adios_datablock * adios_transform_alacrity_pg_reqgroup_completed(adios_transform_read_request *reqgroup,
adios_transform_pg_read_request *completed_pg_reqgroup)
{
//uint64_t raw_size = (uint64_t)completed_pg_reqgroup->raw_var_length;
void* raw_buff = completed_pg_reqgroup->subreqs->data;
uint64_t orig_size = adios_get_type_size(reqgroup->transinfo->orig_type, "");
int d = 0;
for(d = 0; d < reqgroup->transinfo->orig_ndim; d++)
orig_size *= (uint64_t)(completed_pg_reqgroup->orig_varblock->count[d]);
void* orig_buff = malloc(orig_size);
ALPartitionData output_partition;
uint64_t numElements = 0;
// Decompress into output_partition from compressed_buf
memstream_t ms = memstreamInitReturn (raw_buff);
// Deserialize the ALPartitionData from memstream
ALDeserializePartitionData (&output_partition, &ms);
// Decode ALPartitionData into decompresed buffer
int rtn = ALDecode (&output_partition, orig_buff, &numElements);
if (ALErrorNone != rtn)
return NULL;
ALPartitionDataDestroy(&output_partition);
return adios_datablock_new(reqgroup->transinfo->orig_type,
completed_pg_reqgroup->timestep,
completed_pg_reqgroup->pg_bounds_sel,
orig_buff);
}
// Encodes the data from infile into the ALFileStore outfile, closing both afterward
int decodeCommandDecode(ALStore *infile, FILE *outfile) {
ALPartitionData partdata; // Output buffer
void *outbuf;
uint64_t outbufCount;
uint64_t totalElemsWritten = 0;
ALError err;
size_t writelen;
while (!ALStoreEOF(infile)) {
err = ALStoreReadPartition(infile, &partdata);
if (err != ALErrorNone) {
fprintf(stderr, "Error reading the next partition from the input files\n");
return 1;
}
outbuf = malloc(ALGetDecodeLength(&partdata));
if (!outbuf) {
fprintf(stderr, "Error allocating %llu btyes of temporary memory for decoding\n", ALGetDecodeLength(&partdata));
return 1;
}
err = ALDecode(&partdata, outbuf, &outbufCount);
if (err != ALErrorNone) {
fprintf(stderr, "Error decoding partition from input files\n");
return 1;
}
writelen = fwrite(outbuf, partdata.metadata.elementSize, outbufCount, outfile);
if (writelen != outbufCount) {
fprintf(stderr, "Error writing decoded elements to file (wrote %llu, expected to write %llu)\n",
(uint64_t)writelen, (uint64_t)partdata.metadata.elementSize);
return 1;
}
totalElemsWritten += outbufCount;
free(outbuf);
ALPartitionDataDestroy(&partdata);
}
// Cleanup
fclose(outfile);
printf("Decoding complete, wrote out %llu elements\n", totalElemsWritten);
dbprintf("Closing ALACRITY input files...\n");
if (ALStoreClose(infile) != ALErrorNone) {
fprintf(stderr, "Error closing ALACRITY input file, aborting (output should still be correct)\n");
return 1;
}
return 0;
}
// Encodes the data from infile into the ALFileStore outfile, closing both afterward
int encodeCommandEncode(FILE *infile, uint64_t infile_len, ALStore *outfile) {
const int datatypeLen = ALDatatypeGetSize(OPTIONS.datatype);
// Allocate the input buffer
uint64_t buflen;
if (infile_len > (OPTIONS.part_size_in_elem * datatypeLen))
buflen = (OPTIONS.part_size_in_elem * datatypeLen);
else
buflen = infile_len;
void *inbuf = malloc(buflen); // Input buffer
// Prepare the output buffer (encoder)
ALIndexForm index_form = OPTIONS.index_form;
if (index_form >= ALCompressedInvertedIndex) // all other compressed index based on inverted index
index_form = ALInvertedIndex;
ALEncoderConfig econfig;
ALEncoderConfigure(&econfig, OPTIONS.significant_bits, OPTIONS.datatype, index_form);
ALPartitionData partdata; // Output buffer
size_t bytesread;
int i = 0;
double s ;
encode_time = 0;
compress_time = 0;
write_time = 0;
total_time = 0;
double ss = dclock();
while (!feof(infile) && !ferror(infile) && (bytesread = fread(inbuf, 1, buflen, infile)) != 0) {
i++;
dbprintf("Encoding partition %d with size %llu...\n", i, bytesread);
s = dclock();
ALEncode(&econfig, inbuf, bytesread / datatypeLen, &partdata);
encode_time = encode_time + (dclock() - s);
s = dclock();
if (OPTIONS.index_form >= ALCompressedInvertedIndex) // all other compressed index based on inverted index
ALConvertIndexForm(&partdata.metadata, &partdata.index, OPTIONS.index_form);
compress_time = compress_time + (dclock() - s);
s = dclock();
if (ALStoreWritePartition(outfile, &partdata) != ALErrorNone) {
fprintf(stderr, "Error appending ALACRITY partition to file, aborting\n");
abort();
return 1;
}
write_time = write_time + (dclock() - s);
ALPartitionDataDestroy(&partdata); // TODO: make this automatic when encoding over an existing partition data
dbprintf("Partition %d done!\n", i);
}
total_time = dclock() - ss;
printf("[read: %9.3lf] [encode: %9.3lf] [compress: %9.3lf] [write: %9.3lf] [total: %9.3lf]\n", total_time - (encode_time + compress_time + write_time ), encode_time, compress_time, write_time, total_time);
if (ferror(infile)) {
fprintf(stderr, "Error reading from input file, aborting\n");
return 1;
}
// Cleanup
free(inbuf);
fclose(infile);
printf("Encoding complete, %llu bytes of input data successfully encoded into %llu partitions\n", infile_len, outfile->cur_partition);
dbprintf("Closing ALACRITY output file...\n");
if (ALStoreClose(outfile) != ALErrorNone) {
fprintf(stderr, "Error closing ALACRITY output file, aborting\n");
return 1;
}
return 0;
}
