios_groupsize--- %lf\t%lf\t%lf\t%lf\n", write1_max, write1_min, write_avg1, write1_std);
            printf("---write+close---                %lf\t%lf\t%lf\t%lf\n", write2_max, write2_min, write_avg2, write2_std);
            printf("---total_write---                %lf\t%lf\t%lf\t%lf\n", twrite_max, twrite_min, twrite_avg, twrite_std);
            printf("---total---                      %lf\t%lf\t%lf\t%lf\n", total_max, total_min, total_avg, total_std);
            free(rb);

        }

    }

    //    if (TIMING==100 && rank==0) {
    //        printf("------------------------------------------------------------------\n");
    //        printf("Define variables     = %lf\n",total_time[0]);
    //        printf("Read   variables     = %lf\n",total_time[1]);
    //        printf("Write  variables     = %lf\n",total_time[2]);
    //        printf("Close File for write = %lf\n",total_time[3]);
    //        printf("Total write time     = %lf\n",total_time[2] + total_time[3]);
    //        for (itime=0;itime<timers-1;itime++)
    //            total_time[timers-1]+=total_time[itime];
    //        printf("Total I/O time       = %lf\n",total_time[timers-1]);
    //    }
    MPI_Finalize();


    return(0);
}
Beispiel #12
0
int write_blocks () 
{
    int         NX, G, O; 
    double      *t;
    /* ADIOS variables declarations for matching gwrite_temperature.ch */
    int         it, i, r;
    uint64_t    adios_groupsize, adios_totalsize;

    if (!rank) printf ("------- Write blocks -------\n");
    // We will have "3 steps * 2 blocks per process * number of processes" blocks
    nsteps = 3;
    nblocks_per_step = 2;
    block_offset = (uint64_t*) malloc (sizeof(uint64_t) * nsteps * nblocks_per_step * size);
    block_count  = (uint64_t*) malloc (sizeof(uint64_t) * nsteps * nblocks_per_step * size);
    gdims        = (uint64_t*) malloc (sizeof(uint64_t) * nsteps);

    adios_init_noxml (comm);
    adios_set_max_buffer_size (10);

    int64_t       m_adios_group;
    int64_t       m_adios_file;

    adios_declare_group (&m_adios_group, "restart", "", adios_flag_yes);
    adios_select_method (m_adios_group, "MPI", "", "");

    adios_define_var (m_adios_group, "NX"
            ,"", adios_integer
            ,0, 0, 0);

    adios_define_var (m_adios_group, "G"
            ,"", adios_integer
            ,0, 0, 0);

    /* have to define O and temperature as many times as we 
       write them within one step (twice) */
    for (it=0; it < nblocks_per_step; it++) {
        adios_define_var (m_adios_group, "O"
                ,"", adios_integer
                ,0, 0, 0);

        adios_define_var (m_adios_group, "t"
                ,"", adios_double
                ,"NX", "G", "O");
    }

    for (it =0; it < nsteps; it++) {
        if (!rank) printf ("Step %d:\n", it);
        NX = 10+it;
        G = nblocks_per_step * NX * size;

        t = (double *) malloc (NX*sizeof(double));

        for (i = 0; i < NX; i++)
            t[i] = rank + it*0.1 + 0.01;

        MPI_Barrier (comm);
        if (it==0) 
            adios_open (&m_adios_file, "restart", fname, "w", comm);
        else
            adios_open (&m_adios_file, "restart", fname, "a", comm);
        adios_groupsize = 4 + 4 + 4 + NX * 8
            + 4 + 4 + 4 + NX * 8;
        adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);

        adios_write(m_adios_file, "NX", (void *) &NX);
        adios_write(m_adios_file, "G", (void *) &G);
        O = rank * nblocks_per_step * NX;
        adios_write(m_adios_file, "O", (void *) &O);
        adios_write(m_adios_file, "t", t);

        printf ("rank %d: block 1: size=%d, offset=%d\n", rank, NX, O);
        for (r = 0; r < size; r++) {
            block_count  [it*nblocks_per_step*size + nblocks_per_step*r] = NX; 
            block_offset [it*nblocks_per_step*size + nblocks_per_step*r] = r * nblocks_per_step * NX; 
        }

        for (i = 0; i < NX; i++)
            t[i] += 0.01;

        O = rank * nblocks_per_step * NX + NX;
        adios_write(m_adios_file, "O", (void *) &O);
        adios_write(m_adios_file, "t", t);

        printf ("rank %d: block 2: size=%d, offset=%d\n", rank, NX, O);
        for (r = 0; r < size; r++) {
            block_count  [it*nblocks_per_step*size + nblocks_per_step*r + 1] = NX; 
            block_offset [it*nblocks_per_step*size + nblocks_per_step*r + 1] = r * nblocks_per_step * NX + NX; 
        }
        gdims [it] = G;

        adios_close (m_adios_file);
        MPI_Barrier (comm);

        free(t);
    }

    adios_finalize (rank);

    return 0;
}
Beispiel #13
0
int main (int argc, char ** argv) 
{
	char        filename [256];
	int         rank, size, i, block;
	int         NX = 100, Global_bounds, Offsets; 
	double      t[NX];
        int         sub_blocks = 3;
	MPI_Comm    comm = MPI_COMM_WORLD;

	/* ADIOS variables declarations for matching gwrite_temperature.ch */
	uint64_t    adios_groupsize, adios_totalsize;

	MPI_Init (&argc, &argv);
	MPI_Comm_rank (comm, &rank);
	MPI_Comm_size (comm, &size);

        Global_bounds = sub_blocks * NX * size;

	strcpy (filename, "adios_global_no_xml.bp");

	adios_init_noxml (comm);
        adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 10);

        int64_t       m_adios_group;
        int64_t       m_adios_file;

        adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);
        adios_select_method (m_adios_group, "MPI", "", "");


        adios_define_var (m_adios_group, "NX"
			,"", adios_integer
			,0, 0, 0);
   
	adios_define_var (m_adios_group, "Global_bounds"
			,"", adios_integer
			,0, 0, 0);

        for (i=0;i<sub_blocks;i++) {
   
           adios_define_var (m_adios_group, "Offsets"
                        ,"", adios_integer
                        ,0, 0, 0);
   
           int64_t varid;
           varid = adios_define_var (m_adios_group, "temperature"
                        ,"", adios_double
                        ,"NX", "Global_bounds", "Offsets");
           adios_set_transform (varid, "none");
        }
   
        adios_open (&m_adios_file, "restart", filename, "w", comm);

        adios_groupsize = sub_blocks * (4 + 4 + 4 + NX * 8);

        adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
	adios_write(m_adios_file, "NX", (void *) &NX);
	adios_write(m_adios_file, "Global_bounds", (void *) &Global_bounds);
/* now we will write the data for each sub block */
        for (block=0;block<sub_blocks;block++) {

           Offsets = rank * sub_blocks * NX + block*NX;
           adios_write(m_adios_file, "Offsets", (void *) &Offsets);

           for (i = 0; i < NX; i++)
               t[i] = Offsets + i;

           adios_write(m_adios_file, "temperature", t);
        }

        adios_close (m_adios_file);

        MPI_Barrier (comm);

	adios_finalize (rank);

	MPI_Finalize ();
	return 0;
}
Beispiel #14
0
int main (int argc, char** argv) 
{
  fastbit_init(0);
  fastbit_set_verbose_level(0);

  ADIOS_FILE * f;
  //MPI_Comm    comm_dummy = 0;  // MPI_Comm is defined through adios_read.h 
  MPI_Comm comm_dummy = MPI_COMM_WORLD;

  int         rank, size;
  MPI_Init (&argc, &argv);			   
  MPI_Comm_rank (comm_dummy, &rank);
  MPI_Comm_size (comm_dummy, &size);

  adios_init_noxml (comm_dummy);
  
  if (argc < 2) {
    printf("Usage: index_fastbit fileName (attrName)");
    return 0;
  }

  f = adios_read_open_file (argv[1], ADIOS_READ_METHOD_BP, comm_dummy);
  if (f == NULL) {
    printf ("::%s\n", adios_errmsg());
    return -1;
  }
  
  /*
  adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, (f->file_size)*2/1048576 + 5); // +5MB for extra room in buffer
  adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_flag_yes);
  adios_select_method (gAdios_group, "MPI", "", "");
  */
  gIdxFileName = fastbit_adios_util_getFastbitIndexFileName(argv[1]);
  unlink(gIdxFileName);

      adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 500); // +5MB for extra room in buffer
      adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_flag_yes);
      adios_select_method (gAdios_group, "MPI", "", "");

      adios_open (&gAdios_write_file, gGroupNameFastbitIdx, gIdxFileName, "w", MPI_COMM_WORLD);

#ifdef MULTI_BLOCK
      int testid = adios_define_var (gAdios_group, "pack", "", adios_integer , 0, 0, 0);
#endif
#ifdef BOX
      int testid = adios_define_var (gAdios_group, "elements", "", adios_integer , 0, 0, 0);
#endif
      //uint64_t estimatedbytes = (nb+nk+no)*adios_type_size(adios_double, NULL);
      int jobCounter = getJobCounter(f);
      uint64_t estimatedbytes =  getByteEstimationOnFile(f, rank);
      if (size > 1) {
	int maxJobsPP = jobCounter/size + 1;
        estimatedbytes = estimatedbytes * maxJobsPP /jobCounter +1048576;
      }

      estimatedbytes += 1048576;

      uint64_t adios_totalsize;      // adios_group_size needs to be call before any write_byid, Otherwise write_byid does nothing 
      adios_group_size (gAdios_write_file, estimatedbytes , &adios_totalsize);     

      printf("=> .. adios open output file: %s, rank %d allocated %" PRIu64 " bytes... \n", gIdxFileName, rank, adios_totalsize);
      // IMPORTANT: 
      // can only call open/close once in a process
      // otherwise data is tangled or only the data in the last open/close call is recorded

#ifdef MULTI_BLOCK
      adios_write_byid(gAdios_write_file, testid, &pack);
#endif
#ifdef BOX
      adios_write_byid(gAdios_write_file, testid, &recommended_index_ele);
#endif


  sumLogTime(-1);
  sumLogTimeMillis(-1);

  
  if (argc >= 3) {
     int i=2;
     while (i<argc) {
        const char* varName = argv[i];
	if(strstr(varName, "<binning prec") != NULL) {
	  if (gBinningOption == NULL) {
	    gBinningOption = argv[i];
	  }
	  if (argc == 3) {
	    buildIndexOnAllVar(f, rank, size);
	    break;
	  }
	  i++;
	  continue;
	} else {
	  ADIOS_VARINFO * v = adios_inq_var(f, varName);
	  if (v == NULL) {
	     printf("No such variable: %s\n", varName);
	     return 0;
	   }	
	  printf("building fastbit index on  variable: %s\n", varName);
	  buildIndex_mpi(f, v, rank, size);
	  adios_free_varinfo(v);
	  i++;
	}
     }
  } else {
    buildIndexOnAllVar(f, rank, size);
  }


  sumLogTime(0);
  sumLogTimeMillis(0);

  adios_close(gAdios_write_file);
  adios_read_close(f);

  //
  // writing file clean up
  //


  // read back:
  f = adios_read_open_file (gIdxFileName, ADIOS_READ_METHOD_BP, comm_dummy);
  if (f == NULL) {
    printf("No such file: %s \n", gIdxFileName);
    return 0;
  }

  int numVars = f->nvars;
  
  int i=0;
  int k=0;
  int j=0;
  for (i=0; i<numVars; i++) {
      char* varName = f->var_namelist[i];
      ADIOS_VARINFO* v = adios_inq_var(f, varName);

       adios_inq_var_blockinfo(f,v);      
      int timestep = 0;
      for (k=0; k<v->sum_nblocks; k++) {
	  verifyData(f, v, k, timestep);
      }

      adios_free_varinfo(v);
  }

  adios_read_close(f);

  if (rank == 0) {
    printf(" ==>  index file is at: %s\n", gIdxFileName);
  }

  // clean up
  MPI_Barrier (comm_dummy);
  adios_finalize (rank);
  MPI_Finalize ();
  free (gIdxFileName);

  fastbit_cleanup();
  return 0;
}
Beispiel #15
0
int main (int argc, char ** argv) 
{
	char        filename [256];
	int         rank, size, i, j, step, block;
        int         Offset; 

	int         NX = 2; // number of records written per step per process
        int         Width=20;
        int         sub_blocks = 2; // number of record-blocks written per process in one step
        int         steps = 3;

	char        t[NX][Width];
	MPI_Comm    comm = MPI_COMM_WORLD;

	/* ADIOS variables declarations for matching gwrite_temperature.ch */
	int         adios_err;
	uint64_t    adios_groupsize, adios_totalsize;
	int64_t     adios_handle;

	MPI_Init (&argc, &argv);
	MPI_Comm_rank (comm, &rank);
	MPI_Comm_size (comm, &size);

        //Global_bounds = sub_blocks * NX * size;

	strcpy (filename, "steps.bp");

	adios_init_noxml (comm);
        adios_set_max_buffer_size (1);

        int64_t       m_adios_group;
        int64_t       m_adios_file;

        adios_declare_group (&m_adios_group, "steps", "", adios_flag_yes);
        adios_select_method (m_adios_group, "MPI", "", "");


        adios_define_var (m_adios_group, "NX" ,"", adios_integer ,0, 0, 0);
        adios_define_var (m_adios_group, "Width" ,"", adios_integer ,0, 0, 0);
        adios_define_var (m_adios_group, "nproc" ,"", adios_integer ,0, 0, 0);
   
        for (i=0;i<sub_blocks;i++) {
   
           adios_define_var (m_adios_group, "record" ,"", adios_byte ,"NX,Width", "", "");
        }


        for (step=0; step<steps; step++) {

            adios_open (&m_adios_file, "steps", filename, "a", comm);

            adios_groupsize = sub_blocks * (4 + 4 + 4 + (uint64_t) NX * (uint64_t)Width);

            adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
            adios_write(m_adios_file, "nproc", (void *) &size);
            adios_write(m_adios_file, "NX", (void *) &NX);
            adios_write(m_adios_file, "Width", (void *) &Width);
            /* now we will write the data for each sub block */
            for (block=0;block<sub_blocks;block++) {

                for (i = 0; i < NX; i++)
                    //print 19 chars here + '\0'
                    sprintf (t[i], "r%2d  b%2d  s%2d  i%2d ", rank, block, step, i); 

                adios_write(m_adios_file, "record", t);
            }

            adios_close (m_adios_file);
        }

        MPI_Barrier (comm);

	adios_finalize (rank);

	MPI_Finalize ();
	return 0;
}
Beispiel #16
0
int process_metadata(int step)
{
    int retval = 0;
    int i, j;
    char gdims[256], ldims[256], offs[256];
    uint64_t sum_count;
    ADIOS_VARINFO *v; // shortcut pointer

    if (step > 1)
    {
        // right now, nothing to prepare in later steps
        print("Step %d. return immediately\n",step);
        return 0;
    }

    /* First step processing */

    // get groupname of stream, then declare for output
    adios_get_grouplist(f, &group_namelist);
    print0("Group name is %s\n", group_namelist[0]);
    adios_declare_group(&gh,group_namelist[0],"",adios_flag_yes);


    varinfo = (VarInfo *) malloc (sizeof(VarInfo) * f->nvars);
    if (!varinfo) {
        print("ERROR: rank %d cannot allocate %lu bytes\n", rank, sizeof(VarInfo)*f->nvars);
        return 1;
    }

    write_total = 0;
    largest_block = 0;

    // Decompose each variable and calculate output buffer size
    for (i=0; i<f->nvars; i++) 
    {
        print0 ("Get info on variable %d: %s\n", i, f->var_namelist[i]); 
        varinfo[i].v = adios_inq_var_byid (f, i);
        v = varinfo[i].v; // just a shortcut
        if (v == NULL) {
            print ("rank %d: ERROR: Variable %s inquiry failed: %s\n", 
                   rank, f->var_namelist[i], adios_errmsg());
            return 1;
        }

        // print variable type and dimensions
        print0("    %-9s  %s", adios_type_to_string(v->type), f->var_namelist[i]);
        if (v->ndim > 0) {
            print0("[%llu", v->dims[0]);
            for (j = 1; j < v->ndim; j++)
                print0(", %llu", v->dims[j]);
            print0("] :\n");
        } else {
            print0("\tscalar\n");
        }

        // determine subset we will write
        decompose (numproc, rank, v->ndim, v->dims, decomp_values,
                   varinfo[i].count, varinfo[i].start, &sum_count);
        varinfo[i].writesize = sum_count * adios_type_size(v->type, v->value);

        if (varinfo[i].writesize != 0) {
            write_total += varinfo[i].writesize;
            if (largest_block < varinfo[i].writesize)
                largest_block = varinfo[i].writesize; 
        }

    }

    // determine output buffer size and allocate it
    uint64_t bufsize = write_total + f->nvars*128 + f->nattrs*32 + 1024; 
    if (bufsize > max_write_buffer_size) {
        print ("ERROR: rank %d: write buffer size needs to hold about %llu bytes, "
                "but max is set to %d\n", rank, bufsize, max_write_buffer_size);
        return 1;
    }
    print0 ("Rank %d: allocate %llu MB for output buffer\n", rank, bufsize/1048576+1);
    adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, bufsize/1048576+1); 

    // allocate read buffer
    bufsize = largest_block + 128;
    if (bufsize > max_read_buffer_size) {
        print ("ERROR: rank %d: read buffer size needs to hold at least %llu bytes, "
                "but max is set to %d\n", rank, bufsize, max_read_buffer_size);
        return 1;
    }
    print0 ("Rank %d: allocate %g MB for input buffer\n", rank, (double)bufsize/1048576.0);
    readbuf = (char *) malloc ((size_t)bufsize);
    if (!readbuf) {
        print ("ERROR: rank %d: cannot allocate %llu bytes for read buffer\n",
               rank, bufsize);
        return 1;
    }

    // Select output method
    adios_select_method (gh, wmethodname, wmethodparams, "");

    // Define variables for output based on decomposition
    char *vpath, *vname;
    for (i=0; i<f->nvars; i++) 
    {
        v = varinfo[i].v;
        if (varinfo[i].writesize != 0) {
            // define variable for ADIOS writes
            getbasename (f->var_namelist[i], &vpath, &vname);

            if (v->ndim > 0) 
            {
                int64s_to_str (v->ndim, v->dims, gdims);
                int64s_to_str (v->ndim, varinfo[i].count, ldims);
                int64s_to_str (v->ndim, varinfo[i].start, offs);

                print ("rank %d: Define variable path=\"%s\" name=\"%s\"  "
                       "gdims=%s  ldims=%s  offs=%s\n", 
                       rank, vpath, vname, gdims, ldims, offs);

                adios_define_var (gh, vname, vpath, v->type, ldims, gdims, offs);
            }
            else 
            {
                print ("rank %d: Define scalar path=\"%s\" name=\"%s\"\n",
                       rank, vpath, vname);

                adios_define_var (gh, vname, vpath, v->type, "", "", "");
            }
            free(vpath);
            free(vname);
        }
    }

    if (rank == 0)
    {
        // get and define attributes
        enum ADIOS_DATATYPES attr_type;
        void * attr_value;
        char * attr_value_str;
        int  attr_size;
        for (i=0; i<f->nattrs; i++) 
        {
            adios_get_attr_byid (f, i, &attr_type, &attr_size, &attr_value);
            attr_value_str = (char *)value_to_string (attr_type, attr_value, 0);
            getbasename (f->attr_namelist[i], &vpath, &vname);
            if (vpath && !strcmp(vpath,"/__adios__")) { 
                // skip on /__adios/... attributes 
                print ("rank %d: Ignore this attribute path=\"%s\" name=\"%s\" value=\"%s\"\n",
                        rank, vpath, vname, attr_value_str);
            } else {
                adios_define_attribute (gh, vname, vpath,
                        attr_type, attr_value_str, "");
                print ("rank %d: Define attribute path=\"%s\" name=\"%s\" value=\"%s\"\n",
                        rank, vpath, vname, attr_value_str);
                free (attr_value);
            }
        }
    }

    return retval;
}
int main (int argc, char ** argv) 
{
	char        filename [256];
        char        color_str[256];
	int         rank, size, i, color;
	int         NX = 100, Global_bounds, Offsets; 
	double      t[NX];
	MPI_Comm    comm = MPI_COMM_WORLD;

	/* ADIOS variables declarations for matching gwrite_temperature.ch */
	uint64_t    adios_groupsize, adios_totalsize;

	MPI_Init (&argc, &argv);
	MPI_Comm_rank (comm, &rank);
	MPI_Comm_size (comm, &size);

        Global_bounds = NX * size;

	strcpy (filename, "adios_global_aggregate_by_color.bp");

	adios_init_noxml (comm);
        adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 10);

        int64_t       m_adios_group;
        int64_t       m_adios_file;

        adios_declare_group (&m_adios_group, "restart", "iter", adios_flag_yes);

        // split into 2 groups 
        color = (rank % 2 == 0 ? 0 : 1);
        sprintf (color_str, "color=%d", color);
        adios_select_method (m_adios_group, "MPI", color_str, "");

        adios_define_var (m_adios_group, "NX"
			,"", adios_integer
			,0, 0, 0);
   
	adios_define_var (m_adios_group, "Global_bounds"
			,"", adios_integer
			,0, 0, 0);

        adios_define_var (m_adios_group, "Offsets"
                         ,"", adios_integer
                         ,0, 0, 0);
   
       adios_define_var (m_adios_group, "temperature"
                        ,"", adios_double
                        ,"NX", "Global_bounds", "Offsets");
   
        adios_open (&m_adios_file, "restart", filename, "w", comm);

        adios_groupsize = 4 + 4 + 4 + NX * 8;

        adios_group_size (m_adios_file, adios_groupsize, &adios_totalsize);
	adios_write(m_adios_file, "NX", (void *) &NX);
	adios_write(m_adios_file, "Global_bounds", (void *) &Global_bounds);

        Offsets = rank * NX;
        adios_write(m_adios_file, "Offsets", (void *) &Offsets);

        for (i = 0; i < NX; i++)
            t[i] = Offsets + i;

        adios_write(m_adios_file, "temperature", t);

        adios_close (m_adios_file);

        MPI_Barrier (comm);

	adios_finalize (rank);

	MPI_Finalize ();
	return 0;
}