From 26cbb30187656d1714448dd374293276c2d0873e Mon Sep 17 00:00:00 2001 From: Metin Balaban Date: Thu, 29 Aug 2019 15:00:40 -0700 Subject: [PATCH] output and error file locations are configurable via cluster.json --- {{cookiecutter.profile_name}}/pbs-submit.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/{{cookiecutter.profile_name}}/pbs-submit.py b/{{cookiecutter.profile_name}}/pbs-submit.py index 42f2aaf..62684c8 100644 --- a/{{cookiecutter.profile_name}}/pbs-submit.py +++ b/{{cookiecutter.profile_name}}/pbs-submit.py @@ -136,6 +136,15 @@ if walltime: resourceparams = resourceparams + walltime if nodes or mem or walltime: resourceparams = resourceparams + "\"" +if "cluster" in job_properties: + cluster = job_properties["cluster"] + if "error" in cluster: + os.makedirs(os.path.dirname(cluster["error"]), exist_ok=True) + se = " -e " + cluster["error"] + if "output" in cluster: + os.makedirs(os.path.dirname(cluster["output"]), exist_ok=True) + so = " -o " + cluster["output"] + cmd = "qsub {a}{A}{b}{c}{C}{d}{D}{e}{f}{h}{j}{l}{m}{M}{N}{o}{p}{P}{q}{t}{u}{v}{V}{w}{W}{rp}{dep}{ex}".format(\ a=atime,A=acc_string,b=pbs_time,c=chkpt,C=pref,d=dd,D=rd,e=se,f=ft,h=hold,j=j,l=resource,m=mail,M=mailuser,\ N=jname,o=so,p=priority,P=proxy,q=q,t=ar,u=user,v=ev,V=eall,w=wd,W=add,rp=resourceparams,dep=depend,ex=extras)