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Clang-Tidy changes in Src/Extern
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@WeiqunZhang
WeiqunZhang committed Aug 3, 2023
1 parent 1ce0303 commit 9c0a2ce
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Showing 10 changed files with 139 additions and 107 deletions.
65 changes: 38 additions & 27 deletions Src/Extern/HDF5/AMReX_ParticleHDF5.H
View file
Original file line number Diff line number Diff line change
Expand Up @@ -155,10 +155,10 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
AMREX_ASSERT( int_comp_names.size() == NStructInt + NumIntComps() );

Vector<int> write_real_comp;
for (int i = 0; i < NStructReal + NumRealComps(); ++i) write_real_comp.push_back(1);
for (int i = 0; i < NStructReal + NumRealComps(); ++i) { write_real_comp.push_back(1); }

Vector<int> write_int_comp;
for (int i = 0; i < NStructInt + NumIntComps(); ++i) write_int_comp.push_back(1);
for (int i = 0; i < NStructInt + NumIntComps(); ++i) { write_int_comp.push_back(1); }

WriteHDF5ParticleData(dir, name,
write_real_comp, write_int_comp,
Expand Down Expand Up @@ -312,10 +312,10 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
AMREX_ASSERT( int_comp_names.size() == NStructInt + NArrayInt );

Vector<int> write_real_comp;
for (int i = 0; i < NStructReal + NumRealComps(); ++i) write_real_comp.push_back(1);
for (int i = 0; i < NStructReal + NumRealComps(); ++i) { write_real_comp.push_back(1); }

Vector<int> write_int_comp;
for (int i = 0; i < NStructInt + NumIntComps(); ++i) write_int_comp.push_back(1);
for (int i = 0; i < NStructInt + NumIntComps(); ++i) { write_int_comp.push_back(1); }

WriteHDF5ParticleData(dir, name,
write_real_comp, write_int_comp,
Expand All @@ -335,10 +335,10 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
AMREX_ASSERT(real_comp_names.size() == NStructReal + NumRealComps());

Vector<int> write_real_comp;
for (int i = 0; i < NStructReal + NumRealComps(); ++i) write_real_comp.push_back(1);
for (int i = 0; i < NStructReal + NumRealComps(); ++i) { write_real_comp.push_back(1); }

Vector<int> write_int_comp;
for (int i = 0; i < NStructInt + NumIntComps(); ++i) write_int_comp.push_back(1);
for (int i = 0; i < NStructInt + NumIntComps(); ++i) { write_int_comp.push_back(1); }

Vector<std::string> int_comp_names;
for (int i = 0; i < NStructInt + NumIntComps(); ++i )
Expand Down Expand Up @@ -604,8 +604,9 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
hsize_t chunk_dim = 1024;

chunk_env = getenv("HDF5_CHUNK_SIZE");
if (chunk_env != NULL)
if (chunk_env != NULL) {
chunk_dim = atoi(chunk_env);
}

H5Pset_chunk(dcpl_int, 1, &chunk_dim);
H5Pset_chunk(dcpl_real, 1, &chunk_dim);
Expand All @@ -626,7 +627,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
pos = compression.find("ZFP");
if (pos != std::string::npos) {
ret = H5Z_zfp_initialize();
if (ret < 0) amrex::Abort("ZFP initialize failed!");
if (ret < 0) { amrex::Abort("ZFP initialize failed!"); }
}
#endif

Expand Down Expand Up @@ -815,22 +816,25 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
H5Sclose(real_dset_space);

real_file_offset = 0;
for (int i = 0; i < ParallelDescriptor::MyProc(); i++)
for (int i = 0; i < ParallelDescriptor::MyProc(); i++) {
real_file_offset += all_mfi_real_total_size[i];
}
my_real_offset = real_file_offset;
my_real_count = 0;

int max_mfi_count = 0, write_count = 0;
for (int i = 0; i < ParallelDescriptor::MyProc(); i++)
if (max_mfi_count < all_mfi_cnt[i])
for (int i = 0; i < ParallelDescriptor::MyProc(); i++) {
if (max_mfi_count < all_mfi_cnt[i]) {
max_mfi_count = all_mfi_cnt[i];
}
}


for (MFIter mfi(state); mfi.isValid(); ++mfi)
{
const int grid = mfi.index();

if (count[grid] == 0) continue;
if (count[grid] == 0) { continue; }

Vector<int> istuff;
Vector<ParticleReal> rstuff;
Expand All @@ -851,7 +855,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
#else
ret = H5Dwrite(int_dset_id, H5T_NATIVE_INT, int_mem_space, int_dset_space, dxpl_col, istuff.dataPtr());
#endif
if (ret < 0) amrex::Abort("H5Dwrite int_dset failed!");
if (ret < 0) { amrex::Abort("H5Dwrite int_dset failed!"); }

H5Sclose(int_dset_space);
H5Sclose(int_mem_space);
Expand All @@ -864,20 +868,21 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
/* my_real_offset << ", my_real_count = " << my_real_count << ", total_real_size = " << total_real_size << '\n'; */
real_dset_space = H5Screate_simple(1, &total_real_size, NULL);
H5Sselect_hyperslab (real_dset_space, H5S_SELECT_SET, &my_real_offset, NULL, &my_real_count, NULL);
if (sizeof(typename ParticleType::RealType) == 4)
if (sizeof(typename ParticleType::RealType) == 4) {
#ifdef AMREX_USE_HDF5_ASYNC
ret = H5Dwrite_async(real_dset_id, H5T_NATIVE_FLOAT, real_mem_space, real_dset_space, dxpl_col, rstuff.dataPtr(), es_par_g);
#else
ret = H5Dwrite(real_dset_id, H5T_NATIVE_FLOAT, real_mem_space, real_dset_space, dxpl_col, rstuff.dataPtr());
#endif
else
} else {
#ifdef AMREX_USE_HDF5_ASYNC
ret = H5Dwrite_async(real_dset_id, H5T_NATIVE_DOUBLE, real_mem_space, real_dset_space, dxpl_col, rstuff.dataPtr(), es_par_g);
#else
ret = H5Dwrite(real_dset_id, H5T_NATIVE_DOUBLE, real_mem_space, real_dset_space, dxpl_col, rstuff.dataPtr());
#endif
}

if (ret < 0) amrex::Abort("H5Dwrite real_dset failed!");
if (ret < 0) { amrex::Abort("H5Dwrite real_dset failed!"); }

H5Sclose(real_mem_space);
H5Sclose(real_dset_space);
Expand All @@ -896,16 +901,18 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>

#ifdef AMREX_USE_HDF5_ASYNC
H5Dwrite_async(int_dset_id, H5T_NATIVE_INT, int_dset_space, int_dset_space, dxpl_col, NULL, es_par_g);
if (sizeof(typename ParticleType::RealType) == 4)
if (sizeof(typename ParticleType::RealType) == 4) {
H5Dwrite_async(real_dset_id, H5T_NATIVE_FLOAT, real_dset_space, real_dset_space, dxpl_col, NULL, es_par_g);
else
} else {
H5Dwrite_async(real_dset_id, H5T_NATIVE_DOUBLE, real_dset_space, real_dset_space, dxpl_col, NULL, es_par_g);
}
#else
H5Dwrite(int_dset_id, H5T_NATIVE_INT, int_dset_space, int_dset_space, dxpl_col, NULL);
if (sizeof(typename ParticleType::RealType) == 4)
if (sizeof(typename ParticleType::RealType) == 4) {
H5Dwrite(real_dset_id, H5T_NATIVE_FLOAT, real_dset_space, real_dset_space, dxpl_col, NULL);
else
} else {
H5Dwrite(real_dset_id, H5T_NATIVE_DOUBLE, real_dset_space, real_dset_space, dxpl_col, NULL);
}
#endif

H5Sclose(int_dset_space);
Expand All @@ -931,8 +938,9 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
#endif

my_int_offset = 0;
for (int i = 0; i < ParallelDescriptor::MyProc(); i++)
for (int i = 0; i < ParallelDescriptor::MyProc(); i++) {
my_int_offset += all_mfi_cnt[i];
}
my_int_count = my_mfi_cnt;
int_mem_space = H5Screate_simple(1, &my_int_count, NULL);
/* std::cout << "Rank " << ParallelDescriptor::MyProc() << ": my_int_offset = " << */
Expand All @@ -944,7 +952,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
#else
ret = H5Dwrite(offset_id, H5T_NATIVE_INT, int_mem_space, offset_space, dxpl_col, &(my_nparticles[0]));
#endif
if (ret < 0) amrex::Abort("H5Dwrite offset failed!");
if (ret < 0) { amrex::Abort("H5Dwrite offset failed!"); }

H5Pclose(dcpl_int);
H5Pclose(dcpl_real);
Expand Down Expand Up @@ -986,8 +994,9 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
const auto strttime = amrex::second();

std::string fullname = dir;
if (!fullname.empty() && fullname[fullname.size()-1] != '/')
if (!fullname.empty() && fullname[fullname.size()-1] != '/') {
fullname += '/';
}

fullname += file;
fullname += ".h5";
Expand Down Expand Up @@ -1097,8 +1106,9 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
msg += aname;
amrex::Abort(msg.c_str());
}
if (ni != NStructInt + NumIntComps())
if (ni != NStructInt + NumIntComps()) {
amrex::Abort("ParticleContainer::Restart(): ni != NStructInt");
}

aname = "nparticles";
Long nparticles;
Expand Down Expand Up @@ -1285,7 +1295,7 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>

const int rank = ParallelDescriptor::MyProc();
const int NReaders = MaxReaders();
if (rank >= NReaders) return;
if (rank >= NReaders) { return; }

const int Navg = ngrids[lev] / NReaders;
const int Nleft = ngrids[lev] - Navg * NReaders;
Expand Down Expand Up @@ -1378,10 +1388,11 @@ ParticleContainer_impl<ParticleType, NArrayReal, NArrayInt, Allocator>
hsize_t real_offset = offset*rChunkSize;
real_dspace = H5Screate_simple(1, &real_cnt, NULL);
H5Sselect_hyperslab (real_fspace, H5S_SELECT_SET, &real_offset, NULL, &real_cnt, NULL);
if (sizeof(RTYPE) == 4)
if (sizeof(RTYPE) == 4) {
H5Dread(real_dset, H5T_NATIVE_FLOAT, real_dspace, real_fspace, H5P_DEFAULT, rstuff.dataPtr());
else
} else {
H5Dread(real_dset, H5T_NATIVE_DOUBLE, real_dspace, real_fspace, H5P_DEFAULT, rstuff.dataPtr());
}

H5Sclose(real_fspace);
H5Sclose(real_dspace);
Expand Down
20 changes: 11 additions & 9 deletions Src/Extern/HDF5/AMReX_PlotFileUtilHDF5.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -470,7 +470,7 @@ void WriteMultiLevelPlotfileHDF5SingleDset (const std::string& plotfilename,
pos = compression.find("ZFP");
if (pos != std::string::npos) {
ret = H5Z_zfp_initialize();
if (ret < 0) amrex::Abort("ZFP initialize failed!");
if (ret < 0) { amrex::Abort("ZFP initialize failed!"); }
}
#endif

Expand Down Expand Up @@ -912,15 +912,15 @@ void WriteMultiLevelPlotfileHDF5MultiDset (const std::string& plotfilename,
pos = compression.find("ZFP");
if (pos != std::string::npos) {
ret = H5Z_zfp_initialize();
if (ret < 0) amrex::Abort("ZFP initialize failed!");
if (ret < 0) { amrex::Abort("ZFP initialize failed!"); }
}
#endif

#ifdef AMREX_USE_HDF5_SZ
pos = compression.find("SZ");
if (pos != std::string::npos) {
ret = H5Z_SZ_Init((char*)value_env.c_str());
if (ret < 0) amrex::Abort("ZFP initialize failed, check SZ config file!");
if (ret < 0) { amrex::Abort("ZFP initialize failed, check SZ config file!"); }
}
#endif

Expand Down Expand Up @@ -1161,24 +1161,26 @@ void WriteMultiLevelPlotfileHDF5MultiDset (const std::string& plotfilename,
snprintf(dataname, sizeof dataname, "data:datatype=%d", jj);
#ifdef AMREX_USE_HDF5_ASYNC
dataset = H5Dcreate_async(grp, dataname, H5T_NATIVE_DOUBLE, dataspace, H5P_DEFAULT, lev_dcpl_id, H5P_DEFAULT, es_id_g);
if(dataset < 0) std::cout << ParallelDescriptor::MyProc() << "create data failed! ret = " << dataset << std::endl;
if(dataset < 0) { std::cout << ParallelDescriptor::MyProc() << "create data failed! ret = " << dataset << std::endl; }

if (hs_procsize[0] == 0)
if (hs_procsize[0] == 0) {
H5Sselect_none(dataspace);
else
} else {
H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, ch_offset, NULL, hs_procsize, NULL);
}

ret = H5Dwrite_async(dataset, H5T_NATIVE_DOUBLE, memdataspace, dataspace, dxpl_col, a_buffer_ind.dataPtr(), es_id_g);
if(ret < 0) { std::cout << ParallelDescriptor::MyProc() << "Write data failed! ret = " << ret << std::endl; break; }
H5Dclose_async(dataset, es_id_g);
#else
dataset = H5Dcreate(grp, dataname, H5T_NATIVE_DOUBLE, dataspace, H5P_DEFAULT, lev_dcpl_id, H5P_DEFAULT);
if(dataset < 0) std::cout << ParallelDescriptor::MyProc() << "create data failed! ret = " << dataset << std::endl;
if(dataset < 0) { std::cout << ParallelDescriptor::MyProc() << "create data failed! ret = " << dataset << std::endl; }

if (hs_procsize[0] == 0)
if (hs_procsize[0] == 0) {
H5Sselect_none(dataspace);
else
} else {
H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, ch_offset, NULL, hs_procsize, NULL);
}

ret = H5Dwrite(dataset, H5T_NATIVE_DOUBLE, memdataspace, dataspace, dxpl_col, a_buffer_ind.dataPtr());
if(ret < 0) { std::cout << ParallelDescriptor::MyProc() << "Write data failed! ret = " << ret << std::endl; break; }
Expand Down
30 changes: 18 additions & 12 deletions Src/Extern/HDF5/AMReX_WriteBinaryParticleDataHDF5.H
View file
Original file line number Diff line number Diff line change
Expand Up @@ -147,7 +147,7 @@ void WriteHDF5ParticleDataSync (PC const& pc,
#endif

std::string pdir = dir;
if ( ! pdir.empty() && pdir[pdir.size()-1] != '/') pdir += '/';
if ( ! pdir.empty() && pdir[pdir.size()-1] != '/') { pdir += '/'; }
pdir += name;

if ( ! pc.GetLevelDirectoriesCreated()) {
Expand Down Expand Up @@ -250,7 +250,7 @@ void WriteHDF5ParticleDataSync (PC const& pc,
}

fid = H5Fcreate(HDF5FileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if (fid < 0) amrex::FileOpenFailed(HDF5FileName.c_str());
if (fid < 0) { amrex::FileOpenFailed(HDF5FileName.c_str()); }

//
// First thing written is our Checkpoint/Restart version string.
Expand All @@ -259,20 +259,23 @@ void WriteHDF5ParticleDataSync (PC const& pc,
// particles so that we can Restart from the checkpoint files.
//
std::string versionName = is_checkpoint ? PC::CheckpointVersion() : PC::PlotfileVersion();
if (sizeof(typename PC::ParticleType::RealType) == 4)
if (sizeof(typename PC::ParticleType::RealType) == 4) {
versionName += "_single";
else
} else {
versionName += "_double";
}

CreateWriteHDF5AttrString(fid, "version_name", versionName.c_str());

int num_output_real = 0;
for (int i = 0; i < pc.NumRealComps() + NStructReal; ++i)
if (write_real_comp[i]) ++num_output_real;
for (int i = 0; i < pc.NumRealComps() + NStructReal; ++i) {
if (write_real_comp[i]) { ++num_output_real; }
}

int num_output_int = 0;
for (int i = 0; i < pc.NumIntComps() + NStructInt; ++i)
if (write_int_comp[i]) ++num_output_int;
for (int i = 0; i < pc.NumIntComps() + NStructInt; ++i) {
if (write_int_comp[i]) { ++num_output_int; }
}

// AMREX_SPACEDIM and N for sanity checking.
int ndim = AMREX_SPACEDIM;
Expand Down Expand Up @@ -392,8 +395,9 @@ void WriteHDF5ParticleDataSync (PC const& pc,
#else
fid = H5Fopen(HDF5FileName.c_str(), H5F_ACC_RDWR, fapl);
#endif
if (fid < 0)
if (fid < 0) {
FileOpenFailed(HDF5FileName.c_str());
}

char level_name[64];
for (int lev = 0; lev <= pc.finestLevel(); lev++)
Expand All @@ -406,10 +410,11 @@ void WriteHDF5ParticleDataSync (PC const& pc,
#endif

bool gotsome;
if(pc.usePrePost)
if(pc.usePrePost) {
gotsome = (pc.nParticlesAtLevelPrePost[lev] > 0);
else
} else {
gotsome = (pc.NumberOfParticlesAtLevel(lev) > 0);
}

MFInfo info;
info.SetAlloc(false);
Expand All @@ -423,8 +428,9 @@ void WriteHDF5ParticleDataSync (PC const& pc,
Vector<int > count(state.size(),0);
Vector<Long> where(state.size(),0);

if(pc.usePrePost)
if(pc.usePrePost) {
pc.filePrefixPrePost[lev] = HDF5FileName;
}

if (gotsome)
{
Expand Down
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