RemoteSlurmJob: add support for passing addl_slurm_kwargs (0.2.0 rele…

…ase) (#4)

* RemoteSlurm: implement addl_slurm_kwargs

crimpl/common.py

@@ -5,7 +5,7 @@
 import json as _json
 from time import sleep as _sleep
 
-__version__ = '0.1.0'
+__version__ = '0.2.0'
 
 def _new_job_name():
     return _datetime.now().strftime('%Y.%m.%d-%H.%M.%S')
@@ -18,9 +18,9 @@ def _run_cmd(cmd, detach=False, log_cmd=True, allow_retries=True):
     while True:
         try:
             if detach:
-                ret = _subprocess.Popen(cmd, shell=True, stderr=_subprocess.DEVNULL)
+                ret = _subprocess.Popen(cmd, shell=True, stderr=_subprocess.STDOUT)
             else:
-                ret = _subprocess.check_output(cmd, shell=True, stderr=_subprocess.DEVNULL).decode('utf-8').strip()
+                ret = _subprocess.check_output(cmd, shell=True, stderr=_subprocess.STDOUT).decode('utf-8').strip()
         except _subprocess.CalledProcessError as err:
             # print("error output: {}".format(err.output))
             if allow_retries and err.returncode == 255 and i < 5:
@@ -315,10 +315,18 @@ def _submit_script_cmds(self, script, files, ignore_files,
         elif not self.conda_installed and conda_env is not False:
             raise ValueError("conda is not installed on the remote server.  Install manually or call server.install_conda()")
 
-        _slurm_kwarg_to_prefix = {'nprocs': '-n ',
-                                  'walltime': '-t ',
-                                  'mail_type': '--mail-type=',
-                                  'mail_user': '--mail-user='}
+        def _slurm_kwarg_to_prefix(k):
+            exceptions = {'nprocs': '-n ',
+                          'walltime': '-t ',
+                          'mail_type': '--mail-type=',
+                          'mail_user': '--mail-user='}
+            if k in exceptions.keys():
+                return exceptions.get(k)
+            elif len(k) == 1:
+                return f"-{k} "
+            else:
+                return f"--{k}="
+
 
         create_env_cmd, conda_env_path = self._create_conda_env(conda_env, isolate_env, job_name=job_name, check_if_exists=True, run_cmd=False)
 
@@ -336,7 +344,7 @@ def _submit_script_cmds(self, script, files, ignore_files,
                     sched_script += ["#SBATCH -J {}".format(job_name)]
                     for k,v in sched_kwargs.items():
                         if v is None: continue
-                        prefix = _slurm_kwarg_to_prefix.get(k, False)
+                        prefix = _slurm_kwarg_to_prefix(k)
                         if prefix is False:
                             raise NotImplementedError("slurm command for {} not implemented".format(k))
                         if k=='mail_type' and isinstance(v, list):

crimpl/remoteslurm.py

@@ -258,6 +258,7 @@ def submit_script(self, script, files=[],
                       walltime='2-00:00:00',
                       mail_type='END,FAIL',
                       mail_user=None,
+                      addl_slurm_kwargs={},
                       ignore_files=[],
                       wait_for_job_status=False,
                       trial_run=False):
@@ -301,6 +302,10 @@ def submit_script(self, script, files=[],
         * `mail_user` (string, optional, default=None): email to send notifications.
             If not provided or None, will default to the value in <RemoteSlurmServer.mail_user>.
             Prepended to `script` as "#SBATCH --mail_user=mail_user"
+        * `addl_slurm_kwargs` (dict, optional, default={}): additional kwargs
+            to pass to slurm.  Entries will be prepended to `script` as
+            "#SBATCH -<k> <v>" or "#SBATCH --<k>=<v>" depending on whether the
+            key (`k`) is a single character or multiple characters, respectively.
         * `ignore_files` (list, optional, default=[]): list of filenames on the
             remote server to ignore when calling <<class>.check_output>
         * `wait_for_job_status` (bool or string or list, optional, default=False):
@@ -341,7 +346,8 @@ def submit_script(self, script, files=[],
                                                nprocs=nprocs,
                                                walltime=walltime,
                                                mail_type=mail_type,
-                                               mail_user=mail_user if mail_user is not None else self.server.mail_user)
+                                               mail_user=mail_user if mail_user is not None else self.server.mail_user,
+                                               **addl_slurm_kwargs)
 
         if trial_run:
             return cmds
@@ -351,7 +357,13 @@ def submit_script(self, script, files=[],
             # TODO: get around need to add IP to known hosts (either by
             # expecting and answering yes, or by looking into subnet options)
 
-            out = self.server._run_server_cmd(cmd)
+            try:
+                out = self.server._run_server_cmd(cmd)
+            except _subprocess.CalledProcessError as e:
+                if addl_slurm_kwargs:
+                    raise ValueError(f"failed to submit to scheduler, addl_slurm_kwargs may be invalid.  Original error: {e.output}")
+                raise ValueError(f"failed to submit to scheduler.  Original error: {e.output}")
+
             if "sbatch" in cmd:
                 self._slurm_id = out.split(' ')[-1]
 
@@ -507,6 +519,7 @@ def submit_job(self, script, files=[],
                    walltime='2-00:00:00',
                    mail_type='END,FAIL',
                    mail_user=None,
+                   addl_slurm_kwargs={},
                    ignore_files=[],
                    wait_for_job_status=False,
                    trial_run=False):
@@ -525,6 +538,7 @@ def submit_job(self, script, files=[],
         * `walltime`: passed to <RemoteSlurmJob.submit_script>
         * `mail_type`: passed to <RemoteSlurmJob.submit_script>
         * `mail_user`: passed to <RemoteSlurmJob.submit_script>
+        * `addl_slurm_kwargs': pass to <RemoteSlurmJob.submit_script>`
         * `ignore_files`: passed to <RemoteSlurmJob.submit_script>
         * `wait_for_job_status`: passed to <RemoteSlurmJob.submit_script>
         * `trial_run`: passed to <RemoteSlurmJob.submit_script>
@@ -543,6 +557,7 @@ def submit_job(self, script, files=[],
                                walltime=walltime,
                                mail_type=mail_type,
                                mail_user=mail_user,
+                               addl_slurm_kwargs=addl_slurm_kwargs,
                                ignore_files=ignore_files,
                                wait_for_job_status=wait_for_job_status,
                                trial_run=trial_run)

setup.py

@@ -6,14 +6,14 @@
     long_description = fh.read()
 
 setup(name='crimpl',
-      version='0.1.0',
+      version='0.2.0',
       description='Compute Resources Made Simple',
       long_description=long_description,
       long_description_content_type="text/markdown",
       author='Kyle Conroy',
       author_email='[email protected]',
       url='https://www.github.com/kecnry/crimpl',
-      download_url = 'https://github.com/kecnry/crimpl/tarball/0.1.0',
+      download_url = 'https://github.com/kecnry/crimpl/tarball/0.2.0',
       packages=['crimpl'],
       install_requires=['boto3'],
       classifiers=[