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define and use LMP_MAX_VAR_DIMS instead of NC_MAX_VAR_DIMS to avoid stack overflows

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This commit is contained in:
Axel Kohlmeyer
2021-12-26 17:15:13 -05:00
parent 84765f4b81
commit 30af0cb325
3 changed files with 35 additions and 27 deletions
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27
src/NETCDF/dump_netcdf.cpp
View File

@ -46,6 +46,7 @@ using namespace LAMMPS_NS;
using namespace MathConst;
using NetCDFUnits::Quantity;
using NetCDFUnits::get_unit_for;
using NetCDFUnits::LMP_MAX_VAR_DIMS;
static const char NC_FRAME_STR[] = "frame";
static const char NC_SPATIAL_STR[] = "spatial";
@ -206,7 +207,7 @@ DumpNetCDF::~DumpNetCDF()
closefile();
delete[] perat;
if (thermovar) delete[] thermovar;
delete[] thermovar;
if (int_buffer) memory->sfree(int_buffer);
if (double_buffer) memory->sfree(double_buffer);
@ -234,7 +235,7 @@ void DumpNetCDF::openfile()
}
if (thermo && !singlefile_opened) {
if (thermovar) delete[] thermovar;
delete[] thermovar;
thermovar = new int[output->thermo->nfield];
}
@ -300,18 +301,18 @@ void DumpNetCDF::openfile()
NCERRX( nc_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR );
for (int i = 0; i < n_perat; i++) {
int dims = perat[i].dims;
if (vector_dim[dims] < 0) {
int dim = perat[i].dims;
if (vector_dim[dim] < 0) {
char dimstr[1024];
if (dims == 3) {
if (dim == 3) {
strcpy(dimstr, NC_SPATIAL_STR);
} else if (dims == 6) {
} else if (dim == 6) {
strcpy(dimstr, NC_VOIGT_STR);
} else {
sprintf(dimstr, "vec%i", dims);
sprintf(dimstr, "vec%i", dim);
}
if (dims != 1) {
NCERRX( nc_inq_dimid(ncid, dimstr, &vector_dim[dims]), dimstr );
if (dim != 1) {
NCERRX( nc_inq_dimid(ncid, dimstr, &vector_dim[dim]), dimstr );
}
}
}
@ -349,8 +350,8 @@ void DumpNetCDF::openfile()
if (framei != 0 && !multifile)
error->all(FLERR,"at keyword requires use of 'append yes'");
int dims[NC_MAX_VAR_DIMS];
size_t index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
int dims[LMP_MAX_VAR_DIMS];
size_t index[LMP_MAX_VAR_DIMS], count[LMP_MAX_VAR_DIMS];
if (singlefile_opened) return;
singlefile_opened = 1;
@ -720,8 +721,8 @@ void DumpNetCDF::write_header(bigint n)
void DumpNetCDF::write_data(int n, double *mybuf)
{
size_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
ptrdiff_t stride[NC_MAX_VAR_DIMS];
size_t start[LMP_MAX_VAR_DIMS], count[LMP_MAX_VAR_DIMS];
ptrdiff_t stride[LMP_MAX_VAR_DIMS];
if (!int_buffer) {
n_buffer = n;

32
src/NETCDF/dump_netcdf_mpiio.cpp
View File

@ -46,6 +46,7 @@ using namespace LAMMPS_NS;
using namespace MathConst;
using NetCDFUnits::Quantity;
using NetCDFUnits::get_unit_for;
using NetCDFUnits::LMP_MAX_VAR_DIMS;
static const char NC_FRAME_STR[] = "frame";
static const char NC_SPATIAL_STR[] = "spatial";
@ -203,7 +204,7 @@ DumpNetCDFMPIIO::~DumpNetCDFMPIIO()
closefile();
delete[] perat;
if (thermovar) delete[] thermovar;
delete[] thermovar;
if (int_buffer) memory->sfree(int_buffer);
if (double_buffer) memory->sfree(double_buffer);
@ -231,7 +232,7 @@ void DumpNetCDFMPIIO::openfile()
}
if (thermo && !singlefile_opened) {
if (thermovar) delete[] thermovar;
delete[] thermovar;
thermovar = new int[output->thermo->nfield];
}
@ -296,18 +297,18 @@ void DumpNetCDFMPIIO::openfile()
NCERRX( ncmpi_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR );
for (int i = 0; i < n_perat; i++) {
int dims = perat[i].dims;
if (vector_dim[dims] < 0) {
int dim = perat[i].dims;
if (vector_dim[dim] < 0) {
char dimstr[1024];
if (dims == 3) {
if (dim == 3) {
strcpy(dimstr, NC_SPATIAL_STR);
} else if (dims == 6) {
} else if (dim == 6) {
strcpy(dimstr, NC_VOIGT_STR);
} else {
sprintf(dimstr, "vec%i", dims);
sprintf(dimstr, "vec%i", dim);
}
if (dims != 1) {
NCERRX( ncmpi_inq_dimid(ncid, dimstr, &vector_dim[dims]), dimstr );
if (dim != 1) {
NCERRX( ncmpi_inq_dimid(ncid, dimstr, &vector_dim[dim]), dimstr );
}
}
}
@ -345,8 +346,8 @@ void DumpNetCDFMPIIO::openfile()
if (framei != 0 && !multifile)
error->all(FLERR,"at keyword requires use of 'append yes'");
int dims[NC_MAX_VAR_DIMS];
MPI_Offset index[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
int dims[LMP_MAX_VAR_DIMS];
MPI_Offset index[LMP_MAX_VAR_DIMS], count[LMP_MAX_VAR_DIMS];
if (singlefile_opened) return;
singlefile_opened = 1;
@ -360,6 +361,11 @@ void DumpNetCDFMPIIO::openfile()
NCERRX( ncmpi_def_dim(ncid, NC_CELL_ANGULAR_STR, 3, &cell_angular_dim), NC_CELL_ANGULAR_STR );
NCERRX( ncmpi_def_dim(ncid, NC_LABEL_STR, 10, &label_dim), NC_LABEL_STR );
if (vector_dim[3] < 0)
NCERRX( ncmpi_def_dim(ncid, NC_SPATIAL_STR, 3, &vector_dim[3]), NC_SPATIAL_STR );
if (vector_dim[6] < 0)
NCERRX( ncmpi_def_dim(ncid, NC_VOIGT_STR, 6, &vector_dim[6]), NC_VOIGT_STR );
for (int i = 0; i < n_perat; i++) {
int dim = perat[i].dims;
if (vector_dim[dim] < 0) {
@ -384,7 +390,6 @@ void DumpNetCDFMPIIO::openfile()
dims[0] = vector_dim[3];
dims[1] = label_dim;
NCERRX( ncmpi_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims, &cell_angular_var), NC_CELL_ANGULAR_STR );
dims[0] = frame_dim;
NCERRX( ncmpi_def_var(ncid, NC_TIME_STR, type_nc_real, 1, dims, &time_var), NC_TIME_STR);
dims[0] = frame_dim;
@ -731,8 +736,7 @@ void DumpNetCDFMPIIO::write_time_and_cell()
void DumpNetCDFMPIIO::write_data(int n, double *mybuf)
{
MPI_Offset start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
MPI_Offset stride[NC_MAX_VAR_DIMS];
MPI_Offset start[LMP_MAX_VAR_DIMS], count[LMP_MAX_VAR_DIMS], stride[LMP_MAX_VAR_DIMS];
if (!int_buffer) {
n_buffer = std::max(1, n);

3
src/NETCDF/netcdf_units.h
View File

@ -36,6 +36,9 @@ namespace NetCDFUnits {
DIPOLE_MOMENT,
};
// for compatibility with older NetCDF versions
static constexpr int LMP_MAX_VAR_DIMS = 1024;
// get the name of the unit for the given `quantity` in the given LAMMPS
// `unit_style` any error will be reported through `error`
std::string get_unit_for(const char *unit_style, int quantity, Error *error);