pbs qdel not done jobs on rm

[django_unres.git] / django_simple / todo / jobfiles.py

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index e38d7ae..e7ee716 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -72,7 +72,7 @@ def write_ssbond(ssbond):
 
 @receiver(post_save, sender=Task)
 def write_on_task_save(sender, instance, **kwargs):
-   if instance.ready and not instance.done and instance.running==0:
+   if instance.ready and not instance.done and instance.running==0 and instance.pbsjob=='':
      if (not os.path.isdir(instance.jobdirname)):
         os.mkdir(instance.jobdirname)
 #     os.chdir(instance.jobdirname)
@@ -183,7 +183,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
            + ' BOXZ='+str(instance.boxz) +' '
           
           if instance.type == 'dock':
-             control_line = control_line+'CONSTR_HOMOL=20 '             
+             control_line = control_line+'CONSTR_HOMOL=24 '             
            
           if instance.md_pdbref:
              control_line = control_line+'pdbref '
@@ -272,7 +272,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
 
        if instance.type == 'min' or instance.md_start == 'pdbstart':
           if instance.type == 'dock':
-            f.write('model01.pdb\n')
+            f.write('plik1ter.pdb\n')
           else:  
             f.write('plik.pdb\n')
           f.write(write_ssbond(instance.ssbond))
@@ -289,7 +289,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           f.write('READ2SIGMA START_FROM_MODELS\n')
           for i in range(1,10):
            f.write('model0'+str(i)+'.pdb\n')
-          for i in range(10,21):
+          for i in range(10,25):
            f.write('model'+str(i)+'.pdb\n')
 
        if instance.type == 'md' and instance.md_start != 'pdbstart':
@@ -408,7 +408,13 @@ CUTOFF=7.00000 WCORR4=0.00000"""
            f2.write(line.replace('$ssbond',tmp_ss))
           elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
             f2.write(line)
-            f2.write('../files/generator_v7 plik.pdb plik2.pdb\n')
+            if instance.dock_peptide:
+             f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n')
+            else:
+             f2.write('../files/generator_v13 plik.pdb plik2.pdb 0 \n')
+            f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n")
+            f2.write("echo TER >>  plik1ter.pdb \n")
+            f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n")            
           else:
            tmp1=json.loads(instance.remd_multi_t)
            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
@@ -439,7 +445,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if instance.md_2d != '':
                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
           if instance.type == 'dock':
-               f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=20')+'&\n')
+               f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=24')+'&\n')
           if instance.unres_ff =='NEWCT-9P':
                f.write('{:79}'.format('tormode=2 ')+'&\n')
           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
@@ -456,7 +462,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
             f.write('READ2SIGMA \n')
             for i in range(1,10):
               f.write('model0'+str(i)+'.pdb\n')
-            for i in range(10,21):
+            for i in range(10,25):
               f.write('model'+str(i)+'.pdb\n')
 
           if instance.md_2d != '':
@@ -497,7 +503,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           f.write('file_MD000\n')
           if instance.md_pdbref:
              f.write('pdbref\n')
-             f.write('plik.pdb\n')
+             if instance.type == 'dock':
+              f.write('plik1ter.pdb\n')
+             else:
+              f.write('plik.pdb\n')
 
            
       with open(instance.jobdirname+'/file_cluster.inp','w') as f:
@@ -508,7 +517,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if instance.md_2d != '':
                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
           if instance.type == 'dock':
-               f.write('{:79}'.format(' CONSTR_HOMOL=20')+'&\n')
+               f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n')
           if instance.unres_ff =='NEWCT-9P':
                f.write('{:79}'.format('tormode=2 ')+'&\n')
           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
@@ -522,7 +531,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
             f.write('READ2SIGMA \n')
             for i in range(1,10):
               f.write('model0'+str(i)+'.pdb\n')
-            for i in range(10,21):
+            for i in range(10,25):
               f.write('model'+str(i)+'.pdb\n')
           if instance.md_2d != '':
              f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
@@ -536,14 +545,28 @@ CUTOFF=7.00000 WCORR4=0.00000"""
       os.chdir(instance.jobdirname)  
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
       os.chdir('..')
+      
+     output = str(ret_code.communicate()[0])
+     output=output.strip()
+     if output=='':
+       output='error'
+     logger.warning("PBS \"%s\" " % output)
+     instance.pbsjob = output
+     instance.save()
      
-     print ret_code.stdout.readlines()
+#     print ret_code.stdout.readlines()
      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
      
 @receiver(post_delete, sender=Task)
 def delete_on_task_del(sender, instance, **kwargs):     
    if instance.jobdirname:
       if os.path.isdir(instance.jobdirname):
+         if not instance.done:
+           ret_code_qdel = subprocess.Popen(' /opt/torque/bin/qdel '+str(instance.pbsjob), shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+           output = str(ret_code_qdel.communicate()[0])
+           output=output.strip()
+           logger.warning("PBS qdel \"%s\" " % instance.pbsjob)
+           logger.warning("QDEL \"%s\" " % output)
          shutil.rmtree(instance.jobdirname)
          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)         
          
\ No newline at end of file