# -*- coding: utf-8 -*-
###########################################################################
# Copyright (c), The AiiDA team. All rights reserved. #
# This file is part of the AiiDA code. #
# #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida_core #
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################
from aiida.scheduler.plugins.pbspro import *
from aiida.scheduler.datastructures import job_states
import unittest
# import logging
import uuid
text_qstat_f_to_test = """Job Id: 68350.mycluster
Job_Name = cell-Qnormal
Job_Owner = usernum1@mycluster.cluster
job_state = Q
queue = Q_express
server = mycluster
Checkpoint = u
ctime = Tue Apr 9 15:01:47 2013
Error_Path = mycluster.cluster:/home/usernum1/scratch/cptest/scaletest/PTOs
caletest/testjob.err
Hold_Types = n
Join_Path = n
Keep_Files = n
Mail_Points = a
mtime = Mon Apr 22 13:13:53 2013
Output_Path = mycluster.cluster:/home/usernum1/scratch/cptest/scaletest/PTO
scaletest/testjob.out
Priority = 0
qtime = Tue Apr 9 18:26:32 2013
Rerunable = False
Resource_List.mpiprocs = 15
Resource_List.ncpus = 240
Resource_List.nodect = 15
Resource_List.place = free
Resource_List.select = 15:ncpus=16
Resource_List.walltime = 01:00:00
substate = 10
Variable_List = PBS_O_SYSTEM=Linux,PBS_O_SHELL=/bin/bash,
PBS_O_HOME=/home/usernum1,PBS_O_LOGNAME=usernum1,
PBS_O_WORKDIR=/home/usernum1/scratch/cptest/scaletest/PTOscaletest,
PBS_O_LANG=en_US.UTF-8,
PBS_O_PATH=/opt/xcat/bin:/opt/xcat/sbin:/usr/lib64/qt-3.3/bin:/usr/loc
al/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/b
in:/opt/software/python/3.3.0/bin:/opt/software/bin,
PBS_O_MAIL=/var/spool/mail/usernum1,PBS_O_QUEUE=P_share_queue,
PBS_O_HOST=mycluster.cluster
comment = Not Running: Node is in an ineligible state: offline
etime = Tue Apr 9 18:26:32 2013
Submit_arguments = job-PTO64cell-Qnormal.6.15.1.64.4
project = _pbs_project_default
Job Id: 68351.mycluster
Job_Name = cell-Qnormal
Job_Owner = usernum1@mycluster.cluster
job_state = Q
queue = Q_express
server = mycluster
Checkpoint = u
ctime = Tue Apr 9 15:01:47 2013
Error_Path = mycluster.cluster:/home/usernum1/scratch/cptest/scaletest/PTOs
caletest/testjob.err
Hold_Types = n
Join_Path = n
Keep_Files = n
Mail_Points = a
mtime = Mon Apr 22 13:13:53 2013
Output_Path = mycluster.cluster:/home/usernum1/scratch/cptest/scaletest/PTO
scaletest/testjob.out
Priority = 0
qtime = Tue Apr 9 18:26:32 2013
Rerunable = False
Resource_List.mpiprocs = 15
Resource_List.ncpus = 240
Resource_List.nodect = 15
Resource_List.place = free
Resource_List.select = 15:ncpus=16
Resource_List.walltime = 01:00:00
substate = 10
Variable_List = PBS_O_SYSTEM=Linux,PBS_O_SHELL=/bin/bash,
PBS_O_HOME=/home/usernum1,PBS_O_LOGNAME=usernum1,
PBS_O_WORKDIR=/home/usernum1/scratch/cptest/scaletest/PTOscaletest,
PBS_O_LANG=en_US.UTF-8,
PBS_O_PATH=/opt/xcat/bin:/opt/xcat/sbin:/usr/lib64/qt-3.3/bin:/usr/loc
al/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/b
in:/opt/software/python/3.3.0/bin:/opt/software/bin,
PBS_O_MAIL=/var/spool/mail/usernum1,PBS_O_QUEUE=P_share_queue,
PBS_O_HOST=mycluster.cluster
comment = Not Running: Node is in an ineligible state: offline
etime = Tue Apr 9 18:26:32 2013
Submit_arguments = job-PTO64cell-Qnormal.6.15.1.64.8
project = _pbs_project_default
Job Id: 69301.mycluster
Job_Name = Cu-dbp
Job_Owner = user02@mycluster.cluster
resources_used.cpupercent = 6384
resources_used.cput = 4090:56:03
resources_used.mem = 13378420kb
resources_used.ncpus = 64
resources_used.vmem = 9866188kb
resources_used.walltime = 64:26:16
job_state = R
queue = P_lsu
server = mycluster
Account_Name = lsu
Checkpoint = u
ctime = Wed Apr 10 17:10:29 2013
depend = afterok:69299.mycluster@mycluster.cluster,
beforeok:69302.mycluster@mycluster.cluster
Error_Path = mycluster.cluster:/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN7/C
u-dbp.e69301
exec_host = b141/0*16+b142/0*16+b143/0*16+b144/0*16
exec_vnode = (b141:ncpus=16)+(b142:ncpus=16)+(b143:ncpus=16)+(b144:ncpus=16
)
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = a
mtime = Sat Apr 20 01:37:01 2013
Output_Path = mycluster.cluster:/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN7/
Cu-dbp.o69301
Priority = 0
qtime = Wed Apr 10 17:10:29 2013
Rerunable = False
Resource_List.mpiprocs = 4
Resource_List.ncpus = 64
Resource_List.nodect = 4
Resource_List.place = excl
Resource_List.select = 4:ncpus=16
Resource_List.walltime = 72:00:00
stime = Sat Apr 20 01:36:59 2013
session_id = 118473
Shell_Path_List = /bin/tcsh
jobdir = /home/user02
substate = 42
Variable_List = SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass,
PERL_BADLANG=0,KDE_IS_PRELINKED=1,PBS_O_HOME=/home/user02,
module=() { eval `/usr/bin/modulecmd bash $*`,},
LESSOPEN=|/usr/bin/lesspipe.sh %s,PBS_O_LOGNAME=user02,
SSH_CLIENT=128.178.54.94 46714 22,CVS_RSH=ssh,PBS_O_LANG=C,USER=user02,
HOME=/home/user02,LIBGL_ALWAYS_INDIRECT=yes,
PATH=/opt/xcat/bin:/opt/xcat/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin
:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/bin:/op
t/software/python/3.3.0/bin:/opt/software/bin,
LD_LIBRARY_PATH=/opt/software/python/3.3.0/lib,
SSH_CONNECTION=128.178.54.94 46714 128.178.209.70 22,LANG=C,
QTLIB=/usr/lib64/qt-3.3/lib,TERM=xterm,SHELL=/bin/bash,
QTINC=/usr/lib64/qt-3.3/include,G_BROKEN_FILENAMES=1,HISTSIZE=1000,
PBS_O_WORKDIR=/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN7,
PBS_O_PATH=/opt/xcat/bin:/opt/xcat/sbin:/usr/lib64/qt-3.3/bin:/usr/loc
al/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/b
in:/opt/software/python/3.3.0/bin:/opt/software/bin,
MANPATH=/opt/xcat/share/man:,XCATROOT=/opt/xcat,
MODULESHOME=/usr/share/Modules,PBS_O_SYSTEM=Linux,MSM_PRODUCT=MSM,
HOST=mycluster,MAIL=/var/spool/mail/user02,
PBS_O_MAIL=/var/spool/mail/user02,_=/opt/pbs/default/bin/qsub,
MODULEPATH=/etc/modulefiles:/opt/software/modulefiles:/opt/software/cs
e-software/modulefiles,KDEDIRS=/usr,PBS_O_SHELL=/bin/bash,
SSH_TTY=/dev/pts/55,OLDPWD=/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN6,
LOADEDMODULES=,HISTCONTROL=ignoredups,SHLVL=1,
PWD=/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN7,HOSTNAME=mycluster,
MSM_HOME=/usr/local/MegaRAID Storage Manager,LOGNAME=user02,
PBS_O_HOST=mycluster.cluster
comment = Job run at Sat Apr 20 at 01:36 on (b141:ncpus=16)+(b142:ncpus=16)
+(b143:ncpus=16)+(b144:ncpus=16)
etime = Sat Apr 20 01:36:59 2013
Submit_arguments = job.sh
project = _pbs_project_default
Job Id: 69302.mycluster
Job_Name = Cu-dbp
Job_Owner = user02@mycluster.cluster
job_state = H
queue = P_lsu
server = mycluster
Account_Name = lsu
Checkpoint = u
ctime = Wed Apr 10 17:11:21 2013
depend = afterok:69301.mycluster@mycluster.cluster
Error_Path = mycluster.cluster:/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN8/C
u-dbp.e69302
Hold_Types = s
Join_Path = oe
Keep_Files = n
Mail_Points = a
mtime = Wed Apr 10 17:11:21 2013
Output_Path = mycluster.cluster:/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN8/
Cu-dbp.o69302
Priority = 0
qtime = Wed Apr 10 17:11:21 2013
Rerunable = False
Resource_List.mpiprocs = 4
Resource_List.ncpus = 64
Resource_List.nodect = 4
Resource_List.place = excl
Resource_List.select = 4:ncpus=16
Resource_List.walltime = 72:00:00
Shell_Path_List = /bin/tcsh
substate = 22
Variable_List = SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass,
PERL_BADLANG=0,KDE_IS_PRELINKED=1,PBS_O_HOME=/home/user02,
module=() { eval `/usr/bin/modulecmd bash $*`,},
LESSOPEN=|/usr/bin/lesspipe.sh %s,PBS_O_LOGNAME=user02,
SSH_CLIENT=128.178.54.94 46714 22,CVS_RSH=ssh,PBS_O_LANG=C,USER=user02,
HOME=/home/user02,LIBGL_ALWAYS_INDIRECT=yes,
PATH=/opt/xcat/bin:/opt/xcat/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin
:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/bin:/op
t/software/python/3.3.0/bin:/opt/software/bin,
LD_LIBRARY_PATH=/opt/software/python/3.3.0/lib,
SSH_CONNECTION=128.178.54.94 46714 128.178.209.70 22,LANG=C,
QTLIB=/usr/lib64/qt-3.3/lib,TERM=xterm,SHELL=/bin/bash,
QTINC=/usr/lib64/qt-3.3/include,G_BROKEN_FILENAMES=1,HISTSIZE=1000,
PBS_O_WORKDIR=/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN8,
PBS_O_PATH=/opt/xcat/bin:/opt/xcat/sbin:/usr/lib64/qt-3.3/bin:/usr/loc
al/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/b
in:/opt/software/python/3.3.0/bin:/opt/software/bin,
MANPATH=/opt/xcat/share/man:,XCATROOT=/opt/xcat,
MODULESHOME=/usr/share/Modules,PBS_O_SYSTEM=Linux,MSM_PRODUCT=MSM,
HOST=mycluster,MAIL=/var/spool/mail/user02,
PBS_O_MAIL=/var/spool/mail/user02,_=/opt/pbs/default/bin/qsub,
MODULEPATH=/etc/modulefiles:/opt/software/modulefiles:/opt/software/cs
e-software/modulefiles,KDEDIRS=/usr,PBS_O_SHELL=/bin/bash,
SSH_TTY=/dev/pts/55,OLDPWD=/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN7,
LOADEDMODULES=,HISTCONTROL=ignoredups,SHLVL=1,
PWD=/scratch/user02/QMMM-CuPhens/dbp/NOSE/RUN8,HOSTNAME=mycluster,
MSM_HOME=/usr/local/MegaRAID Storage Manager,LOGNAME=user02,
PBS_O_HOST=mycluster.cluster
Submit_arguments = job.sh
project = _pbs_project_default
Job Id: 74164.mycluster
Job_Name = u-100-l-96.job
Job_Owner = user3@mycluster.cluster
resources_used.cpupercent = 3889
resources_used.cput = 343:11:42
resources_used.mem = 1824176kb
resources_used.ncpus = 32
resources_used.vmem = 3796376kb
resources_used.walltime = 10:45:13
job_state = R
queue = Q_normal
server = mycluster
Checkpoint = u
ctime = Fri Apr 12 15:21:55 2013
depend = afterany:74163.mycluster@mycluster.cluster,
beforeany:74165.mycluster@mycluster.cluster
Error_Path = mycluster.cluster:/scratch/user3/ubiquitin/100gL/starting-from
-left/production/u-100-l-96.job.e74164
exec_host = b270/0*16+b275/0*16
exec_vnode = (b270:ncpus=16)+(b275:ncpus=16)
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = abe
Mail_Users = enrico.user3@epfl.ch
mtime = Mon Apr 22 07:17:36 2013
Output_Path = mycluster.cluster:/scratch/user3/ubiquitin/100gL/starting-fro
m-left/production/u-100-l-96.job.o74164
Priority = 0
qtime = Fri Apr 12 15:21:55 2013
Rerunable = False
Resource_List.mpiprocs = 32
Resource_List.ncpus = 32
Resource_List.nodect = 2
Resource_List.place = excl
Resource_List.select = 2:ncpus=16:mpiprocs=16
Resource_List.walltime = 24:00:00
stime = Mon Apr 22 07:17:36 2013
session_id = 14147
jobdir = /home/user3
substate = 42
Variable_List = PBS_O_SYSTEM=Linux,PBS_O_SHELL=/bin/bash,
PBS_O_HOME=/home/user3,PBS_O_LOGNAME=user3,
PBS_O_WORKDIR=/scratch/user3/ubiquitin/100gL/starting-from-left/produc
tion,PBS_O_LANG=en_US.utf8,
PBS_O_PATH=/opt/pbs/default/sbin/:/home/bovigny/bin:/opt/xcat/bin:/opt
/xcat/sbin:/opt/xcat/bin:/opt/xcat/sbin:/usr/lib64/qt-3.3/bin:/usr/loca
l/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/bi
n:/opt/software/python/3.3.0/bin:/opt/software/bin:/opt/pbs/default/bin
:/opt/software/python/3.3.0/bin:/opt/software/bin,
PBS_O_MAIL=/var/spool/mail/user3,PBS_O_QUEUE=P_share_queue,
PBS_O_HOST=mycluster.cluster
comment = Job run at Mon Apr 22 at 07:17 on (b270:ncpus=16)+(b275:ncpus=16)
etime = Mon Apr 22 07:17:34 2013
Submit_arguments = -W depend=afterany:74163 u-100-l-96.job
project = _pbs_project_default
Job Id: 74165.mycluster
Job_Name = u-100-l-97.job
Job_Owner = user3@mycluster.cluster
job_state = H
queue = Q_normal
server = mycluster
Checkpoint = u
ctime = Fri Apr 12 15:22:01 2013
depend = afterany:74164.mycluster@mycluster.cluster,
beforeany:74166.mycluster@mycluster.cluster
Error_Path = mycluster.cluster:/scratch/user3/ubiquitin/100gL/starting-from
-left/production/u-100-l-97.job.e74165
Hold_Types = s
Join_Path = oe
Keep_Files = n
Mail_Points = abe
Mail_Users = enrico.user3@epfl.ch
mtime = Fri Apr 12 15:22:07 2013
Output_Path = mycluster.cluster:/scratch/user3/ubiquitin/100gL/starting-fro
m-left/production/u-100-l-97.job.o74165
Priority = 0
qtime = Fri Apr 12 15:22:01 2013
Rerunable = False
Resource_List.mpiprocs = 32
Resource_List.ncpus = 32
Resource_List.nodect = 2
Resource_List.place = excl
Resource_List.select = 2:ncpus=16:mpiprocs=16
Resource_List.walltime = 24:00:00
substate = 22
Variable_List = PBS_O_SYSTEM=Linux,PBS_O_SHELL=/bin/bash,
PBS_O_HOME=/home/user3,PBS_O_LOGNAME=user3,
PBS_O_WORKDIR=/scratch/user3/ubiquitin/100gL/starting-from-left/produc
tion,PBS_O_LANG=en_US.utf8,
PBS_O_PATH=/opt/pbs/default/sbin/:/home/bovigny/bin:/opt/xcat/bin:/opt
/xcat/sbin:/opt/xcat/bin:/opt/xcat/sbin:/usr/lib64/qt-3.3/bin:/usr/loca
l/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/pbs/default/bi
n:/opt/software/python/3.3.0/bin:/opt/software/bin:/opt/pbs/default/bin
:/opt/software/python/3.3.0/bin:/opt/software/bin,
PBS_O_MAIL=/var/spool/mail/user3,PBS_O_QUEUE=P_share_queue,
PBS_O_HOST=mycluster.cluster
Submit_arguments = -W depend=afterany:74164 u-100-l-97.job
project = _pbs_project_default
"""
## This contains in the 10-th job unexpected newlines
## in the sched_hint field. Still, it should parse correctly.
text_qstat_f_to_test_with_unexpected_newlines = """Job Id: 549159
Job_Name = somejob
Job_Owner = user_549159
job_state = H
queue = ShortQ
server = service1
Account_Name = account_549159
Checkpoint = u
ctime = Sun Jun 21 07:09:41 2015
depend = afterok:549158.service1.head.cb3.ichec.ie@service1.cb3.ichec.ie
Error_Path = host.domain:/some/path/to/sth/ASSP
-1R-p/more/down/the/path/ASSP
-1R.e549159
Hold_Types = s
Join_Path = oe
Keep_Files = n
Mail_Points = bea
Mail_Users = usermail@domain1
mtime = Sun Jun 21 07:09:41 2015
Output_Path = host.domain:/some/path/to/sth/GL
more/down/the/path/ASS
P-1R.o549159
Priority = 0
qtime = Sun Jun 21 07:09:41 2015
Rerunable = False
Resource_List.nodect = 4
Resource_List.nodes = 4:ppn=24
Resource_List.walltime = 09:00:00
euser = user_549159
egroup = users
queue_type = E
submit_args = -W depend=afterok:549158 somejob.pbs
fault_tolerant = False
job_radix = 0
submit_host = host.domain1
Job Id: 555716
Job_Name = ini_J2
Job_Owner = somebody@host.domain
resources_used.cput = 500:13:39
resources_used.energy_used = 0
resources_used.mem = 20716400kb
resources_used.vmem = 23534576kb
resources_used.walltime = 41:45:13
job_state = R
queue = ProdQ
server = service1
Account_Name = dias01
Checkpoint = u
ctime = Fri Jun 26 14:04:56 2015
Error_Path = host:/down/the/path/test
_valg.out
exec_host = r2i4n13/0-23+r1i2n12/0-23+r1i2n11/0-23+r1i1n15/0-23
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = bea
Mail_Users = usermail@mail.domain
mtime = Sun Jun 28 23:20:51 2015
Output_Path = host:/down/the/path/tes
t_valg.out
Priority = 0
qtime = Fri Jun 26 14:04:56 2015
Rerunable = False
Resource_List.nodect = 4
Resource_List.nodes = 4:ppn=24
Resource_List.walltime = 70:00:00
session_id = 21190
euser = somebody
egroup = users
queue_type = E
etime = Fri Jun 26 14:04:56 2015
submit_args = runmem_CB_E
start_time = Sun Jun 28 23:20:51 2015
Walltime.Remaining = 101627
start_count = 1
fault_tolerant = False
job_radix = 0
submit_host = host.domain
Job Id: 556491
Job_Name = somejob010
Job_Owner = user_556491
resources_used.cput = 1850:10:45
resources_used.energy_used = 0
resources_used.mem = 50392860kb
resources_used.vmem = 77507412kb
resources_used.walltime = 78:21:43
job_state = R
queue = LongQ
server = service1
Account_Name = some432472
Checkpoint = u
ctime = Sat Jun 27 10:44:32 2015
Error_Path = host:/down/teh/path/ATc
T/somejob010.e556491
exec_host = r3i1n2/0-23
Hold_Types = n
Join_Path = n
Keep_Files = n
Mail_Points = ea
Mail_Users = user@mail
mtime = Sat Jun 27 10:45:06 2015
Output_Path = host;/down/the/path/AT
cT/somejob-010.o556491
Priority = 0
qtime = Sat Jun 27 10:44:32 2015
Rerunable = False
Resource_List.nodect = 1
Resource_List.nodes = 1:ppn=24
Resource_List.walltime = 144:00:00
session_id = 28668
euser = user_556491
egroup = users
queue_type = E
etime = Sat Jun 27 10:44:32 2015
submit_args = scriptname.pbs
start_time = Sat Jun 27 10:45:06 2015
Walltime.Remaining = 236282
start_count = 1
fault_tolerant = False
job_radix = 0
submit_host = host.domain
Job Id: 546437
Job_Name = job_546437
Job_Owner = user_546437
resources_used.cput = 146:03:05
resources_used.energy_used = 0
resources_used.mem = 4199416kb
resources_used.vmem = 10804052kb
resources_used.walltime = 06:12:22
job_state = C
queue = ShortQ
server = server.service.546437
Account_Name = account_546437
Checkpoint = u
ctime = Thu Jun 18 16:10:46 2015
depend = beforeok:546438@service1
Error_Path = server.domain:/path/to/error/file
-1R-p/more/down/the/path/GLP
-1R.e546437
exec_host = r2i7n16/0-23+r2i6n14/0-23+r2i6n1/0-23+r1i7n8/0-23
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = bea
Mail_Users = usermail_546437@domain.546437
mtime = Thu Jun 18 22:36:03 2015
Output_Path = server.domain:/path/to/output/file
something2/more/down/the/path/GL
P-1R.o546437
Priority = 0
qtime = Thu Jun 18 16:10:46 2015
Rerunable = False
Resource_List.nodect = 4
Resource_List.nodes = 4:ppn=24
Resource_List.walltime = 08:00:00
session_id = 7054
euser = user_546437
egroup = group_546437
queue_type = E
etime = Thu Jun 18 16:10:46 2015
exit_status = 271
submit_args = args_546437.ext
start_time = Thu Jun 18 16:23:35 2015
start_count = 1
fault_tolerant = False
job_radix = 0
submit_host = host_546437.domain
Job Id: 547637
Job_Name = job_546437
Job_Owner = user_546437
job_state = Q
queue = ShortQ
server = server.service.546437
Account_Name = account_546437
Checkpoint = u
ctime = Fri Jun 19 14:00:43 2015
Error_Path = server.domain:/path/to/error/file
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = bea
Mail_Users = usermail_546437@domain.546437
mtime = Fri Jun 19 14:00:43 2015
Output_Path = server.domain:/path/to/output/file
7
Priority = 0
qtime = Fri Jun 19 14:00:43 2015
Rerunable = False
Resource_List.nodect = 1
Resource_List.nodes = 1:ppn=24
Resource_List.walltime = 24:00:00
euser = user_546437
egroup = group_546437
queue_type = E
etime = Fri Jun 19 14:00:43 2015
submit_args = args_546437.ext
fault_tolerant = False
job_radix = 0
submit_host = host_546437.domain
Job Id: 547683
Job_Name = job_547683
Job_Owner = user_547683
job_state = Q
queue = ShortQ
server = server.service.547683
Account_Name = account_547683
Checkpoint = u
ctime = Fri Jun 19 14:58:08 2015
Error_Path = server.domain:/path/to/error/file
83
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = ea
Mail_Users = usermail_547683@domain.547683
mtime = Fri Jun 19 14:58:08 2015
Output_Path = server.domain:/path/to/output/file
683
Priority = 0
qtime = Fri Jun 19 14:58:08 2015
Rerunable = False
Resource_List.nodect = 1
Resource_List.nodes = 1:ppn=24
Resource_List.walltime = 23:30:00
euser = user_547683
egroup = group_547683
queue_type = E
etime = Fri Jun 19 14:58:08 2015
submit_args = args_547683.ext
fault_tolerant = False
job_radix = 0
submit_host = host_547683.domain
Job Id: 549004
Job_Name = job_549004
Job_Owner = user_549004
job_state = Q
queue = ProdQ
server = server.service.549004
Account_Name = account_549004
Checkpoint = u
ctime = Sat Jun 20 21:25:20 2015
Error_Path = server.domain:/path/to/error/file
_something1_202.e549004
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = bea
mtime = Sat Jun 20 21:25:20 2015
Output_Path = server.domain:/path/to/output/file
w_something1_202.o549004
Priority = 0
qtime = Sat Jun 20 21:25:20 2015
Rerunable = False
Resource_List.nodect = 1
Resource_List.nodes = 1:ppn=24
Resource_List.walltime = 48:00:00
euser = user_549004
egroup = group_549004
queue_type = E
etime = Sat Jun 20 21:25:20 2015
submit_args = args_549004ext
fault_tolerant = False
job_radix = 0
submit_host = host_549004.domain
Job Id: 549005
Job_Name = job_549004
Job_Owner = user_549004
job_state = Q
queue = ProdQ
server = server.service.549004
Account_Name = account_549004
Checkpoint = u
ctime = Sat Jun 20 21:25:24 2015
Error_Path = server.domain:/path/to/error/file
_something1_102.e549005
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = bea
mtime = Sat Jun 20 21:25:24 2015
Output_Path = server.domain:/path/to/output/file
w_something1_102.o549005
Priority = 0
qtime = Sat Jun 20 21:25:24 2015
Rerunable = False
Resource_List.nodect = 1
Resource_List.nodes = 1:ppn=24
Resource_List.walltime = 48:00:00
euser = user_549004
egroup = group_549004
queue_type = E
etime = Sat Jun 20 21:25:24 2015
submit_args = args_549004.ext
fault_tolerant = False
job_radix = 0
submit_host = host_549004.domain
Job Id: 549008
Job_Name = job_549008
Job_Owner = user_549008
job_state = Q
queue = ProdQ
server = server.service.549008
Account_Name = account_549008
Checkpoint = u
ctime = Sat Jun 20 21:25:39 2015
Error_Path = server.domain:/path/to/error/file
something1_102.e549008
Hold_Types = n
Join_Path = oe
Keep_Files = n
Mail_Points = bea
mtime = Sat Jun 20 21:25:39 2015
Output_Path = server.domain:/path/to/output/file
_something1_102.o549008
Priority = 0
qtime = Sat Jun 20 21:25:39 2015
Rerunable = False
Resource_List.nodect = 1
Resource_List.nodes = 1:ppn=24
Resource_List.walltime = 48:00:00
euser = user_549008
egroup = group_549008
queue_type = E
etime = Sat Jun 20 21:25:39 2015
submit_args = args_549008.ext
fault_tolerant = False
job_radix = 0
submit_host = host_549008.domain
Job Id: 543984
Job_Name = job_543984
Job_Owner = user_543984
resources_used.cput = 641:36:16
resources_used.energy_used = 0
resources_used.mem = 3815752kb
resources_used.vmem = 12122136kb
resources_used.walltime = 35:47:31
job_state = C
queue = ProdQ
server = server.service.543984
Account_Name = account_543984
Checkpoint = u
ctime = Wed Jun 17 09:16:05 2015
depend = beforeany:545943@service1
Error_Path = server.domain:/path/to/error/file
P_Mp=318.,NVF=1e5,tau=0.10,ddZ,AD,1T,iFlr,xyz.e543984
exec_host = r2i7n17/0-23+r2i0n11/0-23+r2i6n17/0-23+r2i0n5/0-23+r2i7n1/0-23
+r2i5n8/0-23+r2i4n11/0-23+r2i4n8/0-23+r2i2n8/0-23+r2i0n2/0-23+r2i3n16/
0-23+r2i3n2/0-23+r2i1n2/0-23+r2i4n3/0-23+r2i1n15/0-23+r2i1n9/0-23+r2i2
n2/0-23+r2i3n8/0-23+r2i3n5/0-23+r2i1n11/0-23+r2i0n16/0-23+r2i2n5/0-23+
r2i1n3/0-23+r2i0n17/0-23+r2i0n8/0-23+r1i3n0/0-23+r1i7n7/0-23+r1i6n1/0-
23+r1i7n3/0-23+r1i7n5/0-23+r1i6n17/0-23+r1i7n4/0-23
Hold_Types = n
Join_Path = n
Keep_Files = n
Mail_Points = n
Mail_Users = usermail_543984@domain.543984
mtime = Thu Jun 18 22:36:12 2015
Output_Path = server.domain:/path/to/output/file
EP_Mp=318.,NVF=1e5,tau=0.10,ddZ,AD,1T,iFlr,xyz.o543984
Priority = 0
qtime = Wed Jun 17 09:16:05 2015
Rerunable = False
Resource_List.nodect = 32
Resource_List.nodes = 32:ppn=24
Resource_List.walltime = 71:59:59
session_id = 47630
euser = user_543984
egroup = group_543984
queue_type = E
sched_hint = Post job file processing error; job 543984 on host r2i7n17
U
nable to copy file 543984.OU to /some/path/on/the/cluster/MHD
something_Mp=318.,NVF=1e5,tau=0.10,ddZ,AD,1T,iFlr,xyz.o543984,
error 1
*** error from copy
/bin/cp: cannot stat `543984.OU': No suc
h file or directory
*** end error output
Unable to copy file 543984.E
R to /some/path/on/the/cluster/something_Mp=318.,
NVF=1e5,tau=0.10,ddZ,AD,1T,iFlr,xyz.e543984,
error 1
*** error from copy
/bin/cp: cannot stat `543984.ER': No suc
h file or directory
*** end error output
etime = Wed Jun 17 09:16:05 2015
exit_status = 271
submit_args = args_XX.ext
xyz -l nodes=32:ppn=24,walltime=71:59:59 -v RESUME=true,SMP=24,
NND=32,
NOPFS=false -d /some/path/ /some/other/pa
th/NIx/que/runN.sth
start_time = Wed Jun 17 10:48:24 2015
start_count = 1
fault_tolerant = False
job_radix = 0
submit_host = host_XX.domain
"""
[docs]class TestParserQstat(unittest.TestCase):
"""
Tests to verify if teh function _parse_joblist_output behave correctly
The tests is done parsing a string defined above, to be used offline
"""
[docs] def test_parse_common_joblist_output(self):
"""
Test whether _parse_joblist can parse the qstat -f output
"""
s = PbsproScheduler()
retval = 0
stdout = text_qstat_f_to_test
stderr = ''
job_list = s._parse_joblist_output(retval, stdout, stderr)
# The parameters are hard coded in the text to parse
job_on_cluster = 6
job_parsed = len(job_list)
self.assertEquals(job_parsed, job_on_cluster)
job_running = 2
job_running_parsed = len([j for j in job_list if j.job_state \
and j.job_state == job_states.RUNNING])
self.assertEquals(job_running, job_running_parsed)
job_held = 2
job_held_parsed = len([j for j in job_list if j.job_state \
and j.job_state == job_states.QUEUED_HELD])
self.assertEquals(job_held, job_held_parsed)
job_queued = 2
job_queued_parsed = len([j for j in job_list if j.job_state \
and j.job_state == job_states.QUEUED])
self.assertEquals(job_queued, job_queued_parsed)
running_users = ['user02', 'user3']
parsed_running_users = [j.job_owner for j in job_list if j.job_state \
and j.job_state == job_states.RUNNING]
self.assertEquals(set(running_users), set(parsed_running_users))
running_jobs = ['69301.mycluster', '74164.mycluster']
parsed_running_jobs = [j.job_id for j in job_list if j.job_state \
and j.job_state == job_states.RUNNING]
self.assertEquals(set(running_jobs), set(parsed_running_jobs))
for j in job_list:
if j.allocated_machines:
num_machines = 0
num_cpus = 0
for n in j.allocated_machines:
num_machines += 1
num_cpus += n.num_cpus
self.assertTrue(j.num_machines == num_machines)
self.assertTrue(j.num_cpus == num_cpus)
# TODO : parse the env_vars
[docs] def test_parse_with_unexpected_newlines(self):
"""
Test whether _parse_joblist can parse the qstat -f output
also when there are unexpected newlines
"""
s = PbsproScheduler()
retval = 0
stdout = text_qstat_f_to_test_with_unexpected_newlines
stderr = ''
job_list = s._parse_joblist_output(retval, stdout, stderr)
# The parameters are hard coded in the text to parse
job_on_cluster = 10
job_parsed = len(job_list)
self.assertEquals(job_parsed, job_on_cluster)
job_running = 2
job_running_parsed = len([j for j in job_list if j.job_state \
and j.job_state == job_states.RUNNING])
self.assertEquals(job_running, job_running_parsed)
job_held = 1
job_held_parsed = len([j for j in job_list if j.job_state \
and j.job_state == job_states.QUEUED_HELD])
self.assertEquals(job_held, job_held_parsed)
job_queued = 5
job_queued_parsed = len([j for j in job_list if j.job_state \
and j.job_state == job_states.QUEUED])
self.assertEquals(job_queued, job_queued_parsed)
running_users = ['somebody', 'user_556491']
parsed_running_users = [j.job_owner for j in job_list if j.job_state \
and j.job_state == job_states.RUNNING]
self.assertEquals(set(running_users), set(parsed_running_users))
running_jobs = ['555716', '556491']
parsed_running_jobs = [j.job_id for j in job_list if j.job_state \
and j.job_state == job_states.RUNNING]
self.assertEquals(set(running_jobs), set(parsed_running_jobs))
for j in job_list:
if j.allocated_machines:
num_machines = 0
num_cpus = 0
for n in j.allocated_machines:
num_machines += 1
num_cpus += n.num_cpus
self.assertTrue(j.num_machines == num_machines)
self.assertTrue(j.num_cpus == num_cpus)
# TODO : parse the env_vars
# TODO: WHEN WE USE THE CORRECT ERROR MANAGEMENT, REIMPLEMENT THIS TEST
# def test_parse_with_error_retval(self):
# """
# The qstat -f command has received a retval != 0
# """
# s = PbsproScheduler()
# retval = 1
# stdout = text_qstat_f_to_test
# stderr = ''
# # Disable logging to avoid excessive output during test
# logging.disable(logging.ERROR)
# with self.assertRaises(SchedulerError):
# job_list = s._parse_joblist_output(retval, stdout, stderr)
# # Reset logging level
# logging.disable(logging.NOTSET)
# def test_parse_with_error_stderr(self):
# """
# The qstat -f command has received a stderr
# """
# s = PbsproScheduler()
# retval = 0
# stdout = text_qstat_f_to_test
# stderr = 'A non empty error message'
# # TODO : catch the logging error
# job_list = s._parse_joblist_output(retval, stdout, stderr)
# # print s._logger._log, dir(s._logger._log),'!!!!'
[docs]class TestSubmitScript(unittest.TestCase):
[docs] def test_submit_script(self):
"""
Test to verify if scripts works fine with default options
"""
from aiida.scheduler.datastructures import JobTemplate
from aiida.common.datastructures import CodeInfo, code_run_modes
s = PbsproScheduler()
job_tmpl = JobTemplate()
job_tmpl.shebang = '#!/bin/bash -l'
job_tmpl.job_resource = s.create_job_resource(num_machines=1, num_mpiprocs_per_machine=1)
job_tmpl.uuid = str(uuid.uuid4())
job_tmpl.max_wallclock_seconds = 24 * 3600
code_info = CodeInfo()
code_info.cmdline_params = ["mpirun", "-np", "23", "pw.x", "-npool", "1"]
code_info.stdin_name = 'aiida.in'
job_tmpl.codes_info = [code_info]
job_tmpl.codes_run_mode = code_run_modes.SERIAL
submit_script_text = s.get_submit_script(job_tmpl)
self.assertTrue('#PBS -r n' in submit_script_text)
self.assertTrue(submit_script_text.startswith('#!/bin/bash -l'))
self.assertTrue('#PBS -l walltime=24:00:00' in submit_script_text)
self.assertTrue('#PBS -l select=1' in submit_script_text)
self.assertTrue("'mpirun' '-np' '23' 'pw.x' '-npool' '1'" + \
" < 'aiida.in'" in submit_script_text)
[docs] def test_submit_script_bad_shebang(self):
"""
Test to verify if scripts works fine with default options
"""
from aiida.scheduler.datastructures import JobTemplate
from aiida.common.datastructures import CodeInfo, code_run_modes
s = PbsproScheduler()
code_info = CodeInfo()
code_info.cmdline_params = ["mpirun", "-np", "23", "pw.x", "-npool", "1"]
code_info.stdin_name = 'aiida.in'
for (shebang, expected_first_line) in ((None, '#!/bin/bash'), ("",""), ("NOSET", '#!/bin/bash')):
job_tmpl = JobTemplate()
if shebang == "NOSET":
pass
else:
job_tmpl.shebang = shebang
job_tmpl.job_resource = s.create_job_resource(num_machines=1, num_mpiprocs_per_machine=1)
job_tmpl.codes_info = [code_info]
job_tmpl.codes_run_mode = code_run_modes.SERIAL
submit_script_text = s.get_submit_script(job_tmpl)
# This tests if the implementation correctly chooses the default:
self.assertEquals(submit_script_text.split('\n')[0], expected_first_line)
[docs] def test_submit_script_with_num_cores_per_machine(self):
"""
Test to verify if script works fine if we specify only
num_cores_per_machine value.
"""
from aiida.scheduler.datastructures import JobTemplate
from aiida.common.datastructures import CodeInfo, code_run_modes
s = PbsproScheduler()
job_tmpl = JobTemplate()
job_tmpl.shebang = '#!/bin/bash'
job_tmpl.job_resource = s.create_job_resource(
num_machines=1,
num_mpiprocs_per_machine=2,
num_cores_per_machine=24
)
job_tmpl.uuid = str(uuid.uuid4())
job_tmpl.max_wallclock_seconds = 24 * 3600
code_info = CodeInfo()
code_info.cmdline_params = ["mpirun", "-np", "23",
"pw.x", "-npool", "1"]
code_info.stdin_name = 'aiida.in'
job_tmpl.codes_info = [code_info]
job_tmpl.codes_run_mode = code_run_modes.SERIAL
submit_script_text = s.get_submit_script(job_tmpl)
self.assertTrue('#PBS -r n' in submit_script_text)
self.assertTrue(submit_script_text.startswith('#!/bin/bash'))
self.assertTrue('#PBS -l select=1:mpiprocs=2' in submit_script_text)
# Note: here 'num_cores_per_machine' should NOT override the mpiprocs
self.assertTrue("'mpirun' '-np' '23' 'pw.x' '-npool' '1'" +
" < 'aiida.in'" in submit_script_text)
[docs] def test_submit_script_with_num_cores_per_mpiproc(self):
"""
Test to verify if scripts works fine if we pass only
num_cores_per_mpiproc value
"""
from aiida.scheduler.datastructures import JobTemplate
from aiida.common.datastructures import CodeInfo, code_run_modes
s = PbsproScheduler()
job_tmpl = JobTemplate()
job_tmpl.shebang = '#!/bin/bash'
job_tmpl.job_resource = s.create_job_resource(
num_machines=1,
num_mpiprocs_per_machine=1,
num_cores_per_mpiproc=24
)
job_tmpl.uuid = str(uuid.uuid4())
job_tmpl.max_wallclock_seconds = 24 * 3600
code_info = CodeInfo()
code_info.cmdline_params = [
"mpirun", "-np", "23",
"pw.x", "-npool", "1"
]
code_info.stdin_name = 'aiida.in'
job_tmpl.codes_info = [code_info]
job_tmpl.codes_run_mode = code_run_modes.SERIAL
submit_script_text = s.get_submit_script(job_tmpl)
self.assertTrue('#PBS -r n' in submit_script_text)
self.assertTrue(submit_script_text.startswith('#!/bin/bash'))
self.assertTrue('#PBS -l select=1:mpiprocs=1:ppn=24' in submit_script_text)
# Note: here 'num_cores_per_machine' should NOT override the mpiprocs
self.assertTrue("'mpirun' '-np' '23' 'pw.x' '-npool' '1'" +
" < 'aiida.in'" in submit_script_text)
[docs] def test_submit_script_with_num_cores_per_machine_and_mpiproc1(self):
"""
Test to verify if scripts works fine if we pass both
num_cores_per_machine and num_cores_per_mpiproc correct values.
It should pass in check:
res.num_cores_per_mpiproc * res.num_mpiprocs_per_machine = res.num_cores_per_machine
"""
from aiida.scheduler.datastructures import JobTemplate
from aiida.common.datastructures import CodeInfo, code_run_modes
s = PbsproScheduler()
job_tmpl = JobTemplate()
job_tmpl.shebang = '#!/bin/bash'
job_tmpl.job_resource = s.create_job_resource(
num_machines=1,
num_mpiprocs_per_machine=1,
num_cores_per_machine=24,
num_cores_per_mpiproc=24
)
job_tmpl.uuid = str(uuid.uuid4())
job_tmpl.max_wallclock_seconds = 24 * 3600
code_info = CodeInfo()
code_info.cmdline_params = [
"mpirun", "-np", "23",
"pw.x", "-npool", "1"
]
code_info.stdin_name = 'aiida.in'
job_tmpl.codes_info = [code_info]
job_tmpl.codes_run_mode = code_run_modes.SERIAL
submit_script_text = s.get_submit_script(job_tmpl)
self.assertTrue('#PBS -r n' in submit_script_text)
self.assertTrue(submit_script_text.startswith('#!/bin/bash'))
self.assertTrue('#PBS -l select=1:mpiprocs=1:ppn=24' in submit_script_text)
# Note: here 'num_cores_per_machine' should NOT override the mpiprocs
self.assertTrue("'mpirun' '-np' '23' 'pw.x' '-npool' '1'" +
" < 'aiida.in'" in submit_script_text)
[docs] def test_submit_script_with_num_cores_per_machine_and_mpiproc2(self):
"""
Test to verify if scripts works fine if we pass
num_cores_per_machine and num_cores_per_mpiproc wrong values.
It should fail in check:
res.num_cores_per_mpiproc * res.num_mpiprocs_per_machine = res.num_cores_per_machine
"""
from aiida.scheduler.datastructures import JobTemplate
from aiida.common.datastructures import CodeInfo, code_run_modes
s = PbsproScheduler()
job_tmpl = JobTemplate()
with self.assertRaises(ValueError):
job_tmpl.job_resource = s.create_job_resource(
num_machines=1,
num_mpiprocs_per_machine=1,
num_cores_per_machine=24,
num_cores_per_mpiproc=23
)