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adding basic example of writing out an hdf5 blueprint data set using …
…rel… (#474) * adding basic example of writing out hdf5 blueprint data set using relay and mpi * guard hdf5 example with check for hdf5 support
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| //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// | ||
| // Copyright (c) 2014, Lawrence Livermore National Security, LLC. | ||
| // | ||
| // Produced at the Lawrence Livermore National Laboratory | ||
| // | ||
| // LLNL-CODE-666778 | ||
| // | ||
| // All rights reserved. | ||
| // | ||
| // This file is part of Conduit. | ||
| // | ||
| // For details, see https://lc.llnl.gov/conduit/. | ||
| // | ||
| // Please also read conduit/LICENSE | ||
| // | ||
| // Redistribution and use in source and binary forms, with or without | ||
| // modification, are permitted provided that the following conditions are met: | ||
| // | ||
| // * Redistributions of source code must retain the above copyright notice, | ||
| // this list of conditions and the disclaimer below. | ||
| // | ||
| // * Redistributions in binary form must reproduce the above copyright notice, | ||
| // this list of conditions and the disclaimer (as noted below) in the | ||
| // documentation and/or other materials provided with the distribution. | ||
| // | ||
| // * Neither the name of the LLNS/LLNL nor the names of its contributors may | ||
| // be used to endorse or promote products derived from this software without | ||
| // specific prior written permission. | ||
| // | ||
| // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | ||
| // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | ||
| // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | ||
| // ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY, | ||
| // LLC, THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY | ||
| // DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL | ||
| // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS | ||
| // OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) | ||
| // HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, | ||
| // STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING | ||
| // IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE | ||
| // POSSIBILITY OF SUCH DAMAGE. | ||
| // | ||
| //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// | ||
|
|
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| //----------------------------------------------------------------------------- | ||
| /// | ||
| /// file: t_blueprint_mpi_relay.cpp | ||
| /// | ||
| //----------------------------------------------------------------------------- | ||
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| #include "conduit.hpp" | ||
| #include "conduit_blueprint.hpp" | ||
| #include "conduit_relay.hpp" | ||
| #include "conduit_relay_mpi.hpp" | ||
| #include "conduit_utils.hpp" | ||
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| #include <mpi.h> | ||
| #include <iostream> | ||
| #include <sstream> | ||
| #include <string> | ||
| #include "gtest/gtest.h" | ||
|
|
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| using namespace conduit; | ||
| using namespace conduit::relay; | ||
| using namespace conduit::relay::mpi; | ||
| using namespace conduit::utils; | ||
|
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| using namespace std; | ||
|
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| //----------------------------------------------------------------------------- | ||
| void mesh_blueprint_save(const Node &data, | ||
| const std::string &path, | ||
| const std::string &file_protocol) | ||
| { | ||
| Node io_protos; | ||
| relay::io::about(io_protos["io"]); | ||
| bool hdf5_enabled = io_protos["io/protocols/hdf5"].as_string() == "enabled"; | ||
|
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| // only run this test if hdf5 is enabled | ||
| if(!hdf5_enabled) | ||
| { | ||
| CONDUIT_INFO("hdf5 is disabled, skipping hdf5 dependent test"); | ||
| return; | ||
| } | ||
|
|
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| // For simplicity, this code assumes that all ranks have | ||
| // data and that data is NOT multi-domain. | ||
|
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| int par_rank = mpi::rank(MPI_COMM_WORLD); | ||
| int par_size = mpi::size(MPI_COMM_WORLD); | ||
|
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| // setup the directory | ||
| char fmt_buff[64]; | ||
| int cycle = data["state/cycle"].to_int32(); | ||
| snprintf(fmt_buff, sizeof(fmt_buff), "%06d",cycle); | ||
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| std::string output_base_path = path; | ||
|
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| ostringstream oss; | ||
| oss << output_base_path << ".cycle_" << fmt_buff; | ||
| string output_dir = oss.str(); | ||
|
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| bool dir_ok = false; | ||
|
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| // let rank zero handle dir creation | ||
| if(par_rank == 0) | ||
| { | ||
| // check of the dir exists | ||
| dir_ok = is_directory(output_dir); | ||
|
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||
| if(!dir_ok) | ||
| { | ||
| // if not try to let rank zero create it | ||
| dir_ok = create_directory(output_dir); | ||
| } | ||
| } | ||
|
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| int local_domains, global_domains; | ||
| local_domains = 1; | ||
|
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| // use an mpi sum to check if the dir exists | ||
| Node n_src, n_reduce; | ||
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| if(dir_ok) | ||
| n_src = (int)1; | ||
| else | ||
| n_src = (int)0; | ||
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| mpi::sum_all_reduce(n_src, | ||
| n_reduce, | ||
| MPI_COMM_WORLD); | ||
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| dir_ok = (n_reduce.as_int() == 1); | ||
|
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| // find out how many domains there are | ||
| n_src = local_domains; | ||
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| mpi::sum_all_reduce(n_src, | ||
| n_reduce, | ||
| MPI_COMM_WORLD); | ||
|
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| global_domains = n_reduce.as_int(); | ||
|
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| if(!dir_ok) | ||
| { | ||
| CONDUIT_ERROR("Error: failed to create directory " << output_dir); | ||
| } | ||
|
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| // write out our local domain | ||
| uint64 domain = data["state/domain_id"].to_uint64(); | ||
|
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| snprintf(fmt_buff, sizeof(fmt_buff), "%06llu",domain); | ||
| oss.str(""); | ||
| oss << "domain_" << fmt_buff << "." << file_protocol; | ||
| string output_file = join_file_path(output_dir,oss.str()); | ||
| relay::io::save(data, output_file); | ||
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| int root_file_writer = 0; | ||
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| // let rank zero write out the root file | ||
| if(par_rank == root_file_writer) | ||
| { | ||
| snprintf(fmt_buff, sizeof(fmt_buff), "%06d",cycle); | ||
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| oss.str(""); | ||
| oss << path | ||
| << ".cycle_" | ||
| << fmt_buff | ||
| << ".root"; | ||
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| string root_file = oss.str(); | ||
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| string output_dir_base, output_dir_path; | ||
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| rsplit_string(output_dir, | ||
| "/", | ||
| output_dir_base, | ||
| output_dir_path); | ||
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| string output_file_pattern = join_file_path(output_dir_base, "domain_%06d." + file_protocol); | ||
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| Node root; | ||
| Node &bp_idx = root["blueprint_index"]; | ||
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| blueprint::mesh::generate_index(data, | ||
| "", | ||
| global_domains, | ||
| bp_idx["mesh"]); | ||
|
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| // work around conduit and manually add state fields | ||
| // sometimes they were not present and bad things happened | ||
| if(data.has_path("state/cycle")) | ||
| { | ||
| bp_idx["mesh/state/cycle"] = data["state/cycle"].to_int32(); | ||
| } | ||
|
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| if(data.has_path("state/time")) | ||
| { | ||
| bp_idx["mesh/state/time"] = data["state/time"].to_double(); | ||
| } | ||
|
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| root["protocol/name"] = file_protocol; | ||
| root["protocol/version"] = "0.4.0"; | ||
|
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| root["number_of_files"] = global_domains; | ||
| // for now we will save one file per domain, so trees == files | ||
| root["number_of_trees"] = global_domains; | ||
| // TODO: make sure this is relative | ||
| root["file_pattern"] = output_file_pattern; | ||
| root["tree_pattern"] = "/"; | ||
|
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| relay::io::save(root,root_file,file_protocol); | ||
| } | ||
| } | ||
| //----------------------------------------------------------------------------- | ||
| TEST(blueprint_mpi_relay, basic_use) | ||
| { | ||
| Node io_protos; | ||
| relay::io::about(io_protos["io"]); | ||
| bool hdf5_enabled = io_protos["io/protocols/hdf5"].as_string() == "enabled"; | ||
|
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| // only run this test if hdf5 is enabled | ||
| if(!hdf5_enabled) | ||
| { | ||
| CONDUIT_INFO("hdf5 is disabled, skipping hdf5 dependent test"); | ||
| return; | ||
| } | ||
|
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| int rank = mpi::rank(MPI_COMM_WORLD); | ||
| int com_size = mpi::size(MPI_COMM_WORLD); | ||
| std::cout<<"Rank "<<rank<<" of "<<com_size<<"\n"; | ||
| index_t npts_x = 10; | ||
| index_t npts_y = 10; | ||
| index_t npts_z = 10; | ||
|
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| Node dset; | ||
| blueprint::mesh::examples::braid("uniform", | ||
| npts_x, | ||
| npts_y, | ||
| npts_z, | ||
| dset); | ||
|
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| // the example data set has the bounds -10 to 10 in all dims | ||
| // Offset this along x to create mpi 'pencil' | ||
|
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| dset["coordsets/coords/origin/x"] = -10.0 + 20.0 * rank; | ||
| dset["state/domain_id"] = rank; | ||
|
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| string protocol = "hdf5"; | ||
| //string protocol = "conduit_bin"; | ||
| string output_path = "test_blueprint_mpi_relay"; | ||
| mesh_blueprint_save(dset, output_path, protocol); | ||
| } | ||
|
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| //----------------------------------------------------------------------------- | ||
| int main(int argc, char* argv[]) | ||
| { | ||
| int result = 0; | ||
|
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| ::testing::InitGoogleTest(&argc, argv); | ||
| MPI_Init(&argc, &argv); | ||
| result = RUN_ALL_TESTS(); | ||
| MPI_Finalize(); | ||
|
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| return result; | ||
| } | ||
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