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Merge pull request #311 from LBL-EESA/cf_reader_thread_bug
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lock all NetCDF calls in the CF reader
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@burlen
burlen authored Dec 6, 2019
2 parents c82a0e0 + cccac6d commit 73fa98f
Showing 1 changed file with 103 additions and 19 deletions.
122 changes: 103 additions & 19 deletions io/teca_cf_reader.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,10 @@ class read_variable
nc_type var_type = 0;

int ierr = 0;
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
if (((ierr = nc_inq_dimid(file_id, m_variable.c_str(), &var_id)) != NC_NOERR)
|| ((ierr = nc_inq_dimlen(file_id, var_id, &var_size)) != NC_NOERR)
|| ((ierr = nc_inq_varid(file_id, m_variable.c_str(), &var_id)) != NC_NOERR)
Expand All @@ -140,6 +144,9 @@ class read_variable
<< "\" from \"" << m_file << "\". " << nc_strerror(ierr))
return std::make_pair(m_id, nullptr);
}
#if !defined(HDF5_THREAD_SAFE)
}
#endif

// allocate a buffer and read the variable.
NC_DISPATCH(var_type,
Expand Down Expand Up @@ -421,20 +428,11 @@ teca_metadata teca_cf_reader::get_output_metadata(
return teca_metadata();
}

if (((ierr = nc_inq_dimid(fh.get(), x_axis_variable.c_str(), &x_id)) != NC_NOERR)
|| ((ierr = nc_inq_dimlen(fh.get(), x_id, &n_x)) != NC_NOERR)
|| ((ierr = nc_inq_varid(fh.get(), x_axis_variable.c_str(), &x_id)) != NC_NOERR)
|| ((ierr = nc_inq_vartype(fh.get(), x_id, &x_t)) != NC_NOERR))
{
this->clear_cached_metadata();
TECA_ERROR(
<< "Failed to query x axis variable \"" << x_axis_variable
<< "\" in file \"" << file << "\"" << endl
<< nc_strerror(ierr))
return teca_metadata();
}

// query mesh axes
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
if (((ierr = nc_inq_dimid(fh.get(), x_axis_variable.c_str(), &x_id)) != NC_NOERR)
|| ((ierr = nc_inq_dimlen(fh.get(), x_id, &n_x)) != NC_NOERR)
|| ((ierr = nc_inq_varid(fh.get(), x_axis_variable.c_str(), &x_id)) != NC_NOERR)
Expand All @@ -447,6 +445,11 @@ teca_metadata teca_cf_reader::get_output_metadata(
<< nc_strerror(ierr))
return teca_metadata();
}
#if !defined(HDF5_THREAD_SAFE)
}
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif

if (!y_axis_variable.empty()
&& (((ierr = nc_inq_dimid(fh.get(), y_axis_variable.c_str(), &y_id)) != NC_NOERR)
Expand All @@ -461,6 +464,11 @@ teca_metadata teca_cf_reader::get_output_metadata(
<< nc_strerror(ierr))
return teca_metadata();
}
#if !defined(HDF5_THREAD_SAFE)
}
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif

if (!z_axis_variable.empty()
&& (((ierr = nc_inq_dimid(fh.get(), z_axis_variable.c_str(), &z_id)) != NC_NOERR)
Expand All @@ -475,6 +483,11 @@ teca_metadata teca_cf_reader::get_output_metadata(
<< nc_strerror(ierr))
return teca_metadata();
}
#if !defined(HDF5_THREAD_SAFE)
}
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif

// enumerate mesh arrays and their attributes
if (((ierr = nc_inq_nvars(fh.get(), &n_vars)) != NC_NOERR))
Expand All @@ -486,6 +499,9 @@ teca_metadata teca_cf_reader::get_output_metadata(
<< nc_strerror(ierr))
return teca_metadata();
}
#if !defined(HDF5_THREAD_SAFE)
}
#endif

for (int i = 0; i < n_vars; ++i)
{
Expand All @@ -495,6 +511,10 @@ teca_metadata teca_cf_reader::get_output_metadata(
int dim_id[NC_MAX_VAR_DIMS] = {0};
int n_atts = 0;

#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
if ((ierr = nc_inq_var(fh.get(), i, var_name,
&var_type, &n_dims, dim_id, &n_atts)) != NC_NOERR)
{
Expand All @@ -504,6 +524,9 @@ teca_metadata teca_cf_reader::get_output_metadata(
<< file << endl << nc_strerror(ierr))
return teca_metadata();
}
#if !defined(HDF5_THREAD_SAFE)
}
#endif

// skip scalars
if (n_dims == 0)
Expand All @@ -516,6 +539,10 @@ teca_metadata teca_cf_reader::get_output_metadata(
{
char dim_name[NC_MAX_NAME + 1] = {'\0'};
size_t dim = 0;
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
if ((ierr = nc_inq_dim(fh.get(), dim_id[ii], dim_name, &dim)) != NC_NOERR)
{
this->clear_cached_metadata();
Expand All @@ -524,7 +551,9 @@ teca_metadata teca_cf_reader::get_output_metadata(
<< var_name << ", " << file << endl << nc_strerror(ierr))
return teca_metadata();
}

#if !defined(HDF5_THREAD_SAFE)
}
#endif
dim_names.push_back(dim_name);
dims.push_back(dim);
}
Expand All @@ -544,6 +573,10 @@ teca_metadata teca_cf_reader::get_output_metadata(
char att_name[NC_MAX_NAME + 1] = {'\0'};
nc_type att_type = 0;
size_t att_len = 0;
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
if (((ierr = nc_inq_attname(fh.get(), i, ii, att_name)) != NC_NOERR)
|| ((ierr = nc_inq_att(fh.get(), i, att_name, &att_type, &att_len)) != NC_NOERR))
{
Expand All @@ -553,29 +586,59 @@ teca_metadata teca_cf_reader::get_output_metadata(
free(att_buffer);
return teca_metadata();
}

#if !defined(HDF5_THREAD_SAFE)
}
#endif
if (att_type == NC_CHAR)
{
char *tmp = static_cast<char*>(realloc(att_buffer, att_len + 1));
tmp[att_len] = '\0';
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
nc_get_att_text(fh.get(), i, att_name, tmp);
#if !defined(HDF5_THREAD_SAFE)
}
#endif
teca_netcdf_util::crtrim(tmp, att_len);
atts.set(att_name, std::string(tmp));
}
else if (att_type == NC_STRING)
{
char *strs[1] = {nullptr};
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
nc_get_att_string(fh.get(), i, att_name, strs);
#if !defined(HDF5_THREAD_SAFE)
}
#endif
atts.set(att_name, std::string(strs[0]));
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
nc_free_string(1, strs);
#if !defined(HDF5_THREAD_SAFE)
}
#endif
}
else
{
NC_DISPATCH(att_type,
NC_T *tmp = static_cast<NC_T*>(realloc(att_buffer, att_len));
nc_get_att(fh.get(), i, att_name, tmp);
atts.set(att_name, tmp, att_len);
)
NC_T *tmp = static_cast<NC_T*>(realloc(att_buffer, att_len));
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
nc_get_att(fh.get(), i, att_name, tmp);
#if !defined(HDF5_THREAD_SAFE)
}
#endif
atts.set(att_name, tmp, att_len);
)
}
}
free(att_buffer);
Expand All @@ -587,6 +650,10 @@ teca_metadata teca_cf_reader::get_output_metadata(
NC_DISPATCH_FP(x_t,
size_t x_0 = 0;
p_teca_variant_array_impl<NC_T> x = teca_variant_array_impl<NC_T>::New(n_x);
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
if ((ierr = nc_get_vara(fh.get(), x_id, &x_0, &n_x, x->get())) != NC_NOERR)
{
this->clear_cached_metadata();
Expand All @@ -595,6 +662,9 @@ teca_metadata teca_cf_reader::get_output_metadata(
<< file << endl << nc_strerror(ierr))
return teca_metadata();
}
#if !defined(HDF5_THREAD_SAFE)
}
#endif
x_axis = x;
)

Expand All @@ -603,6 +673,10 @@ teca_metadata teca_cf_reader::get_output_metadata(
NC_DISPATCH_FP(y_t,
size_t y_0 = 0;
p_teca_variant_array_impl<NC_T> y = teca_variant_array_impl<NC_T>::New(n_y);
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
if ((ierr = nc_get_vara(fh.get(), y_id, &y_0, &n_y, y->get())) != NC_NOERR)
{
this->clear_cached_metadata();
Expand All @@ -611,6 +685,9 @@ teca_metadata teca_cf_reader::get_output_metadata(
<< file << endl << nc_strerror(ierr))
return teca_metadata();
}
#if !defined(HDF5_THREAD_SAFE)
}
#endif
y_axis = y;
)
}
Expand All @@ -628,6 +705,10 @@ teca_metadata teca_cf_reader::get_output_metadata(
NC_DISPATCH_FP(z_t,
size_t z_0 = 0;
p_teca_variant_array_impl<NC_T> z = teca_variant_array_impl<NC_T>::New(n_z);
#if !defined(HDF5_THREAD_SAFE)
{
std::lock_guard<std::mutex> lock(teca_netcdf_util::get_netcdf_mutex());
#endif
if ((ierr = nc_get_vara(fh.get(), z_id, &z_0, &n_z, z->get())) != NC_NOERR)
{
this->clear_cached_metadata();
Expand All @@ -636,6 +717,9 @@ teca_metadata teca_cf_reader::get_output_metadata(
<< file << endl << nc_strerror(ierr))
return teca_metadata();
}
#if !defined(HDF5_THREAD_SAFE)
}
#endif
z_axis = z;
)
}
Expand Down

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