# increase memory and walltime
# TODO: consider how to scale mem/time here
oldmem = sendjob_dict['mem']
sendjob_dict['mem'] = int(oldmem) * 2
oldtime = sendjob_dict['walltime']
sendjob_dict['walltime'] = int(oldtime) * 4
# replace chunk file and set number of new jobs
sendjob_dict['njobs'] = int(nummiss)
job_dict['cfile'] = tmp_chunk_file_name
# re-save new settings (primarily to track updating mem and walltime)
save_job(jfile=orig_job_conf,
cmd_templ=cmd_templ,
job_dict=job_dict,
sendjob_dict=sendjob_dict)
# submit
imp_cmd = cmd_templ.format(**job_dict)
jobres = send_job(jobname=sendjob_dict['jobname'],
cmd=imp_cmd,
logname=sendjob_dict['logname'],
mem=sendjob_dict['mem'],
walltime=sendjob_dict['walltime'],
njobs=sendjob_dict['njobs'],
sleep=sendjob_dict['sleep'],
forcearray=True)
print 'GWAS jobs resubmitted for %d chunks.\n' % nummiss
# get number of chunks (-1 is for header)
nchunks = file_len(outdot+'.chunks.txt')-1
# store job information for possible resubs
job_store_file = 'imp.chunks.'+str(outdot)+'.pkl'
clust_dict = init_sendjob_dict()
clust_dict['jobname'] = 'imp.chunks.'+str(outdot)
clust_dict['logname'] = str('imp.chunks.'+str(outdot)+'.'+str(clust_conf['log_task_id'])+'.sub.log')
clust_dict['mem'] = 8000
clust_dict['walltime'] = 2
clust_dict['njobs'] = int(nchunks)
clust_dict['sleep'] = args.sleep
save_job(jfile=job_store_file, cmd_templ=imp_templ, job_dict=jobdict, sendjob_dict=clust_dict)
# submit
cmd_imp = imp_templ.format(**jobdict)
jobres2 = send_job(jobname='imp.chunks.'+str(outdot),
cmd=cmd_imp,
logname=str('imp.chunks.'+str(outdot)+'.'+str(clust_conf['log_task_id'])+'.sub.log'),
mem=8000,
walltime=2,
njobs=int(nchunks),
sleep=args.sleep)
print 'Imputation jobs submitted for %d chunks.\n' % nchunks
# increase memory and walltime
# TODO: consider how to scale mem/time here
oldmem = sendjob_dict['mem']
sendjob_dict['mem'] = int(oldmem)*2
oldtime = sendjob_dict['walltime']
sendjob_dict['walltime'] = int(oldtime)*4
# replace chunk file and set number of new jobs
sendjob_dict['njobs'] = int(nummiss)
job_dict['cfile'] = tmp_chunk_file_name
# re-save new settings (primarily to track updating mem and walltime)
save_job(jfile=orig_job_conf, cmd_templ=cmd_templ, job_dict=job_dict, sendjob_dict=sendjob_dict)
# submit
gwas_cmd = cmd_templ.format(**job_dict)
jobres = send_job(jobname=sendjob_dict['jobname'],
cmd=gwas_cmd,
logname=sendjob_dict['logname'],
mem=sendjob_dict['mem'],
walltime=sendjob_dict['walltime'],
njobs=sendjob_dict['njobs'],
maxpar=sendjob_dict['maxpar'],
sleep=sendjob_dict['sleep'],
forcearray=True)