Esempio n. 1
0
int read_file (char *fname)
{
    ADIOS_SELECTION *sel;
    ADIOS_FILE * f;
    ADIOS_VARINFO * vi;
    int err=0,i,n;

    uint64_t start[1] = {0};
    uint64_t count[2] = {NX};
    uint64_t ndim;

    reset_rarrays();

    log ("Read and check data in %s\n", fname);
    f = adios_read_open_file (fname, ADIOS_READ_METHOD_BP, comm);
    if (f == NULL) {
        printE ("Error at opening file: %s\n", adios_errmsg());
        return 1;
    }

    sel = adios_selection_boundingbox (1, start, count);
    adios_schedule_read (f, sel, "t1", 0, 1, r1);
    adios_schedule_read (f, sel, "t2", 0, 1, r2);
    adios_perform_reads (f, 1);
    adios_selection_delete (sel);

    CHECK_ARRAY (t, r1, NX);
    CHECK_ARRAY (t, r2, NX);

endread:
    adios_read_close(f);
    MPI_Barrier (comm);
    return err;
}
AdiosCheckpointInput::~AdiosCheckpointInput()
{
  adios_read_close(adios_file_handle);
  adios_read_finalize_method(method);
  for (int i = 0; i < buffers.size(); i++)
    free(buffers[i]);
}
Esempio n. 3
0
void ADIOS1CommonRead::Close()
{
    if (m_IsFileOpen)
    {
        adios_read_close(m_fh);
        m_IsFileOpen = false;
    }
}
Esempio n. 4
0
/// Test if the file is present.  This function accomplishes its task by
/// actually attempting to open it.  It returns true if the open attempt
/// was successful, returns false otherwise.
bool ADIOS_File::exists(const std::string& fileName)
{
    ADIOS_FILE* f = adios_read_open_file
        (fileName.c_str(), ADIOS_READ_METHOD_BP, MPI_COMM_WORLD);
    if (f != 0) {
        adios_read_close(f);
        return true;
    }
    return false;
}
Esempio n. 5
0
eavlXGCImporter::~eavlXGCImporter()
{
    if (fp)
        adios_read_close(fp);
    if (mesh_fp)
        adios_read_close(mesh_fp);

    fp = NULL;
    mesh_fp = NULL;

    map<string, ADIOS_VARINFO*>::const_iterator it;
    for (it = variables.begin(); it != variables.end(); it++)
	adios_free_varinfo(it->second);
    variables.clear();
    if (points)
	adios_free_varinfo(points);    
    if (cells)
	adios_free_varinfo(cells);
    points = NULL;
    cells = NULL;
}
Esempio n. 6
0
int read_stepbystep ()
{
    ADIOS_FILE * f;
    float timeout_sec = 0.0; 
    int steps = 0;
    int retval = 0;
    MPI_Comm    comm = MPI_COMM_SELF;

    adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");
    printf ("\n--------- Read as stream  ------------\n");
    f = adios_read_open (fname, ADIOS_READ_METHOD_BP,
                          comm, ADIOS_LOCKMODE_NONE, timeout_sec);
    if (adios_errno == err_file_not_found)
    {
        printf ("Stream not found after waiting %f seconds: %s\n",
                timeout_sec, adios_errmsg());
        retval = adios_errno;
    }
    else if (adios_errno == err_end_of_stream)
    {
        printf ("Stream terminated before open. %s\n", adios_errmsg());
        retval = adios_errno;
    }
    else if (f == NULL) {
        printf ("Error at opening stream: %s\n", adios_errmsg());
        retval = adios_errno;
    }
    else
    {
        /* Processing loop over the steps (we are already in the first one) */
        while (adios_errno != err_end_of_stream) {
            steps++; // steps start counting from 1
            printf ("Step: %d\n", f->current_step);
            print_varinfo (f, f->current_step);

            // advance to 1) next available step with 2) blocking wait
            adios_advance_step (f, 0, timeout_sec);
            if (adios_errno == err_step_notready)
            {
                //printf ("No new step arrived within the timeout. Quit. %s\n",
                //        adios_errmsg());
                break; // quit while loop
            }
        }
        adios_read_close (f);
    }
    adios_read_finalize_method (ADIOS_READ_METHOD_BP);
    //printf ("We have processed %d steps\n", steps);
    return retval;
}
Esempio n. 7
0
/// Close the open file.  This function frees the content of the ADIOS_FILE
/// object under the control of this object.
void ADIOS_File::close()
{
    if (m_handle == 0) return;

    int ierr = adios_read_close(m_handle);
    if (ierr == 0) {
        LOGGER(ibis::gVerbose > 4)
            << "ADIOS_File::close successfully closed file \"" << m_fname
            << '"';
    }
    else {
        LOGGER(ibis::gVerbose >= 0)
            << "Warning -- ADIOS_File::close failed to close file \""
            << m_fname << "\" because of " << adios_errmsg();
    }
    m_handle = 0;
} // ADIOS_File::close
static void test_file_mode_reads(const char *bp_filename) {
	int i;
	ADIOS_FILE *fp = adios_read_open_file(bp_filename, ADIOS_READ_METHOD_BP, COMM);
	MPI_Assert(COMM, fp);

	fprintf(stderr, "[rank %d/%d] Starting file-mode writeblock reads on %s\n", rank, size, bp_filename);

	for (i = 0; i < fp->nvars; ++i) {
		const char *varname = fp->var_namelist[i];
		test_file_mode_reads_on_var(fp, bp_filename, varname);

		MPI_Barrier(COMM);
	}

	adios_read_close(fp);

	fprintf(stderr, "[rank %d/%d] Finished file-mode writeblock reads on %s\n", rank, size, bp_filename);
}
Esempio n. 9
0
/// Open the named file in read-only mode.  If a write operation is
/// desired, the caller is expected to close this file and call adios_open
/// explicitly.  This object is used to carry the file name when any write
/// operations are to be performed.  Furthermore, the file is always open
/// in streaming mode.
void ADIOS_File::open(const std::string &fn, ADIOS_READ_METHOD rm,
                      float to, bool strm)
{
    const char *cptr = (fn.empty() ? m_fname.c_str() : fn.c_str());
    if (*cptr == 0) // can not proceed with a valid file name
        return;

    if (m_handle)
        (void) adios_read_close(m_handle);

    if (strm) { // variables are visible one step at a time
        m_handle = adios_read_open_stream
            (cptr, rm, m_comm, ADIOS_LOCKMODE_CURRENT, to);
        if (m_handle != 0) { // successfully opened the stream for reading
            if (m_fname.compare(cptr) != 0)
                m_fname = cptr;
            LOGGER(ibis::gVerbose > 4)
                << "ADIOS_File::open(" << m_fname
                << ") successfully opened the name file in streaming mode";
        }
        else {
            LOGGER(ibis::gVerbose >= 0)
                << "Warning -- ADIOS_File::open(" << cptr
                << ") failed to locate an active stream";
        }
    }
    else { // open_file makes all variables visible at once
        if (m_fname.compare(cptr) != 0)
            m_fname = cptr;
        m_handle = adios_read_open_file(cptr, rm, m_comm);
        if (m_handle != 0) {
            LOGGER(ibis::gVerbose > 4)
                << "ADIOS_File::open(" << m_fname
                << ") opened the named file for reading";
        }
        else {
            LOGGER(ibis::gVerbose >= 0)
                << "Warning -- ADIOS_File::open(" << cptr
                << ") failed to open the named file in read-only mode";
        }
    }
} // ADIOS_File::open
Esempio n. 10
0
eavlXGCParticleImporter::~eavlXGCParticleImporter()
{
    if(fp)
        adios_read_close(fp);
    fp = NULL;

    map<string, ADIOS_VARINFO*>::const_iterator it;
    for(it = ephase.begin(); it != ephase.end(); it++)
        adios_free_varinfo(it->second);
    ephase.clear();
    for(it = iphase.begin(); it != iphase.end(); it++)
        adios_free_varinfo(it->second);
    iphase.clear();
    for(it = egid.begin(); it != egid.end(); it++)
        adios_free_varinfo(it->second);
    egid.clear();
    for(it = igid.begin(); it != igid.end(); it++)
        adios_free_varinfo(it->second);
    igid.clear();
}
Esempio n. 11
0
int main (int argc, char ** argv) 
{
	char        filename [256];
	int         rank, size, i;
	int         NX = 4096; 
	double      t[NX];
	MPI_Comm    comm = MPI_COMM_WORLD;

	/* ADIOS variables declarations for matching gwrite_temperature.ch */
	ADIOS_FILE *fp;
	ADIOS_SELECTION *s;

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

	strcpy (filename, "adios_global.bp");

    //adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "");

    fp = adios_read_open_file ("adios_global.bp", ADIOS_READ_METHOD_BP, comm);

    #include "gread_temperature.ch"

    adios_read_close (fp);

    // Verify data
	for (i = 0; i < NX; i++)
		if (t[i] != rank*NX + i)
        {
            fprintf (stderr, "Error detected\n");
        }

    
    adios_read_finalize_method (ADIOS_READ_METHOD_BP);

	MPI_Finalize ();
	return 0;
}
Esempio n. 12
0
int read_all ()
{
        ADIOS_FILE * f;
        float timeout_sec = 0.0; 
        int steps = 0;
    int retval = 0;
    MPI_Comm    comm = MPI_COMM_SELF;

    adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");
    printf ("\n--------- Read as file  ------------\n");
    f = adios_read_open_file (fname, ADIOS_READ_METHOD_BP, comm);
    if (f == NULL) {
        printf ("Error at opening file: %s\n", adios_errmsg());
        retval = adios_errno;
    }
    else
    {
        /* Processing all the steps at once */
        print_varinfo (f, 0);
        adios_read_close (f);
    }
    adios_read_finalize_method (ADIOS_READ_METHOD_BP);
    return retval;
}
Esempio n. 13
0
int read_scalar ()
{
    ADIOS_FILE * f;
    float timeout_sec = 0.0; 
    int steps = 0;
    int retval = 0;
    MPI_Comm    comm = MPI_COMM_SELF;

    adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");
    printf ("\n--------- Read all instances of the scalar 'O'  ------------\n");
    f = adios_read_open_file (fname, ADIOS_READ_METHOD_BP, comm);
    if (f == NULL) {
        printf ("Error at opening file: %s\n", adios_errmsg());
        retval = adios_errno;
    }
    else
    {
        /* Read the scalar O with writeblock selection */
        print_scalar (f, "O");
        adios_read_close (f);
    }
    adios_read_finalize_method (ADIOS_READ_METHOD_BP);
    return retval;
}
Esempio n. 14
0
int main (int argc, char ** argv) 
{
    char        filename [256] = "stream.bp";
    int         rank, size;
    int         NX, NY; 
    int         len, off;
    double      *t = NULL;
    MPI_Comm    comm = MPI_COMM_WORLD;

    int64_t     adios_handle;
	uint64_t    adios_groupsize, adios_totalsize;

    uint64_t    start[2], count[2];

    ADIOS_SELECTION *sel;
    int         steps = 0;

    MPI_Init (&argc, &argv);
    MPI_Comm_rank (comm, &rank);
    MPI_Comm_size (comm, &size);
    
    // ADIOS read init
    adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");
    
    ADIOS_FILE* fp = adios_read_open_file ("kstar.bp", 
                                           ADIOS_READ_METHOD_BP,
                                           comm);
    assert(fp != NULL);

    ADIOS_VARINFO* nx_info = adios_inq_var( fp, "N");
    ADIOS_VARINFO* ny_info = adios_inq_var( fp, "L");

    NX = *((int *)nx_info->value);
    NY= *((int*)ny_info->value);

    len = NX / size;
    off = len * rank;

    if (rank == size-1)
        len = len + NX % size;

    printf("\trank=%d: NX,NY,len,off = %d\t%d\t%d\t%d\n", rank, NX, NY, len, off);
    assert(len > 0);

    t = (double *) malloc(sizeof(double) * len * NY);
    memset(t, '\0', sizeof(double) * len * NY);
    assert(t != NULL);

    start[0] = off;
    start[1] = 0;
    count[0] = len;
    count[1] = NY;
    sel = adios_selection_boundingbox (2, start, count);

    // ADIOS write init
    adios_init ("adios.xml", comm);
    
    remove (filename);
    //int ii;
    //for(ii = 0; ii<10; ii++){
    //    for (i = 0; i < len * NY; i++)
    //        t[i] = ii*1000 + rank;

    while(adios_errno != err_end_of_stream && adios_errno != err_step_notready)
    {
        steps++;
        // Reading
        adios_schedule_read (fp, sel, "var", 0, 1, t);
        adios_perform_reads (fp, 1);

        // Debugging
        //for (i = 0; i < len*NY; i++)  t[i] = off * NY + i;

        printf("step=%d\trank=%d\t[%d,%d]\n", steps, rank, len, NY);

        // Writing
        adios_open (&adios_handle, "writer", filename, "a", comm);
        adios_groupsize = 4*4 + 8*len*NY;
        adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
        adios_write (adios_handle, "NX", &NX);
        adios_write (adios_handle, "NY", &NY);
        adios_write (adios_handle, "len", &len);
        adios_write (adios_handle, "off", &off);
        adios_write (adios_handle, "var_2d_array", t);
        adios_close (adios_handle);


        // Advance
        MPI_Barrier (comm);
        adios_advance_step(fp, 0, TIMEOUT_SEC);
    }
    free(t);

    MPI_Barrier (comm);
    adios_read_close(fp);

    if (rank==0) 
        printf ("We have processed %d steps\n", steps);

    MPI_Barrier (comm);
    adios_read_finalize_method(ADIOS_READ_METHOD_BP);

    adios_finalize (rank);

    MPI_Finalize ();

    return 0;
}
Esempio n. 15
0
int main (int argc, char ** argv) 
{
    int         rank, size, i;
    MPI_Comm    comm = MPI_COMM_WORLD;
    enum ADIOS_DATATYPES attr_type;
    enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
    int attr_size;
    void * data = NULL;

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

    adios_read_init_method (method, comm, "verbose=3");
    adios_logger_open ("log_read_C", rank);
    ADIOS_FILE * f = adios_read_open ("attributes_C.bp", method, comm, ADIOS_LOCKMODE_NONE, 0.0);
    if (f == NULL)
    {
        log_error ("%s\n", adios_errmsg());
        return -1;
    }

    for (i = 0; i < f->nattrs; i++)
    {

        adios_get_attr (f, f->attr_namelist[i], &attr_type, &attr_size, &data);

        log_test("rank %d: attr: %s %s = ", rank, adios_type_to_string(attr_type), f->attr_namelist[i]);
        int type_size = adios_type_size (attr_type, data);
        int nelems = attr_size / type_size;
        int k;
        char *p = (char*)data;
        for (k=0; k<nelems; k++) 
        {
            if (k>0) log_test(", ");
            switch (attr_type)  
            {
                case adios_integer:
                    log_test ("%d", *(int *)p);
                    break;
                case adios_double:
                    log_test ("%e", *(double *)p);
                    break;
                case adios_string:
                    log_test ("\"%s\"", (char *)p);
                    break;
                case adios_string_array:
                    log_test ("\"%s\"", *(char **)p);
                    break;
                default:
                    log_test ("??????\n");
            }
            p=p+type_size;
        }
        log_test("\n");
        free (data);
        data = 0;
    }

    adios_read_close (f);
    MPI_Barrier (comm);
    adios_read_finalize_method (ADIOS_READ_METHOD_BP);
    adios_logger_close();
    MPI_Finalize ();
    return 0;
}
Esempio n. 16
0
int main (int argc, char ** argv) 
{
    char        filename [256];
    int         rank;
    MPI_Comm    comm = MPI_COMM_WORLD;
    enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
    ADIOS_SELECTION * sel1=NULL;

    int8_t  v1 = 0;
    int16_t v2 = 0;
    int32_t v3 = 0;
    int64_t v4 = 0;

    uint8_t  v5 = 0;
    uint16_t v6 = 0;
    uint32_t v7 = 0;
    uint64_t v8 = 0;

    float v9 = 0.0;
    double v10 = 0.0;

    char v11[256];

    complex v12;
    v12.r = 0.0;
    v12.i = 0.0;

    double_complex v13;
    v13.r = 0.0;
    v13.i = 0.0;

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

    strcpy (filename, "scalars.bp");

    adios_read_init_method (method, comm, "verbose=3");
    ADIOS_FILE * f = adios_read_open (filename, method, comm, ADIOS_LOCKMODE_NONE, 0.0);

    adios_schedule_read (f, sel1, "var_byte",           0, 1, &v1);
    adios_schedule_read (f, sel1, "var_short",          0, 1, &v2);
    adios_schedule_read (f, sel1, "var_int",            0, 1, &v3);
    adios_schedule_read (f, sel1, "var_long",           0, 1, &v4);
    adios_schedule_read (f, sel1, "var_ubyte",          0, 1, &v5);
    adios_schedule_read (f, sel1, "var_ushort",         0, 1, &v6);
    adios_schedule_read (f, sel1, "var_uint",           0, 1, &v7);
    adios_schedule_read (f, sel1, "var_ulong",          0, 1, &v8);
    adios_schedule_read (f, sel1, "var_real",           0, 1, &v9);
    adios_schedule_read (f, sel1, "var_double",         0, 1, &v10);
    /* note that a string is an array and thus v11 a pointer already, 
       so we pass the v11 instead of &v11 here */
    adios_schedule_read (f, sel1, "var_string",         0, 1, v11);
    adios_schedule_read (f, sel1, "var_complex",        0, 1, &v12);
    adios_schedule_read (f, sel1, "var_double_complex", 0, 1, &v13);
    adios_perform_reads (f,1);

    if (rank == 0) {
        printf("byte        v1  = %d\n", v1);
        printf("short       v2  = %d\n", v2);
        printf("integer     v3  = %d\n", v3);
        printf("long        v4  = %" PRId64 "\n", v4);

        printf("uns.byte    v5  = %u\n", v5);
        printf("uns.short   v6  = %u\n", v6);
        printf("uns.int     v7  = %u\n", v7);
        printf("uns.long    v8  = %" PRIu64 "\n", v8);

        printf("float       v9  = %g\n", v9);
        printf("double      v10 = %g\n", v10);

        printf("string      v11 = %s\n", v11);

        printf("complex     v12 = (%g, i%g)\n", v12.r, v12.i);
        printf("dbl-complex v13 = (%g, i%g)\n", v13.r, v13.i);
    }

    adios_read_close (f);
    MPI_Barrier (comm);
    adios_read_finalize_method (ADIOS_READ_METHOD_BP);
    MPI_Finalize ();

    return 0;
}
Esempio n. 17
0
int read_scalar_stepbystep ()
{
    ADIOS_FILE * f;
    float timeout_sec = 0.0; 
    int steps = 0;
    int retval = 0;
    MPI_Comm    comm = MPI_COMM_SELF;

    adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");
    printf ("\n--------- Read scalar in stream using varinfo->value  ------------\n");
    f = adios_read_open (fname, ADIOS_READ_METHOD_BP,
                          comm, ADIOS_LOCKMODE_NONE, timeout_sec);
    if (adios_errno == err_file_not_found)
    {
        printf ("Stream not found after waiting %f seconds: %s\n",
                timeout_sec, adios_errmsg());
        retval = adios_errno;
    }
    else if (adios_errno == err_end_of_stream)
    {
        printf ("Stream terminated before open. %s\n", adios_errmsg());
        retval = adios_errno;
    }
    else if (f == NULL) {
        printf ("Error at opening stream: %s\n", adios_errmsg());
        retval = adios_errno;
    }
    else
    {
        /* Processing loop over the steps (we are already in the first one) */
        while (adios_errno != err_end_of_stream) {
            steps++; // steps start counting from 1
            printf ("Step: %d\n", f->current_step);

            /* Check the scalar O with varinfo->value */
            ADIOS_VARINFO * v = adios_inq_var (f, "NX");
            int value =  *(int*)v->value;
            printf ("Scalar NX = %d", value);
            if (value != 
                    block_count [f->current_step*nblocks_per_step*size]) 
            {
                printf ("\tERROR expected = %llu", 
                        block_count [f->current_step*nblocks_per_step*size]);
                nerrors++;
            }
            printf ("\n");

            // advance to 1) next available step with 2) blocking wait
            adios_advance_step (f, 0, timeout_sec);
            if (adios_errno == err_step_notready)
            {
                //printf ("No new step arrived within the timeout. Quit. %s\n",
                //        adios_errmsg());
                break; // quit while loop
            }
        }
        adios_read_close (f);
    }
    adios_read_finalize_method (ADIOS_READ_METHOD_BP);
    //printf ("We have processed %d steps\n", steps);
    return retval;
}
Esempio n. 18
0
int main(int argc, char ** argv) {

    char xmlFileName[256];
    enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;

    MPI_Comm comm = MPI_COMM_WORLD;

    ADIOS_QUERY_TEST_INFO *queryInfo;
    ADIOS_FILE *f;


    MPI_Init(&argc, &argv);

    if (argc < 4 || argc > 7) {
        fprintf(stderr," usage: %s {input bp file} {xml file} {query engine (ALACRITY/FASTBIT)} [mode (FILE/stream)] [print points? (TRUE/false)] [read results? (true/FALSE)]\n", argv[0]);
        MPI_Abort(comm, 1);
    }
    else {
        strcpy(xmlFileName,  argv[2]);
    }

    enum ADIOS_QUERY_METHOD query_method = ADIOS_QUERY_METHOD_UNKNOWN;
    if (strcasecmp(argv[3], "ALACRITY") == 0) {
        // init with ALACRITY
        //adios_query_init(ADIOS_QUERY_TOOL_ALACRITY);
    	query_method = ADIOS_QUERY_METHOD_ALACRITY;
    }
    else if (strcasecmp(argv[3], "FASTBIT") == 0) {
        // init with FastBit
    	query_method = ADIOS_QUERY_METHOD_FASTBIT;
    	//fprintf(stderr,"FastBit not supported in this test yet, exiting...\n");
    	//MPI_Abort(comm, 1);
    }
    else {
    	fprintf(stderr,"Unsupported query engine %s, exiting...\n", argv[3]);
        MPI_Abort(comm, 1);
    }

    const int use_streaming = (argc >= 5) && (strcasecmp(argv[4], "stream") == 0);
    const int read_results = (argc >= 6) && (strcasecmp(argv[5], "true") == 0);
    const int print_points = !(argc >= 7) || (strcasecmp(argv[6], "true") == 0);

    fprintf(stderr, "NOTE: Running the query in %s mode\n", use_streaming ? "STREAM" : "FILE");
    fprintf(stderr, "NOTE: %s print query result points\n", print_points ? "WILL" : "WILL NOT");
    fprintf(stderr, "NOTE: %s read data using query result point selection\n", read_results ? "WILL" : "WILL NOT");

    // ADIOS init
    adios_read_init_method(method, comm, NULL);

    f = use_streaming ?
    		adios_read_open(argv[1], method, comm, ADIOS_LOCKMODE_ALL, -1) :
    		adios_read_open_file(argv[1], method, comm);
    if (f == NULL) {
        fprintf(stderr," can not open file %s \n", argv[1]);
        MPI_Abort(comm, 1);
    }

    // Parse the xml file to generate query info
    queryInfo = parseXml(xmlFileName, f);

    // perform query
    adios_query_set_method(queryInfo->query, query_method);
    performQuery(queryInfo, f, use_streaming, print_points, read_results);


    adios_read_close(f);
    adios_read_finalize_method(ADIOS_READ_METHOD_BP);

    MPI_Finalize();
    return 0;
}
Esempio n. 19
0
int main (int argc, char ** argv) 
{
    int         err;
    int         steps = 0, curr_step;
    int         retval = 0;

    MPI_Init (&argc, &argv);
    comm = MPI_COMM_WORLD;
    MPI_Comm_rank (comm, &rank);
    MPI_Comm_size (comm, &numproc);

    if (processArgs(argc, argv)) {
        return 1;
    }
    
    print0("Input stream            = %s\n", infilename);
    print0("Output stream           = %s\n", outfilename);
    print0("Read method             = %s (id=%d)\n", rmethodname, read_method);
    print0("Read method parameters  = \"%s\"\n", rmethodparams);
    print0("Write method            = %s\n", wmethodname);
    print0("Write method parameters = \"%s\"\n", wmethodparams);
    

    err = adios_read_init_method(read_method, comm, 
                                 "max_chunk_size=100; "
                                 "app_id =32767; \n"
                                 "verbose= 3;"
                                 "poll_interval  =  100;"
                                );

    if (!err) {
        print0 ("%s\n", adios_errmsg());
    }

    adios_init_noxml(comm);

    print0 ("Waiting to open stream %s...\n", infilename);
    f = adios_read_open_stream (infilename, read_method, comm, 
                                             ADIOS_LOCKMODE_ALL, timeout_sec);
    if (adios_errno == err_file_not_found) 
    {
        print ("rank %d: Stream not found after waiting %d seconds: %s\n", 
               rank, timeout_sec, adios_errmsg());
        retval = adios_errno;
    } 
    else if (adios_errno == err_end_of_stream) 
    {
        print ("rank %d: Stream terminated before open. %s\n", rank, adios_errmsg());
        retval = adios_errno;
    } 
    else if (f == NULL) {
        print ("rank %d: Error at opening stream: %s\n", rank, adios_errmsg());
        retval = adios_errno;
    } 
    else 
    {
        // process steps here... 
        if (f->current_step != 0) {
            print ("rank %d: WARNING: First %d steps were missed by open.\n", 
                   rank, f->current_step);
        }

        while (1)
        {
            steps++; // start counting from 1

            print0 ("File info:\n");
            print0 ("  current step:   %d\n", f->current_step);
            print0 ("  last step:      %d\n", f->last_step);
            print0 ("  # of variables: %d:\n", f->nvars);

            retval = process_metadata(steps);
            if (retval) break;

            retval = read_write(steps);
            if (retval) break;

            // advance to 1) next available step with 2) blocking wait 
            curr_step = f->current_step; // save for final bye print
            adios_advance_step (f, 0, timeout_sec);

            if (adios_errno == err_end_of_stream) 
            {
                break; // quit while loop
            }
            else if (adios_errno == err_step_notready) 
            {
                print ("rank %d: No new step arrived within the timeout. Quit. %s\n", 
                        rank, adios_errmsg());
                break; // quit while loop
            } 
            else if (f->current_step != curr_step+1) 
            {
                // we missed some steps
                print ("rank %d: WARNING: steps %d..%d were missed when advancing.\n", 
                        rank, curr_step+1, f->current_step-1);
            }

        }

        adios_read_close (f);
    } 
    print0 ("Bye after processing %d steps\n", steps);

    adios_read_finalize_method (read_method);
    adios_finalize (rank);
    MPI_Finalize ();

    return retval;
}
int main (int argc, char ** argv) 
{
    int         rank, size, i, j;
    MPI_Comm    comm = MPI_COMM_WORLD;
    ADIOS_FILE * f;
    ADIOS_VARINFO * v;
    ADIOS_SELECTION * sel;
    int steps = 0;
    int retval = 0;
    float timeout_sec = 1.0; 

    void * data = NULL;
    uint64_t start[2], count[2];

    MPI_Init (&argc, &argv);

    MPI_Comm_rank (comm, &rank);
    MPI_Comm_size (comm, &size);

    adios_read_init_method (ADIOS_READ_METHOD_BP, comm, "verbose=3");

    f = adios_read_open ("adios_globaltime.bp", ADIOS_READ_METHOD_BP,
                          comm, ADIOS_LOCKMODE_NONE, timeout_sec);
    if (adios_errno == err_file_not_found)
    {
        printf ("rank %d: Stream not found after waiting %f seconds: %s\n",
                rank, timeout_sec, adios_errmsg());
        retval = adios_errno;
    }
    else if (adios_errno == err_end_of_stream)
    {
        printf ("rank %d: Stream terminated before open. %s\n", rank, adios_errmsg());
        retval = adios_errno;
    }
    else if (f == NULL) {
        printf ("rank %d: Error at opening stream: %s\n", rank, adios_errmsg());
        retval = adios_errno;
    }
    else
    {
        /* process file here... */
        v = adios_inq_var (f, "temperature");
        adios_inq_var_blockinfo (f, v);

        printf ("ndim = %d\n",  v->ndim);
        //printf ("nsteps = %d\n",  v->nsteps);
        printf ("dims[%llu][%llu]\n",  v->dims[0], v->dims[1]);

        uint64_t slice_size = v->dims[0]/size;
        if (rank == size-1)
            slice_size = slice_size + v->dims[0]%size;

        start[0] = rank * slice_size;
        count[0] = slice_size;
        start[1] = 0;
        count[1] = v->dims[1];

        data = malloc (slice_size * v->dims[1] * 8);

        /* Processing loop over the steps (we are already in the first one) */
        while (adios_errno != err_end_of_stream) {
            steps++; // steps start counting from 1

            sel = adios_selection_boundingbox (v->ndim, start, count);
            adios_schedule_read (f, sel, "temperature", 0, 1, data);
            adios_perform_reads (f, 1);

            if (rank == 0)
                printf ("--------- Step: %d --------------------------------\n", 
                        f->current_step);

            printf("rank=%d: [0:%lld,0:%lld] = [", rank, v->dims[0], v->dims[1]);
            for (i = 0; i < slice_size; i++) {
                printf (" [");
                for (j = 0; j < v->dims[1]; j++) {
                    printf ("%g ", *((double *)data + i * v->dims[1] + j));
                }
                printf ("]");
            }
            printf (" ]\n\n");

            // advance to 1) next available step with 2) blocking wait
            adios_advance_step (f, 0, timeout_sec);
            if (adios_errno == err_step_notready)
            {
                printf ("rank %d: No new step arrived within the timeout. Quit. %s\n",
                        rank, adios_errmsg());
                break; // quit while loop
            }

        }

        adios_read_close (f);
    }

    if (rank==0) 
        printf ("We have processed %d steps\n", steps);

    adios_read_finalize_method (ADIOS_READ_METHOD_BP);
    free (data);
    MPI_Finalize ();

    return retval;
}
Esempio n. 21
0
int read_points ()
{
    ADIOS_SELECTION *sel0,*sel1,*sel2,*sel3;
    ADIOS_FILE * f;
    ADIOS_VARINFO * vi;
    int err=0,n,n1, i,j,k;
    int nsteps_a, nsteps_b, nsteps_c;
    int v; 

    uint64_t *pts1;
    uint64_t *pts2;
    uint64_t *pts3;
    uint64_t start[3] = {offs1,offs2,offs3};
    uint64_t count[3] = {ldim1,ldim2,ldim3};
    
    pts1 = (uint64_t*) malloc (1*sizeof(uint64_t)*ldim1);
    pts2 = (uint64_t*) malloc (2*sizeof(uint64_t)*ldim1*ldim2);
    pts3 = (uint64_t*) malloc (3*sizeof(uint64_t)*ldim1*ldim2*ldim3);

    for (i=0; i<ldim1; i++) 
    {
        pts1[i] = offs1 + i;
        for (j=0; j<ldim2; j++) 
        {
            pts2[i*2*ldim2 + 2*j]   = offs1 + i;
            pts2[i*2*ldim2 + 2*j+1] = j; 
            for (k=0; k<ldim3; k++) 
            {
                pts3[i*3*ldim2*ldim3+j*3*ldim3+3*k]   = offs1 + i;
                pts3[i*3*ldim2*ldim3+j*3*ldim3+3*k+1] = j;
                pts3[i*3*ldim2*ldim3+j*3*ldim3+3*k+2] = k;
            }
        }
    }

    //Force error on very last point: pts3[3*ldim1*ldim2*ldim3-1] = 0;

    reset_readvars();

    log ("Read and check data in %s using point selections\n", FILENAME);
    f = adios_read_open (FILENAME, read_method, comm,
                         ADIOS_LOCKMODE_CURRENT, 0.0);
    if (f == NULL) {
        printE ("Error at opening file: %s\n", rank, adios_errmsg());
        return 1;
    }

    sel1 = adios_selection_points (1, ldim1, pts1); 
    sel2 = adios_selection_points (2, ldim1*ldim2, pts2); 
    sel3 = adios_selection_points (3, ldim1*ldim2*ldim3, pts3); 

#ifdef DEBUG_PRINTS
    fprintf(stderr, "1D selection: {");
    for (i=0; i<ldim1; i++) {
        fprintf (stderr, "%d ", i, i, pts1[i]);
    }
    fprintf(stderr, "}\n");

    fprintf(stderr, "2D selection :\n");
    for (i=0; i<ldim1; i++) {
        fprintf (stderr, "i=%d, idx=%2d- = ", i, i*2*ldim2);
        for (j=0; j<ldim2; j++) {
            n = i*2*ldim2+2*j;
            fprintf (stderr, "{%d,%d} ", pts2[n], pts2[n+1]); 
        }
        fprintf(stderr, "\n");
    }

    fprintf(stderr, "3D selection :\n");
    for (i=0; i<ldim1; i++) {
        for (j=0; j<ldim2; j++) {
            fprintf (stderr, "i=%d, j=%d, idx=%3d- = ", i, j, i*3*ldim2*ldim3+j*3*ldim3); 
            for (k=0; k<ldim3; k++) {
                n = i*3*ldim2*ldim3+j*3*ldim3+3*k;
                fprintf (stderr, "{%d,%d,%d} ", pts3[n], pts3[n+1], pts3[n+2]); 
            }
            fprintf(stderr, "\n");
        }
    }
#endif

    n1=0;
    while (n1 < NSTEPS && adios_errno != err_end_of_stream) {
        n1++;
        log ("  Step %d\n", f->current_step);


        log ("  Check 1D variable a1...\n");
        adios_schedule_read (f, sel1, "a1",  0, 1, r1);
        adios_perform_reads (f, 1);

#ifdef DEBUG_PRINTS
        fprintf(stderr, "1D result: {");
        for (i=0; i<ldim1; i++) {
            fprintf (stderr, "%d ", i, i, r1[i]);
        }
        fprintf(stderr, "}\n");
#endif

        for (i=0; i<ldim1; i++) {
            v = VALUE1D(rank,f->current_step,i);
            if (r1[i] != v) {
                printE ("Error: a1[%d]=%d  !=  read=%d\n", i, v, r1[i]); 
                //goto endread;
            }
        }



        log ("  Check 2D variable a2...\n");
        adios_schedule_read (f, sel2, "a2",  0, 1, r2);
        adios_perform_reads (f, 1);

#ifdef DEBUG_PRINTS
        fprintf(stderr, "2D result :\n");
        n = 0;
        for (i=0; i<ldim1; i++) {
            fprintf (stderr, "row=%2d- = {", i);
            for (j=0; j<ldim2; j++) {
                fprintf (stderr, "%d ", r2[n]); 
                n++;
            }
            fprintf(stderr, "}\n");
        }
#endif

        n = 0;
        for (i=0; i<ldim1; i++) {
            for (j=0; j<ldim2; j++) {
                v = VALUE2D(rank,f->current_step,i,j);
                if (v != r2[n]) {
                    printE ("Error: a2[%d,%d]=%d  !=  read=%d\n", i, j, v, r2[n]); 
                    //goto endread;
                }
                n++;
            }
        }




        log ("  Check 3D variable a3...\n");
        adios_schedule_read (f, sel3, "a3",  0, 1, r3);
        adios_perform_reads (f, 1);

#ifdef DEBUG_PRINTS
        fprintf(stderr, "3D selection :\n");
        n=0;
        for (i=0; i<ldim1; i++) {
            for (j=0; j<ldim2; j++) {
                fprintf (stderr, "[%d,%d] = {", i, j); 
                for (k=0; k<ldim3; k++) {
                    fprintf (stderr, "%d ", r3[n]); 
                    n++;
                }
                fprintf(stderr, "}\n");
            }
        }
#endif
        n = 0;
        for (i=0; i<ldim1; i++) {
            for (j=0; j<ldim2; j++) {
                for (k=0; k<ldim3; k++) {
                    v = VALUE3D(rank,f->current_step,i,j,k);
                    if (v != r3[n]) {
                        printE ("Error: a3[%d,%d,%d]=%d  !=  read=%d\n", i, j, k, v, r3[n]); 
                        //goto endread;
                    }
                    n++;
                }
            }
        }

        if (n1 < NSTEPS)
        {
            adios_advance_step (f, 0, -1.0);
        }
    }


endread:

    adios_selection_delete (sel1);
    adios_selection_delete (sel2);
    adios_selection_delete (sel3);

    free(pts1);
    free(pts2);
    free(pts3);

    adios_read_close(f);
    MPI_Barrier (comm);
    return err;
}
Esempio n. 22
0
int main (int argc, char ** argv) 
{
    int         rank, size;
    int         NX, NY; 
    int         len, off;
    double      *t = NULL;
    MPI_Comm    comm = MPI_COMM_WORLD;

    uint64_t    start[2], count[2];

    ADIOS_SELECTION *sel;
    int         steps = 0;

#ifdef _USE_GNUPLOT
    int         i, j;
    double      *tmp;
    FILE        *pipe;
#else
    // Variables for ADIOS write
    int64_t     adios_handle;
    uint64_t    adios_groupsize, adios_totalsize;
    char        outfn[256];
#endif

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

    adios_read_init_method(ADIOS_READ_METHOD_FLEXPATH, comm, "");

    ADIOS_FILE* fp = adios_read_open("stream.bp", 
                                     ADIOS_READ_METHOD_FLEXPATH, 
                                     comm, ADIOS_LOCKMODE_NONE, 0.0);
    assert(fp != NULL);
    
    ADIOS_VARINFO* nx_info = adios_inq_var( fp, "NX");
    ADIOS_VARINFO* ny_info = adios_inq_var( fp, "NY");

    NX = *((int *)nx_info->value);
    NY= *((int*)ny_info->value);
    
    len = NX / size;
    off = len * rank;

    if (rank == size-1)
        len = len + NX % size;
    
    printf("\trank=%d: NX,NY,len,off = %d\t%d\t%d\t%d\n", rank, NX, NY, len, off);
    assert(len > 0);

    t = (double *) malloc(sizeof(double) * len * NY);
    memset(t, '\0', sizeof(double) * len * NY);
    assert(t != NULL);

    start[0] = off;
    start[1] = 0;
    count[0] = len;
    count[1] = NY;
    // Not working ... 
    //sel = adios_selection_boundingbox (2, start, count);

    sel = malloc(sizeof(ADIOS_SELECTION));
    sel->type=ADIOS_SELECTION_WRITEBLOCK;
    sel->u.block.index = rank;

#ifdef _USE_GNUPLOT
    if ((NX % size) > 0)
    {
        fprintf(stderr, "Equal distribution is required\n");
        return -1;
    }

    if (rank == 0) {
        pipe = popen("gnuplot", "w");
        fprintf(pipe, "set view map\n");
        fprintf(pipe, "set xrange [0:%d]\n", NX-1);

        tmp = (double *) malloc(sizeof(double) * NX * NY);
        assert(tmp != NULL);
    }

#else
    // ADIOS write init
    adios_init ("adios.xml", comm);
#endif

    //while(adios_errno != err_end_of_stream && adios_errno != err_step_notready)
    while(1)
    {
        steps++;
        // Reading
        adios_schedule_read (fp, sel, "var_2d_array", 0, 1, t);
        adios_perform_reads (fp, 1);
        
        printf("step=%d\trank=%d\tfp->current_step=%d\t[%d,%d]\n", 
                steps, rank, fp->current_step, len, NY);
        /*
        // Debugging
        for (i=0; i<len; i++) {
            printf("%d: rank=%d: t[%d,0:4] = ", steps, rank, off+i);
            for (j=0; j<5; j++) {
                printf(", %g", t[i*NY + j]);
            }
            printf(" ...\n");
        }
        */

        // Do something 
#ifdef _USE_GNUPLOT         // Option 1: plotting

        MPI_Gather(t, len * NY, MPI_DOUBLE, tmp, len * NY, MPI_DOUBLE, 0, comm);
        
        if (rank == 0)
        {
            fprintf(pipe, "set title 'Soft X-Rray Signal (shot #%d)'\n", steps);
            fprintf(pipe, "set xlabel 'Channel#'\n");
            fprintf(pipe, "set ylabel 'Timesteps'\n");
            fprintf(pipe, "set cblabel 'Voltage (eV)'\n");

#  ifndef _GNUPLOT_INTERACTIVE
            fprintf(pipe, "set terminal png\n");
            fprintf(pipe, "set output 'fig%03d.png'\n", steps);
#  endif

            fprintf(pipe, "splot '-' matrix with image\n");
            //fprintf(pipe, "plot '-' with lines, '-' with lines, '-' with lines\n");

            double *sum = calloc(NX, sizeof(double));

            for (j = 0; j < NY; j++) {
                for (i = 0; i < NX; i++) {
                    sum[i] += tmp[i * NY + j];
                }
            }

            for (j = 0; j < NY; j++) {
                for (i = 0; i < NX; i++) {
                    fprintf (pipe, "%g ", (-tmp[i * NY + j] + sum[i]/NY)/3276.8);
                }
                fprintf(pipe, "\n");
            }
            fprintf(pipe, "e\n");
            fprintf(pipe, "e\n");
            fflush (pipe);

#  ifdef _GNUPLOT_INTERACTIVE
            printf ("Press [Enter] to continue . . .");
            fflush (stdout);
            getchar ();
#  endif

            free(sum);
        }


#else        // Option 2: BP writing

        snprintf (outfn, sizeof(outfn), "reader_%3.3d.bp", steps);
        adios_open (&adios_handle, "reader", outfn, "w", comm);
        adios_groupsize = 4 * sizeof(int) + sizeof(double) * len * NY; 
        adios_group_size (adios_handle, adios_groupsize, &adios_totalsize);
        adios_write (adios_handle, "NX", &NX);
        adios_write (adios_handle, "NY", &NY);
        adios_write (adios_handle, "len", &len);
        adios_write (adios_handle, "off", &off);
        adios_write (adios_handle, "var", t);
        adios_close (adios_handle);

#endif        

        // Advance
        MPI_Barrier (comm);
        adios_advance_step(fp, 0, TIMEOUT_SEC);
        if (adios_errno == err_end_of_stream)
        {
            printf("rank %d, Stream terminated. Quit\n", rank);
            break; // quit while loop
        }
        else if (adios_errno == err_step_notready)
        {
            printf ("rank %d: No new step arrived within the timeout. Quit.\n", rank);
            break; // quit while loop
        }
        else if (adios_errno != err_no_error) {
            printf("ADIOS returned code=%d, msg:%s\n", 
                    adios_errno, adios_get_last_errmsg()); 
            break; // quit while loop
        }
    }
    //
    free(t);

    adios_read_close(fp);
    //printf("rank %d, Successfully closed stream\n", rank);

    adios_read_finalize_method(ADIOS_READ_METHOD_FLEXPATH);
    //printf("rank %d, Successfully finalized read method\n", rank);

#ifndef _USE_GNUPLOT
    adios_finalize (rank);
    //printf("rank %d, Successfully finalized adios\n", rank);
#else
    if (rank==0) {
        free(tmp);
        pclose(pipe);
    }
#endif

    MPI_Finalize ();

    return 0;
}
Esempio n. 23
0
int main (int argc, char ** argv) 
{
    /* application data structures */
    int         rank;
    int         NX, NY; 
    double      *t;
    int         *p;

    /* MPI and ADIOS data structures */
    MPI_Comm    comm = MPI_COMM_WORLD;

    /* MPI and ADIOS setup */
    MPI_Init (&argc, &argv);
    MPI_Comm_rank (comm, &rank);
    adios_read_init_method(ADIOS_READ_METHOD_FLEXPATH, comm, "");

    /* First read in the scalars to calculate the size of the arrays */

    /* get everything from single process - rank 0 for now*/
    ADIOS_SELECTION process_select;
    process_select.type=ADIOS_SELECTION_WRITEBLOCK;
    process_select.u.block.index = rank;

    /* read the size of arrays using local inq_var */

    /* Note: at this moment, timeout is not handled. It blocks until writer appears */
    ADIOS_FILE* afile = adios_read_open("arrays", ADIOS_READ_METHOD_FLEXPATH, comm, 
                                        ADIOS_LOCKMODE_NONE, 30.0);
    /* Read arrays for each time step */
    while(adios_errno != err_end_of_stream){

	ADIOS_VARINFO* nx_info = adios_inq_var( afile, "NX");
	if(nx_info->value) {
	    NX = *((int *)nx_info->value);
	}

	ADIOS_VARINFO* ny_info = adios_inq_var( afile, "NY");
	if(ny_info->value) {
	    NY = *((int *)ny_info->value);
	}
    
	/* Allocate space for the arrays */
	t = (double *) malloc (NX*NY*sizeof(double));    
	p = (int *) malloc (NX*sizeof(int));
	memset(t, 0, NX*NY*sizeof(double));
	memset(p, 0, NX*sizeof(int));
        /* schedule a read of the arrays */
        adios_schedule_read (afile, &process_select, "var_double_2Darray", 0, 1, t);
        adios_schedule_read (afile, &process_select, "var_int_1Darray", 0, 1, p);	
        /* commit request and retrieve data */
        adios_perform_reads (afile, 1);

        /* print result */
        printf("Results Rank=%d Step=%d p[] = [%d, %d,...] t[][] = [%.2f, %.2f]\n", 
                rank, afile->current_step, p[0], p[1], t[0], t[1]);
    
	/* block until next step is available (30 sec timeout unsupported) */
	adios_release_step(afile);
        adios_advance_step(afile, 0, 30);
	MPI_Barrier (comm);
	
	/* shutdown ADIOS and MPI */
    }
    adios_read_close(afile);	
    /* wait until all readers finish */
    adios_read_finalize_method(ADIOS_READ_METHOD_FLEXPATH);
    MPI_Finalize ();

    return 0;
}
Esempio n. 24
0
File: map.c Progetto: Dumbear/ADIOS
int main (int argc, char ** argv) 
{
    int         i, j, k,l;
    MPI_Comm    comm_dummy = 0;  /* MPI_Comm is defined through adios_read.h */

    if (argc < 2) {
        printf("Usage: %s <BP-file>\n", argv[0]);
        return 1;
    }

    adios_read_init_method (ADIOS_READ_METHOD_BP, comm_dummy, "show_hidden_attrs");
    ADIOS_FILE * f;
    f = adios_read_open_file (argv[1], ADIOS_READ_METHOD_BP, comm_dummy);
    if (f == NULL) {
        printf ("%s\n", adios_errmsg());
        return -1;
    }

    /* For all variables */
    printf("  Variables=%d:\n", f->nvars);
    for (i = 0; i < f->nvars; i++) {
        ADIOS_VARINFO * v = adios_inq_var_byid (f, i);
        adios_inq_var_stat (f, v, 0, 1);
        adios_inq_var_blockinfo (f, v);

        uint64_t total_size = adios_type_size (v->type, v->value);
        for (j = 0; j < v->ndim; j++)
            total_size *= v->dims[j];

        printf("    %-9s  %s", adios_type_to_string(v->type), f->var_namelist[i]);
        if (v->ndim == 0) {
            /* Scalars do not need to be read in, we get it from the metadata
               when using adios_inq_var */
            printf(" = %s\n", value_to_string(v->type, v->value, 0));
        } else {
            /* Arrays, print min/max statistics*/
            printf("[%lld",v->dims[0]);
            for (j = 1; j < v->ndim; j++)
                printf(", %lld",v->dims[j]);
            //printf("] = \n");

            if (v->type == adios_integer)
                printf("] : min=%d  max=%d\n", 
                        (*(int*)v->statistics->min), (*(int*)v->statistics->max));
            else if (v->type == adios_double)
                printf("] : min=%lg  max=%lg\n", 
                        (*(double*)v->statistics->min), (*(double*)v->statistics->max));

            /* Print block info */
            for (l=0; l<v->nsteps; l++) {
                printf("        step %3d: \n", l);
                for (j=0; j<v->nblocks[l]; j++) {
                    printf("          block %3d: [", j);
                    for (k=0; k<v->ndim; k++) {
                        printf("%3lld:%3lld", v->blockinfo[j].start[k],
                                v->blockinfo[j].start[k]+v->blockinfo[j].count[k]-1);
                        if (k<v->ndim-1)
                            printf(", ");
                    }
                    printf("]\n");
                }
            }

        }

        adios_free_varinfo (v);
    } /* variables */

    /* For all attributes */
    printf("  Attributes=%d:\n", f->nattrs);
    for (i = 0; i < f->nattrs; i++) {
        enum ADIOS_DATATYPES atype;
        int  asize;
        void *adata;
        adios_get_attr_byid (f, i, &atype, &asize, &adata);
        printf("    %-9s  %s = %s\n", adios_type_to_string(atype), 
                f->attr_namelist[i], value_to_string(atype, adata, 0));
        free(adata);
    } /* attributes */

    adios_read_close (f);

    return 0;
}
Esempio n. 25
0
int main (int argc, char ** argv) 
{
    int         rank, size, i, j;
    MPI_Comm    comm = MPI_COMM_WORLD;
    enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
    ADIOS_SELECTION * sel;
    void * data = NULL;
    uint64_t start[2], count[2];

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

    adios_read_init_method (method, comm, "verbose=4");
    adios_logger_open ("log_read_C", rank);

    ADIOS_FILE * f = adios_read_open ("global_array_C.bp", method, comm, ADIOS_LOCKMODE_NONE, 0);
    if (f == NULL)
    {
        log_error ("%s\n", adios_errmsg());
        return -1;
    }

    ADIOS_VARINFO * v = adios_inq_var (f, "temperature");

    /* Using less readers to read the global array back, i.e., non-uniform */
    uint64_t slice_size = v->dims[0]/size;
    start[0] = slice_size * rank;
    if (rank == size-1) /* last rank may read more lines */
        slice_size = slice_size + v->dims[0]%size;
    count[0] = slice_size;

    start[1] = 0;
    count[1] = v->dims[1];
       

    data = malloc (slice_size * v->dims[1] * sizeof (double));
    if (data == NULL)
    {
        log_error (stderr, "malloc failed.\n");
        return -1;
    }

    /* Read a subset of the temperature array */
    sel = adios_selection_boundingbox (v->ndim, start, count);
    adios_schedule_read (f, sel, "temperature", 0, 1, data);
    adios_perform_reads (f, 1);

    for (i = 0; i < slice_size; i++) {
        log_test ("rank %d: [%lld,%d:%lld]", rank, start[0]+i, 0, slice_size);
        for (j = 0; j < v->dims[1]; j++)
            log_test (" %6.6g", * ((double *)data + i * v->dims[1] + j));
        log_test ("\n");
    }

    free (data);

    adios_read_close (f);
    MPI_Barrier (comm);
    adios_read_finalize_method (method);
    adios_logger_close();
    MPI_Finalize ();
    return 0;
}
Esempio n. 26
0
int worker(int argc, char* argv[]) {
    TAU_PROFILE_TIMER(timer, __func__, __FILE__, TAU_USER);
    TAU_PROFILE_START(timer);
    my_printf("%d of %d In worker B\n", myrank, commsize);
    static bool announced = false;

    /* validate input */
    validate_input(argc, argv);

    my_printf("Worker B will execute until it sees n iterations.\n", iterations);

    /* ADIOS: These declarations are required to match the generated
     *        gread_/gwrite_ functions.  (And those functions are
     *        generated by calling 'gpp.py adios_config.xml') ...
     *        EXCEPT THAT THE generation of Reader code is broken.
     *        So, we will write the reader code manually.
     */
    uint64_t  adios_groupsize;
    uint64_t  adios_totalsize;
    uint64_t  adios_handle;
    void * data = NULL;
    uint64_t start[2], count[2];
    int i, j, steps = 0;
    int NX = 10;
    int NY = 1;
    double t[NX];
    double p[NX];

    /* ADIOS: Can duplicate, split the world, whatever.
     *        This allows you to have P writers to N files.
     *        With no splits, everyone shares 1 file, but
     *        can write lock-free by using different areas.
     */
    MPI_Comm  adios_comm, adios_comm_b_to_c;
    adios_comm = MPI_COMM_WORLD;
    //MPI_Comm_dup(MPI_COMM_WORLD, &adios_comm);
    adios_comm_b_to_c = MPI_COMM_WORLD;
    //MPI_Comm_dup(MPI_COMM_WORLD, &adios_comm_b_to_c);

    enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_FLEXPATH;
    adios_read_init_method(method, adios_comm, "verbose=3");
    if (adios_errno != err_no_error) {
        fprintf (stderr, "rank %d: Error %d at init: %s\n", myrank, adios_errno, adios_errmsg());
        exit(4);
    }
    if (send_to_c) {
        adios_init("adios_config.xml", adios_comm);
    }

    /* ADIOS: Set up the adios communications and buffers, open the file.
    */
    ADIOS_FILE *fp; // file handler
    ADIOS_VARINFO *vi; // information about one variable 
    ADIOS_SELECTION * sel;
    char      adios_filename_a_to_b[256];
    char      adios_filename_b_to_c[256];
    enum ADIOS_LOCKMODE lock_mode = ADIOS_LOCKMODE_NONE;
    double timeout_sec = 1.0;
    sprintf(adios_filename_a_to_b, "adios_a_to_b.bp");
    sprintf(adios_filename_b_to_c, "adios_b_to_c.bp");
    my_printf ("rank %d: Worker B opening file: %s\n", myrank, adios_filename_a_to_b);
    fp = adios_read_open(adios_filename_a_to_b, method, adios_comm, lock_mode, timeout_sec);
    if (adios_errno == err_file_not_found) {
        fprintf (stderr, "rank %d: Stream not found after waiting %d seconds: %s\n",
        myrank, timeout_sec, adios_errmsg());
        exit(1);
    } else if (adios_errno == err_end_of_stream) {
        // stream has been gone before we tried to open
        fprintf (stderr, "rank %d: Stream terminated before open. %s\n", myrank, adios_errmsg());
        exit(2);
    } else if (fp == NULL) {
        // some other error happened
        fprintf (stderr, "rank %d: Error %d at opening: %s\n", myrank, adios_errno, adios_errmsg());
        exit(3);
    } else {
        my_printf("Found file %s\n", adios_filename_a_to_b);
        my_printf ("File info:\n");
        my_printf ("  current step:   %d\n", fp->current_step);
        my_printf ("  last step:      %d\n", fp->last_step);
        my_printf ("  # of variables: %d:\n", fp->nvars);

        vi = adios_inq_var(fp, "temperature");
        adios_inq_var_blockinfo(fp, vi);

        printf ("ndim = %d\n",  vi->ndim);
        printf ("nsteps = %d\n",  vi->nsteps);
        printf ("dims[%llu][%llu]\n",  vi->dims[0], vi->dims[1]);

        uint64_t slice_size = vi->dims[0]/commsize;
        if (myrank == commsize-1) {
            slice_size = slice_size + vi->dims[0]%commsize;
        }

        start[0] = myrank * slice_size;
        count[0] = slice_size;
        start[1] = 0;
        count[1] = vi->dims[1];

        data = malloc (slice_size * vi->dims[1] * 8);

        /* Processing loop over the steps (we are already in the first one) */
        while (adios_errno != err_end_of_stream && steps < iterations) {
            steps++; // steps start counting from 1

            TAU_PROFILE_TIMER(adios_recv_timer, "ADIOS recv", __FILE__, TAU_USER);
            TAU_PROFILE_START(adios_recv_timer);
            sel = adios_selection_boundingbox (vi->ndim, start, count);
            adios_schedule_read (fp, sel, "temperature", 0, 1, data);
            adios_perform_reads (fp, 1);

            if (myrank == 0)
                printf ("--------- B Step: %d --------------------------------\n",
                        fp->current_step);

#if 0
            printf("B rank=%d: [0:%lld,0:%lld] = [", myrank, vi->dims[0], vi->dims[1]);
            for (i = 0; i < slice_size; i++) {
                printf (" [");
                for (j = 0; j < vi->dims[1]; j++) {
                    printf ("%g ", *((double *)data + i * vi->dims[1] + j));
                }
                printf ("]");
            }
            printf (" ]\n\n");
#endif

            // advance to 1) next available step with 2) blocking wait
            adios_advance_step (fp, 0, timeout_sec);
            if (adios_errno == err_step_notready)
            {
                printf ("B rank %d: No new step arrived within the timeout. Quit. %s\n",
                        myrank, adios_errmsg());
                break; // quit while loop
            }
            TAU_PROFILE_STOP(adios_recv_timer);

            /* Do some exchanges with neighbors */
            //do_neighbor_exchange();
            /* "Compute" */
            compute(steps);

            for (i = 0; i < NX; i++) {
                t[i] = steps*100.0 + myrank*NX + i;
            }

            for (i = 0; i < NY; i++) {
                p[i] = steps*1000.0 + myrank*NY + i;
            }

            if (send_to_c) {
                TAU_PROFILE_TIMER(adios_send_timer, "ADIOS send", __FILE__, TAU_USER);
                TAU_PROFILE_START(adios_send_timer);
                /* ADIOS: write to the next application in the workflow */
                if (steps == 0) {
                    adios_open(&adios_handle, "b_to_c", adios_filename_b_to_c, "w", adios_comm_b_to_c);
                } else {
                    adios_open(&adios_handle, "b_to_c", adios_filename_b_to_c, "a", adios_comm_b_to_c);
                }
                /* ADIOS: Actually write the data out.
                *        Yes, this is the recommended method, and this way, changes in
                *        configuration with the .XML file will, even in the worst-case
                *        scenario, merely require running 'gpp.py adios_config.xml'
                *        and typing 'make'.
                */
                #include "gwrite_b_to_c.ch"
                /* ADIOS: Close out the file completely and finalize.
                *        If MPI is being used, this must happen before MPI_Finalize().
                */
                adios_close(adios_handle);
                TAU_PROFILE_STOP(adios_send_timer);
            #if 1
            if (!announced) {
                SOS_val foo;
                foo.i_val = NX;
                SOS_pack(example_pub, "NX", SOS_VAL_TYPE_INT, foo);
                SOS_announce(example_pub);
                SOS_publish(example_pub);
                announced = true;
            }
            #endif
            }
            MPI_Barrier(adios_comm_b_to_c);
        }
        MPI_Barrier(MPI_COMM_WORLD);
        adios_read_close(fp);
        /* ADIOS: Close out the file completely and finalize.
        *        If MPI is being used, this must happen before MPI_Finalize().
        */
        adios_read_finalize_method(method);
    }
    if (send_to_c) {
        adios_finalize(myrank);
    }

    free(data);
    //MPI_Comm_free(&adios_comm);
    //MPI_Comm_free(&adios_comm_b_to_c);

    TAU_PROFILE_STOP(timer);
    /* exit */
    return 0;
}
Esempio n. 27
0
int main (int argc, char ** argv) 
{
    int         rank, size, i, j;
    MPI_Comm    comm = MPI_COMM_WORLD;
    enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;

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

    adios_read_init_method (method, comm, "verbose=3");
    ADIOS_FILE * f = adios_read_open_file("adios_stat.bp", method, comm);
    if (f == NULL)
    {
        fprintf (stderr, "%s\n", adios_errmsg());
        return -1;
    }

    ADIOS_VARINFO * v = adios_inq_var (f, "temperature");
    if (v) {
        /* get statistics, for each individual time-step */ 
        adios_inq_var_stat (f, v, 1, 0);


        printf("Global MIN of temperature: %lf\n", * (double *) v->statistics->min);
        printf("Global MAX of temperature: %lf\n", * (double *) v->statistics->max);
        printf("Global AVG of temperature: %lf\n", * (double *) v->statistics->avg);
        printf("Global STD DEV of temperature: %lf\n", * (double *) v->statistics->std_dev);

        printf("\n");
        printf("---------------------------------------------------------------------------\n");
        if (v->statistics->steps) {
            printf("MIN\t\tMAX\t\tAVG\t\tSTD_DEV\t\tHISTOGRAM\n");
            for(i = 0; i < v->nsteps; i++)
            {
                if (v->statistics->steps->mins[i]) 
                    printf("%lf\t", * (double *) v->statistics->steps->mins[i]);
                else
                    printf("--\t\t");
                if (v->statistics->steps->maxs[i]) 
                    printf("%lf\t", * (double *) v->statistics->steps->maxs[i]);
                else
                    printf("--\t\t");
                if (v->statistics->steps->avgs[i]) 
                    printf("%lf\t", * (double *) v->statistics->steps->avgs[i]);
                else
                    printf("--\t\t");
                if (v->statistics->steps->std_devs[i]) 
                    printf("%lf\t", * (double *) v->statistics->steps->std_devs[i]);
                else
                    printf("--\t\t");
                if (v->statistics->histogram) {
                    for(j = 0; j <= v->statistics->histogram->num_breaks; j++) {
                        printf("%d ", v->statistics->histogram->frequencies[i][j]);
                    }
                    printf("\n");
                } else {
                    printf("--\t\t");
                }
                printf("\n");
            }	
        } else {
            printf ("Per step statistics is missing\n"); 
        }
        printf("---------------------------------------------------------------------------\n");
        printf("\n");

        if (v->statistics->histogram) {
            printf("Break points:\t\t\t");
            for(j = 0; j < v->statistics->histogram->num_breaks; j++)
                printf("%6.2lf\t", v->statistics->histogram->breaks[j]);

            printf("\n");

            printf("Frequencies:\t\t\t");
            for(j = 0; j <= v->statistics->histogram->num_breaks; j++)
                printf("%6d\t", v->statistics->histogram->gfrequencies[j]);
        }

        printf("\n\n");

#if 0 
        printf ("Auto covariance of MIN values of temperature over time: %lf\n", adios_stat_cov (v, v, "min", 0, 12, 0));
        printf ("Auto correlation of MAX values of temperature over time, with lag 2 units: %lf\n", adios_stat_cor (v, v, "max", 0, 8, 2));
        printf("\n\n");
#endif 

        adios_free_varinfo (v);

    } else {
        fprintf (stderr, "ERROR: Cannot inquire statistics of variable 'temperature': %s\n", adios_errmsg());
    }

    v = adios_inq_var (f, "complex");
    if (v) {
        adios_inq_var_stat (f, v, 1, 0);
        double *C = v->statistics->min;
        printf("Global Minimum of variable complex - Magnitude: %lf\n", C[0]);
        printf("Global Minimum of variable complex - Real part: %lf\n", C[1]);
        printf("Global Minimum of variable complex - Imaginary part: %lfi\n", C[2]);

        double ** Cmin;
        Cmin = (double **) v->statistics->steps->mins;

        printf("\nMagnitude\t\tReal\t\t\tImaginary\n");
        for (j = 0; j < v->nsteps; j++)
        {
            printf ("%lf\t\t%lf\t\t%lf\n", Cmin[j][0], Cmin[j][1], Cmin[j][2]);
        }
        printf("\n");
        adios_free_varinfo (v);

    } else {
        fprintf (stderr, "ERROR: Cannot inquire statistics of variable 'complex': %s\n", adios_errmsg());
    }

    adios_read_close (f);
    MPI_Barrier (comm);
    adios_read_finalize_method (method);
    MPI_Finalize ();
    return 0;
}
Esempio n. 28
0
int main (int argc, char ** argv)
{
    int         i, j, datasize;
    MPI_Comm    comm = MPI_COMM_WORLD;
    enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
    ADIOS_SELECTION * sel1;
    double * data = NULL;
    uint64_t start[2], count[2];

    MPI_Init (&argc, &argv);
#ifdef WITH_NCSU_TIMER
    timer_init();
#endif

    adios_read_init_method (method, comm, NULL);

    ADIOS_FILE * f = adios_read_open_file ("adios_global.bp", method, comm);
    ADIOS_VARINFO * varinfo = adios_inq_var (f, "temperature");
    if (varinfo)
    {
        int nranks;

        assert(varinfo->ndim == 2);

        nranks = varinfo->dims[0];
        assert(nranks % 4 == 0);
        assert(varinfo->dims[1] == 10);

        datasize = (nranks / 2) * varinfo->dims[1] * sizeof(double);
        data = malloc (datasize);

        start[0] = nranks / 4;
        start[1] = 2;
        count[0] = nranks / 2;
        count[1] = 6;

        sel1 = adios_selection_boundingbox (varinfo->ndim, start, count);

        adios_schedule_read (f, sel1, "temperature", 0, 1, data);
        adios_perform_reads (f, 1);

        printf("Subvolume at (%" PRIu64 ",%" PRIu64 ") of size (%" PRIu64 ",%" PRIu64 "):\n", start[0], start[1], count[0], count[1]);
        for (i = 0; i < count[0]; i++) {
            printf("[ ");
            for (j = 0; j < count[1]; j++) {
                printf("%.0lf ", data[i * count[1] + j]);
            }
            printf("]\n");
        }

        adios_selection_delete (sel1);
    }

    adios_free_varinfo (varinfo);
    adios_read_close (f);

    adios_read_finalize_method (ADIOS_READ_METHOD_BP);


#ifdef WITH_NCSU_TIMER
    printf("[TIMERS] ");
    timer_result_t *results = timer_get_results_sorted();
    for (i = 0; i < timer_get_num_timers(); i++) {
        printf("%s: %0.4lf ", results[i].name, results[i].time);
    }
    printf("\n");
    free(results);
#endif

#ifdef WITH_NCSU_TIMER
    timer_finalize();
#endif
    MPI_Finalize ();
    return 0;
}
int main(int argc, char ** argv)
{
    int rank, size, varid, numvars;
    int bins, step, mod;
    char *filename, *in_stream, *data_var_name;
    MPI_Comm comm = MPI_COMM_WORLD;
    enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_FLEXPATH;
    //enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
    ADIOS_SELECTION * global_range_select;
    double *data;
    uint64_t tstep, global_size, mysize, mystart, sz;

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

    /* Command line parsing */
    if (rank == 0 && argc < 4) {
      fprintf(stderr, "\nHistogram usage: <exec> input-stream-name num-bins" 
         " arr1 [arr2] [arr3] [...]\n"
         "\t where arr1, arr2, arr3 ... are the names of the arrays to be analyzed.\n");
      MPI_Abort(comm, -1);
    }
    MPI_Barrier(comm); 
    in_stream = argv[1];

    //Parse cmd line
    bins = atoi(argv[2]);
    numvars = argc - 3;
    const char *vars[numvars];
    for (varid=0; varid < numvars; varid++)
    {
      vars[varid] = argv[varid + 3];
    }

    /* Adios open and init */
    adios_read_init_method (method, comm, "verbose=1");
    ADIOS_FILE * f = adios_read_open (in_stream, method, comm, ADIOS_LOCKMODE_ALL, -1);
    step = 0; //not used now
    while (adios_errno != err_end_of_stream){
      //resource monitor

      /*loop over different arrays inside stream*/
      for (varid = 0; varid < numvars; varid++){         
#ifdef ENABLE_MONITOR
        //double t1 = wfgettimeofday();
        lib_mem_init();
        ind_timer_start(0, "whole timestep");
#endif
        //Init variables....
        global_size = 0; tstep = 0;
        mod = 0; mysize = 0; mystart = 0;
        adios_schedule_read (f, NULL, "ntimestep", 0, 1, &tstep);
        adios_perform_reads (f, 1);
        ADIOS_VARINFO * glob_info = adios_inq_var (f, vars[varid]);
        global_size = glob_info->dims[0];
        //printf("[DEBUG] global_size = %" PRIu64 " ntimestep = %" PRIu64 "\n", 
        //  global_size, tstep);

        //printf("[HIST%d] received data for timestep %" PRIu64 " with ndim: %d and globalsize:%"
        //    PRIu64 " \n", rank, tstep, ndim, global_size); 
        //sleep(800);
        //debug
        //Array slice computation
        mod = global_size % size;//size = MPI size
        if (mod == 0){
          mysize = global_size / size;
          mystart = mysize * rank;
        }
        else {
          mysize = global_size / (size);
          if (rank < mod){
            mysize++;
            mystart = mysize * rank;
          }
          else {
            mystart = (mod * (mysize + 1)) +
                      ((rank - mod) * mysize);
          }
        }

#ifdef ENABLE_MONITOR
        nohandler_mem(rank);
#endif

        //printf("[HISTO%d]: mysize = %" PRIu64" mystart = %" PRIu64 "\n", rank, mysize, mystart);
        //debug
        //if (step == 0) sleep(800);
        uint64_t starts[] = {mystart};
        uint64_t counts[] = {mysize};
        global_range_select = adios_selection_boundingbox (1, starts, counts);
        
        //Allocate space for arrays
        uint64_t msize = ((uint64_t) sizeof(double) * mysize);
        //printf("[DEBUG] mysize = %" PRIu64 " msize= %" PRIu64" \n", mysize, msize);
        //data = (double *) malloc(sizeof(double) * mysize);
        data = new double[mysize];
        if (data == NULL){
          //printf("DEBUG: malloc returned NULL, size was %d\n", msize);
        }
        else {
          if (rank == 0)
            printf("[HIST0] DEBUG: malloc successful, size was %d\n", mysize);
        }
        //memset (data, 0, sizeof(double) * mysize);

        //Read data
        adios_schedule_read (f,
                             global_range_select,
                             vars[varid],
                             0, 1, data);
        adios_perform_reads 

        (f, 1);
        
#ifdef ENABLE_MONITOR
        nohandler_mem(rank);
#endif

        //printf("PERFORM_READS success of variable: %s\n", vars[varid]); 
        /*
           Data check


        if (step == 4) {
          FILE *fp;
          char *log;
          asprintf(&log, "histo-input%d-%d.log", step, rank);
          fp = fopen(log, "w");
          fprintf(fp, "timestep: %" PRIu64 " mysize: %"PRIu64 "\n", 
              tstep, mysize);
          for (i=0; i<(int)mysize; i++){
            fprintf(fp, "%lf\n", data[i]);
          }
          fclose(fp);
          sleep(800);
        }
        */

         
        // find max and min
        sz = 0;
        sz = mysize; 
        double min = data[0];
        double max = data[0];
        for (uint64_t i = 1; i < sz; ++i)
        {
            if (data[i] > max) max = data[i];
            if (data[i] < min) min = data[i];
        }//local max, min found.
        //local data should just use shared mem.


        double g_min, g_max;

        // Find the global max/min
        MPI_Allreduce (&min, &g_min, 1, MPI_DOUBLE, MPI_MIN, comm);
        MPI_Allreduce (&max, &g_max, 1, MPI_DOUBLE, MPI_MAX, comm);

        //printf("[HIST%d] glob-min: %f, glob-max: %f\n", rank, g_min, g_max);
        
        nohandler_mem(rank);

        double width = (g_max - g_min)/bins;
        std::vector<uint64_t>   hist(bins);
        for (uint64_t i = 0; i < sz; ++i)//fill local bins
        {
            //printf("[HISTO%d] local filling adding index %" PRIu64 "\n", rank, i);
            int idx = int((data[i] - g_min)/width);//discover index
            if (idx == bins)        // we hit the max
                --idx;
            //printf("[%d]: %f -> %d\n", rank, data[i], idx);
            ++hist[idx];
        }

        delete[] data;
        // Global reduce histograms
        std::vector<uint64_t> g_hist(bins);
        MPI_Reduce(&hist[0], &g_hist[0], bins, MPI_UINT64_T, MPI_SUM, 0, comm);
        
        //debug
        //printf("[Completed histogram routine]\n");

        if (rank == 0) //print histogram to file
        {
          FILE *fp;
          const char *log = "histograms.log";
          fp = fopen(log, "a");
          fprintf(fp, "Histogram for %s, timestep %" PRIu64"\n", vars[varid], tstep);
          for (int i = 0; i < bins; ++i)
            fprintf(fp, "  %f-%f: %" PRIu64 "\n", g_min + i*width, g_min + (i+1)*width, g_hist[i]);
          fclose (fp);
        }

#ifdef ENABLE_MONITOR
        nohandler_mem(rank);
#endif

        if (rank == 0) //print histogram to terminal
        {
          printf("Histogram for %s, timestep %" PRIu64"\n", vars[varid], tstep);
          for (int i = 0; i < bins; ++i)
            printf("  %f-%f: %" PRIu64 "\n", 
              g_min + i*width, g_min + (i+1)*width, g_hist[i]);
        }
        
        //resource monitor
#ifdef ENABLE_MONITOR
        //double t2 = wfgettimeofday();
        ind_timer_end(0);
        char monitor_title[40];
        sprintf(monitor_title, "histogram-%s", vars[varid]);
        monitor_out (rank, size, tstep, msize, t1, t2, comm, monitor_title);
#endif
      }
      //end of read + analysis for 3 variables


      
      adios_release_step(f);
      //delete[] data;
      if (rank == 0) printf("[HIST%d] read and wrote data for timestep %" PRIu64 "\n", rank, tstep);

      step++;
      adios_advance_step(f, 0, -1);
      /*
      if (step == 6){ 
        double t1 = wfgettimeofday();
        FILE *tfp;
        tfp = fopen("time.log", "a");
        fprintf(tfp, "rank %d histogram end time: %f\n", rank, t1);
        fclose(tfp);
      }
      */ 
    }//end of adios stream while loop
    if (rank == 0) printf("[HIST%d] out of read loop\n", rank);
    /* performance measurement */
    /*
    if (rank == 0){ 
      double t3 = wfgettimeofday();
      FILE *tfp;
      tfp = fopen("time.log", "a");
      fprintf(tfp, "master histogram end time: %f\n", t3);
      fclose(tfp);
    }
    */
#ifdef ENABLE_MONITOR
    outer_timer_end(rank, "histogram");
#endif
    adios_read_close(f);
    adios_read_finalize_method(method);
    MPI_Finalize();
    return 0;
}
Esempio n. 30
0
int main (int argc, char ** argv) 
{
    char        filename [256];
    int         rank, size, i, j, k, token;
    MPI_Comm    comm = MPI_COMM_WORLD;
    MPI_Status  status;
    enum ADIOS_READ_METHOD method = ADIOS_READ_METHOD_BP;
    ADIOS_SELECTION * sel;
    void * data = NULL;
    uint64_t start[3], count[3], step = 0;

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

    adios_read_init_method (method, comm, "verbose=3");

    /* adios_read_open_file() allows for seeing all timesteps in the file */
    ADIOS_FILE * f = adios_read_open_file ("adios_globaltime.bp", method, comm);
    if (f == NULL)
    {
        printf ("%s\n", adios_errmsg());
        return -1;
    }

    ADIOS_VARINFO * v = adios_inq_var (f, "temperature");

    // read in two timesteps
    data = malloc (2 * v->dims[0] * v->dims[1] * sizeof (double));
    if (data == NULL)
    {
        fprintf (stderr, "malloc failed.\n");
        return -1;
    }

    // read in timestep 'rank' (up to 12)
    step = rank % 13;

    start[0] = 0;
    count[0] = v->dims[0];

    start[1] = 0;
    count[1] = v->dims[1];

    /* Read a subset of the temperature array */
    sel = adios_selection_boundingbox (v->ndim, start, count);
    /*    2 steps from 'step' */
    adios_schedule_read (f, sel, "temperature", step, 2, data);
    adios_perform_reads (f, 1);

    if (rank == 0) 
        printf ("Array size of temperature [0:%lld,0:%lld]\n", v->dims[0], v->dims[1]);   

    if (rank > 0) {
        MPI_Recv (&token, 1, MPI_INT, rank-1, 0, comm, &status);
    }

    printf("------------------------------------------------\n", rank);
    printf("rank=%d: \n", rank);
    for (i = 0; i < 2; i++) {
        printf ("step %lld = [\n", step+i);   
        for (j = 0; j < v->dims[0]; j++) {
            printf (" [");
            for (k = 0; k < v->dims[1]; k++) {
                printf ("%g ", ((double *)data) [ i * v->dims[0] * v->dims[1] + j * v->dims[1] + k]);
            }
            printf ("]\n");
        }
        printf ("]\n");
    }
    printf ("\n");

    if (rank < size-1) {
        MPI_Send (&token, 1, MPI_INT, rank+1, 0, comm);
    }

    free (data);
    adios_free_varinfo (v);

    adios_read_close (f);
    MPI_Barrier (comm);
    adios_read_finalize_method (method);
    MPI_Finalize ();
    return 0;
}