/*writes properties of the current run related to implementation and command line choices*/
herr_t /*hdf5 error*/
append_meta_properties(hdf5block_t *h5block,/*hdf5 file ids*/
double *seed,/*random number seed*/
size_t *BurnInSampleSize, /*tuning iterations*/
char *h5file, /*name of hdf5 file containing the experimental data and prior set-up*/
char *lib_base)/*basename of the library file @code .so@ file*/{
herr_t status;
int omp_n,omp_np,i;
status&=H5LTset_attribute_double(h5block->file_id, "LogParameters", "seed", seed, 1);
status&=H5LTset_attribute_ulong(h5block->file_id, "LogParameters", "BurnIn", BurnInSampleSize, 1);
status&=H5LTset_attribute_string(h5block->file_id, "LogParameters", "DataFrom", h5file);
status&=H5LTmake_dataset_string(h5block->file_id,"Model",lib_base);
// here we make a short test to see what the automatic choice of the
// number of threads turns out to be.
#pragma omp parallel private(omp_n,omp_np) reduction(+:i)
{
i=1;
omp_n=omp_get_num_threads();
omp_np=omp_get_num_procs();
}
if (i!=omp_n){
fprintf(stderr,"[append_meta_properties] warning: finding out number of threads possibly failed reduction of (n×1: %i) != get_num_threads():%i.\n",i,omp_n);
} else {
h5block->size[0]=1;
h5block->size[1]=1;
status&=H5LTmake_dataset_int(h5block->file_id,"OMP_NUM_THREADS",1,h5block->size,&omp_n);
status&=H5LTmake_dataset_int(h5block->file_id,"OMP_NUM_PROCS",1,h5block->size,&omp_np);
}
return status;
}
static herr_t make_attributes( hid_t loc_id, const char* obj_name )
{
int rank_out;
hsize_t *dims_out = 0;
H5T_class_t type_class;
size_t type_size;
int i;
char attr_str_in[] = {"My attribute"};
char attr_str_out[20];
char attr_char_in[5] = {1,2,3,4,5};
char attr_char_out[5];
short attr_short_in[5] = {1,2,3,4,5};
short attr_short_out[5];
int attr_int_in[5] = {1,2,3,4,5};
int attr_int_out[5];
long attr_long_in[5] = {1,2,3,4,5};
long attr_long_out[5];
float attr_float_in[5] = {1,2,3,4,5};
float attr_float_out[5];
double attr_double_in[5] = {1,2,3,4,5};
double attr_double_out[5];
unsigned char attr_uchar_in[5] = {1,2,3,4,5};
unsigned char attr_uchar_out[5];
unsigned short attr_ushort_in[5] = {1,2,3,4,5};
unsigned short attr_ushort_out[5];
unsigned int attr_uint_in[5] = {1,2,3,4,5};
unsigned int attr_uint_out[5];
unsigned long attr_ulong_in[5] = {1,2,3,4,5};
unsigned long attr_ulong_out[5];
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_string");
/* Set the attribute */
if ( H5LTset_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_in ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_string");
/* Get the attribute */
if ( H5LTget_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_out ) < 0 )
return -1;
if ( strcmp( attr_str_in, attr_str_out ) != 0 )
{
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_char");
/* Set the attribute */
if ( H5LTset_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_char");
/* Get the attribute */
if ( H5LTget_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR2_NAME, H5T_NATIVE_CHAR, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_short");
/* Set the attribute */
if ( H5LTset_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_short");
/* Get the attribute */
if ( H5LTget_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR3_NAME, H5T_NATIVE_SHORT, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_int");
/* Set the attribute */
if ( H5LTset_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_int");
/* Get the attribute */
if ( H5LTget_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR4_NAME, H5T_NATIVE_INT, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_long");
/* Set the attribute */
if ( H5LTset_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_long");
/* Get the attribute */
if ( H5LTget_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR5_NAME, H5T_NATIVE_LONG, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uchar");
/* Set the attribute */
if ( H5LTset_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uchar");
/* Get the attribute */
if ( H5LTget_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR6_NAME, H5T_NATIVE_UCHAR, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ushort");
/* Set the attribute */
if ( H5LTset_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ushort");
/* Get the attribute */
if ( H5LTget_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR7_NAME, H5T_NATIVE_USHORT, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uint");
/* Set the attribute */
if ( H5LTset_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uint");
/* Get the attribute */
if ( H5LTget_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR8_NAME, H5T_NATIVE_UINT, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ulong test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ulong");
/* Set the attribute */
if ( H5LTset_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ulong");
/* Get the attribute */
if ( H5LTget_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR9_NAME, H5T_NATIVE_ULONG, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_float");
/* Set the attribute */
if ( H5LTset_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_float");
/* Get the attribute */
if ( H5LTget_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR10_NAME, H5T_NATIVE_FLOAT, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_double");
/* Set the attribute */
if ( H5LTset_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_double");
/* Get the attribute */
if ( H5LTget_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR11_NAME, H5T_NATIVE_DOUBLE, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ndims test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ndims");
if ( H5LTget_attribute_ndims( loc_id, obj_name, ATTR2_NAME, &rank_out ) < 0 )
return -1;
if ( rank_out != 1 ) {
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_info test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_info");
dims_out = (hsize_t*) malloc( sizeof(hsize_t) * rank_out );
if ( H5LTget_attribute_info( loc_id, obj_name, ATTR2_NAME, dims_out, &type_class,
&type_size) < 0 )
return -1;
for (i = 0; i < rank_out; i++)
{
if ( dims_out[i] != 5 ) {
return -1;
}
}
if ( type_class != H5T_INTEGER ) {
return -1;
}
if ( dims_out )
free( dims_out );
PASSED();
return 0;
}
/*main mcmc loop, records sampled values, performs no tuning of the step size.*/
int /*always returns success*/
mcmc_foreach(int rank, /*MPI rank*/
int R, /*MPI Comm size*/
size_t SampleSize, /*number of iterations of MCMC*/
ode_model_parameters *omp, /*ODE problem cpecification and pre-allocated space*/
mcmc_kernel *kernel, /* MCMC kernel sturct, holds MCMC-algorithm's parameters*/
hdf5block_t *h5block, /*defines the hdf5 file to write into, holds ids and sizes*/
void *buffer, /* for MPI communication, similar to kernel*/
main_options *option)/*options from defaults, files and command line*/{
clock_t ct=clock();
gsl_matrix *log_para_chunk;
gsl_vector *log_post_chunk;
int D=get_number_of_MCMC_variables(omp);
log_para_chunk=gsl_matrix_alloc(CHUNK,D);
log_post_chunk=gsl_vector_alloc(CHUNK);
gsl_vector_view current;
gsl_vector_view x_state;
int swaps = 0; // swap success counter
int acc=no; // acceptance flag
int acc_c=0; // acceptance counter
double acc_rate=0.0;
size_t it;
int master=no;
int DEST;
double beta=mcmc_get_beta(kernel);
herr_t status;
int resume_EC;
int last_chunk=no, not_written_yet=yes;
for (it = 0; it < SampleSize; it++) {
mcmc_sample(kernel, &acc);
last_chunk=SampleSize-it<CHUNK;
if (acc && last_chunk && not_written_yet){
resume_EC=write_resume_state(option->resume_file, rank, R, kernel);
if (resume_EC==EXIT_SUCCESS){
not_written_yet=no;
}
}
acc_c += acc;
master=(it%2==rank%2);
if (master){
DEST=(rank+1)%R; // this process is the master process for swap decisions
} else {
DEST=(R+rank-1)%R; // this process has to accept swap decisions from DEST
}
//their_beta=BETA(DEST,R); // the other proc's
if (R>1){
mcmc_exchange_information(kernel,DEST,buffer);
swaps+=mcmc_swap_chains(kernel,master,rank,DEST,buffer);
}
/* save sampled point for writing */
current=gsl_matrix_row(log_para_chunk,it%CHUNK);
x_state=gsl_vector_view_array(kernel->x,D);
gsl_vector_memcpy(&(current.vector),&(x_state.vector));
gsl_vector_set(log_post_chunk,it%CHUNK,kernel->fx[0]);
/* print sample log and statistics every 100 samples */
if ( ((it + 1) % CHUNK) == 0 ) {
acc_rate = ((double) acc_c) / ((double) CHUNK);
fprintf(stdout, "# [rank % 2i/% 2i; β=%5f; %3li%% done] (it %5li)\tacc. rate: %3.2f;\t%3i %% swap success\t",rank,R,beta,(100*it)/SampleSize,it,acc_rate,swaps);
mcmc_print_stats(kernel, stdout);
acc_c = 0;
// print chunk to hdf5 file
status=h5write_current_chunk(h5block,log_para_chunk,log_post_chunk);
h5block->offset[0]=it+1;
swaps=0;
}
}
assert(status==0);
// write remaining data to the output hdf5 file
int Rest=SampleSize % CHUNK;
printf("[main] last iteration done %i points remain to write.\n",Rest);
if (Rest > 0){
h5block->chunk_size[0]=Rest;
h5block->chunk_size[1]=D;
h5block->para_chunk_id=H5Screate_simple(2, h5block->chunk_size, NULL);
h5block->chunk_size[0]=Rest;
h5block->chunk_size[1]=1;
h5block->post_chunk_id=H5Screate_simple(2, h5block->chunk_size, NULL);
printf("[main] writing the remaining %i sampled parametrisations to file.\n",Rest);
h5block->block[0]=Rest;
h5block->block[1]=D;
display_chunk_properties(h5block);
status = H5Sselect_hyperslab(h5block->para_dataspace_id, H5S_SELECT_SET, h5block->offset, h5block->stride, h5block->count, h5block->block);
H5Dwrite(h5block->parameter_set_id, H5T_NATIVE_DOUBLE, h5block->para_chunk_id, h5block->para_dataspace_id, H5P_DEFAULT, log_para_chunk->data);
h5block->block[1]=1;
printf("[main] writing their %i log-posterior values to file.\n",Rest);
display_chunk_properties(h5block);
status &= H5Sselect_hyperslab(h5block->post_dataspace_id, H5S_SELECT_SET, h5block->offset, h5block->stride, h5block->count, h5block->block);
H5Dwrite(h5block->posterior_set_id, H5T_NATIVE_DOUBLE, h5block->post_chunk_id, h5block->post_dataspace_id, H5P_DEFAULT, log_post_chunk->data);
assert(status>=0);
}
// annotate written sample with all necessary information
//printf("[main] writing some annotation about the sampled points as hdf5 attributes.\n");
status&=H5LTset_attribute_int(h5block->file_id, "LogParameters", "MPI_RANK", &rank, 1);
status&=H5LTset_attribute_ulong(h5block->file_id, "LogParameters", "SampleSize", &SampleSize, 1);
status&=H5LTset_attribute_double(h5block->file_id, "LogParameters", "InverseTemperature_Beta", &beta, 1);
ct=clock()-ct;
double sampling_time=((double) ct)/((double) CLOCKS_PER_SEC);
int ts=round(sampling_time);
int hms[3]; // hours, minutes, seconds
hms[0]=ts/3600;
hms[1]=(ts%3600)/60;
hms[2]=(ts%60);
printf("# computation time spend sampling: %i:%i:%i\n",hms[0],hms[1],hms[2]);
h5block->size[0]=1;
status&=H5LTmake_dataset_double (h5block->file_id, "SamplingTime_s", 1, h5block->size, &sampling_time);
h5block->size[0]=3;
status&=H5LTmake_dataset_int(h5block->file_id, "SamplingTime_hms", 1, h5block->size, hms);
if(status){
printf("[rank %i] statistics written to file.\n",rank);
}
return EXIT_SUCCESS;
}
