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 seq_2d_write(line):
  17    line=line.replace(" ", "")
  18    out='{:d}\n{:6.1f}\n'.format(len(line),50.0)
  19    for i in range(1,4):
  20      out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
  21    for e in line[:-3]:
  22      i+=1
  23      if e=='-':
  24        out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
  25      elif e=='H':
  26        out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
  27      elif e=='E':
  28        out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0)
  29    return(out)
  30
  31 def seq_2d_write_50(line):
  32    line=line.replace(" ", "")
  33    out='{:d}\n'.format(len(line))
  34    for i in range(1,4):
  35      out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
  36    for e in line[:-3]:
  37      i+=1
  38      if e=='-':
  39        out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
  40      elif e=='H':
  41        out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0,50.0)
  42      elif e=='E':
  43        out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0,50.0)
  44    return(out)
  45
  46 def write_ssbond(ssbond):
  47    list=[]
  48    if ssbond!='':
  49      ssbond=json.loads(ssbond)
  50      for e in ssbond:
  51            list.append(e[0])
  52            list.append(e[1])
  53      list_sorted=sorted(list)
  54
  55    if len(list)>0:
  56        return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\
  57             str(len(ssbond))+' '+' '.join(map(str,list))+'\n'
  58    else:
  59        return '0\n'
  60
  61
  62 @receiver(post_save, sender=Task)
  63 def write_on_task_save(sender, instance, **kwargs):
  64    if instance.ready and not instance.done and instance.running==0:
  65      if (not os.path.isdir(instance.jobdirname)):
  66         os.mkdir(instance.jobdirname)
  67 #     os.chdir(instance.jobdirname)
  68
  69
  70
  71 #md=Template('nstep=$nstep ntwe=100  ntwx=100   dt=0.20 damax=10.0 lang=1'+
  72 #   't_bath=300 reset_vel=0 respa ntime_split=1 maxtime_split=512 mdpdb')
  73 #wrapper = textwrap.TextWrapper(width=70)
  74 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
  75
  76      if  instance.unres_ff =='E0LL2Y':
  77       w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
  78 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000        &
  79 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000    &
  80 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25                                        &
  81 CUTOFF=7.00000 WCORR4=0.00000"""
  82      else:
  83       w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542              &
  84 WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000        &
  85 WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000    &
  86 WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000                      &
  87 CUTOFF=7.00000 WCORR4=0.00000"""
  88
  89
  90      with open(instance.jobdirname+'/file.inp','w') as f:
  91        f.write(instance.name + ' UNRES server job'+ '\n')
  92
  93        if instance.type == 'min' :
  94
  95           control_line = 'SEED='+str(instance.md_seed)+' ' \
  96              + instance.min_choice \
  97              + ' pdbstart pdbref ' \
  98              + ' BOXX='+str(instance.boxx) \
  99              + ' BOXY='+str(instance.boxy) \
 100              + ' BOXZ='+str(instance.boxz) +' '
 101           if not instance.min_overlap:
 102             control_line = control_line+'overlap '
 103           if not instance.min_searchsc:
 104             control_line = control_line+'nosearchsc '
 105           if instance.min_pdbout:
 106             control_line = control_line+'pdbout '
 107           if instance.min_unres_pdb:
 108             control_line = control_line+'unres_pdb '
 109
 110           type_line = 'print_min_ini print_min_res print_min_stat'\
 111             +' MAXMIN='+str(instance.min_maxmin)\
 112             +' MAXFUN='+str(instance.min_maxfun)
 113
 114
 115        seq=instance.md_seq.replace(" ","")
 116        dimen3=len(seq)
 117        if dimen3>1:
 118           if seq[0]=='X':
 119             dimen3-=1
 120           if seq[-1]=='X':
 121             dimen3-=1
 122
 123        nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym'
 124        seq2 = ''.join([c for c in seq if c in nogly])
 125
 126        dimen3=(dimen3+len(seq2))*3
 127
 128
 129        if instance.type == 'md' :
 130           control_line = 'SEED='+str(instance.md_seed)+' '\
 131            +instance.md_start +' md one_letter'\
 132            + ' BOXX='+str(instance.boxx) \
 133            + ' BOXY='+str(instance.boxy) \
 134            + ' BOXZ='+str(instance.boxz) +' '
 135
 136           if instance.md_pdbref:
 137              control_line = control_line+'pdbref '
 138
 139           type_line = 'reset_vel=0'\
 140              +' t_bath='+str(instance.md_temp)\
 141              +' nstep='+str(instance.md_nstep)\
 142              +' ntwe='+str(instance.md_ntwe)\
 143              +' ntwx='+str(instance.md_ntwx)\
 144              +' dt='+str(instance.md_dt)
 145           if instance.md_lang == 'langevin':
 146             type_line = type_line + ' lang=1 '
 147             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 148           if instance.md_lang == 'berendsen':
 149             type_line = type_line + ' lang=0 tbf '
 150             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 151           if instance.md_respa:
 152             type_line = type_line + ' respa '
 153           if instance.md_mdpdb:
 154             type_line = type_line + ' mdpdb '
 155
 156        if instance.type == 'remd' :
 157           control_line = 'SEED='+str(instance.md_seed)+' '\
 158            +instance.md_start +' re one_letter'\
 159            + ' BOXX='+str(instance.boxx) \
 160            + ' BOXY='+str(instance.boxy) \
 161            + ' BOXZ='+str(instance.boxz) +' '
 162
 163           if instance.md_pdbref:
 164              control_line = control_line+'pdbref '
 165
 166           cntrl_saxs=''
 167           if instance.saxs_data != '':
 168              lines=instance.saxs_data.split('\n')
 169              nsaxs=0
 170              for line in lines:
 171               if len(line.split())==2:
 172                nsaxs+=1
 173              cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad)
 174              control_line += cntrl_saxs
 175
 176           type_line = 'reset_vel='+ str(instance.remd_nstex)\
 177              +' nstep='+str(instance.md_nstep)\
 178              +' ntwe='+str(instance.md_ntwe)\
 179              +' ntwx='+str(instance.md_ntwx)\
 180              +' dt='+str(instance.md_dt)
 181           if instance.md_lang == 'langevin':
 182             type_line = type_line + ' lang=1 '
 183             type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
 184           if instance.md_lang == 'berendsen':
 185             type_line = type_line + ' lang=0 tbf '
 186             type_line = type_line + 'tau_bath='+str(instance.md_tau)
 187           if instance.md_respa:
 188             type_line = type_line + ' respa '
 189           if instance.md_mdpdb:
 190             type_line = type_line + ' mdpdb '
 191
 192           type_line2 = 'nrep='+str(instance.remd_nrep) \
 193              +' nstex='+str(instance.remd_nstex) \
 194              +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
 195              +' traj1file  rest1file TRAJCACHE=200'
 196
 197        if instance.md_start == 'pdbstart':
 198              type_line = type_line + ' preminim cart'
 199
 200        wrapper = textwrap.TextWrapper(width=70)
 201
 202        word_list = wrapper.wrap(text=control_line)
 203        for element in word_list[:-1]:
 204            f.write('{:79}'.format(element)+'&\n')
 205        f.write(word_list[-1]+'\n')
 206
 207        word_list = wrapper.wrap(text=type_line)
 208        for element in word_list[:-1]:
 209            f.write('{:79}'.format(element)+'&\n')
 210        f.write(word_list[-1]+'\n')
 211
 212        if instance.md_start == 'pdbstart':
 213          f.write('print_min_ini print_min_res print_min_stat\n')
 214
 215
 216        if instance.type == 'remd' :
 217           word_list = wrapper.wrap(text=type_line2)
 218           for element in word_list[:-1]:
 219               f.write('{:79}'.format(element)+'&\n')
 220           f.write(word_list[-1]+'\n')
 221
 222           tmp1=json.loads(instance.remd_multi_t)
 223           string1=" "
 224           word_list = wrapper.wrap(text=string1.join(tmp1))
 225           for element in word_list[:-1]:
 226               f.write('{:79}'.format(element)+'&\n')
 227           f.write(word_list[-1]+'\n')
 228
 229           tmp1=json.loads(instance.remd_multi_m)
 230           string1=" "
 231           word_list = wrapper.wrap(text=string1.join(tmp1))
 232           for element in word_list[:-1]:
 233               f.write('{:79}'.format(element)+'&\n')
 234           f.write(word_list[-1]+'\n')
 235
 236        if instance.saxs_data != '':
 237          w+=' wsaxs='+str(instance.wsaxs)
 238        f.write(w+'\n')
 239
 240
 241        if instance.type == 'min' or instance.md_start == 'pdbstart':
 242           f.write('plik.pdb\n')
 243           f.write(write_ssbond(instance.ssbond))
 244           if instance.md_seq_2d == '':
 245             f.write('0\n')
 246           else:
 247             f.write(seq_2d_write(instance.md_seq_2d))
 248
 249        if instance.type == 'md' and instance.md_start != 'pdbstart':
 250
 251           if instance.md_pdbref:
 252              f.write('plik.pdb\n')
 253           f.write(str(len(seq))+'\n')
 254           for i in range(0,len(seq),80):
 255              f.write(seq[i:i+80]+'\n')
 256           f.write('0\n')
 257           if instance.md_2d == '':
 258             f.write('0\n')
 259           else:
 260             f.write(seq_2d_write(instance.md_2d))
 261
 262
 263        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 264
 265           if instance.md_pdbref:
 266              f.write('plik.pdb\n')
 267           f.write(str(len(seq))+'\n')
 268           for i in range(0,len(seq),80):
 269              f.write(seq[i:i+80]+'\n')
 270           f.write('0\n')
 271           if instance.md_2d == '':
 272             f.write('0\n')
 273           else:
 274             f.write(seq_2d_write(instance.md_2d))
 275
 276
 277        if instance.saxs_data != '':
 278              lines=instance.saxs_data.split('\n')
 279              for line in lines:
 280               tmp=line.split()
 281               if len(tmp)==2:
 282                f.write(tmp[0]+' '+tmp[1]+'\n')
 283
 284
 285      if instance.type == 'min':
 286       os.chdir(instance.jobdirname)
 287       if  instance.unres_ff =='E0LL2Y':
 288         shutil.copy('../files/pbs.csh','.')
 289       else:
 290         shutil.copy('../files/pbs_new.csh','pbs.csh')
 291       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 292       os.chdir('..')
 293      elif instance.type == 'md':
 294       os.chdir(instance.jobdirname)
 295       if  instance.unres_ff =='E0LL2Y':
 296         f1 = open('../files/pbs_md.csh', 'r')
 297       else:
 298         f1 = open('../files/pbs_md_new.csh', 'r')
 299       f2 = open('pbs.csh', 'w')
 300       for line in f1:
 301            f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
 302       f1.close()
 303       f2.close()
 304
 305       f1 = open('file.seq', 'w')
 306       for i in range(0,len(seq),80):
 307              f1.write(seq[i:i+80]+'\n')
 308       f1.close()
 309
 310       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 311       os.chdir('..')
 312      else:
 313 # instance.type == 'remd'
 314       tmp1=json.loads(instance.remd_multi_m)
 315       nreplicas=sum(map(int, tmp1))
 316 # hardcoded for 4 core nodes with FGPROC=2
 317       nodes=int(nreplicas*2/4)
 318       reszta = nreplicas*2-nodes*4
 319       if reszta == 0 :
 320         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
 321       else:
 322         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
 323
 324       tmp_ss=''
 325       if instance.ssbond!='':
 326         ix=[]
 327         ii=0
 328         for i in range(0,len(seq)):
 329            if seq[i]=='X':
 330               ii=ii+1
 331            ix.append(ii)
 332         l=[]
 333         ss=json.loads(instance.ssbond)
 334         for e in ss:
 335            l.append(e[0]-ix[e[0]])
 336            l.append(e[1]-ix[e[1]])
 337         tmp_ss=' '.join(map(str,l))
 338
 339       os.chdir(instance.jobdirname)
 340       if  instance.unres_ff =='E0LL2Y':
 341         f1 = open('../files/pbs8.csh', 'r')
 342       else:
 343         f1 = open('../files/pbs8_new.csh', 'r')
 344       f2 = open('pbs8.csh', 'w')
 345       for line in f1:
 346           if '#PBS -l nodes=4:ppn=4' in line:
 347            f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
 348           elif '$ssbond' in line:
 349            f2.write(line.replace('$ssbond',tmp_ss))
 350           else:
 351            tmp1=json.loads(instance.remd_multi_t)
 352            f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
 353       f1.close()
 354       f2.close()
 355       os.chdir('..')
 356
 357 # write wham & cluster input
 358       with open(instance.jobdirname+'/file_wham.inp','w') as f:
 359           if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
 360               isampl=1
 361           else:
 362               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
 363
 364           if instance.md_pdbref:
 365             f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
 366                ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
 367           else:
 368             f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
 369               ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
 370           if instance.md_2d != '':
 371                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 372           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 373                     ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 374
 375           f.write('nres='+str(len(seq))+' one_letter\n')
 376           for i in range(0,len(seq),80):
 377              f.write(seq[i:i+80]+'\n')
 378
 379           f.write(write_ssbond(instance.ssbond))
 380
 381           if instance.md_2d != '':
 382              f.write(seq_2d_write_50(instance.md_2d))
 383
 384           if instance.saxs_data != '':
 385              fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
 386              lines=instance.saxs_data.split('\n')
 387              for line in lines:
 388               tmp=line.split()
 389               if len(tmp)==2:
 390                f.write(tmp[0]+' '+tmp[1]+'\n')
 391                fsaxs.write(tmp[0]+' '+tmp[1]+'\n')
 392              fsaxs.close()
 393
 394           f.write(w+'\n')
 395           f.write('\n')
 396           f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
 397           tmp1=json.loads(instance.remd_multi_t)
 398           for element in tmp1:
 399               f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
 400               f.write('kh= 0.0 Q0=0.0\n')
 401           rec=instance.md_nstep/instance.md_ntwx
 402           f.write('nfile_cx=1 rec_start='+str(rec/10)
 403                   +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
 404           f.write('file_MD000\n')
 405           if instance.md_pdbref:
 406              f.write('pdbref\n')
 407              f.write('plik.pdb\n')
 408
 409
 410       with open(instance.jobdirname+'/file_cluster.inp','w') as f:
 411           f.write(instance.name + ' UNRES server job'+ '\n')
 412           f.write('{:79}'.format('nres='+str(len(seq))
 413              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
 414              +' temper='+str(instance.remd_cluter_temp))+'&\n')
 415           if instance.md_2d != '':
 416                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
 417           f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
 418                   ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
 419           f.write(w+'\n')
 420           for i in range(0,len(seq),80):
 421              f.write(seq[i:i+80]+'\n')
 422           f.write(write_ssbond(instance.ssbond))
 423           if instance.md_2d != '':
 424              f.write(seq_2d_write_50(instance.md_2d))
 425           if instance.saxs_data != '':
 426              lines=instance.saxs_data.split('\n')
 427              for line in lines:
 428               tmp=line.split()
 429               if len(tmp)==2:
 430                f.write(tmp[0]+' '+tmp[1]+'\n')
 431
 432       os.chdir(instance.jobdirname)
 433       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 434       os.chdir('..')
 435
 436      print ret_code.stdout.readlines()
 437      logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
 438
 439 @receiver(post_delete, sender=Task)
 440 def delete_on_task_del(sender, instance, **kwargs):
 441    if instance.jobdirname:
 442       if os.path.isdir(instance.jobdirname):
 443          shutil.rmtree(instance.jobdirname)
 444          logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)
 445