Merge pull request #346 from Cloudac7/jump

supporting rev_mat parameters when using sys_rev_mat(#328) and other fix

Author: amcadmus

dpgen/__init__.py

@@ -8,7 +8,7 @@
 SHORT_CMD="dpgen"
 dlog = logging.getLogger(__name__)
 dlog.setLevel(logging.INFO)
-dlogf = logging.FileHandler(os.getcwd()+os.sep+SHORT_CMD+'.log')
+dlogf = logging.FileHandler(os.getcwd()+os.sep+SHORT_CMD+'.log', delay=True)
 dlogf_formatter=logging.Formatter('%(asctime)s - %(levelname)s : %(message)s')
 #dlogf_formatter=logging.Formatter('%(asctime)s - %(name)s - [%(filename)s:%(funcName)s - %(lineno)d ] - %(levelname)s \n %(message)s')
 dlogf.setFormatter(dlogf_formatter)

dpgen/dispatcher/LSF.py

@@ -108,7 +108,7 @@ def sub_script_head(self, res):
             if res['node_cpu']:
                 ret += '#BSUB -R span[ptile=%d]\n' % res['node_cpu']
             if res.get('new_lsf_gpu', False):
-                # supportted in LSF >= 10.1.0 SP6
+                # supported in LSF >= 10.1.0 SP6
                 # ref: https://www.ibm.com/support/knowledgecenter/en/SSWRJV_10.1.0/lsf_resource_sharing/use_gpu_res_reqs.html
                 ret += '#BSUB -n %d\n#BSUB -gpu "num=%d:mode=shared:j_exclusive=yes"\n' % (
                     res['numb_gpu'], res['task_per_node'])

dpgen/dispatcher/Slurm.py

@@ -81,6 +81,8 @@ def sub_script_head(self, res):
         ret += "#SBATCH -t %s\n" % res['time_limit']
         if res['mem_limit'] > 0 :
             ret += "#SBATCH --mem=%dG \n" % res['mem_limit']
+        if len(res['job_name']) > 0:
+            ret += '#SBATCH --job-name=%s\n' % res['job_name']
         if len(res['account']) > 0 :
             ret += "#SBATCH --account=%s \n" % res['account']
         if len(res['partition']) > 0 :

dpgen/generator/run.py

@@ -869,8 +869,10 @@ def _make_model_devi_revmat(iter_index, jdata, mdata, conf_systems):
                     shutil.copyfile(plm_templ, 'input.plumed')
                     with open('input.plumed') as fp:
                         plm_lines = fp.readlines()
+                    # allow using the same list as lmp
+                    # user should not use the same key name for plm
                     plm_lines = revise_by_keys(
-                        plm_lines, total_rev_keys[total_num_lmp:], total_rev_item[total_num_lmp:]
+                        plm_lines, total_rev_keys, total_rev_item
                     )
                     with open('input.plumed', 'w') as fp:
                         fp.write(''.join(plm_lines))