/** Prepare the write operation:
* Define ADIOS variable, increase params.adiosGroupSize and write attribute (if attrName is non-empty)
*
* Must be called before executing the functor
*/
void prepare(ThreadParams& params, T_Attribute attribute = T_Attribute())
{
typedef traits::PICToAdios<T_Scalar> AdiosSkalarType;
typedef pmacc::math::UInt64<simDim> Dimensions;
log<picLog::INPUT_OUTPUT> ("ADIOS: prepare write %1%D scalars: %2%") % simDim % name;
params.adiosGroupSize += sizeof(T_Scalar);
if(!attrName.empty())
params.adiosGroupSize += sizeof(T_Attribute);
// Size over all processes
Dimensions globalDomainSize = Dimensions::create(1);
// Offset for this process
Dimensions localDomainOffset = Dimensions::create(0);
for (uint32_t d = 0; d < simDim; ++d)
{
globalDomainSize[d] = Environment<simDim>::get().GridController().getGpuNodes()[d];
localDomainOffset[d] = Environment<simDim>::get().GridController().getPosition()[d];
}
std::string datasetName = params.adiosBasePath + name;
varId = defineAdiosVar<simDim>(
params.adiosGroupHandle,
datasetName.c_str(),
nullptr,
AdiosSkalarType().type,
Dimensions::create(1),
globalDomainSize,
localDomainOffset,
true,
params.adiosCompression);
if(!attrName.empty())
{
typedef traits::PICToAdios<T_Attribute> AdiosAttrType;
log<picLog::INPUT_OUTPUT> ("ADIOS: write attribute %1% of %2%D scalars: %3%") % attrName % simDim % name;
ADIOS_CMD( adios_define_attribute_byvalue(params.adiosGroupHandle,
attrName.c_str(), datasetName.c_str(),
AdiosAttrType().type, 1, (void*)&attribute) );
}
}
/**
* Define attributes in the bp file
*/
SEXP R_define_attr(SEXP R_group,
SEXP R_attrname,
SEXP R_nelems,
SEXP R_values)
{
int64_t m_adios_group = (int64_t)(REAL(R_group)[0]);
const char *attrname = CHARPT(R_attrname, 0);
int nelems = asInteger(R_nelems);
char **values;
values = malloc(nelems);
int i;
for(i = 0; i < nelems; i++)
values[i] = (char*)CHAR(STRING_ELT(R_values,i));
adios_define_attribute_byvalue(m_adios_group,
attrname, "",
adios_string_array,
nelems,
values);
return R_NilValue;
}
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;
}