load from PBS presets correctly

lmn/cli/_config_loader.py

@@ -124,6 +124,7 @@ def load_config(machine_name: str):
     # Parse special config params
     preset_conf = {
         'slurm-configs': config.get('slurm-configs', {}),
+        'pbs-configs': config.get('pbs-configs', {}),
         'docker-images': config.get('docker-images', {}),
     }
 

lmn/cli/_utils.py

@@ -42,7 +42,6 @@ def rsync(source_dir: Union[Path, str], target_dir: Union[Path, str], remote_con
         cmd = f"rsync {options_str} {remote_conf.base_uri}:{source_dir} {target_dir}"
     else:
         cmd = f"rsync {options_str} {source_dir} {remote_conf.base_uri}:{target_dir}"
-    logger.debug(f'running command: {cmd}')
 
     if not dry_run:
         run_cmd(cmd, shell=True)

lmn/cli/run.py

@@ -370,7 +370,7 @@ def handler_scheduler(
                 logger.error(f'Slurm config preset: "{parsed.sconf}" cannot be found in "slurm-configs" or is empty.')
                 import sys; sys.exit(1)
             scheduler_conf = SlurmConfig(**_sconf)
-            logger.debug(f'Using preset: {parsed.sconf}')
+            logger.info(f'Using Slurm preset: [{parsed.sconf}]')
 
         runner = SlurmRunner(ssh_client, lmndirs)
 
@@ -381,24 +381,25 @@ def handler_scheduler(
             raise ValueError('Configuration must have an entry for "pbs" to use PBS mode.')
 
         # Create PBSConfig object
-        if parsed.sconf is None:
+        if parsed.pbsconf is None:
             scheduler_conf = machine.parsed_conf.pbs
         else:
             # Try to load from the slurm conf presets
             logger.debug('parsed.sconf is specified. Loading custom preset conf.')
-            _pconf = preset.get('pbs-configs', {}).get(parsed.pconf, {})
+            _pconf = preset.get('pbs-configs', {}).get(parsed.pbsconf, {})
             if not _pconf:
-                logger.error(f'PBS config preset: "{parsed.pconf}" cannot be found in "pbs-configs" or is empty.')
+                logger.error(f'PBS config preset: "{parsed.pbsconf}" cannot be found in "pbs-configs" or is empty.')
                 import sys; sys.exit(1)
             scheduler_conf = PBSConfig(**_pconf)
-            logger.debug(f'Using preset: {parsed.pconf}')
+            logger.info(f'Using PBS preset: [{parsed.pbsconf}]')
 
         runner = PBSRunner(ssh_client, lmndirs)
 
     else:
-        raise ValueError(f'Unrecognized mode: {mode}')
+        logger.error(f'Unrecognized mode: {mode}')
+        import sys; sys.exit(1)
 
-    # NOTE: Slurm seems to be fine with duplicated name. (How about PBS?)
+    # NOTE: Slurm / PBS seem to be fine with duplicated name.
     proj_name_maxlen = 15
     rand_num = random.randint(0, 100)
     job_name = f'lmn-{project.name[:proj_name_maxlen]}-{randomname.get_name()}-{rand_num}'
@@ -407,7 +408,7 @@ def handler_scheduler(
     scheduler_conf.job_name = job_name
 
     if run_opt.force:
-        logger.warn("`-f / --force` option has no effect in slurm mode")
+        logger.warn("`-f / --force` option has no effect in Slurm / PBS mode")
 
     # Specify job name
     name = f'{machine.user}-lmn-{project.name}'

lmn/runner.py

@@ -371,7 +371,7 @@ def exec(self, cmd: str, relative_workdir, conf: PBSConfig, env: Optional[dict]
             # NOTE: without `-S` option, `bash -i` will be considered a single command and will end up in command not found.
             # Reference: https://unix.stackexchange.com/a/657774/556831
             # '#!/usr/bin/env -S bash -i' if interactive else '#!/usr/bin/env bash',
-            f'#!/bin/{s.shell} -i',  # ^ This only works with a recent version of coreutils (8.30) and that cannot be taken for granted.
+            f'#!/bin/{conf.shell} -i',  # ^ This only works with a recent version of coreutils (8.30) and that cannot be taken for granted.
             *slurm_options,
             *exports,
             cmd

lmn/scheduler/pbs.py

@@ -8,7 +8,7 @@ class PBSConfig(BaseModel):
     job_name: str = 'default-job-name'  # To be filled
     account: str = 'SuperBERT'  # Account string
     queue: str = 'debug'  # debug, small, medium, large, etc. (Check `qstat -q`)
-    shell: str = '/usr/bin/env bash'
+    shell: str = 'bash'  # It will be fed to `/bin/{shell}` template
     filesystems: str = 'home:grand'  # Request access to /home and /grand directories
     select: int = 1  # Request 1 node
     place: str = 'free'  # scatter, pack (default): specify how to distribute allocations (I believe it only matters for multi-node allocation ?)