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Merge pull request #297 from iulian787/iulian787/pnetcdf_indep_writes
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replace nonblocking collective with independent
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@hklion
hklion authored Nov 21, 2024
2 parents ce191ae + 021572d commit c4a72eb
Showing 1 changed file with 21 additions and 54 deletions.
75 changes: 21 additions & 54 deletions Source/IO/NCPlotFile.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -332,17 +332,13 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
//nc_plot_var.par_access(NC_COLLECTIVE);
nc_plot_var.put(&t_new[lev], { local_start_nt }, { local_nt });
}
ncmpi_end_indep_data(ncf.ncid);

// temporary
//ncf.close();
// do all independent writes
//ncmpi_end_indep_data(ncf.ncid);

cons_new[lev]->FillBoundary(geom[lev].periodicity());

mask_arrays_for_write(lev, (Real) fill_value);

std::vector<int> requests;
int irq = 0;
for (MFIter mfi(*cons_new[lev], false); mfi.isValid(); ++mfi) {
auto bx = mfi.validbox();
if (subdomain.contains(bx)) {
Expand Down Expand Up @@ -384,9 +380,7 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("h");
//nc_plot_var.par_access(NC_INDEPENDENT);
requests.push_back(0);
nc_plot_var.iput(tmp_bathy.dataPtr(), { local_start_y, local_start_x }, { local_ny, local_nx }, &requests[irq++]);
nc_plot_var.put(tmp_bathy.dataPtr(), { local_start_y, local_start_x }, { local_ny, local_nx });
}

{
Expand All @@ -396,10 +390,8 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("zeta");
//nc_plot_var.par_access(NC_INDEPENDENT);
requests.push_back(0);
nc_plot_var.iput(tmp_zeta.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny,
local_nx }, &requests[irq++]);
nc_plot_var.put(tmp_zeta.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny,
local_nx });
}

{
Expand All @@ -409,10 +401,8 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("temp");
//nc_plot_var.par_access(NC_INDEPENDENT);
requests.push_back(0);
nc_plot_var.iput(tmp_temp.dataPtr(), { local_start_nt, local_start_z, local_start_y, local_start_x }, { local_nt,
local_nz, local_ny, local_nx }, &requests[irq++]);
nc_plot_var.put(tmp_temp.dataPtr(), { local_start_nt, local_start_z, local_start_y, local_start_x }, { local_nt,
local_nz, local_ny, local_nx });
}

{
Expand All @@ -422,17 +412,15 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("salt");
//nc_plot_var.par_access(NC_INDEPENDENT);
requests.push_back(0);
nc_plot_var.iput(tmp_salt.dataPtr(), { local_start_nt, local_start_z, local_start_y, local_start_x }, { local_nt,
local_nz, local_ny, local_nx }, &requests[irq++]);
nc_plot_var.put(tmp_salt.dataPtr(), { local_start_nt, local_start_z, local_start_y, local_start_x }, { local_nt,
local_nz, local_ny, local_nx });
}
} // subdomain
} // mfi

ncf.wait_all(irq, &requests[0]);
requests.resize(0);
irq = 0;
//ncf.wait_all(irq, &requests[0]);
//requests.resize(0);
//irq = 0;
// Writing u (we loop over cons to get cell-centered box)
for (MFIter mfi(*cons_new[lev], false); mfi.isValid(); ++mfi) {
Box bx = mfi.validbox();
Expand Down Expand Up @@ -469,10 +457,8 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("u");
//nc_plot_var.par_access(NC_INDEPENDENT);
requests.push_back(0);
nc_plot_var.iput(tmp.dataPtr(), { local_start_nt, local_start_z, local_start_y, local_start_x }, { local_nt,
local_nz, local_ny, local_nx }, &requests[irq++]);
nc_plot_var.put(tmp.dataPtr(), { local_start_nt, local_start_z, local_start_y, local_start_x }, { local_nt,
local_nz, local_ny, local_nx });
}

{
Expand All @@ -482,10 +468,7 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("ubar");
//nc_plot_var.par_access(NC_INDEPENDENT);
requests.push_back(0);
nc_plot_var.iput(tmp.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny, local_nx },
&requests[irq++]);
nc_plot_var.put(tmp.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny, local_nx });
}
{
FArrayBox tmp;
Expand All @@ -494,16 +477,11 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("sustr");
//nc_plot_var.par_access(NC_INDEPENDENT);
requests.push_back(0);
nc_plot_var.iput(tmp.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny, local_nx },
&requests[irq++]);
nc_plot_var.put(tmp.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny, local_nx });
}
} // in subdomain
} // mfi
ncf.wait_all(irq, &requests[0]);
requests.resize(0);
irq = 0;

// Writing v (we loop over cons to get cell-centered box)
for (MFIter mfi(*cons_new[lev], false); mfi.isValid(); ++mfi) {
Box bx = mfi.validbox();
Expand Down Expand Up @@ -543,10 +521,8 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("v");
//nc_plot_var.par_access(NC_INDEPENDENT);
requests.push_back(0);
nc_plot_var.iput(tmp.dataPtr(), { local_start_nt, local_start_z, local_start_y, local_start_x }, { local_nt,
local_nz, local_ny, local_nx }, &requests[irq++]);
nc_plot_var.put(tmp.dataPtr(), { local_start_nt, local_start_z, local_start_y, local_start_x }, { local_nt,
local_nz, local_ny, local_nx });
}

{
Expand All @@ -556,10 +532,7 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("vbar");
//nc_plot_var.par_access(NC_INDEPENDENT);
requests.push_back(0);
nc_plot_var.iput(tmp.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny, local_nx },
&requests[irq++]);
nc_plot_var.put(tmp.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny, local_nx });
}
{
FArrayBox tmp;
Expand All @@ -568,18 +541,12 @@ void REMORA::WriteNCPlotFile_which(int lev, int which_subdomain, bool write_head
Gpu::streamSynchronize();

auto nc_plot_var = ncf.var("svstr");
//nc_plot_var.par_access(NC_INDEPENDENT);
nc_plot_var.iput(tmp.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny, local_nx },
&requests[irq++]);
nc_plot_var.put(tmp.dataPtr(), { local_start_nt, local_start_y, local_start_x }, { local_nt, local_ny, local_nx });
}

} // in subdomain
} // mfi

ncf.wait_all(irq, &requests[0]);
requests.resize(0);
irq = 0;

mask_arrays_for_write(lev, 0.0_rt);

ncf.close();
Expand Down

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