From 354eba80cdce01521a09a7b2c6a19cecc4e3e1c0 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Tue, 2 May 2017 01:26:25 +0200
Subject: [PATCH] Fixing missing files
---
src/HDF5_wr/HDF5_reader.hpp | 24 +++
src/HDF5_wr/HDF5_reader_vd.hpp | 218 +++++++++++++++++++++++++
src/HDF5_wr/HDF5_wr.hpp | 18 ++
src/HDF5_wr/HDF5_writer.hpp | 28 ++++
src/HDF5_wr/HDF5_writer_unit_tests.hpp | 115 +++++++++++++
src/HDF5_wr/HDF5_writer_vd.hpp | 161 ++++++++++++++++++
6 files changed, 564 insertions(+)
create mode 100644 src/HDF5_wr/HDF5_reader.hpp
create mode 100644 src/HDF5_wr/HDF5_reader_vd.hpp
create mode 100644 src/HDF5_wr/HDF5_wr.hpp
create mode 100644 src/HDF5_wr/HDF5_writer.hpp
create mode 100644 src/HDF5_wr/HDF5_writer_unit_tests.hpp
create mode 100644 src/HDF5_wr/HDF5_writer_vd.hpp
diff --git a/src/HDF5_wr/HDF5_reader.hpp b/src/HDF5_wr/HDF5_reader.hpp
new file mode 100644
index 0000000..9f8aa12
--- /dev/null
+++ b/src/HDF5_wr/HDF5_reader.hpp
@@ -0,0 +1,24 @@
+/*
+ * HDF5_loader.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_HPP_
+
+#include "VCluster/VCluster.hpp"
+
+template <unsigned int type>
+class HDF5_reader
+{
+ void load()
+ {
+ std::cerr << __FILE__ << ":" << __LINE__ << " Error: we do not know how to write this type of data" << std::endl;
+ }
+};
+
+#include "HDF5_reader_vd.hpp"
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_HPP_ */
diff --git a/src/HDF5_wr/HDF5_reader_vd.hpp b/src/HDF5_wr/HDF5_reader_vd.hpp
new file mode 100644
index 0000000..36041cc
--- /dev/null
+++ b/src/HDF5_wr/HDF5_reader_vd.hpp
@@ -0,0 +1,218 @@
+/*
+ * HDF5_reader_vd.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_VD_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_VD_HPP_
+
+
+template <>
+class HDF5_reader<VECTOR_DIST>
+{
+private:
+
+ template<unsigned int dim, typename St,typename prp>
+ void load_block(long int bid,
+ hssize_t mpi_size_old,
+ int * metadata_out,
+ openfpm::vector<size_t> metadata_accum,
+ hid_t plist_id,
+ hid_t dataset_2,
+ size_t & g_m,
+ openfpm::vector<Point<dim,St>> & v_pos,
+ openfpm::vector<prp> & v_prp)
+ {
+ hsize_t offset[1];
+ hsize_t block[1];
+
+ if (bid < mpi_size_old && bid != -1)
+ {
+ offset[0] = metadata_accum.get(bid);
+ block[0] = metadata_out[bid];
+ }
+ else
+ {
+ offset[0] = 0;
+ block[0] = 0;
+ }
+
+ hsize_t count[1] = {1};
+
+
+ //Select file dataspace
+ hid_t file_dataspace_id_2 = H5Dget_space(dataset_2);
+
+ H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset, NULL, count, block);
+
+ hsize_t mdim_2[1] = {block[0]};
+
+
+ //Create data space in memory
+ hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
+
+ size_t sum = 0;
+
+ for (int i = 0; i < mpi_size_old; i++)
+ sum += metadata_out[i];
+
+ // allocate the memory
+ HeapMemory pmem;
+
+ ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
+ mem.incRef();
+
+ // Read the dataset.
+ H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer());
+
+ mem.allocate(pmem.size());
+
+ Unpack_stat ps;
+
+ openfpm::vector<Point<dim, St>> v_pos_unp;
+
+ openfpm::vector<prp> v_prp_unp;
+
+ Unpacker<decltype(v_pos_unp),HeapMemory>::unpack(mem,v_pos_unp,ps,1);
+ Unpacker<decltype(v_prp_unp),HeapMemory>::unpack(mem,v_prp_unp,ps,1);
+
+ mem.decRef();
+ delete &mem;
+
+ for (size_t i = 0; i < v_pos_unp.size(); i++)
+ v_pos.add(v_pos_unp.get(i));
+
+ for (size_t i = 0; i < v_prp_unp.size(); i++)
+ v_prp.add(v_prp_unp.get(i));
+
+ g_m = v_pos.size();
+ }
+
+public:
+
+ template<unsigned int dim, typename St, typename prp> inline void load(const std::string & filename,
+ openfpm::vector<Point<dim,St>> & v_pos,
+ openfpm::vector<prp> & v_prp,
+ size_t & g_m)
+ {
+ Vcluster & v_cl = create_vcluster();
+
+ v_pos.clear();
+ v_prp.clear();
+
+ g_m = 0;
+
+ MPI_Comm comm = v_cl.getMPIComm();
+ MPI_Info info = MPI_INFO_NULL;
+
+ int mpi_rank = v_cl.getProcessUnitID();
+
+ // Set up file access property list with parallel I/O access
+ hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ H5Pset_fapl_mpio(plist_id, comm, info);
+
+ //Open a file
+ hid_t file = H5Fopen (filename.c_str(), H5F_ACC_RDONLY, plist_id);
+ H5Pclose(plist_id);
+
+ //Open dataset
+ hid_t dataset = H5Dopen (file, "metadata", H5P_DEFAULT);
+
+ //Create property list for collective dataset read
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+ //Select file dataspace
+ hid_t file_dataspace_id = H5Dget_space(dataset);
+
+ hssize_t mpi_size_old = H5Sget_select_npoints (file_dataspace_id);
+
+ //Where to read metadata
+ int metadata_out[mpi_size_old];
+
+ for (int i = 0; i < mpi_size_old; i++)
+ {
+ metadata_out[i] = 0;
+ }
+
+ //Size for data space in memory
+ hsize_t mdim[1] = {(size_t)mpi_size_old};
+
+ //Create data space in memory
+ hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
+
+ // Read the dataset.
+ H5Dread(dataset, H5T_NATIVE_INT, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
+
+ openfpm::vector<size_t> metadata_accum;
+ metadata_accum.resize(mpi_size_old);
+
+ metadata_accum.get(0) = 0;
+ for (int i = 1 ; i < mpi_size_old ; i++)
+ metadata_accum.get(i) = metadata_accum.get(i-1) + metadata_out[i-1];
+
+ //Open dataset
+ hid_t dataset_2 = H5Dopen (file, "vector_dist", H5P_DEFAULT);
+
+ //Create property list for collective dataset read
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+ openfpm::vector<size_t> n_block;
+ n_block.resize(v_cl.getProcessingUnits());
+
+
+ for(size_t i = 0 ; i < n_block.size() ; i++)
+ n_block.get(i) = mpi_size_old / v_cl.getProcessingUnits();
+
+ size_t rest_block = mpi_size_old % v_cl.getProcessingUnits();
+
+ size_t max_block;
+
+ if (rest_block != 0)
+ max_block = n_block.get(0) + 1;
+ else
+ max_block = n_block.get(0);
+
+ //for(size_t i = 0 ; i < n_block.size() ; i++)
+ for(size_t i = 0 ; i < rest_block ; i++)
+ n_block.get(i) += 1;
+
+ size_t start_block = 0;
+ size_t stop_block = 0;
+
+
+ if (v_cl.getProcessUnitID() != 0)
+ {
+ for(size_t i = 0 ; i < v_cl.getProcessUnitID() ; i++)
+ start_block += n_block.get(i);
+ }
+
+ stop_block = start_block + n_block.get(v_cl.getProcessUnitID());
+
+ if (mpi_rank >= mpi_size_old)
+ load_block(start_block,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,g_m,v_pos,v_prp);
+ else
+ {
+ size_t n_bl = 0;
+ size_t lb = start_block;
+ for ( ; lb < stop_block ; lb++, n_bl++)
+ load_block(lb,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,g_m,v_pos,v_prp);
+
+ if (n_bl < max_block)
+ load_block(-1,mpi_size_old,metadata_out,metadata_accum,plist_id,dataset_2,g_m,v_pos,v_prp);
+ }
+
+ // Close the dataset.
+ H5Dclose(dataset);
+ H5Dclose(dataset_2);
+ // Close the file.
+ H5Fclose(file);
+ H5Pclose(plist_id);
+ }
+};
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_READER_VD_HPP_ */
diff --git a/src/HDF5_wr/HDF5_wr.hpp b/src/HDF5_wr/HDF5_wr.hpp
new file mode 100644
index 0000000..f90c60a
--- /dev/null
+++ b/src/HDF5_wr/HDF5_wr.hpp
@@ -0,0 +1,18 @@
+/*
+ * HDF5_wr.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WR_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WR_HPP_
+
+
+#define VECTOR_DIST 1
+
+#include "HDF5_writer.hpp"
+#include "HDF5_reader.hpp"
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WR_HPP_ */
diff --git a/src/HDF5_wr/HDF5_writer.hpp b/src/HDF5_wr/HDF5_writer.hpp
new file mode 100644
index 0000000..b0ac16c
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer.hpp
@@ -0,0 +1,28 @@
+/*
+ * HDF5_writer.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_HPP_
+
+
+#include "VCluster/VCluster.hpp"
+#include <hdf5.h>
+
+template <unsigned int type>
+class HDF5_writer
+{
+
+ void save()
+ {
+ std::cerr << __FILE__ << ":" << __LINE__ << " Error: we do not know how to write this type of data" << std::endl;
+ }
+
+};
+
+#include "../HDF5_wr/HDF5_writer_vd.hpp"
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_HPP_ */
diff --git a/src/HDF5_wr/HDF5_writer_unit_tests.hpp b/src/HDF5_wr/HDF5_writer_unit_tests.hpp
new file mode 100644
index 0000000..0fc72b1
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer_unit_tests.hpp
@@ -0,0 +1,115 @@
+/*
+ * HDF5_writer_unit_test.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_UNIT_TESTS_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_UNIT_TESTS_HPP_
+
+#include "HDF5_wr.hpp"
+
+#include "hdf5.h"
+
+BOOST_AUTO_TEST_SUITE( vd_hdf5_chckpnt_rstrt_test )
+
+// Dimensionality
+const size_t dim = 3;
+
+BOOST_AUTO_TEST_CASE( vector_dist_hdf5_save_test )
+{
+ openfpm::vector<Point<3,float>> vpos;
+ openfpm::vector<aggregate<float[dim]>> vprp;
+
+ // Put forces
+
+ for (size_t i = 0 ; i < 1024 ; i++)
+ {
+ Point<3,float> p;
+
+ p.get(0) = i;
+ p.get(1) = i+13;
+ p.get(2) = i+17;
+
+ vpos.add(p);
+
+ vprp.add();
+ vprp.template get<0>(vprp.size()-1)[0] = p.get(0) + 100.0;
+ vprp.template get<0>(vprp.size()-1)[1] = p.get(1) + 200.0;
+ vprp.template get<0>(vprp.size()-1)[2] = p.get(2) + 300.0;
+ }
+
+ HDF5_writer<VECTOR_DIST> h5;
+
+ // Save the vector
+ h5.save("vector_dist.h5",vpos,vprp);
+
+ HDF5_reader<VECTOR_DIST> h5r;
+
+ openfpm::vector<Point<3,float>> vpos2;
+ openfpm::vector<aggregate<float[dim]>> vprp2;
+
+ size_t g_m = 0;
+ h5r.load("vector_dist.h5",vpos2,vprp2,g_m);
+
+ BOOST_REQUIRE_EQUAL(1024ul,vpos2.size());
+ BOOST_REQUIRE_EQUAL(1024ul,vprp2.size());
+
+ BOOST_REQUIRE_EQUAL(1024ul,g_m);
+
+ // Check that vpos == vpos2 and vprp2 == vprp2
+
+ bool check = true;
+ for (size_t i = 0 ; i < vpos.size() ; i++)
+ {
+ check &= (vpos.get(i) == vpos2.get(i));
+ check &= (vprp.get_o(i) == vprp2.get_o(i));
+ }
+
+ BOOST_REQUIRE_EQUAL(check,true);
+}
+
+
+
+BOOST_AUTO_TEST_CASE( vector_dist_hdf5_load_test )
+{
+ Vcluster & v_cl = create_vcluster();
+
+ openfpm::vector<Point<3,float>> vpos;
+ openfpm::vector<aggregate<float[dim]>> vprp;
+
+ HDF5_reader<VECTOR_DIST> h5;
+
+ size_t g_m = 0;
+
+ // Load the vector
+ h5.load("test_data/vector_dist_24.h5",vpos,vprp,g_m);
+
+ /////////////////// Checking data ///////////////////////
+
+ // Check total number of particles
+ size_t n_part = vpos.size();
+ v_cl.sum(n_part);
+ v_cl.execute();
+
+ BOOST_REQUIRE_EQUAL(n_part,1024ul*24ul);
+
+ BOOST_REQUIRE_EQUAL(vpos.size(),vprp.size());
+
+ bool check = true;
+
+ for (size_t i = 0 ; i < vpos.size() ; i++)
+ {
+ check &= (vprp.template get<0>(i)[0] == vpos.template get<0>(i)[0] + 100.0);
+ check &= (vprp.template get<0>(i)[1] == vpos.template get<0>(i)[1] + 200.0);
+ check &= (vprp.template get<0>(i)[2] == vpos.template get<0>(i)[2] + 300.0);
+ }
+
+
+}
+
+BOOST_AUTO_TEST_SUITE_END()
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_UNIT_TESTS_HPP_ */
diff --git a/src/HDF5_wr/HDF5_writer_vd.hpp b/src/HDF5_wr/HDF5_writer_vd.hpp
new file mode 100644
index 0000000..d413962
--- /dev/null
+++ b/src/HDF5_wr/HDF5_writer_vd.hpp
@@ -0,0 +1,161 @@
+/*
+ * HDF5_loader_vector_dist.hpp
+ *
+ * Created on: May 1, 2017
+ * Author: i-bird
+ */
+
+#ifndef OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_
+#define OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_
+
+#include "Packer_Unpacker/Pack_selector.hpp"
+#include "Packer_Unpacker/Packer.hpp"
+#include "Packer_Unpacker/Unpacker.hpp"
+
+template <>
+class HDF5_writer<VECTOR_DIST>
+{
+public:
+
+ template<unsigned int dim, typename St, typename prp>
+ inline void save(const std::string & filename,
+ const openfpm::vector<Point<dim,St>> & v_pos,
+ const openfpm::vector<prp> & v_prp) const
+ {
+ Vcluster & v_cl = create_vcluster();
+
+ //Pack_request vector
+ size_t req = 0;
+
+ //std::cout << "V_pos.size() before save: " << v_pos.size() << std::endl;
+
+ //Pack request
+ Packer<typename std::remove_reference<decltype(v_pos)>::type,HeapMemory>::packRequest(v_pos,req);
+ Packer<typename std::remove_reference<decltype(v_prp)>::type,HeapMemory>::packRequest(v_prp,req);
+
+ // allocate the memory
+ HeapMemory pmem;
+ //pmem.allocate(req);
+ ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(req,pmem));
+ mem.incRef();
+
+ //Packing
+
+ Pack_stat sts;
+
+ Packer<typename std::remove_reference<decltype(v_pos)>::type,HeapMemory>::pack(mem,v_pos,sts);
+ Packer<typename std::remove_reference<decltype(v_prp)>::type,HeapMemory>::pack(mem,v_prp,sts);
+
+ /*****************************************************************
+ * Create a new file with default creation and access properties.*
+ * Then create a dataset and write data to it and close the file *
+ * and dataset. *
+ *****************************************************************/
+
+ int mpi_rank = v_cl.getProcessUnitID();
+ int mpi_size = v_cl.getProcessingUnits();
+
+ MPI_Comm comm = v_cl.getMPIComm();
+ MPI_Info info = MPI_INFO_NULL;
+
+ // Set up file access property list with parallel I/O access
+
+ hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ H5Pset_fapl_mpio(plist_id, comm, info);
+
+ // Create a new file collectively and release property list identifier.
+ hid_t file = H5Fcreate (filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
+ H5Pclose(plist_id);
+
+ size_t sz = pmem.size();
+ //std::cout << "Pmem.size: " << pmem.size() << std::endl;
+ openfpm::vector<size_t> sz_others;
+ v_cl.allGather(sz,sz_others);
+ v_cl.execute();
+
+ size_t sum = 0;
+
+ for (size_t i = 0; i < sz_others.size(); i++)
+ sum += sz_others.get(i);
+
+ //Size for data space in file
+ hsize_t fdim[1] = {sum};
+
+ //Size for data space in file
+ hsize_t fdim2[1] = {(size_t)mpi_size};
+
+ //Create data space in file
+ hid_t file_dataspace_id = H5Screate_simple(1, fdim, NULL);
+
+ //Create data space in file
+ hid_t file_dataspace_id_2 = H5Screate_simple(1, fdim2, NULL);
+
+ //Size for data space in memory
+ hsize_t mdim[1] = {pmem.size()};
+
+ //Create data space in memory
+ hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
+
+ //Create data set in file
+ hid_t file_dataset = H5Dcreate (file, "vector_dist", H5T_NATIVE_CHAR, file_dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ //Create data set 2 in file
+ hid_t file_dataset_2 = H5Dcreate (file, "metadata", H5T_NATIVE_INT, file_dataspace_id_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ //H5Pclose(plist_id);
+ H5Sclose(file_dataspace_id);
+ H5Sclose(file_dataspace_id_2);
+
+ hsize_t block[1] = {pmem.size()};
+
+ //hsize_t stride[1] = {1};
+
+ hsize_t count[1] = {1};
+
+ hsize_t offset[1] = {0};
+
+ for (int i = 0; i < mpi_rank; i++)
+ {
+ if (mpi_rank == 0)
+ offset[0] = 0;
+ else
+ offset[0] += sz_others.get(i);
+ }
+
+ int metadata[mpi_size];
+
+ for (int i = 0; i < mpi_size; i++)
+ metadata[i] = sz_others.get(i);
+
+ //Select hyperslab in the file.
+ file_dataspace_id = H5Dget_space(file_dataset);
+ H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset, NULL, count, block);
+
+ file_dataspace_id_2 = H5Dget_space(file_dataset_2);
+
+
+ //Create property list for collective dataset write.
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+
+ //Write a data set to a file
+ H5Dwrite(file_dataset, H5T_NATIVE_CHAR, mem_dataspace_id, file_dataspace_id, plist_id, (const char *)pmem.getPointer());
+
+ //Write a data set 2 to a file
+ H5Dwrite(file_dataset_2, H5T_NATIVE_INT, H5S_ALL, file_dataspace_id_2, plist_id, metadata);
+
+
+ //Close/release resources.
+ H5Dclose(file_dataset);
+ H5Sclose(file_dataspace_id);
+ H5Dclose(file_dataset_2);
+ H5Sclose(file_dataspace_id_2);
+ H5Sclose(mem_dataspace_id);
+ H5Pclose(plist_id);
+ H5Fclose(file);
+ }
+
+};
+
+
+#endif /* OPENFPM_IO_SRC_HDF5_WR_HDF5_WRITER_VD_HPP_ */
--
GitLab