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Merge pull request #541 from frantropy/rc_prior
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Included facultative h5 in rc_prior
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@carlocamilloni
carlocamilloni authored Feb 6, 2025
2 parents e6a993c + 8b9b115 commit 274d9b1
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Showing 4 changed files with 81 additions and 16 deletions.
14 changes: 10 additions & 4 deletions tools/cmdata/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.16)

project(cmdata VERSION 0.1
DESCRIPTION "A programm to calculate contact data from gromacs trajectories for multi-eGO"
LANGUAGES CXX)
LANGUAGES CXX C)

set(CMAKE_CXX_STANDARD 17)
set(CMDATA cmdata)
Expand All @@ -25,10 +25,16 @@ endif()

# find gromacs
find_package(GROMACS REQUIRED NAMES gromacs gromacs_mpi gromacs_d gromacs_mpi_d HINTS "$ENV{GROMACS_DIR}")
find_package(HDF5 REQUIRED COMPONENTS C CXX)
find_package(HDF5 COMPONENTS C CXX)
if(HDF5_FOUND)
message(STATUS "HDF5 found, enabling HDF5 support")
add_definitions(-DUSE_HDF5)
target_include_directories(${CMDATA} PRIVATE ${HDF5_INCLUDE_DIRS})
target_link_libraries(${CMDATA} PRIVATE ${HDF5_CXX_LIBRARIES})
endif()

# include source and header files
target_include_directories(${CMDATA} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/src ${HDF5_INCLUDE_DIRS})
target_include_directories(${CMDATA} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/src)

include(FetchContent)
SET(FETCHCONTENT_QUIET OFF)
Expand All @@ -51,7 +57,7 @@ FetchContent_Declare(
FetchContent_MakeAvailable(xdrfile)

# link libraries
target_link_libraries(${CMDATA} PRIVATE Gromacs::libgromacs xdrfile popt ${HDF5_CXX_LIBRARIES})
target_link_libraries(${CMDATA} PRIVATE Gromacs::libgromacs xdrfile popt)

set_target_properties(${PROJECT_NAME} PROPERTIES INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib)
install(TARGETS ${CMDATA} DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)
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9 changes: 8 additions & 1 deletion tools/cmdata/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,9 @@ int main(int argc, const char** argv)
{"mode", '\0', POPT_ARG_STRING | POPT_ARGFLAG_OPTIONAL, &p_mode, 0, "Mode of operation", "STRING"},
{"weights", '\0', POPT_ARG_STRING | POPT_ARGFLAG_OPTIONAL, &p_weights_path, 0, "Weights file", "FILE"},
{"no_pbc", '\0', POPT_ARG_NONE | POPT_ARGFLAG_OPTIONAL, &p_nopbc, 0, "Ignore pbcs", 0},
#ifdef USE_HDF5
{"h5", '\0', POPT_ARG_NONE | POPT_ARGFLAG_OPTIONAL, &p_h5 , 0, "Write output in HDF5 format", 0},
#endif
POPT_TABLEEND
};

Expand All @@ -73,7 +75,9 @@ int main(int argc, const char** argv)
if ( p_weights_path != NULL ) weights_path = std::string(p_weights_path);
if ( p_out_prefix != NULL ) out_prefix = std::string(p_out_prefix);
if ( p_nopbc != NULL ) nopbc = true;
#ifdef USE_HDF5
if ( p_h5 != NULL ) h5 = true;
#endif

// check if paths are valid
if ( !std::filesystem::exists(std::filesystem::path(traj_path)) )
Expand Down Expand Up @@ -155,7 +159,10 @@ int main(int argc, const char** argv)

cmdata::CMData cmdata(
top_path, traj_path, cutoff, mol_cutoff, nskip, num_threads, mol_threads, dt,
mode, weights_path, nopbc, t_begin, t_end, h5
mode, weights_path, nopbc, t_begin, t_end
#ifdef USE_HDF5
, h5
#endif
);
cmdata.run();
cmdata.process_data();
Expand Down
36 changes: 28 additions & 8 deletions tools/cmdata/src/cmdata/cmdata.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,9 @@ class CMData
// mode selection, booleans and functions
std::string mode_;
bool intra_ = false, same_ = false, cross_ = false;
#ifdef USE_HDF5
bool h5_ = false;
#endif

// function types
using ftype_intra_ = cmdata::ftypes::function_traits<decltype(&cmdata::density::intra_mol_routine)>;
Expand Down Expand Up @@ -235,12 +237,18 @@ class CMData
public:
CMData(
const std::string &top_path, const std::string &traj_path,
float cutoff, float mol_cutoff, int nskip, int num_threads, int num_mol_threads,
double cutoff, double mol_cutoff, int nskip, int num_threads, int num_mol_threads,
int dt, const std::string &mode, const std::string &weights_path,
bool no_pbc, float t_begin, float t_end, bool h5
bool no_pbc, float t_begin, float t_end
#ifdef USE_HDF5
, bool h5
#endif
) : cutoff_(cutoff), mol_cutoff_(mol_cutoff), nskip_(nskip), num_threads_(num_threads), num_mol_threads_(num_mol_threads),
mode_(mode), weights_path_(weights_path),
no_pbc_(no_pbc), dt_(dt), t_begin_(t_begin), t_end_(t_end), h5_(h5)
no_pbc_(no_pbc), dt_(dt), t_begin_(t_begin), t_end_(t_end)
#ifdef USE_HDF5
,h5_(h5)
#endif
{
bool bTop_;
matrix boxtop_;
Expand Down Expand Up @@ -756,27 +764,39 @@ class CMData
void write_output( const std::string &output_prefix )
{
std::cout << "Writing data... " << std::endl;
using ftype_write_intra = cmdata::ftypes::function_traits<decltype(&cmdata::io::f_write_intra_HDF5)>;
using ftype_write_inter_same = cmdata::ftypes::function_traits<decltype(&cmdata::io::f_write_inter_same_HDF5)>;
using ftype_write_inter_cross = cmdata::ftypes::function_traits<decltype(&cmdata::io::f_write_inter_cross_HDF5)>;
using ftype_write_intra = cmdata::ftypes::function_traits<decltype(&cmdata::io::f_write_intra)>;
using ftype_write_inter_same = cmdata::ftypes::function_traits<decltype(&cmdata::io::f_write_inter_same)>;
using ftype_write_inter_cross = cmdata::ftypes::function_traits<decltype(&cmdata::io::f_write_inter_cross)>;
std::function<ftype_write_intra::signature> write_intra = cmdata::ftypes::do_nothing<ftype_write_intra>();
std::function<ftype_write_inter_same::signature> write_inter_same = cmdata::ftypes::do_nothing<ftype_write_inter_same>();
std::function<ftype_write_inter_cross::signature> write_inter_cross = cmdata::ftypes::do_nothing<ftype_write_inter_cross>();

if (intra_)
{
#ifdef USE_HDF5
if(h5_) write_intra = cmdata::io::f_write_intra_HDF5;
else write_intra = cmdata::io::f_write_intra;
else write_intra = cmdata::io::f_write_intra;
#else
write_intra = cmdata::io::f_write_intra;
#endif
}
if (same_)
{
#ifdef USE_HDF5
if(h5_) write_inter_same = cmdata::io::f_write_inter_same_HDF5;
else write_inter_same = cmdata::io::f_write_inter_same;
#else
write_inter_same = cmdata::io::f_write_inter_same;
#endif
}
if (cross_)
{
#ifdef USE_HDF5
if(h5_) write_inter_cross = cmdata::io::f_write_inter_cross_HDF5;
else write_inter_cross = cmdata::io::f_write_inter_cross;
else write_inter_cross = cmdata::io::f_write_inter_cross;
#else
write_inter_cross = cmdata::io::f_write_inter_cross;
#endif
}

for (std::size_t i = 0; i < natmol2_.size(); i++)
Expand Down
38 changes: 35 additions & 3 deletions tools/cmdata/src/cmdata/io.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,9 @@
#include <gromacs/trajectoryanalysis/topologyinformation.h>
#include <gromacs/fileio/tpxio.h>

#ifdef USE_HDF5
#include <H5Cpp.h>
#endif

#include <filesystem>
#include <string>
Expand All @@ -18,7 +20,9 @@

#define COUT_FLOAT_PREC6 std::fixed << std::setprecision(6)

#ifdef USE_HDF5
using namespace H5;
#endif

static inline void mtopGetMolblockIndex(const gmx_mtop_t& mtop,
int globalAtomIndex,
Expand Down Expand Up @@ -176,6 +180,7 @@ std::vector<float> read_weights_file( const std::string &path )
// return mols;
// }

#ifdef USE_HDF5
void f_write_intra_HDF5(const std::string &output_prefix,
std::size_t i, int ii, const std::vector<float> &density_bins, const std::vector<int> &natmol2,
const std::vector<std::vector<std::vector<std::vector<float>>>> &intram_mat_density
Expand All @@ -192,7 +197,11 @@ void f_write_intra_HDF5(const std::string &output_prefix,
// Create dataset creation property list with compression
DSetCreatPropList plist;
plist.setDeflate(6); // Set compression level (0-9, where 9 is maximum compression)
hsize_t chunk_dims[2] = {300, 512}; // Adjust chunk size based on your data
// hsize_t chunk_dims[2] = {300, 512}; // Adjust chunk size based on your data
hsize_t chunk_dims[2] = {
std::min(static_cast<hsize_t>(density_bins.size()), static_cast<hsize_t>(300)),
std::min(static_cast<hsize_t>(natmol2[i] + 1), static_cast<hsize_t>(512))
};
plist.setChunk(2, chunk_dims);

// Create a dataset with compression
Expand All @@ -211,6 +220,7 @@ void f_write_intra_HDF5(const std::string &output_prefix,
// Write the data to the dataset
dataset.write(flat_data.data(), PredType::NATIVE_FLOAT);
}
#endif

void f_write_intra(const std::string &output_prefix,
std::size_t i, int ii, const std::vector<float> &density_bins, const std::vector<int> &natmol2,
Expand All @@ -232,6 +242,7 @@ void f_write_intra(const std::string &output_prefix,
fp_intra.close();
}

#ifdef USE_HDF5
void f_write_inter_same_HDF5(const std::string &output_prefix,
std::size_t i, int ii, const std::vector<float> &density_bins, const std::vector<int> &natmol2,
const std::vector<std::vector<std::vector<std::vector<float>>>> &interm_same_mat_density,
Expand All @@ -251,7 +262,21 @@ void f_write_inter_same_HDF5(const std::string &output_prefix,
// Create dataset creation property list with compression
DSetCreatPropList plist;
plist.setDeflate(6); // Set compression level (0-9, where 9 is maximum compression)
hsize_t chunk_dims[2] = {300, 512}; // Adjust chunk size based on your data
// hsize_t chunk_dims[2] = {
// (static_cast<hsize_t>(density_bins.size()) < 300) ? 300 : static_cast<hsize_t>(density_bins.size()),
// (static_cast<hsize_t>(natmol2[i]+1) < 512) ? 512 : static_cast<hsize_t>(natmol2[i]+1)
// }; // Adjust chunk size based on your data
hsize_t chunk_dims[2] = {
std::min(static_cast<hsize_t>(density_bins.size()), static_cast<hsize_t>(300)),
std::min(static_cast<hsize_t>(natmol2[i] + 1), static_cast<hsize_t>(512))
};
std::cout << "Dataset dimensions: ("
<< density_bins.size() << ", "
<< (natmol2[i] + 1) << ")" << std::endl;
std::cout << "Chunk dimensions: ("
<< chunk_dims[0] << ", "
<< chunk_dims[1] << ")" << std::endl;

plist.setChunk(2, chunk_dims);

// Create a dataset with compression
Expand All @@ -275,6 +300,7 @@ void f_write_inter_same_HDF5(const std::string &output_prefix,
dataset.write(flat_data.data(), PredType::NATIVE_FLOAT);
dataset_c.write(flat_data_c.data(), PredType::NATIVE_FLOAT);
}
#endif

void f_write_inter_same(const std::string &output_prefix,
std::size_t i, int ii, const std::vector<float> &density_bins, const std::vector<int> &natmol2,
Expand Down Expand Up @@ -302,6 +328,7 @@ void f_write_inter_same(const std::string &output_prefix,
fp_inter_cum.close();
}

#ifdef USE_HDF5
void f_write_inter_cross_HDF5(const std::string &output_prefix,
std::size_t i, std::size_t j, int ii, const std::vector<float> &density_bins, const std::vector<int> &natmol2,
const std::vector<std::vector<int>> &cross_index,
Expand All @@ -322,7 +349,11 @@ void f_write_inter_cross_HDF5(const std::string &output_prefix,
// Create dataset creation property list with compression
DSetCreatPropList plist;
plist.setDeflate(6); // Set compression level (0-9, where 9 is maximum compression)
hsize_t chunk_dims[2] = {300, 512}; // Adjust chunk size based on your data
// hsize_t chunk_dims[2] = {300, 512}; // Adjust chunk size based on your data
hsize_t chunk_dims[2] = {
std::min(static_cast<hsize_t>(density_bins.size()), static_cast<hsize_t>(300)),
std::min(static_cast<hsize_t>(natmol2[i] + 1), static_cast<hsize_t>(512))
};
plist.setChunk(2, chunk_dims);

// Create a dataset with compression
Expand All @@ -346,6 +377,7 @@ void f_write_inter_cross_HDF5(const std::string &output_prefix,
dataset.write(flat_data.data(), PredType::NATIVE_FLOAT);
dataset_c.write(flat_data_c.data(), PredType::NATIVE_FLOAT);
}
#endif

void f_write_inter_cross(const std::string &output_prefix,
std::size_t i, std::size_t j, int ii, const std::vector<float> &density_bins, const std::vector<int> &natmol2,
Expand Down

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