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joewallwork wants to merge 16 commits into from
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File behaviour for restarts and diagnostics #989

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2451359
Ensure write test comes before read test
joewallwork Nov 18, 2025
5474f91
Have the read test delete the files from the write test; disable file…
joewallwork Nov 18, 2025
57eaef7
Fix dimension names
joewallwork Nov 18, 2025
1555ee2
Set domain lon/lat values as indices
joewallwork Nov 24, 2025
84d0c95
Have read test read output of write test
joewallwork Nov 24, 2025
94a05c4
Clearer error for missing restart file
joewallwork Nov 24, 2025
c16977a
Use altName for dims
joewallwork Nov 24, 2025
5296d98
Only write landmask once
joewallwork Oct 1, 2025
042eee8
Write diagnostics with averaging
joewallwork Nov 10, 2025
7786fb4
Don't write the mask 'once'
joewallwork Nov 25, 2025
ce5116f
Make XiosWrite_test output fields time-dependent
joewallwork Nov 25, 2025
daea402
Align outputFreq and splitFreq
joewallwork Nov 25, 2025
f73566b
Use consistent date format in split files
joewallwork Nov 25, 2025
3e886cd
Handle patterns in filenames
joewallwork Nov 25, 2025
322f0e4
Overhaul createFile; drop XiosFile_test
joewallwork Nov 25, 2025
33e0a3e
Pull file uniqueness check out of createFile
joewallwork Nov 25, 2025
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368 changes: 157 additions & 211 deletions core/src/Xios.cpp
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11 changes: 2 additions & 9 deletions core/src/include/Xios.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -88,25 +88,19 @@ class Xios : public Configured<Xios> {

/* File */
void createFile(const std::string fileId, const int fieldType);
void setFileType(const std::string fileId, const std::string fileType);
void setFileOutputFreq(const std::string fileId, const Duration outputFreq);
void setFileParAccess(const std::string fileId, const std::string parAccess);
std::string getFileType(const std::string fileId);
void setFileOutputFreq(
const std::string fileId, const Duration outputFreq, const int fieldType);
Duration getFileOutputFreq(const std::string fileId);
std::string getFileMode(const std::string fileId);
std::string getFileParAccess(const std::string fileId);
void fileAddField(const std::string fileId, const std::string fieldId);
std::vector<std::string> fileGetFieldIds(const std::string fileId);

enum {
ENABLED_KEY,
OUTPUT_FIELD_NAMES_KEY,
OUTPUT_SPLITFREQ_KEY,
INPUT_FIELD_NAMES_KEY,
DIAGNOSTIC_PERIOD_KEY,
DIAGNOSTIC_FILE_KEY,
DIAGNOSTIC_FIELD_NAMES_KEY,
DIAGNOSTIC_SPLITFREQ_KEY,
FORCING_PERIOD_KEY,
FORCING_FILE_KEY,
FORCING_FIELD_NAMES_KEY,
Expand Down Expand Up @@ -189,7 +183,6 @@ class Xios : public Configured<Xios> {
/* File */
xios::CFileGroup* getFileGroup();
xios::CFile* getFile(const std::string fileId);
void setFileMode(const std::string fileId, const std::string mode);
std::string outputFileId;
std::string inputFileId;
std::string diagnosticFilename;
Expand Down
10 changes: 7 additions & 3 deletions core/src/include/xios_c_interface.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -90,10 +90,14 @@ bool cxios_is_defined_domain_lat_name(xios::CDomain* domain_hdl);
bool cxios_is_defined_domain_lon_name(xios::CDomain* domain_hdl);
bool cxios_is_defined_domain_ni_glo(xios::CDomain* domain_hdl);
bool cxios_is_defined_domain_nj_glo(xios::CDomain* domain_hdl);
void cxios_set_domain_lonvalue_1d(xios::CDomain* domain_hdl, double* data, const int* ni);
void cxios_set_domain_latvalue_1d(xios::CDomain* domain_hdl, double* data, const int* nj);
bool cxios_is_defined_domain_ni(xios::CDomain* domain_hdl);
bool cxios_is_defined_domain_nj(xios::CDomain* domain_hdl);
bool cxios_is_defined_domain_ibegin(xios::CDomain* domain_hdl);
bool cxios_is_defined_domain_jbegin(xios::CDomain* domain_hdl);
bool cxios_is_defined_domain_lonvalue_1d(xios::CDomain* domain_hdl);
bool cxios_is_defined_domain_latvalue_1d(xios::CDomain* domain_hdl);

// grid group methods
void cxios_gridgroup_handle_create(xios::CGridGroup** _ret, const char* _id, int _id_len);
Expand Down Expand Up @@ -142,16 +146,16 @@ void cxios_set_file_output_freq(xios::CFile* file_hdl, cxios_duration output_fre
void cxios_set_file_split_freq(xios::CFile* file_hdl, cxios_duration split_freq_c);
void cxios_set_file_mode(xios::CFile* file_hdl, const char* mode, int mode_size);
void cxios_set_file_par_access(xios::CFile* file_hdl, const char* par_access, int par_access_size);
void cxios_get_file_type(xios::CFile* file_hdl, char* type, int type_size);
void cxios_set_file_split_freq_format(
xios::CFile* file_hdl, const char* split_freq_format, int split_freq_format_size);
void cxios_get_file_output_freq(xios::CFile* file_hdl, cxios_duration* output_freq_c);
void cxios_get_file_mode(xios::CFile* file_hdl, char* mode, int mode_size);
void cxios_get_file_par_access(xios::CFile* file_hdl, char* par_access, int par_access_size);
bool cxios_is_defined_file_name(xios::CFile* file_hdl);
bool cxios_is_defined_file_type(xios::CFile* file_hdl);
bool cxios_is_defined_file_output_freq(xios::CFile* file_hdl);
bool cxios_is_defined_file_split_freq(xios::CFile* file_hdl);
bool cxios_is_defined_file_mode(xios::CFile* file_hdl);
bool cxios_is_defined_file_par_access(xios::CFile* file_hdl);
bool cxios_is_defined_file_split_freq_format(xios::CFile* file_hdl);
void cxios_xml_tree_add_fieldtofile(
xios::CFile* file, xios::CField** field, const char* _id, int _id_len);

Expand Down
6 changes: 3 additions & 3 deletions core/src/iodef.xml.jinja
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Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,9 @@

<!-- Axes defining extrusions for certain fields based on degrees of freedom per node -->
<axis_definition>
<axis id="DGAxis" n_glo="{{ DGCOMP }}" name="dg_comp" dim_name="DGAxis"/>
<axis id="DGSAxis" n_glo="{{ DGSTRESSCOMP }}" name="dgstress_comp" dim_name="DGSAxis"/>
<axis id="VertexAxis" n_glo="2" name="ncoords" dim_name="VertexAxis"/>
<axis id="DGAxis" n_glo="{{ DGCOMP }}" name="dg_comp" dim_name="dg_comp"/>
<axis id="DGSAxis" n_glo="{{ DGSTRESSCOMP }}" name="dgstress_comp" dim_name="dgstress_comp"/>
<axis id="VertexAxis" n_glo="2" name="ncoords" dim_name="ncoords"/>
</axis_definition>

<grid_definition>
Expand Down
15 changes: 3 additions & 12 deletions core/test/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -217,18 +217,6 @@ if(ENABLE_MPI)
)
target_link_libraries(testXiosField_MPI3 PRIVATE nextsimlib doctest::doctest)

add_executable(testXiosFile_MPI2 "XiosFile_test.cpp" "MainMPI.cpp")
target_compile_definitions(testXiosFile_MPI2 PRIVATE USE_XIOS)
target_include_directories(
testXiosFile_MPI2
PRIVATE
${PHYSICS_INCLUDE_DIRS}
"${MODEL_INCLUDE_DIR}"
"${XIOS_INCLUDE_LIST}"
"${ModulesRoot}/StructureModule"
)
target_link_libraries(testXiosFile_MPI2 PRIVATE nextsimlib doctest::doctest)

add_executable(testXiosRead_MPI2 "XiosRead_test.cpp" "MainMPI.cpp")
target_compile_definitions(testXiosRead_MPI2
PRIVATE
Expand Down Expand Up @@ -271,6 +259,9 @@ if(ENABLE_MPI)
)

add_mpi_test("${XIOS_TESTS}")

# Ensure XiosWrite_test is run before XiosRead_test
set_tests_properties(testXiosRead_MPI2 PROPERTIES DEPENDS testXiosWrite_MPI2)
else()
add_executable(testHaloExchangeCB_MPI3
"HaloExchangeCB_test.cpp"
Expand Down
142 changes: 0 additions & 142 deletions core/test/XiosFile_test.cpp
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22 changes: 16 additions & 6 deletions core/test/XiosRead_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,8 @@
#include <filesystem>

const std::string testFilesDir = TEST_FILES_DIR;
const std::string restartFilename = testFilesDir + "/xios_test_input.nc";
const std::string inputFilename
= testFilesDir + "/restart_2023-03-17T17:11:00Z-2023-03-17T20:10:59Z.nc";
const std::string forcingFilename = testFilesDir + "/xios_test_forcing.nc";

static const int DGCOMP = 6;
Expand All @@ -42,8 +43,7 @@ MPI_TEST_CASE("TestXiosRead", 2)
config << "start = 2023-03-17T17:11:00Z" << std::endl;
config << "stop = 2023-03-17T23:11:00Z" << std::endl;
config << "time_step = P0-0T01:30:00" << std::endl;
config << "init_file = " << restartFilename << std::endl;
config << "restart_period = P0-0T01:30:00" << std::endl;
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@joewallwork joewallwork Dec 5, 2025

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The restart period needs to be provided, otherwise XIOS stalls.

config << "init_file = " << inputFilename << std::endl;
config << "partition_file = xios_test_partition_metadata_2.nc" << std::endl;
config << "[XiosInput]" << std::endl;
config << "field_names = " << maskName << "," << coordsName << "," << hiceName << ","
Expand Down Expand Up @@ -79,8 +79,11 @@ MPI_TEST_CASE("TestXiosRead", 2)

xiosHandler.close_context_definition();

// Check the input files exists
REQUIRE(std::filesystem::exists(restartFilename));
// Check the input files exist
if (!std::filesystem::exists(inputFilename)) {
throw std::runtime_error(
"XiosRead_test: Input file not found. Did you run XiosWrite_test?");
}
REQUIRE(std::filesystem::exists(forcingFilename));

// Check calendar step is zero initially
Expand All @@ -93,7 +96,7 @@ MPI_TEST_CASE("TestXiosRead", 2)
REQUIRE(ModelArray::size(ModelArray::Dimension::DG) == DGCOMP);

// Read restarts from file and check they take the expected values
ModelState restarts = grid.getModelState(restartFilename);
ModelState restarts = grid.getModelState(inputFilename);
int rank;
MPI_Comm_rank(test_comm, &rank);
for (auto& entry : restarts.data) {
Expand Down Expand Up @@ -169,6 +172,13 @@ MPI_TEST_CASE("TestXiosRead", 2)
REQUIRE(xiosHandler.getCalendarStep() == ts + 1);
}

if (rank == 0) {
std::filesystem::remove("restart_2023-03-17T17:11:00Z-2023-03-17T20:10:59Z.nc");
std::filesystem::remove("restart_2023-03-17T20:11:00Z-2023-03-17T23:10:59Z.nc");
std::filesystem::remove("diagnostic_2023-03-17T17:11:00Z-2023-03-17T20:10:59Z.nc");
std::filesystem::remove("diagnostic_2023-03-17T20:11:00Z-2023-03-17T23:10:59Z.nc");
}

xiosHandler.context_finalize();
Finalizer::finalize();
}
Expand Down
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