guilhem_lavaux/cosmotool
0
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

fixed include ordering in h5_readFlash. Expanded limits of kdtree. Better support for NETCDF4/HDF5.

Browse Source
This commit is contained in:
Guilhem Lavaux 2015-06-09 20:01:56 +02:00
parent 59b1b12be8
commit b668f9947d
7 changed files with 60 additions and 47 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
external/external_build.cmake vendored
View File

@ -12,6 +12,7 @@ SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to dow
mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL)
IF(ENABLE_OPENMP)
IF (NOT OPENMP_FOUND)
MESSAGE(ERROR "No known compiler option for enabling OpenMP")
@ -25,6 +26,8 @@ ENDIF(ENABLE_OPENMP)
SET(BUILD_PREFIX ${CMAKE_BINARY_DIR}/external_build)
SET(EXT_INSTALL ${CMAKE_BINARY_DIR}/ext_install)
SET(CONFIGURE_LIBS)
SET(CONFIGURE_CPP_FLAGS)
if (ENABLE_SHARP)
SET(SHARP_SOURCE ${CMAKE_SOURCE_DIR}/external/sharp)
@ -72,6 +75,7 @@ if (INTERNAL_HDF5)
SET(ENV{HDF5_ROOT} ${HDF5_BIN_DIR})
SET(HDF5_ROOTDIR ${HDF5_BIN_DIR})
SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib")
SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl")
else(INTERNAL_HDF5)
find_path(HDF5_INCLUDE_PATH hdf5.h)
find_library(HDF5_LIBRARY hdf5)
@ -92,7 +96,7 @@ if (INTERNAL_NETCDF)
SET(NETCDF_BIN_DIR ${EXT_INSTALL})
SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${NETCDF_BIN_DIR}/include")
SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${NETCDF_BIN_DIR}/lib")
SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_LDFLAGS})
SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LIBS=${CONFIGURE_LIBS} LDFLAGS=${CONFIGURE_LDFLAGS})
ExternalProject_Add(netcdf
DEPENDS ${hdf5_built}
PREFIX ${BUILD_PREFIX}/netcdf-prefix

7
python/cosmotool/grafic.py
View File

@ -72,7 +72,7 @@ def writeWhitePhase(filename, field):
f.write(struct.pack("IIIIII", checkPoint, Nx, Ny, Nz, 0, checkPoint))
field = field.reshape(field.shape, order='F')
checkPoint = struct.pack("I", 4*Nx*Ny)
checkPoint = struct.pack("I", 4*Ny*Nz)
for i in range(Nx):
f.write(checkPoint)
f.write(field[i].astype(np.float32).tostring())
@ -91,7 +91,10 @@ def readWhitePhase(filename):
if struct.unpack("I", f.read(4))[0] != checkPoint_ref:
raise ValueError("Invalid unformatted access")
a[i, :, :] = np.fromfile(f, dtype=np.float32, count=Ny*Nz).reshape((Ny, Nz), order='F')
b = np.fromfile(f, dtype=np.float32, count=Ny*Nz).reshape((Ny, Nz))
if i==0:
print(b)
a[i, : ,:] = b
if struct.unpack("I", f.read(4))[0] != checkPoint_ref:
raise ValueError("Invalid unformatted access")

3
src/h5_readFlash.cpp
View File

@ -212,7 +212,6 @@ void h5_read_runtime_parameters
*numPart = *numPart * *numPart * *numPart;
}
}
}
@ -253,7 +252,6 @@ void h5_read_flash3_particles (H5File* file,
return;
}
/* first determine how many particle properties are
present in the input data file, and determine which of these
are the properties we are interested in */
@ -424,7 +422,6 @@ void h5_read_flash3_particles (H5File* file,
//status = H5Tclose(datatype);
//status = H5Sclose(dataspace);
//status = H5Dclose(dataset);
}

11
src/h5_readFlash.hpp
View File

@ -45,12 +45,13 @@ This file has been developped by P. M. Sutter.
* The functions accept the PARAMESH data through arguments.
*/
#include <stdio.h>
#include <stdlib.h>
#include <stddef.h>
#include <string.h>
#include "hdf5_flash.h"
#include <cstdio>
#include <cstdlib>
//#include <stddef.h>
#include <string>
#include <cstring>
#include "H5Cpp.h"
#include "hdf5_flash.h"
using namespace H5;

12
src/kdtree_splitters.hpp
View File

@ -48,17 +48,17 @@ namespace CosmoTool
typedef typename KDDef<N,CType>::CoordType ctype;
void check_splitting(KDCell<N,ValType,CType> **cells, uint32_t Ncells, int axis, uint32_t split_index, ctype midCoord)
void check_splitting(KDCell<N,ValType,CType> **cells, NodeIntType Ncells, int axis, NodeIntType split_index, ctype midCoord)
{
ctype delta = std::numeric_limits<ctype>::max();
assert(split_index < Ncells);
assert(axis < N);
for (uint32_t i = 0; i < split_index; i++)
for (NodeIntType i = 0; i < split_index; i++)
{
assert(cells[i]->coord[axis] <= midCoord);
delta = min(midCoord-cells[i]->coord[axis], delta);
}
for (uint32_t i = split_index+1; i < Ncells; i++)
for (NodeIntType i = split_index+1; i < Ncells; i++)
{
assert(cells[i]->coord[axis] > midCoord);
delta = min(cells[i]->coord[axis]-midCoord, delta);
@ -67,7 +67,7 @@ namespace CosmoTool
assert (std::abs(cells[split_index]->coord[axis]-midCoord) <= delta);
}
void operator()(KDCell<N,ValType,CType> **cells, uint32_t Ncells, uint32_t& split_index, int axis, coords minBound, coords maxBound)
void operator()(KDCell<N,ValType,CType> **cells, NodeIntType Ncells, NodeIntType& split_index, int axis, coords minBound, coords maxBound)
{
if (Ncells == 1)
{
@ -76,9 +76,9 @@ namespace CosmoTool
}
ctype midCoord = 0.5*(maxBound[axis]+minBound[axis]);
uint32_t below = 0, above = Ncells-1;
NodeIntType below = 0, above = Ncells-1;
ctype delta_min = std::numeric_limits<ctype>::max();
uint32_t idx_min = std::numeric_limits<uint32_t>::max();
NodeIntType idx_min = std::numeric_limits<NodeIntType>::max();
while (below < above)
{

26
src/mykdtree.hpp
View File

@ -46,6 +46,8 @@ knowledge of the CeCILL license and that you accept its terms.
namespace CosmoTool {
typedef uint64_t NodeIntType;
template<int N, typename CType = ComputePrecision>
struct KDDef
{
@ -84,7 +86,7 @@ namespace CosmoTool {
KDTreeNode<N,ValType,CType> *children[2];
typename KDDef<N,CType>::KDCoordinates minBound, maxBound;
#ifdef __KD_TREE_NUMNODES
uint32_t numNodes;
NodeIntType numNodes;
#endif
};
@ -122,7 +124,7 @@ namespace CosmoTool {
template<int N, typename ValType, typename CType = ComputePrecision>
struct KD_default_cell_splitter
{
void operator()(KDCell<N,ValType,CType> **cells, uint32_t Ncells, uint32_t& split_index, int axis, typename KDDef<N,CType>::KDCoordinates minBound, typename KDDef<N,CType>::KDCoordinates maxBound);
void operator()(KDCell<N,ValType,CType> **cells, NodeIntType Ncells, NodeIntType& split_index, int axis, typename KDDef<N,CType>::KDCoordinates minBound, typename KDDef<N,CType>::KDCoordinates maxBound);
};
template<int N, typename ValType, typename CType = ComputePrecision, typename CellSplitter = KD_default_cell_splitter<N,ValType,CType> >
@ -136,7 +138,7 @@ namespace CosmoTool {
CellSplitter splitter;
KDTree(Cell *cells, uint32_t Ncells);
KDTree(Cell *cells, NodeIntType Ncells);
~KDTree();
void setPeriodic(bool on, CoordType replicate)
@ -175,14 +177,14 @@ namespace CosmoTool {
void optimize();
Node *getAllNodes() { return nodes; }
uint32_t getNumNodes() const { return lastNode; }
NodeIntType getNumNodes() const { return lastNode; }
uint32_t countActives() const;
NodeIntType countActives() const;
#ifdef __KD_TREE_NUMNODES
uint32_t getNumberInNode(const Node *n) const { return n->numNodes; }
NodeIntType getNumberInNode(const Node *n) const { return n->numNodes; }
#else
uint32_t getNumberInNode(const Node *n) const {
NodeIntType getNumberInNode(const Node *n) const {
if (n == 0)
return 0;
return 1+getNumberInNode(n->children[0])+getNumberInNode(n->children[1]);
@ -190,15 +192,15 @@ namespace CosmoTool {
#endif
#ifdef __KD_TREE_SAVE_ON_DISK
KDTree(std::istream& i, Cell *cells, uint32_t Ncells)
KDTree(std::istream& i, Cell *cells, NodeIntType Ncells)
throw (InvalidOnDiskKDTree);
void saveTree(std::ostream& o) const;
#endif
protected:
Node *nodes;
uint32_t numNodes;
uint32_t lastNode;
NodeIntType numNodes;
NodeIntType lastNode;
Node *root;
Cell **sortingHelper;
@ -208,7 +210,7 @@ namespace CosmoTool {
coords replicate;
Node *buildTree(Cell **cell0,
uint32_t NumCells,
NodeIntType NumCells,
uint32_t depth,
coords minBound,
coords maxBound);
@ -231,7 +233,7 @@ namespace CosmoTool {
};
template<int N, typename T, typename CType>
uint32_t gatherActiveCells(KDCell<N,T,CType> **cells, uint32_t numCells);
NodeIntType gatherActiveCells(KDCell<N,T,CType> **cells, NodeIntType numCells);
};

42
src/mykdtree.tcc
View File

@ -31,7 +31,7 @@ namespace CosmoTool {
}
template<int N, typename ValType, typename CType, typename CellSplitter>
KDTree<N,ValType,CType,CellSplitter>::KDTree(Cell *cells, uint32_t Ncells)
KDTree<N,ValType,CType,CellSplitter>::KDTree(Cell *cells, NodeIntType Ncells)
{
periodic = false;
@ -40,7 +40,7 @@ namespace CosmoTool {
nodes = new Node[numNodes];
sortingHelper = new Cell *[Ncells];
for (uint32_t i = 0; i < Ncells; i++)
for (NodeIntType i = 0; i < Ncells; i++)
sortingHelper[i] = &cells[i];
optimize();
@ -52,7 +52,7 @@ namespace CosmoTool {
coords absoluteMin, absoluteMax;
std::cout << "Optimizing the tree..." << std::endl;
uint32_t activeCells = gatherActiveCells(sortingHelper, numNodes);
NodeIntType activeCells = gatherActiveCells(sortingHelper, numNodes);
std::cout << " number of active cells = " << activeCells << std::endl;
lastNode = 0;
@ -62,7 +62,7 @@ namespace CosmoTool {
absoluteMax[i] = -std::numeric_limits<typeof (absoluteMax[0])>::max();
}
// Find min and max corner
for (uint32_t i = 0; i < activeCells; i++)
for (NodeIntType i = 0; i < activeCells; i++)
{
KDCell<N,ValType,CType> *cell = sortingHelper[i];
@ -226,11 +226,11 @@ namespace CosmoTool {
}
template<int N, typename ValType, typename CType>
uint32_t gatherActiveCells(KDCell<N,ValType,CType> **cells,
uint32_t Ncells)
NodeIntType gatherActiveCells(KDCell<N,ValType,CType> **cells,
NodeIntType Ncells)
{
uint32_t swapId = Ncells-1;
uint32_t i = 0;
NodeIntType swapId = Ncells-1;
NodeIntType i = 0;
#if __KD_TREE_ACTIVE_CELLS == 1
while (!cells[swapId]->active && swapId > 0)
@ -253,7 +253,10 @@ namespace CosmoTool {
}
template<int N, typename ValType, typename CType>
void KD_default_cell_splitter<N,ValType,CType>::operator()(KDCell<N,ValType,CType> **cells, uint32_t Ncells, uint32_t& split_index, int axis, typename KDDef<N,CType>::KDCoordinates minBound, typename KDDef<N,CType>::KDCoordinates maxBound)
void KD_default_cell_splitter<N,ValType,CType>::operator()(KDCell<N,ValType,CType> **cells, NodeIntType Ncells,
NodeIntType& split_index, int axis,
typename KDDef<N,CType>::KDCoordinates minBound,
typename KDDef<N,CType>::KDCoordinates maxBound)
{
CellCompare<N,ValType,CType> compare(axis);
omptl::sort(cells,cells+Ncells,compare); // std::sort(cells, cells+Ncells, compare);
@ -263,7 +266,7 @@ namespace CosmoTool {
template<int N, typename ValType, typename CType, typename CellSplitter>
KDTreeNode<N,ValType,CType> *KDTree<N,ValType,CType,CellSplitter>::buildTree(Cell **cell0,
uint32_t Ncells,
NodeIntType Ncells,
uint32_t depth,
coords minBound,
coords maxBound)
@ -273,11 +276,14 @@ namespace CosmoTool {
Node *node;
int axis = depth % N;
uint32_t mid;
NodeIntType mid;
coords tmpBound;
NodeIntType nodeId;
#pragma omp critical
node = &nodes[lastNode++];
#pragma omp atomic
nodeId = (this->lastNode)++;
node = &nodes[nodeId];
// Isolate the environment
splitter(cell0, Ncells, mid, axis, minBound, maxBound);
@ -315,10 +321,10 @@ namespace CosmoTool {
}
template<int N, typename ValType, typename CType, typename CellSplitter>
uint32_t KDTree<N,ValType,CType,CellSplitter>::countActives() const
NodeIntType KDTree<N,ValType,CType,CellSplitter>::countActives() const
{
uint32_t numActive = 0;
for (uint32_t i = 0; i < lastNode; i++)
NodeIntType numActive = 0;
for (NodeIntType i = 0; i < lastNode; i++)
{
#if __KD_TREE_ACTIVE_CELLS == 1
if (nodes[i].value->active)
@ -604,7 +610,7 @@ namespace CosmoTool {
}
template<int N, typename ValType, typename CType, typename CellSplitter>
KDTree<N,ValType,CType,CellSplitter>::KDTree(std::istream& in, Cell *cells, uint32_t Ncells)
KDTree<N,ValType,CType,CellSplitter>::KDTree(std::istream& in, Cell *cells, NodeIntType Ncells)
throw (InvalidOnDiskKDTree)
{
KDTreeHeader h;
@ -683,7 +689,7 @@ namespace CosmoTool {
root = &nodes[h.rootId];
sortingHelper = new Cell *[Ncells];
for (uint32_t i = 0; i < Ncells; i++)
for (NodeIntType i = 0; i < Ncells; i++)
sortingHelper[i] = &cells[i];
}
#endif