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Fixes to SEACAS-Snapshot-01-2025 #13782

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merged 2 commits into from
Feb 5, 2025
Merged

Fixes to SEACAS-Snapshot-01-2025 #13782

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a9972b6
EXODUS: Fix so works with non-netcdf4-enabled netCDF
gsjaardema Feb 4, 2025
1632040
IOSS: Fix calling mpi function while in serialize_io mode
gsjaardema Feb 4, 2025
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13 changes: 11 additions & 2 deletions packages/seacas/libraries/exodus/src/ex_get_init_ext.c
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* Copyright(C) 1999-2022, 2024 National Technology & Engineering Solutions
* Copyright(C) 1999-2022, 2024, 2025 National Technology & Engineering Solutions
* of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
* NTESS, the U.S. Government retains certain rights in this software.
*
Expand Down Expand Up @@ -28,14 +28,21 @@ static void exi_get_entity_count(int exoid, ex_init_params *info)
{
int include_parent_group = 0; // Only want dims in current group
int ndims = 0;
#if NC_HAS_NC4
nc_inq_dimids(exoid, &ndims, NULL, include_parent_group);
int *dimids = calloc(ndims, sizeof(int));
nc_inq_dimids(exoid, &ndims, dimids, include_parent_group);

#else
nc_inq(exoid, &ndims, NULL, NULL, NULL);
#endif
for (int dimid = 0; dimid < ndims; dimid++) {
char dim_nm[NC_MAX_NAME + 1] = {'\0'};
size_t dim_sz;
#if NC_HAS_NC4
nc_inq_dim(exoid, dimids[dimid], dim_nm, &dim_sz);
#else
nc_inq_dim(exoid, dimid, dim_nm, &dim_sz);
#endif
/* For assemblies, we check for a dim starting with "num_entity_assembly" */
if (strncmp(dim_nm, "num_entity_assembly", 19) == 0) {
info->num_assembly++;
Expand All @@ -44,7 +51,9 @@ static void exi_get_entity_count(int exoid, ex_init_params *info)
info->num_blob++;
}
}
#if NC_HAS_NC4
free(dimids);
#endif
}

/* Used to reduce repeated code below */
Expand Down
113 changes: 59 additions & 54 deletions packages/seacas/libraries/ioss/src/exodus/Ioex_DatabaseIO.C
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
// Copyright(C) 1999-2024 National Technology & Engineering Solutions
// Copyright(C) 1999-2025 National Technology & Engineering Solutions
// of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
// NTESS, the U.S. Government retains certain rights in this software.
//
Expand Down Expand Up @@ -731,60 +731,65 @@ namespace Ioex {
{
Ioss::SerializeIO serializeIO_(this);
timestepCount = ex_inquire_int(get_file_pointer(), EX_INQ_TIME);
int exTimestepCount = timestepCount;
// Need to sync timestep count across ranks if parallel...
if (isParallel) {
auto min_timestep_count =
util().global_minmax(timestepCount, Ioss::ParallelUtils::DO_MIN);
if (min_timestep_count == 0) {
auto max_timestep_count =
util().global_minmax(timestepCount, Ioss::ParallelUtils::DO_MAX);
if (max_timestep_count != 0) {
if (myProcessor == 0) {
// NOTE: Don't want to warn on all processors if the
// timestep count is zero on some, but not all ranks.
fmt::print(Ioss::WarnOut(),
"At least one database has no timesteps. No times will be read on ANY"
" database for consistency.\n");
}
}
}
timestepCount = min_timestep_count;
}

if (timestepCount <= 0) {
return tsteps;
}

// For an exodus file, timesteps are global and are stored in the region.
// Read the timesteps and add to the region
tsteps.resize(exTimestepCount, -std::numeric_limits<double>::max());

// The `EXODUS_CALL_GET_ALL_TIMES=NO` is typically only used in
// isSerialParallel mode and the client is responsible for
// making sure that the step times are handled correctly. All
// databases will know about the number of timesteps, but if
// this is skipped, then the times will all be zero. Use case
// is that in isSerialParallel, each call to
// `ex_get_all_times` for all files is performed sequentially,
// so if you have hundreds to thousands of files, the time for
// the call is additive and since timesteps are record
// variables in netCDF, accessing the data for all timesteps
// involves lseeks throughout the file.
bool call_ex_get_all_times = true;
Ioss::Utils::check_set_bool_property(properties, "EXODUS_CALL_GET_ALL_TIMES",
call_ex_get_all_times);
if (call_ex_get_all_times) {
int error = ex_get_all_times(get_file_pointer(), Data(tsteps));
if (error < 0) {
Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__);
}
}

// See if the "last_written_time" attribute exists and if it
// does, check that it matches the largest time in 'tsteps'.
exists = Ioex::read_last_time_attribute(get_file_pointer(), &last_time);
}
int exTimestepCount = timestepCount;
// Need to sync timestep count across ranks if parallel...
if (isParallel) {
auto min_timestep_count =
util().global_minmax(timestepCount, Ioss::ParallelUtils::DO_MIN);
if (min_timestep_count == 0) {
auto max_timestep_count =
util().global_minmax(timestepCount, Ioss::ParallelUtils::DO_MAX);
if (max_timestep_count != 0) {
if (myProcessor == 0) {
// NOTE: Don't want to warn on all processors if the
// timestep count is zero on some, but not all ranks.
fmt::print(Ioss::WarnOut(),
"At least one database has no timesteps. No times will be read on ANY"
" database for consistency.\n");
}
}
}
timestepCount = min_timestep_count;
}

if (timestepCount <= 0) {
return tsteps;
}

// For an exodus file, timesteps are global and are stored in the region.
// Read the timesteps and add to the region
tsteps.resize(exTimestepCount, -std::numeric_limits<double>::max());

// The `EXODUS_CALL_GET_ALL_TIMES=NO` is typically only used in
// isSerialParallel mode and the client is responsible for
// making sure that the step times are handled correctly. All
// databases will know about the number of timesteps, but if
// this is skipped, then the times will all be zero. Use case
// is that in isSerialParallel, each call to
// `ex_get_all_times` for all files is performed sequentially,
// so if you have hundreds to thousands of files, the time for
// the call is additive and since timesteps are record
// variables in netCDF, accessing the data for all timesteps
// involves lseeks throughout the file.
bool call_ex_get_all_times = true;
Ioss::Utils::check_set_bool_property(properties, "EXODUS_CALL_GET_ALL_TIMES",
call_ex_get_all_times);
if (call_ex_get_all_times) {
Ioss::SerializeIO serializeIO_(this);
int error = ex_get_all_times(get_file_pointer(), Data(tsteps));
if (error < 0) {
Ioex::exodus_error(get_file_pointer(), __LINE__, __func__, __FILE__);
}
}

// See if the "last_written_time" attribute exists and if it
// does, check that it matches the largest time in 'tsteps'.
{
Ioss::SerializeIO serializeIO_(this);
exists = Ioex::read_last_time_attribute(get_file_pointer(), &last_time);
}

if (exists && isParallel) {
// Assume that if it exists on 1 processor, it exists on
// all... Sync value among processors since could have a
Expand Down
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