Fix bug: messing with LD_LIBRARY_PATH when in conda environment (#223)

* Added is_conda function to fsops and used to
detect conda environment and not muck about with LD_LIBRARY_PATH

* Changed default nodesize and memory to 48 and 192GB respectively
as these are the default values for gadi

payu/cli.py

@@ -18,6 +18,7 @@
 
 import payu
 import payu.envmod as envmod
+from payu.fsops import is_conda
 from payu.models import index as supported_models
 import payu.subcommands
 from payu.scheduler.pbs import generate_command
@@ -83,9 +84,11 @@ def set_env_vars(init_run=None, n_runs=None, lab_path=None, dir_path=None,
     """Construct the environment variables used by payu for resubmissions."""
     payu_env_vars = {}
 
-    # Setup Python dynamic library link
-    lib_paths = sysconfig.get_config_vars('LIBDIR')
-    payu_env_vars['LD_LIBRARY_PATH'] = ':'.join(lib_paths)
+    if not is_conda():
+        # Setup Python dynamic library link
+        lib_paths = sysconfig.get_config_vars('LIBDIR')
+        payu_env_vars['LD_LIBRARY_PATH'] = ':'.join(lib_paths)
+
     if 'PYTHONPATH' in os.environ:
         payu_env_vars['PYTHONPATH'] = os.environ['PYTHONPATH']
 

payu/fsops.py

@@ -10,6 +10,7 @@
 # Standard library
 import errno
 import os
+import sys
 
 # Extensions
 import yaml
@@ -134,3 +135,9 @@ def check_exe_path(payu_path, pbs_script):
     assert os.path.isfile(pbs_script)
 
     return pbs_script
+
+
+def is_conda():
+    """Return True if python interpreter is in a conda environment"""
+
+    return os.path.exists(os.path.join(sys.prefix, 'conda-meta'))

payu/subcommands/run_cmd.py

@@ -29,8 +29,8 @@ def runcmd(model_type, config_path, init_run, n_runs, lab_path, reproduce):
 
     # TODO: Create drivers for servers
     platform = pbs_config.get('platform', {})
-    max_cpus_per_node = platform.get('nodesize', 16)
-    max_ram_per_node = platform.get('nodemem', 32)
+    max_cpus_per_node = platform.get('nodesize', 48)
+    max_ram_per_node = platform.get('nodemem', 192)
 
     # Adjust the CPUs for any model-specific settings
     # TODO: Incorporate this into the Model driver