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GaussianZiggy.py
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GaussianZiggy.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Wed Apr 19 15:56:54 2019
@author: ke291
Contains all of the specific code for running Gaussian jobs on Ziggy.
A lot of code is reused from Gaussian.py. Called by PyDP4.py.
"""
import subprocess
import socket
import os
import time
import math
import Gaussian
SetupNMRCalcs = Gaussian.SetupNMRCalcs
SetupECalcs = Gaussian.SetupECalcs
SetupOptCalcs = Gaussian.SetupOptCalcs
ReadShieldings = Gaussian.ReadShieldings
ReadEnergies = Gaussian.ReadEnergies
ReadGeometries = Gaussian.ReadGeometries
IsGausCompleted = Gaussian.IsGausCompleted
Converged = Gaussian.Converged
def RunNMRCalcs(Isomers, settings):
print('\nRunning Gaussian NMR calculations on Ziggy...')
# Run Gaussian jobs on Ziggy cluster in folder named after date and time
# Split in batches, if needed
jobdir = os.getcwd()
os.chdir('nmr')
GausJobs = []
for iso in Isomers:
GausJobs.extend([x for x in iso.NMRInputFiles if (x[:-4] + '.out') not in iso.NMROutputFiles])
Completed = RunCalcs(GausJobs, settings)
for iso in Isomers:
iso.NMROutputFiles.extend([x[:-4] + '.out' for x in iso.NMRInputFiles if (x[:-4] + '.out') in Completed])
os.chdir(jobdir)
return Isomers
def RunECalcs(Isomers, settings):
print('\nRunning Gaussian DFT energy calculations on Ziggy...')
jobdir = os.getcwd()
os.chdir('e')
GausJobs = []
for iso in Isomers:
GausJobs.extend([x for x in iso.EInputFiles if (x[:-4] + '.out') not in iso.EOutputFiles])
Completed = RunCalcs(GausJobs, settings)
for iso in Isomers:
iso.EOutputFiles.extend([x[:-4] + '.out' for x in iso.EInputFiles if (x[:-4] + '.out') in Completed])
os.chdir(jobdir)
return Isomers
def RunOptCalcs(Isomers, settings):
print('\nRunning Gaussian DFT geometry optimizations on Ziggy...')
jobdir = os.getcwd()
os.chdir('opt')
GausJobs = []
for iso in Isomers:
GausJobs.extend([x for x in iso.OptInputFiles if (x[:-4] + '.out') not in iso.OptOutputFiles])
Completed = RunCalcs(GausJobs, settings)
for iso in Isomers:
iso.OptOutputFiles.extend([x[:-4] + '.out' for x in iso.OptInputFiles if (x[:-4] + '.out') in Completed])
os.chdir(jobdir)
return Isomers
def RunCalcs(GausJobs, settings):
MaxCon = settings.MaxConcurrentJobsZiggy
if len(GausJobs) < MaxCon:
if len(GausJobs) > 0:
RunBatchOnZiggy(0, settings.queue, GausJobs, settings)
else:
if len(GausJobs) > 0:
print("The DFT calculations will be done in " + \
str(math.ceil(len(GausJobs) / MaxCon)) + " batches")
i = 0
while (i + 1) * MaxCon < len(GausJobs):
print("Starting batch nr " + str(i + 1))
RunBatchOnZiggy(str(i + 1), settings.queue, GausJobs[(i * MaxCon):((i + 1) * MaxCon)], settings)
i += 1
print("Starting batch nr " + str(i + 1))
RunBatchOnZiggy(str(i + 1), settings.queue, GausJobs[(i * MaxCon):], settings)
NCompleted = 0
Completed = []
for f in GausJobs:
if IsGausCompleted(f[:-4] + '.out'):
Completed.append(f[:-4] + '.out')
NCompleted += 1
if NCompleted > 0:
print(str(NCompleted) + " Gaussian jobs of " + str(len(GausJobs)) + \
" completed successfully.")
elif len(GausJobs) == 0:
print("There were no jobs to run.")
return Completed
def RunBatchOnZiggy(findex, queue, GausFiles, settings):
# Run Gaussian jobs on Ziggy cluster in folder named after date and time
# Split in batches, if needed
if findex == 0:
folder = settings.StartTime + settings.Title
else:
folder = settings.StartTime + findex + settings.Title
print("Setting up jobs for running on ziggy...\n")
#Check that folder does not exist, create job folder on ziggy
outp = subprocess.check_output('ssh ziggy ls', shell=True)
if folder in outp.decode():
print("Folder exists on ziggy, choose another folder name.")
return
outp = subprocess.check_output('ssh ziggy mkdir ' + folder, shell=True)
print("Results folder: " + folder)
#Write the qsub scripts
for f in GausFiles:
WriteSubScript(f, queue, folder, settings)
print(str(len(GausFiles)) + ' slurm scripts generated')
#Upload .com files and .qsub files to directory
print("Uploading files to ziggy...")
for f in GausFiles:
outp = subprocess.check_output('scp ' + f +' ziggy:~/' + folder,
shell=True)
outp = subprocess.check_output('scp ' + f[:-4] +'slurm ziggy:~/' +
folder, shell=True)
print(str(len(GausFiles)) + ' .com and slurm files uploaded to ziggy')
JobIDs = []
#Launch the calculations
for f in GausFiles:
job = '~/' + folder + '/' + f[:-4]
outp = subprocess.check_output('ssh ziggy sbatch ' + job + 'slurm', shell=True)
status = outp.decode()[:-1]
print(status)
JobIDs.append(status.split('job ')[1])
print(str(len(GausFiles)) + ' jobs submitted to the queue on ziggy')
outp = subprocess.check_output('ssh ziggy qstat', shell=True)
if settings.user in outp.decode():
print("Jobs are running on ziggy")
time.sleep(60)
OldQRes = CheckZiggyQueue(JobIDs, settings)
print('Pending: ' + str(OldQRes[0]) + ', Running: ' + str(OldQRes[1]) + ', Not in queue: ' + str(OldQRes[2]))
Jobs2Complete = list(GausFiles)
n2complete = len(Jobs2Complete)
#Check and report on the progress of calculations
while len(Jobs2Complete) > 0:
JustCompleted = [job for job in Jobs2Complete if
IsZiggyGComplete(job[:-3] + 'out', folder, settings)]
Jobs2Complete[:] = [job for job in Jobs2Complete if
not IsZiggyGComplete(job[:-3] + 'out', folder, settings)]
if n2complete != len(Jobs2Complete):
n2complete = len(Jobs2Complete)
print(str(n2complete) + " remaining.")
QRes = CheckZiggyQueue(JobIDs, settings)
if QRes != OldQRes:
OldQRes = QRes
print('Pending: ' + str(OldQRes[0]) + ', Running: ' + str(OldQRes[1]) + ', Not in queue: ' + str(OldQRes[2]))
if QRes[2] == len(JobIDs):
#check each gaussian file to ascertain the status of individual gaus jobs
print('No jobs left in Ziggy queue')
break
time.sleep(120)
#When done, copy the results back
print("\nCopying the output files back to localhost...")
print('ssh ziggy scp /home/' + settings.user + '/' + folder + '/*.out ' +\
socket.getfqdn() + ':' + os.getcwd())
outp = subprocess.check_output('ssh ziggy scp /home/' + settings.user +
'/' + folder + '/*.out ' + socket.getfqdn()
+ ':' + os.getcwd(), shell=True)
def WriteSubScript(GausJob, queue, ZiggyJobFolder, settings):
if not (os.path.exists(GausJob)):
print("The input file " + GausJob + " does not exist. Exiting...")
return
#Create the submission script
QSub = open(GausJob[:-4] + "slurm", 'w')
#Choose the queue
QSub.write('#!/bin/bash\n\n')
QSub.write('#SBATCH -p ' + settings.queue + '\n')
if settings.nProc >1:
QSub.write('#SBATCH --nodes=1\n#SBATCH --cpus-per-task=' + str(settings.nProc) + '\n')
else:
QSub.write('#SBATCH --nodes=1\n#SBATCH --cpus-per-task=1\n')
QSub.write('#SBATCH --time=' + format(settings.TimeLimit,"02") +':00:00\n\n')
#define input files and output files
QSub.write('file=' + GausJob[:-4] + '\n\n')
QSub.write('inpfile=${file}.com\noutfile=${file}.out\n')
#define cwd and scratch folder and ask the machine
#to make it before running the job
QSub.write('HERE=/home/' + settings.user +'/' + ZiggyJobFolder + '\n')
QSub.write('SCRATCH=/scratch/' + settings.user + '/' +
GausJob[:-4] + '\n')
QSub.write('mkdir ${SCRATCH}\n')
#Setup GAUSSIAN environment variables
QSub.write('set OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK\n')
QSub.write('export GAUSS_EXEDIR=/usr/local/shared/gaussian/em64t/09-D01/g09\n')
QSub.write('export g09root=/usr/local/shared/gaussian/em64t/09-D01\n')
QSub.write('export PATH=/usr/local/shared/gaussian/em64t/09-D01/g09:$PATH\n')
QSub.write('export GAUSS_SCRDIR=$SCRATCH\n')
QSub.write('exe=$GAUSS_EXEDIR/g09\n')
#copy the input file to scratch
QSub.write('cp ${HERE}/${inpfile} $SCRATCH\ncd $SCRATCH\n')
#write useful info to the job output file (not the gaussian)
QSub.write('echo "Starting job $SLURM_JOBID"\necho\n')
QSub.write('echo "SLURM assigned me this node:"\nsrun hostname\necho\n')
QSub.write('ln -s $HERE/$outfile $SCRATCH/$outfile\n')
QSub.write('srun $exe > $outfile < $inpfile\n')
#Cleanup
QSub.write('rm -rf ${SCRATCH}/\n')
QSub.close()
def IsZiggyGComplete(f, folder, settings):
path = '/home/' + settings.user + '/' + folder + '/'
try:
outp1 = subprocess.check_output('ssh ziggy ls ' + path, shell=True)
except subprocess.CalledProcessError as e:
print("ssh ziggy ls failed: " + str(e.output))
return False
if f in outp1.decode():
try:
outp2 = subprocess.check_output('ssh ziggy cat ' + path + f,
shell=True)
except subprocess.CalledProcessError as e:
print("ssh ziggy cat failed: " + str(e.output).decode())
return False
if ("Normal termination" in outp2[-90:].decode()) or \
(('termination' in outp2[-270:].decode()) and ('l9999.exe' in outp2[-270:].decode())):
return True
return False
def CheckZiggyQueue(JobIDs, settings):
outp = subprocess.Popen(['ssh', 'ziggy', 'qstat', '-u ' + settings.user], \
stderr=subprocess.STDOUT, stdout=subprocess.PIPE).communicate()[0]
outp = outp.decode().split('\n')
QStart = 0
for i, line in enumerate(outp):
if '------' in line:
QStart = i+1
break
QueueReport = outp[QStart:-1]
JobStats = []
for job in JobIDs:
status = ''
for i, line in enumerate(QueueReport):
if job in line:
status = list(filter(None, line.split(' ')))[9]
JobStats.append(status)
Pending = JobStats.count('Q')
Running = JobStats.count('R')
NotInQueue = JobStats.count('')
return Pending, Running, NotInQueue