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Add support for H5 format in output (#14)
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This commit adds the option to use h5 as output format. Note that
arbitrary precision is not supported by this (optional) output.
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@jbreue16
jbreue16 committed Nov 25, 2024
1 parent 967dc40 commit 25ef992
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Showing 2 changed files with 186 additions and 12 deletions.
11 changes: 10 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -68,4 +68,13 @@ Suppose your model is contained in the HDF5 file `model.h5`, then you can comput
```
casema-cli.exe model.h5 -o chromatogram.csv -e 1e-100 -p 250 -P 20 -t 4
```
where no extrapolation method is used and, hence, the convergence detection tolerances are set to 0. This command also requests the usage of 250 decimal digits precision arithmetics (but only 20 digits of them are written to file), parallelization using 4 threads, and the total error to be less than 10^(-100). Extrapolation is enabled by adding `-x MET` to the command line, where `MET` is one of `ide`, `ads`, `wem`, `wrm`, `iad`, `lum`, `ltm`, `ibt`, `btm`, `nam`, `rem`, or `sgr`. The results are written to the file `chromatogram.csv`.
where no extrapolation method is used and, hence, the convergence detection tolerances are set to 0.
This command also requests the usage of 250 decimal digits precision arithmetics (but only 20 digits of them are written to file), parallelization using 4 threads, and the total error to be less than 10^(-100).
Extrapolation is enabled by adding `-x MET` to the command line, where `MET` is one of `ide`, `ads`, `wem`, `wrm`, `iad`, `lum`, `ltm`, `ibt`, `btm`, `nam`, `rem`, or `sgr`.
The results are written to the file `chromatogram.csv`.

Alternatively, you can choose to write the output to the H5 input file, following the CADET file format.
Note, however, that in this mode, the output precision is constrained by the H5 format, which does not support arbitrary precision, and is instead limited by the numerical limits of the C++ double type.
```
casema-cli.exe model.h5 -e 1e-100 -p 250 -P 20 -t 4
```
187 changes: 176 additions & 11 deletions src/casema-cli.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -93,11 +93,153 @@ class ProgressBarUpdater
int _prevPhase;
};

#ifdef ENABLE_HDF5
void writeMetaAndResultToH5(const ProgramOptions& opts, const casema::model::ModelSystem* sys, const std::vector<mpfr::mpreal>& solutionTimes, const casema::util::SlicedVector<mpfr::mpreal>& output, const double time_sim, const int timeOffset)
{
casema::io::IFileWriter* writer = casema::io::createWriter("h5");

bool split_ports = true; // from CADET file format
bool single_as_multi_port = false; // from CADET file format

if (opts.outFile.empty()) // write to input file
{
casema::io::IFileReader* reader = casema::io::createReader("h5");
reader->openFile(opts.inFile, "r");
reader->pushGroup("input");
reader->pushGroup("return");
if (reader->exists("SINGLE_AS_MULTI_PORT"))
single_as_multi_port = reader->getBool("SINGLE_AS_MULTI_PORT");

reader->closeFile();
writer->openFile(opts.inFile, "rw");
}
else if (opts.outFile == opts.inFile)
{
casema::io::IFileReader* reader = casema::io::createReader("h5");
reader->openFile(opts.outFile, "r");
reader->pushGroup("input");
reader->pushGroup("return");
if (reader->exists("SINGLE_AS_MULTI_PORT"))
single_as_multi_port = reader->getBool("SINGLE_AS_MULTI_PORT");

reader->closeFile();
writer->openFile(opts.outFile, "rw");
}
else // create output file
writer->openFile(opts.outFile, "co");

// Write meta data
writer->deleteGroup("meta");
writer->pushGroup("meta");
writer->writeString("CASEMA_VERSION", casema::getVersion());
writer->writeString("CASEMA_BRANCH", casema::getBranchRefspec());
writer->writeString("CASEMA_COMMIT", casema::getCommitHash());
writer->writeInt("FILE_FORMAT", casema::getFileFormat());
writer->writeDouble("TIME_SIM", time_sim);
{
std::ostringstream oss;
oss << opts.errorTrunc + opts.errorCons;
writer->writeString("ERROR", oss.str());
}
writer->popGroup();

// Write program options
writer->deleteGroup("program_options");
writer->pushGroup("program_options");
writer->writeBool("KAHAN_SUMMATION", opts.kahan);
writer->writeBool("IGNORE_CSTR", opts.ignoreCSTR);
#ifdef ENABLE_BESSEL_TRUNCATION
writer->writeBool("BESSEL_FUNCTION_TRUNCATION", true);
#else
writer->writeBool("BESSEL_FUNCTION_TRUNCATION", false);
#endif
{
std::ostringstream oss;
oss << mpfr::digits2bits(opts.precision);
writer->writeString("PRECISION", oss.str());
oss.str("");
//writer->writeDouble("OUTPUT_PRECISION", std::numeric_limits<double>::digits10 + 1);

writer->writeBool("EXTRAPOLATION", false);
writer->writeInt("MAX_LAPLACE_SUMMANDS", opts.laplaceSummands);
writer->writeInt("MAX_HANKEL_SUMMANDS", opts.hankelSummands);
oss << opts.abscissa;
writer->writeString("ABSCISSA", oss.str());
oss.str("");
oss << opts.errorCons;
writer->writeString("CONSISTENCY_ERROR", oss.str());
oss.str("");
oss << opts.errorTrunc;
writer->writeString("TRUNCATION_ERROR", oss.str());
oss.str("");
oss << opts.errorTrunc + opts.errorCons;
writer->writeString("ERROR", oss.str());
oss.str("");
oss << opts.error;
writer->writeString("REQUESTED_ERROR", oss.str());
oss.str("");
oss << opts.errorWeight;
writer->writeString("ERROR_WEIGHT", oss.str());
}
writer->popGroup();

writer->deleteGroup("output");
writer->pushGroup("output");

writer->pushGroup("solution");

const int timePoints = solutionTimes.size() - timeOffset;
std::vector<double> solutionBuffer(timePoints);

const int numUnits = sys->numModels();
const int numOutlets = sys->numOutlets();
int numWrittenOutlets = 0;

for (int i = 0; i < timePoints; i++)
solutionBuffer[i] = static_cast<double>(solutionTimes[i + timeOffset]);

void writeMeta(std::ostream& os, const casema::model::ModelSystem& model, const ProgramOptions& opts)
writer->writeVectorDouble("SOLUTION_TIMES", timePoints, &solutionBuffer[0], 1, timePoints);

std::ostringstream oss;

for (int j = 0; j < numUnits; ++j)
{
oss << std::setw(3) << std::setfill('0') << j;
writer->pushGroup("unit_" + oss.str());
oss.str("");

const int nPorts = std::max(1, sys->unitOperation(j)->numOutletPorts());

// always split ports
for (int k = 0; k < nPorts; ++k)
{
for (int i = 0; i < timePoints; i++)
solutionBuffer[i] = static_cast<double>(output(numWrittenOutlets, i));

oss << std::setw(3) << std::setfill('0') << k;
const std::string outName = (single_as_multi_port || nPorts > 1) ? "SOLUTION_OUTLET_PORT_" + oss.str() : "SOLUTION_OUTLET";

writer->writeVectorDouble(outName, timePoints, &solutionBuffer[0], 1, timePoints);
oss.str("");

numWrittenOutlets++;
}
writer->popGroup();
}

writer->closeFile();
}
#endif

void writeMeta(std::ostream& os, const casema::model::ModelSystem& model, const ProgramOptions& opts, const double simTime)
{
os << "# Version: " << casema::getVersion() << "\n";
os << "# Commit: " << casema::getCommitHash() << "\n";
os << "# CASEMA Version: " << casema::getVersion() << "\n";
os << "# CASEMA Branch: " << casema::getBranchRefspec() << "\n";
os << "# CASEMA Commit: " << casema::getCommitHash() << "\n";
os << "# CASEMA File Format: " << casema::getFileFormat() << "\n";
if(simTime > 0.0)
os << "# Compute time: " << simTime << "\n";

if (opts.kahan)
os << "# Kahan summation: On\n";
else
Expand Down Expand Up @@ -434,23 +576,46 @@ int main(int argc, char** argv)
std::cout << "[DONE]" << std::endl;
}

writeMeta(std::cout, *sys, opts);
writeMeta(std::cout, *sys, opts, -1.0);

std::cout << "Starting Laplace inversion" << std::endl;

const auto start = std::chrono::high_resolution_clock::now();

const casema::util::SlicedVector<mpfr::mpreal> output = invert(*sys, maxTime, st.solutionTimes, timeOffset, opts);

const double time_sim = std::chrono::duration_cast<std::chrono::duration<double>>(std::chrono::high_resolution_clock::now() - start).count();

std::cout << "Writing output" << std::endl;
if (opts.outFile.empty())

#ifdef ENABLE_HDF5
// Check if input file is h5 file and if so, write to that. Otherwise, print to console
bool inIsH5 = false;
const std::size_t dotPos = opts.inFile.find_last_of('.');

if (dotPos != std::string::npos && dotPos != 0)
{
writeResult(std::cout, st.solutionTimes, output, opts.outPrecision, timeOffset, *sys);
if ((opts.inFile.substr(dotPos + 1) == "h5"))
{
inIsH5 = true;

writeMetaAndResultToH5(opts, sys, st.solutionTimes, output, time_sim, timeOffset);
}
}
else
if (!inIsH5)
#endif
{
std::ofstream fs(opts.outFile, std::ofstream::out | std::ofstream::trunc);

writeMeta(fs, *sys, opts);
writeResult(fs, st.solutionTimes, output, opts.outPrecision, timeOffset, *sys);
if (opts.outFile.empty())
{
writeResult(std::cout, st.solutionTimes, output, opts.outPrecision, timeOffset, *sys);
}
else
{
std::ofstream fs(opts.outFile, std::ofstream::out | std::ofstream::trunc);

writeMeta(fs, *sys, opts, time_sim);
writeResult(fs, st.solutionTimes, output, opts.outPrecision, timeOffset, *sys);
}
}

::mpfr_free_cache();
Expand Down

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