Initial log compression for cice4

payu/models/cice.py

@@ -17,6 +17,8 @@
 import sys
 import shutil
 import datetime
+import re
+import tarfile
 
 # Extensions
 import f90nml
@@ -51,6 +53,13 @@ def __init__(self, expt, name, config):
 
         self.copy_inputs = False
 
+        # regex patterns for matching log files. When empty, no logs compressed
+        self.logs_to_compress = [r"iceout[0-9]{3}",
+                                 r"debug\.root\.[0-9]{2}",
+                                 r"ice_diag\.d",
+                                 r"ice_diag_out"]
+        self.log_tar_name = "logfiles.tar.gz"
+
     def set_model_pathnames(self):
         super(Cice, self).set_model_pathnames()
 
@@ -333,6 +342,25 @@ def archive(self, **kwargs):
         else:
             shutil.rmtree(self.work_input_path)
 
+        if self.expt.config.get('compress_logs', False):
+            self.compress_log_files()
+
+    def get_log_files(self):
+        log_files = []
+        for filename in os.listdir(self.work_path):
+            if any((re.match(pattern, filename)
+                    for pattern in self.logs_to_compress)):
+                log_files.append(os.path.join(self.work_path, filename))
+        return log_files
+
+    def compress_log_files(self):
+        log_files = self.get_log_files()
+        with tarfile.open(name=os.path.join(self.work_path, self.log_tar_name),
+                          mode="w:gz") as tar:
+            for file in log_files:
+                tar.add(file, arcname=os.path.basename(file))
+                os.remove(file)
+
     def collate(self):
         pass
 

payu/models/cice5.py

@@ -42,6 +42,9 @@ def __init__(self, expt, name, config):
         self.copy_restarts = True
         self.copy_inputs = True
 
+        # Empty list means no log files will be compressed
+        self.logs_to_compress = []
+
     def set_local_timestep(self, t_step):
         dt = self.ice_in['setup_nml']['dt']
         npt = self.ice_in['setup_nml']['npt']

test/models/test_cice.py

@@ -3,6 +3,7 @@
 
 import pytest
 import f90nml
+import tarfile
 
 import payu
 
@@ -124,41 +125,47 @@ def empty_workdir():
     workdir.symlink_to(expt_workdir)
 
     yield expt_workdir
-    shutil.rmtree(expt_workdir)
+    try:
+        shutil.rmtree(expt_workdir)
+    except FileNotFoundError:
+        pass
     workdir.unlink()
 
 
+@pytest.fixture
+def cice_nml():
+    nml_path = os.path.join(ctrldir, CICE_NML_NAME)
+    f90nml.write(DEFAULT_CICE_NML, nml_path)
+
+    yield nml_path
+
+    # Cleanup
+    os.remove(nml_path)
+
 # Important to test None case without separate ice history file
 @pytest.fixture(params=[None,
                         {"icefields_nml": {"f_icy": "m"}},
                         {"icefields_nml": {"f_icy": "m", "f_new": "y"}}])
-def cice_config_files(request):
+def cice_history_nml(request):
     """
-    Write the default cice_in.nml namelist, and if included, separate ice
-    history namelist used by ESM1.5.
+    Write separate ice history namelist used by ESM1.5, if provided.
     """
-    cice_nml = DEFAULT_CICE_NML
     ice_history = request.param
+    ice_history_path = os.path.join(ctrldir, HIST_NML_NAME)
 
-    with cd(ctrldir):
-        # 2. Create config.nml
-        f90nml.write(cice_nml, CICE_NML_NAME)
-
-        if ice_history:
-            f90nml.write(ice_history, HIST_NML_NAME)
+    if ice_history:
+        f90nml.write(ice_history, ice_history_path)
 
     yield {'ice_history': ice_history}
 
     # cleanup
-    with cd(ctrldir):
-        os.remove(CICE_NML_NAME)
-        if ice_history:
-            os.remove(HIST_NML_NAME)
+    if ice_history:
+        os.remove(ice_history_path)
 
 
 @pytest.mark.parametrize("config", [DEFAULT_CONFIG],
                          indirect=True)
-def test_setup(config, cice_config_files):
+def test_setup(config, cice_nml, cice_history_nml):
     """
     Confirm that
         1: payu overwrites cice_in with ice_history
@@ -183,9 +190,9 @@ def test_setup(config, cice_config_files):
     # Check cice_in was patched with ice_history
     work_input_fpath = os.path.join(model.work_path, CICE_NML_NAME)
     input_nml = f90nml.read(work_input_fpath)
-    if cice_config_files['ice_history']:
+    if cice_history_nml['ice_history']:
         assert (input_nml["icefields_nml"] ==
-                cice_config_files["ice_history"]["icefields_nml"])
+                cice_history_nml["ice_history"]["icefields_nml"])
     else:
         assert input_nml["icefields_nml"] == DEFAULT_CICE_NML["icefields_nml"]
 
@@ -238,7 +245,7 @@ def prior_restart_cice4(run_timing_params):
 
 @pytest.mark.parametrize("config", [CONFIG_WITH_RESTART],
                          indirect=True)
-def test_restart_setup(config, cice_config_files, prior_restart_cice4,
+def test_restart_setup(config, cice_nml, cice_history_nml, prior_restart_cice4,
                        run_timing_params):
     """
     Test that seting up an experiment from a cloned control directory
@@ -280,7 +287,7 @@ def test_restart_setup(config, cice_config_files, prior_restart_cice4,
 
 @pytest.mark.parametrize("config", [DEFAULT_CONFIG],
                          indirect=True)
-def test_no_restart_ptr(config, cice_config_files):
+def test_no_restart_ptr(config, cice_nml, cice_history_nml):
     """
     Test that payu raises an error if no prior restart path is specified,
     restart is `true` in cice_in.nml, and the restart pointer is missing.
@@ -300,3 +307,85 @@ def test_no_restart_ptr(config, cice_config_files):
         with pytest.raises(RuntimeError,
                            match="Cannot find previous restart file"):
             model.setup()
+
+
+CONFIG_WITH_COMPRESSION = {
+    "laboratory": "lab",
+    "jobname": "testrun",
+    "model": "cice",
+    "exe": "test.exe",
+    "experiment": ctrldir_basename,
+    "metadata": {"enable": False},
+    "compress_logs": True
+}
+
+
+@pytest.fixture
+def cice4_log_files():
+    """
+    Create cice log files matching those produced during ESM1.5 simulations.
+    """
+    log_names = ["ice_diag_out", "ice_diag.d", "debug.root.03",
+                 "iceout086", "iceout088", "iceout090", "iceout092",
+                 "iceout094", "iceout096", "iceout085", "iceout087",
+                 "iceout089", "iceout091", "iceout093", "iceout095"]
+    log_paths = [os.path.join(expt_workdir, name) for name in log_names]
+
+    for log_file in log_paths:
+        with open(log_file, "w") as f:
+            f.close()
+
+    yield log_paths
+
+    # Cleanup
+    for log_file in log_paths:
+        try:
+            os.remove(log_file)
+        except FileNotFoundError:
+            pass
+
+
+@pytest.fixture
+def non_log_file():
+    """
+    Create a cice4 output file to be ignored by log compression.
+    Use cice_in.nml which is copied to the work directory in ESM1.5.
+    """
+    non_log_path = os.path.join(expt_workdir, CICE_NML_NAME)
+    with open(non_log_path, "w") as f:
+        f.close()
+
+    yield non_log_path
+
+    # Cleanup
+    os.remove(non_log_path)
+
+
+@pytest.mark.parametrize("config", [CONFIG_WITH_COMPRESSION],
+                         indirect=True)
+def test_log_compression(config, cice4_log_files, non_log_file,
+                         cice_nml # Required by expt.__init__
+                         ):
+    """
+    Test that logfiles produced by cice during ESM1.5 simulations are
+    properly compressed into a tarball by cice.compress_log_files().
+    """
+    with cd(ctrldir):
+        # Initialise laboratory and experiment
+        lab = payu.laboratory.Laboratory(lab_path=str(labdir))
+        expt = payu.experiment.Experiment(lab, reproduce=False)
+        model = expt.models[0]
+
+        # Function to test
+        model.compress_log_files()
+
+    # Check that log tarball created and no original logs remain
+    assert set(os.listdir(expt_workdir)) == {model.log_tar_name,
+                                             os.path.basename(non_log_file)}
+
+    # Check all logs present in tarball
+    log_file_names = {os.path.basename(log_path) for
+                      log_path in cice4_log_files}
+    with tarfile.open(os.path.join(expt_workdir, model.log_tar_name),
+                      "r") as tar:
+        assert set(tar.getnames()) == log_file_names