Merge branch 'feature/tweak-slurm' into develop

TurTLE/_code.py

@@ -4,18 +4,18 @@
 #                                                                              #
 #  This file is part of bfps.                                                  #
 #                                                                              #
-#  TurTLE is free software: you can redistribute it and/or modify                #
+#  TurTLE is free software: you can redistribute it and/or modify              #
 #  it under the terms of the GNU General Public License as published           #
 #  by the Free Software Foundation, either version 3 of the License,           #
 #  or (at your option) any later version.                                      #
 #                                                                              #
-#  TurTLE is distributed in the hope that it will be useful,                     #
+#  TurTLE is distributed in the hope that it will be useful,                   #
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of              #
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               #
 #  GNU General Public License for more details.                                #
 #                                                                              #
 #  You should have received a copy of the GNU General Public License           #
-#  along with TurTLE.  If not, see <http://www.gnu.org/licenses/>                #
+#  along with TurTLE.  If not, see <http://www.gnu.org/licenses/>              #
 #                                                                              #
 # Contact: Cristian.Lalescu@ds.mpg.de                                          #
 #                                                                              #
@@ -678,9 +678,9 @@ class _code(_base):
             script_file.write('#SBATCH -o ' + out_file + '\n')
 
         # set up environment
-        script_file.write('#SBATCH --get-user-env\n')
-        script_file.write('#SBATCH --partition={0}\n'.format(
-                self.host_info['environment']))
+        if self.host_info['explicit_slurm_environment']:
+            script_file.write('#SBATCH --partition={0}\n'.format(
+                    self.host_info['environment']))
         if 'account' in self.host_info.keys():
             script_file.write('#SBATCH --account={0}\n'.format(
                     self.host_info['account']))
@@ -717,11 +717,15 @@ class _code(_base):
 
         script_file.write('#SBATCH --mail-type=none\n')
         script_file.write('#SBATCH --time={0}:{1:0>2d}:00\n'.format(hours, minutes))
+        if 'extra_slurm_lines' in self.host_info.keys():
+            for line in self.host_info['extra_slurm_lines']:
+                script_file.write(line + '\n')
         ## following cleans up environment for job.
+        ## put these in the 'extra_slurm_lines' list if you need them
         ## make sure that "~/.config/TurTLE/bashrc" exists and builds desired job environment
-        script_file.write('#SBATCH --export=NONE\n')
-        script_file.write('#SBATCH --get-user-env\n')
-        script_file.write('source ~/.config/TurTLE/bashrc\n')
+        #script_file.write('#SBATCH --export=NONE\n')
+        #script_file.write('#SBATCH --get-user-env\n')
+        #script_file.write('source ~/.config/TurTLE/bashrc\n')
         if nb_threads_per_process > 1:
             script_file.write('export OMP_NUM_THREADS={0}\n'.format(nb_threads_per_process))
             script_file.write('export OMP_PLACES=cores\n')

pc_host_info.py

@@ -32,7 +32,9 @@ host_info = {'type' : 'pc'}
 #                  'deltanprocs' : info_template_deltanprocs,
 #                  'mail_address': info_template_mail_address,
 #                  'account'     : info_template_account,
-#                  'executable_launcher': info_template_executable_launcher}
+#                  'executable_launcher'         : info_template_executable_launcher,
+#                  'extra_slurm_lines'           : info_template_extra_slurm_lines,
+#                  'explicit_slurm_environment'  : info_template_explicit_slurm_environment}
 
 # info_template_type can be one of:
 # 'pc'            --- jobs run interactively
@@ -59,3 +61,13 @@ host_info = {'type' : 'pc'}
 # info_template_executable_launcher, relevant for 'SLURM' clusters,
 # is the binary that should be called to execute the hybrid MPI/OpenMP code.
 # by default it is 'srun', but it may be 'mpiexec' for some machines.
+
+# info_template_extra_slurm_lines, relevant for 'SLURM' clusters,
+# is a list of strings, written as extra options within the SLURM file.
+# for example something like `#SBATCH --get-user-env`
+
+# info_template_explicit_slurm_environment, relevant for `SLURM` clusters,
+# is a bool specifying whether the environment must be mentioned explicitly
+# in the submission script, or whether the cluster chooses it based on the
+# resources requested
+