django_simple/todo/jobfiles.py

   1 import logging
   2
   3 from django.db.models.signals import post_save, post_delete
   4 from django.dispatch import receiver
   5 from .models import Task
   6 import os
   7 import shutil
   8 import subprocess
   9 import json
  10 from string import Template
  11 import textwrap
  12
  13 logging.basicConfig()
  14 logger = logging.getLogger(__name__)
  15
  16 def write_ssbond(ssbond):
  17      list=[]
  18      ssbond=json.loads(ssbond)
  19      for e in ssbond:
  20            list.append(e[0])
  21            list.append(e[1])
  22      list_sorted=sorted(list)
  23
  24      if len(list)>0:
  25        return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\
  26             str(len(ssbond))+' '+' '.join(map(str,list))+'\n'
  27      else:
  28        return '0\n'
  29
  30
  31 @receiver(post_save, sender=Task)
  32 def write_on_task_save(sender, instance, **kwargs):
  33    if instance.ready and not instance.done and instance.running==0:
  34      if (not os.path.isdir(instance.jobdirname)):
  35         os.mkdir(instance.jobdirname)
  36 #     os.chdir(instance.jobdirname)
  37
  38
  39
  40 #md=Template('nstep=$nstep ntwe=100  ntwx=100   dt=0.20 damax=10.0 lang=1'+
  41 #   't_bath=300 reset_vel=0 respa ntime_split=1 maxtime_split=512 mdpdb')
  42 #wrapper = textwrap.TextWrapper(width=70)
  43 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
  44
  45      if  instance.unres_ff =='E0LL2Y':
  46       w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
  47 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000        &
  48 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000    &
  49 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25                                        &
  50 CUTOFF=7.00000 WCORR4=0.00000
  51 """
  52      else:
  53       w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542              &
  54 WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000        &
  55 WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000    &
  56 WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000                      &
  57 CUTOFF=7.00000 WCORR4=0.00000
  58 """
  59
  60
  61      with open(instance.jobdirname+'/file.inp','w') as f:
  62        f.write(instance.name + ' UNRES server job'+ '\n')
  63
  64        if instance.type == 'min' :
  65
  66           control_line = 'SEED='+str(instance.md_seed)+' ' \
  67              + instance.min_choice \
  68              + ' pdbstart pdbref BOXX=1000. BOXY=1000. BOXZ=1000. '
  69           if not instance.min_overlap:
  70             control_line = control_line+'overlap '
  71           if not instance.min_searchsc:
  72             control_line = control_line+'nosearchsc '
  73           if instance.min_pdbout:
  74             control_line = control_line+'pdbout '
  75           if instance.min_unres_pdb:
  76             control_line = control_line+'unres_pdb '
  77
  78           type_line = 'print_min_ini print_min_res print_min_stat'\
  79             +' MAXMIN='+str(instance.min_maxmin)\
  80             +' MAXFUN='+str(instance.min_maxfun)
  81
  82
  83        seq=instance.md_seq.replace(" ","")
  84        dimen3=len(seq)
  85        if dimen3>1:
  86           if seq[0]=='X':
  87             dimen3-=1
  88           if seq[-1]=='X':
  89             dimen3-=1
  90
  91        nogly ='CDSQKIPTFNHLRWAVEYM'
  92        seq2 = ''.join([c for c in seq if c in nogly])
  93
  94        dimen3=(dimen3+len(seq2))*3
  95
  96
  97        if instance.type == 'md' :
  98           control_line = 'SEED='+str(instance.md_seed)+' '\
  99            +instance.md_start +' md one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
 100           if instance.md_pdbref:
 101              control_line = control_line+'pdbref '
 102
 103           type_line = 'reset_vel=0'\
 104              +' t_bath='+str(instance.md_temp)\
 105              +' nstep='+str(instance.md_nstep)\
 106              +' ntwe='+str(instance.md_ntwe)\
 107              +' ntwx='+str(instance.md_ntwx)\
 108              +' dt='+str(instance.md_dt)
 109           if instance.md_lang == 'langevin':
 110             type_line = type_line + ' lang=1 '
 111             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 112           if instance.md_lang == 'berendsen':
 113             type_line = type_line + ' lang=0 tbf '
 114             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 115           if instance.md_respa:
 116             type_line = type_line + ' respa '
 117           if instance.md_mdpdb:
 118             type_line = type_line + ' mdpdb '
 119
 120        if instance.type == 'remd' :
 121           control_line = 'SEED='+str(instance.md_seed)+' '\
 122            +instance.md_start +' re one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
 123           if instance.md_pdbref:
 124              control_line = control_line+'pdbref '
 125
 126
 127           type_line = 'reset_vel='+ str(instance.remd_nstex)\
 128              +' nstep='+str(instance.md_nstep)\
 129              +' ntwe='+str(instance.md_ntwe)\
 130              +' ntwx='+str(instance.md_ntwx)\
 131              +' dt='+str(instance.md_dt)
 132           if instance.md_lang == 'langevin':
 133             type_line = type_line + ' lang=1 '
 134             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 135           if instance.md_lang == 'berendsen':
 136             type_line = type_line + ' lang=0 tbf '
 137             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 138           if instance.md_respa:
 139             type_line = type_line + ' respa '
 140           if instance.md_mdpdb:
 141             type_line = type_line + ' mdpdb '
 142
 143           type_line2 = 'nrep='+str(instance.remd_nrep) \
 144              +' nstex='+str(instance.remd_nstex) \
 145              +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
 146              +' traj1file  rest1file TRAJCACHE=200'
 147
 148        if instance.md_start == 'pdbstart':
 149              type_line = type_line + ' preminim cart'
 150
 151        wrapper = textwrap.TextWrapper(width=70)
 152
 153        word_list = wrapper.wrap(text=control_line)
 154        for element in word_list[:-1]:
 155            f.write('{:79}'.format(element)+'&\n')
 156        f.write(word_list[-1]+'\n')
 157
 158        word_list = wrapper.wrap(text=type_line)
 159        for element in word_list[:-1]:
 160            f.write('{:79}'.format(element)+'&\n')
 161        f.write(word_list[-1]+'\n')
 162
 163        if instance.md_start == 'pdbstart':
 164          f.write('print_min_ini print_min_res print_min_stat\n')
 165
 166
 167        if instance.type == 'remd' :
 168           word_list = wrapper.wrap(text=type_line2)
 169           for element in word_list[:-1]:
 170               f.write('{:79}'.format(element)+'&\n')
 171           f.write(word_list[-1]+'\n')
 172
 173           tmp1=json.loads(instance.remd_multi_t)
 174           string1=" "
 175           word_list = wrapper.wrap(text=string1.join(tmp1))
 176           for element in word_list[:-1]:
 177               f.write('{:79}'.format(element)+'&\n')
 178           f.write(word_list[-1]+'\n')
 179
 180           tmp1=json.loads(instance.remd_multi_m)
 181           string1=" "
 182           word_list = wrapper.wrap(text=string1.join(tmp1))
 183           for element in word_list[:-1]:
 184               f.write('{:79}'.format(element)+'&\n')
 185           f.write(word_list[-1]+'\n')
 186
 187        f.write(w)
 188
 189
 190        if instance.type == 'min' or instance.md_start == 'pdbstart':
 191           f.write('plik.pdb\n')
 192           f.write(write_ssbond(instance.ssbond))
 193           f.write('0\n')
 194
 195
 196        if instance.type == 'md' and instance.md_start != 'pdbstart':
 197
 198           if instance.md_pdbref:
 199              f.write('plik.pdb\n')
 200           f.write(str(len(seq))+'\n')
 201           for i in range(0,len(seq),80):
 202              f.write(seq[i:i+80]+'\n')
 203           f.write('0\n0\n')
 204
 205        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 206
 207           if instance.md_pdbref:
 208              f.write('plik.pdb\n')
 209           f.write(str(len(seq))+'\n')
 210           for i in range(0,len(seq),80):
 211              f.write(seq[i:i+80]+'\n')
 212           f.write('0\n0\n')
 213
 214
 215
 216
 217      if instance.type == 'min':
 218       os.chdir(instance.jobdirname)
 219       if  instance.unres_ff =='E0LL2Y':
 220         shutil.copy('../files/pbs.csh','.')
 221       else:
 222         shutil.copy('../files/pbs_new.csh','pbs.csh')
 223       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 224       os.chdir('..')
 225      elif instance.type == 'md':
 226       os.chdir(instance.jobdirname)
 227       if  instance.unres_ff =='E0LL2Y':
 228         f1 = open('../files/pbs_md.csh', 'r')
 229       else:
 230         f1 = open('../files/pbs_md_new.csh', 'r')
 231       f2 = open('pbs.csh', 'w')
 232       for line in f1:
 233            f2.write(line.replace('$dimen3',str(dimen3) ))
 234       f1.close()
 235       f2.close()
 236
 237       f1 = open('file.seq', 'w')
 238       for i in range(0,len(seq),80):
 239              f1.write(seq[i:i+80]+'\n')
 240       f1.close()
 241
 242       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 243       os.chdir('..')
 244      else:
 245 # instance.type == 'remd'
 246       tmp1=json.loads(instance.remd_multi_m)
 247       nreplicas=sum(map(int, tmp1))
 248 # hardcoded for 4 core nodes with FGPROC=2
 249       nodes=int(nreplicas*2/4)
 250       reszta = nreplicas*2-nodes*4
 251       if reszta == 0 :
 252         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
 253       else:
 254         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
 255
 256       os.chdir(instance.jobdirname)
 257       if  instance.unres_ff =='E0LL2Y':
 258         f1 = open('../files/pbs8.csh', 'r')
 259       else:
 260         f1 = open('../files/pbs8_new.csh', 'r')
 261       f2 = open('pbs8.csh', 'w')
 262       for line in f1:
 263           if '#PBS -l nodes=4:ppn=4' in line:
 264            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
 265           else:
 266            tmp1=json.loads(instance.remd_multi_t)
 267            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
 268       f1.close()
 269       f2.close()
 270       os.chdir('..')
 271
 272 # write wham & cluster input
 273       with open(instance.jobdirname+'/file_wham.inp','w') as f:
 274           if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
 275               isampl=1
 276           else:
 277               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
 278
 279           if instance.md_pdbref:
 280             f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
 281                ' einicheck=1 rescale=2 delta=0.02 cxfile classify\n')
 282           else:
 283             f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
 284               ' einicheck=1 rescale=2 delta=0.02 cxfile\n')
 285           f.write('nres='+str(len(seq))+' one_letter\n')
 286           for i in range(0,len(seq),80):
 287              f.write(seq[i:i+80]+'\n')
 288
 289           f.write(write_ssbond(instance.ssbond))
 290
 291
 292           f.write(w)
 293           f.write('\n')
 294           f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
 295           tmp1=json.loads(instance.remd_multi_t)
 296           for element in tmp1:
 297               f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
 298               f.write('kh= 0.0 Q0=0.0\n')
 299           rec=instance.md_nstep/instance.md_ntwx
 300           f.write('nfile_cx=1 rec_start='+str(rec/10)
 301                   +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
 302           f.write('file_MD000\n')
 303           if instance.md_pdbref:
 304              f.write('pdbref\n')
 305              f.write('plik.pdb\n')
 306
 307
 308       with open(instance.jobdirname+'/file_cluster.inp','w') as f:
 309           f.write(instance.name + ' UNRES server job'+ '\n')
 310           f.write('nres='+str(len(seq))
 311              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
 312              +' temper='+str(instance.remd_cluter_temp)+'\n')
 313           f.write(w)
 314           for i in range(0,len(seq),80):
 315              f.write(seq[i:i+80]+'\n')
 316           f.write(write_ssbond(instance.ssbond))
 317
 318       os.chdir(instance.jobdirname)
 319       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 320       os.chdir('..')
 321
 322      print ret_code.stdout.readlines()
 323      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
 324
 325 @receiver(post_delete, sender=Task)
 326 def delete_on_task_del(sender, instance, **kwargs):
 327    if instance.jobdirname:
 328       if os.path.isdir(instance.jobdirname):
 329          shutil.rmtree(instance.jobdirname)
 330          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)
 331