/** 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; }