elif first == True: cmd.extend(["--ab", "1"]) first = False else: cmd.extend(["--ab", "2"]) if args.v: cmd.append("--v") if args.low: cmd.append("--low") if args.flip: cmd.append("--flip") if args.capC: cmd.append("--capC") cmd = " ".join(cmd) job = General.jobOnCluster( ["pyr", cmd], pepid + " model" + str(m), pepid + "/model" + str(m) + ".out/.finished" ) job.submit(12) # job.submit(16) jobs.append(job) sleep(1) while len(jobs) > 0: sleep(300) for j in jobs: j.checkjob() if j.running == 0: jobs.remove(j) if j.checkfinish() == 0: print "Job about " + j.myid + " may have died ..." if j.tried > 3:
pdbs.sort() jobs = [] odir = os.getcwd() # h**o = '/home/anthill/fzheng/home/termanal_upgrade/caspHomoStrict/' h**o = "/home/anthill/fzheng/ironfs/prepareCASP/CASP10_benchmark/h**o/" for pdb in pdbs: caspid = pdb.split("/")[0] # caspid = pdb.split('.')[0] label = args.d + "/" + caspid + "/" + General.getBase(pdb) + "." + args.label if os.path.isfile(label): continue cmd = ["python", src, "--p", pdb, "--o", args.d + "/" + caspid, "--dontuse", h**o + caspid + ".h**o", "--hrs", "3"] cmd.append(args.opts) cmd = " ".join(cmd) job = General.jobOnCluster([cmd], os.getcwd(), os.path.realpath(label)) job.submit(3) jobs.append(job) sleep(0.5) while len(jobs) > 0: sleep(120) for j in jobs: j.checkjob() if j.running == 0: jobs.remove(j) if j.checkfinish() == 0: print "Job about " + j.myid + " may have died ..." # never gives up # if j.tried > 3: # print 'have failed 3 times, give up ...'
if args.wgap != None: pdb = args.wgap + '/' + mut.dir + '/' + pdb ## pos = PDB.findPositionInPDB(pdb, str(mut.n), mut.c) if pos == -1: print('cannot found the residue in fragment pdb: '+ pdb) continue pdb = General.removePath(pdb) cmd = ['python', selfbin +'/envForMatches.py','--m', matchf, '--n', str(pos-1), '--o', outname] if args.uplimit != None: cmd.extend(['--uplimit', args.uplimit]) if args.wgap != None: cmd.append('--wgap') cmd = ' '.join(cmd) job = General.jobOnCluster([cmd], mut.dir, os.path.realpath(outname)) job.submit(3) jobs.append(job) sleep(0.5) os.chdir(odir) while (len(jobs) > 0): sleep(120) for j in jobs: j.checkjob() if j.running == 0: jobs.remove(j) if j.checkfinish() == 0: print('Job about ' + j.myid + ' may have died ...') if j.tried > 3: