#!/usr/bin/python import time, os, LGI; import math, sys; from shutil import rmtree # FUNCTION ENDS HERE #---------------------------------------------------------------------------------------------------------- def check_finished(CURRENT_DIRECTORY, Client, functional, millerindex ): print "Entering check_finished function...." print "Current date & time " + time.strftime("%c") LIST_FINISHED = Client.GetJobList( Application = "vasp535", State = "finished", Limit=1024); N_FINISHED = LIST_FINISHED[ 'LGI' ][ 'response' ][ 'number_of_jobs' ]; if (N_FINISHED > 1): #for JOB_FINISHED in LIST_FINISHED[ 'LGI' ][ 'response' ][ 'job' ][ : ][ 'job' ]: for job_num in range(0, N_FINISHED): #GET THE JOB ID JOB_FINISHED = LIST_FINISHED[ 'LGI' ][ 'response' ][ 'job' ][ job_num ][ 'job' ]; job_id = JOB_FINISHED[ 'job_id' ] job_specifics = JOB_FINISHED[ 'job_specifics' ] project = job_specifics[ 'project' ] if ( project == "NN" ): repository_url = job_specifics[ 'repository_url' ] folder = job_specifics[ 'foldername' ] func = job_specifics[ 'functional' ] mill = job_specifics[ 'millerindex' ] #only do something if the job is from batch if ( func == functional ) and ( str(mill) == millerindex ): #TRANSFER FILES #CHANGE THE DIRECTORY os.chdir("LGI_OUTPUT"); #MAKE A NEW DIRECTORY if os.path.isdir( folder ): rmtree( folder ) os.mkdir("%s" %(folder)); os.chdir("%s" %(folder)); #TRANFER FILE #Client.LGI_filetransfer download repository_url OUTCAR OSZICAR POSCAR vasprun.xml ; print "downloading: ", repository_url FileTransferClient = LGI.LGI_Client( URL = repository_url ); FileTransferClient.DownLoadFiles( [ "OUTCAR", "OSZICAR", "POSCAR", "vasprun.xml" ], "./" ); print "deleting job nr ", job_id Client.DeleteJob( job_id ); del FileTransferClient; #GO BACK TO WORKING DIRECTORY os.chdir(CURRENT_DIRECTORY); # FUNCTION ENDS HERE #---------------------------------------------------------------------------------------------------------- #ASK FOR THE CURRENT DIRECTORY CURRENT_DIRECTORY = os.getcwd() project = "NN" functional = "PBEa57-DF2" Queue = "long" maxwalltime= "72:00:00" maxram = "55" NCores = "16" Client = LGI.LGI_Client() Ntot = 10000 layers = 5 supercellx = 1 supercelly = 3 mil_h = 9 mil_k = 7 mil_l = 7 #LGI allows 2500 jobs to be in the queue per VASP version for all users combined: includes running, queued, and finished MAX_NUM_JOBS = 1000; #os.mkdir("LGI_OUTPUT"); COUNT = 0 COUNTFINISH = 0 restart_file = "restart_file_{0:d}{1:d}{2:d}".format( mil_h, mil_k, mil_l ) start_val = 0 #check whether the restart_file exists # and if it exists, then read the start value if os.path.isfile(restart_file) : data_list = open(restart_file, "r").readline() start_val = int(data_list) + 1 # plus 1 as this is the geometry we want to submit, the restart file contains the last submitted geometry print "RESTART FILE FOUND" else : start_val = 0 print "NO RESTART_FILE, START FROM SCRATCH" print "START VALUE IS ", start_val, "\n" foldername = "LGI_OUTPUT/{:d}{:d}{:d}-{:d}x{:d}-{:d}L".format(mil_h, mil_k, mil_l, supercellx, supercelly, layers) if not os.path.isdir( foldername ): os.mkdir( foldername ) start_val = 0 #start submit loop for idx in range(start_val, Ntot): #folder name we are going to give to job_specifics together with functional foldername = "{:d}{:d}{:d}-{:d}x{:d}-{:d}L/{:0>6d}".format(mil_h, mil_k, mil_l, supercellx, supercelly, layers, idx) print(foldername) if os.path.isdir( "LGI_OUTPUT/" + foldername ): print('WARNING: folder already exists') continue # exit(1) if idx < 2000: Zmin = 2.0 Zmax = 8.0 rmin = 0.5 rmax = 1.5 surface_motion = False elif idx > 1999 and idx < 10000: Zmin = 0.3 Zmax = 2.5 rmin = 0.5 rmax = 2.5 surface_motion = False else: print('WARNING: Z and r are not defined') exit(1) os.system( './slab_H2-poscar.py {:d} {:d} {:d} {:d} {:d} {:d} {:f} {:f} {:f} {:f} {:s}'.format( layers, supercellx, supercelly, mil_h, mil_k, mil_l, Zmin, Zmax, rmin, rmax, str(surface_motion) ) ) # FIRST: ASK LGI HOW MANY JOBS ARE RUNNING # AND HOW MANY JOBS ARE QUEUED # IF THE NUMBER OF QUEUED JOBS IS LARGER THEN MAX_NUM_QUEUED_JOB # THEN FALL ASLEEP, OTHERWISE CONTINUE WITH SUBMITTING JOBS CONTINUE_VAR = 1 ; while CONTINUE_VAR == 1 : LIST_QUEUED = Client.GetJobList( Application = "vasp535", State = "queued", Limit=0 ); LIST_RUNNING = Client.GetJobList( Application = "vasp535", State = "running", Limit=0); N_QUEUED = LIST_QUEUED[ 'LGI' ][ 'response' ][ 'number_of_jobs' ] ; N_RUNNING = LIST_RUNNING[ 'LGI' ][ 'response' ][ 'number_of_jobs' ]; print "queued:", N_QUEUED, "running: ", N_RUNNING #Check if not too many jobs if (N_QUEUED + N_RUNNING < MAX_NUM_JOBS ): CONTINUE_VAR = 0 else: time.sleep(600) #IF THERE ARE ABORTED JOBS THEN DELETE THEM LIST_ABORTED = Client.GetJobList( Application = "vasp535", State = "aborted", Limit=1024); N_ABORTED = LIST_ABORTED[ 'LGI' ][ 'response' ][ 'number_of_jobs' ]; if N_ABORTED > 1: for job_num in range(0, N_ABORTED): JOB_ABORTED = LIST_ABORTED[ 'LGI' ][ 'response' ][ 'job' ][ job_num ][ 'job' ]; job_id = JOB_ABORTED[ 'job_id' ]; job_specifics = JOB_ABORTED[ 'job_specifics' ]; repository_url = job_specifics[ 'repository_url' ] ; Client.DeleteJob( job_id ); ## SECOND: CREATE AND SUBMIT A JOB # you can add your own keys to the job by adding to job specifics value JOB = Client.SubmitJob( Application = "vasp535", TargetResources = "mark@octo.wks.gorlaeus.net,mark@erc1.wks.gorlaeus.net,mark@erc2.wks.gorlaeus.net,mark@epyc.tc.lic.leidenuniv.nl", #TargetResources = "mark@octo.wks.gorlaeus.net,mark@erc1.wks.gorlaeus.net,mark@erc2.wks.gorlaeus.net,mark@epyc.tc.lic.leidenuniv.nl,somers@cartesius.surfsara.nl", FileList = [ "./INPUTS/INCAR", "./INPUTS/vdw_kernel.bindat", "./INPUTS/POTCAR", "./POSCAR", "./INPUTS/KPOINTS" ], #now job specifics -- here we can give specifiers for the job in xml format JobSpecifics = " {0} {1} {2} {3} {4} {5} {6} {7} {8} ".format(functional, foldername, maxwalltime, maxram, project, Queue, NCores, idx, str(mil_h)+str(mil_k)+str(mil_l)) ) COUNT = COUNT + 1; print " Number of Jobs submitted ", COUNT #write restart file fout_file = open(restart_file, "w") fout_file.write("{:d}".format( idx )) fout_file.close() #now check for finished jobs check_finished(CURRENT_DIRECTORY, Client, functional, str(mil_h)+str(mil_k)+str(mil_l) ) print print "entering retrieval loop" CONTINUE_VAR = 1 ; while CONTINUE_VAR == 1 : check_finished(CURRENT_DIRECTORY, Client, functional, str(mil_h)+str(mil_k)+str(mil_l) ) print "Going to sleep ......" time.sleep(1800);