if instance.ready and not instance.done and instance.running==0:
if (not os.path.isdir(instance.jobdirname)):
os.mkdir(instance.jobdirname)
- os.chdir(instance.jobdirname)
+# os.chdir(instance.jobdirname)
#wrapper = textwrap.TextWrapper(width=70)
#word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
- w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
+ if instance.unres_ff =='E0LL2Y':
+ w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &
WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &
WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25 &
CUTOFF=7.00000 WCORR4=0.00000
"""
+ else:
+ w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542 &
+WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000 &
+WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000 &
+CUTOFF=7.00000 WCORR4=0.00000
+"""
+
- with open('file.inp','w') as f:
+ with open(instance.jobdirname+'/file.inp','w') as f:
f.write(instance.name + ' UNRES server job'+ '\n')
if instance.type == 'min' :
if instance.type == 'min':
- shutil.copy('../files/pbs.csh','.')
+ os.chdir(instance.jobdirname)
+ if instance.unres_ff =='E0LL2Y':
+ shutil.copy('../files/pbs.csh','.')
+ else:
+ shutil.copy('../files/pbs_new.csh','pbs.csh')
ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+ os.chdir('..')
elif instance.type == 'md':
- f1 = open('../files/pbs_md.csh', 'r')
+ os.chdir(instance.jobdirname)
+ if instance.unres_ff =='E0LL2Y':
+ f1 = open('../files/pbs_md.csh', 'r')
+ else:
+ f1 = open('../files/pbs_md_new.csh', 'r')
f2 = open('pbs.csh', 'w')
for line in f1:
f2.write(line.replace('$dimen3',str(dimen3) ))
f1.close()
ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+ os.chdir('..')
else:
+# instance.type == 'remd'
tmp1=json.loads(instance.remd_multi_m)
nreplicas=sum(map(int, tmp1))
-
# hardcoded for 4 core nodes with FGPROC=2
nodes=int(nreplicas*2/4)
reszta = nreplicas*2-nodes*4
else:
pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
- f1 = open('../files/pbs8.csh', 'r')
+ os.chdir(instance.jobdirname)
+ if instance.unres_ff =='E0LL2Y':
+ f1 = open('../files/pbs8.csh', 'r')
+ else:
+ f1 = open('../files/pbs8_new.csh', 'r')
f2 = open('pbs8.csh', 'w')
for line in f1:
if '#PBS -l nodes=4:ppn=4' in line:
f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
else:
tmp1=json.loads(instance.remd_multi_t)
- f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'"'))
+ f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
f1.close()
- f2.close()
+ f2.close()
+ os.chdir('..')
# write wham & cluster input
- with open('file_wham.inp','w') as f:
+ with open(instance.jobdirname+'/file_wham.inp','w') as f:
if instance.md_nstep/instance.remd_nstex*nreplicas<=8000:
isampl=1
else:
f.write('plik.pdb\n')
- with open('file_cluster.inp','w') as f:
+ with open(instance.jobdirname+'/file_cluster.inp','w') as f:
f.write(instance.name + ' UNRES server job'+ '\n')
f.write('nres='+str(len(seq))
+' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
for i in range(0,len(seq),80):
f.write(seq[i:i+80]+'\n')
f.write(write_ssbond(instance.ssbond))
-
+
+ os.chdir(instance.jobdirname)
ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+ os.chdir('..')
print ret_code.stdout.readlines()
- os.chdir('..')
logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
@receiver(post_delete, sender=Task)