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Fixes to provenance/timing saving #1201

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merged 9 commits into from
Jan 26, 2017
Merged

Fixes to provenance/timing saving #1201

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779d8f5
Fixes to provenance/timing saving
jgfouca Dec 30, 2016
9e3f14f
Fixes based on review
jgfouca Jan 3, 2017
6cdaf97
Address additional feedback for PR.
jgfouca Jan 4, 2017
585d13b
Change gzip utility function to preserve timestamps of original file
jgfouca Jan 5, 2017
d8aed6b
Add timestamp to output_error_path
jgfouca Jan 12, 2017
d2cc172
Revert "Add timestamp to output_error_path"
jgfouca Jan 17, 2017
02ced13
Better solution for getting the jobid into slurm output files
jgfouca Jan 17, 2017
2868e50
Fix syslog_jobid path name
jgfouca Jan 17, 2017
0dcecbf
rename corip1 as cori-haswell and cori-knl
Jan 21, 2017
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2 changes: 1 addition & 1 deletion cime/cime_config/acme/machines/config_batch.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,7 @@
<directives>
<directive> --job-name={{ job_id }}</directive>
<directive> --nodes={{ num_nodes }}</directive>
<directive> --output={{ output_error_path }} </directive>
<directive> --output={{ output_error_path }}.%j </directive>
<directive> --exclusive </directive>
<directive> --time={{ job_wallclock_time }}</directive>
<directive> --partition={{ job_queue }}</directive>
Expand Down
10 changes: 5 additions & 5 deletions cime/cime_config/acme/machines/syslog.cetus
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,11 @@ set timing = $5
set dir = $6

# wait until output file is nonempty before checking remaining time
# (note that calling script 'touch'es the cesm log file before spawning this script, so that 'wc' does not fail)
# (note that calling script 'touch'es the acme log file before spawning this script, so that 'wc' does not fail)
set outlth = 0
while ($outlth < 1)
sleep 10
set outlth = `wc \-l $run/cesm.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
set outlth = `wc \-l $run/acme.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
end

set TimeRemaining = `qstat -lf $jid | grep TimeRemaining | sed 's/^ *TimeRemaining *: *\([0-9]*:[0-9]*:[0-9]*\) */\1/' `
Expand All @@ -29,16 +29,16 @@ if ("X$rem_secs" == "X") set rem_secs = 0
cat > $run/Walltime.Remaining <<EOF1
$remaining $sample_interval
EOF1
/bin/cp -p $run/cesm.log.$lid $dir/cesm.log.$lid.$remaining
/bin/cp --preserve=timestamps $run/acme.log.$lid $dir/acme.log.$lid.$remaining

while ($remaining > 0)
grep -a -i -e "nstep" -e "model date" $run/*atm.log.$lid | tail > $dir/atm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/cesm.log.$lid | tail > $dir/cesm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/acme.log.$lid | tail > $dir/acme.log.$lid.nstep.$remaining
grep -a -i -e "timestep" -e "model date" $run/*lnd.log.$lid | tail > $dir/lnd.log.$lid.timestep.$remaining
grep -a -i -e "timestep" -e "Step number" -e "model date" $run/*ocn.log.$lid | tail > $dir/ocn.log.$lid.stepnum.$remaining
grep -a -i -e "timestep" -e "istep" -e "model date" $run/*ice.log.$lid | tail > $dir/ice.log.$lid.istep.$remaining
grep -a -i "model date" $run/*cpl.log.$lid | tail > $dir/cpl.log.$lid.modeldata.$remaining
cp -p -u $timing/* $dir
/bin/cp --preserve=timestamps -u $timing/* $dir
chmod a+r $dir/*
sleep $sample_interval
set TimeRemaining = `qstat -lf $jid | grep TimeRemaining | sed 's/^ *TimeRemaining *: *\([0-9]*:[0-9]*:[0-9]*\) */\1/' `
Expand Down
72 changes: 72 additions & 0 deletions cime/cime_config/acme/machines/syslog.cori-haswell
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Original file line number Diff line number Diff line change
@@ -0,0 +1,72 @@
#!/bin/csh -f
# cori-haswell syslog script:
# mach_syslog <sampling interval (in seconds)> <job identifier> <time stamp> <run directory> <timing directory> <output directory>

set sec = 0
set sample_interval = $1
set jid = $2
set lid = $3
set run = $4
set timing = $5
set dir = $6

# wait until job mapping information is output before saving output file
# (note that calling script 'touch'es the acme log file before spawning this script, so that 'wc' does not fail)
set nnodes = `sqs -f $jid | grep NumNodes | sed 's/^ *NumNodes= *\([0-9]*\).*/\1/' `
set outlth = 0
while ($outlth < $nnodes)
sleep 10
set outlth = `wc \-l $run/acme.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
end

set TimeLimit = `sqs -f $jid | grep TimeLimit | sed 's/^ *RunTime=.*TimeLimit=\([0-9]*:[0-9]*:[0-9]*\) .*/\1/' `
set limit_hours = `echo $TimeLimit | sed 's/^0*\([0-9]*\):0*\([0-9]*\):0*\([0-9]*\)/\1/' `
set limit_mins = `echo $TimeLimit | sed 's/^0*\([0-9]*\):0*\([0-9]*\):0*\([0-9]*\)/\2/' `
set limit_secs = `echo $TimeLimit | sed 's/^0*\([0-9]*\):0*\([0-9]*\):0*\([0-9]*\)/\3/' `
if ("X$limit_hours" == "X") set limit_hours = 0
if ("X$limit_mins" == "X") set limit_mins = 0
if ("X$limit_secs" == "X") set limit_secs = 0
@ limit = 3600 * $limit_hours + 60 * $limit_mins + $limit_secs

set RunTime = `sqs -f $jid | grep RunTime | sed 's/^ *RunTime=\([0-9]*:[0-9]*:[0-9]*\) .*/\1/' `
set runt_hours = `echo $RunTime | sed 's/^0*\([0-9]*\):0*\([0-9]*\):0*\([0-9]*\)/\1/' `
set runt_mins = `echo $RunTime | sed 's/^0*\([0-9]*\):0*\([0-9]*\):0*\([0-9]*\)/\2/' `
set runt_secs = `echo $RunTime | sed 's/^0*\([0-9]*\):0*\([0-9]*\):0*\([0-9]*\)/\3/' `
if ("X$runt_hours" == "X") set runt_hours = 0
if ("X$runt_mins" == "X") set runt_mins = 0
if ("X$runt_secs" == "X") set runt_secs = 0
@ runt = 3600 * $runt_hours + 60 * $runt_mins + $runt_secs

@ remaining = $limit - $runt
cat > $run/Walltime.Remaining <<EOF1
$remaining $sample_interval
EOF1
/bin/cp --preserve=timestamps $run/acme.log.$lid $dir/acme.log.$lid.$remaining

while ($remaining > 0)
grep -a -i -e "nstep" -e "model date" $run/*atm.log.$lid | tail > $dir/atm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/acme.log.$lid | tail > $dir/acme.log.$lid.nstep.$remaining
grep -a -i -e "timestep" -e "model date" $run/*lnd.log.$lid | tail > $dir/lnd.log.$lid.timestep.$remaining
grep -a -i -e "timestep" -e "Step number" -e "model date" $run/*ocn.log.$lid | tail > $dir/ocn.log.$lid.stepnum.$remaining
grep -a -i -e "timestep" -e "istep" -e "model date" $run/*ice.log.$lid | tail > $dir/ice.log.$lid.istep.$remaining
grep -a -i "model date" $run/*cpl.log.$lid | tail > $dir/cpl.log.$lid.modeldata.$remaining
/bin/cp --preserve=timestamps -u $timing/* $dir
# xtnodestat > $dir/xtnodestat.$lid.$remaining
sqs -w -a > $dir/sqsw.$lid.$remaining
chmod a+r $dir/*
sleep $sample_interval
set RunTime = `sqs -f $jid | grep RunTime | sed 's/^ *RunTime=\([0-9]*:[0-9]*:[0-9]*\) .*/\1/' `
set runt_hours = `echo $RunTime | sed 's/^0*\([0-9]*\):0*\([0-9]*\):0*\([0-9]*\)/\1/' `
set runt_mins = `echo $RunTime | sed 's/^0*\([0-9]*\):0*\([0-9]*\):0*\([0-9]*\)/\2/' `
set runt_secs = `echo $RunTime | sed 's/^0*\([0-9]*\):0*\([0-9]*\):0*\([0-9]*\)/\3/' `
if ("X$runt_hours" == "X") set runt_hours = 0
if ("X$runt_mins" == "X") set runt_mins = 0
if ("X$runt_secs" == "X") set runt_secs = 0
@ runt = 3600 * $runt_hours + 60 * $runt_mins + $runt_secs
@ remaining = $limit - $runt
cat > $run/Walltime.Remaining << EOF2
$remaining $sample_interval
EOF2

end

12 changes: 6 additions & 6 deletions cime/cime_config/acme/machines/syslog.corip1 → ...cime_config/acme/machines/syslog.cori-knl
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#!/bin/csh -f
# corip1 syslog script:
# cori-knl syslog script:
# mach_syslog <sampling interval (in seconds)> <job identifier> <time stamp> <run directory> <timing directory> <output directory>

set sec = 0
Expand All @@ -11,12 +11,12 @@ set timing = $5
set dir = $6

# wait until job mapping information is output before saving output file
# (note that calling script 'touch'es the cesm log file before spawning this script, so that 'wc' does not fail)
# (note that calling script 'touch'es the acme log file before spawning this script, so that 'wc' does not fail)
set nnodes = `sqs -f $jid | grep NumNodes | sed 's/^ *NumNodes= *\([0-9]*\).*/\1/' `
set outlth = 0
while ($outlth < $nnodes)
sleep 10
set outlth = `wc \-l $run/cesm.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
set outlth = `wc \-l $run/acme.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
end

set TimeLimit = `sqs -f $jid | grep TimeLimit | sed 's/^ *RunTime=.*TimeLimit=\([0-9]*:[0-9]*:[0-9]*\) .*/\1/' `
Expand All @@ -41,16 +41,16 @@ if ("X$runt_secs" == "X") set runt_secs = 0
cat > $run/Walltime.Remaining <<EOF1
$remaining $sample_interval
EOF1
/bin/cp -p $run/cesm.log.$lid $dir/cesm.log.$lid.$remaining
/bin/cp --preserve=timestamps $run/acme.log.$lid $dir/acme.log.$lid.$remaining

while ($remaining > 0)
grep -a -i -e "nstep" -e "model date" $run/*atm.log.$lid | tail > $dir/atm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/cesm.log.$lid | tail > $dir/cesm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/acme.log.$lid | tail > $dir/acme.log.$lid.nstep.$remaining
grep -a -i -e "timestep" -e "model date" $run/*lnd.log.$lid | tail > $dir/lnd.log.$lid.timestep.$remaining
grep -a -i -e "timestep" -e "Step number" -e "model date" $run/*ocn.log.$lid | tail > $dir/ocn.log.$lid.stepnum.$remaining
grep -a -i -e "timestep" -e "istep" -e "model date" $run/*ice.log.$lid | tail > $dir/ice.log.$lid.istep.$remaining
grep -a -i "model date" $run/*cpl.log.$lid | tail > $dir/cpl.log.$lid.modeldata.$remaining
cp -p -u $timing/* $dir
/bin/cp --preserve=timestamps -u $timing/* $dir
# xtnodestat > $dir/xtnodestat.$lid.$remaining
sqs -w -a > $dir/sqsw.$lid.$remaining
chmod a+r $dir/*
Expand Down
10 changes: 5 additions & 5 deletions cime/cime_config/acme/machines/syslog.edison
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Original file line number Diff line number Diff line change
Expand Up @@ -11,12 +11,12 @@ set timing = $5
set dir = $6

# wait until job mapping information is output before saving output file
# (note that calling script 'touch'es the cesm log file before spawning this script, so that 'wc' does not fail)
# (note that calling script 'touch'es the acme log file before spawning this script, so that 'wc' does not fail)
set nnodes = `sqs -f $jid | grep NumNodes | sed 's/^ *NumNodes= *\([0-9]*\).*/\1/' `
set outlth = 0
while ($outlth < $nnodes)
sleep 10
set outlth = `wc \-l $run/cesm.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
set outlth = `wc \-l $run/acme.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
end

set TimeLimit = `sqs -f $jid | grep TimeLimit | sed 's/^ *RunTime=.*TimeLimit=\([0-9]*:[0-9]*:[0-9]*\) .*/\1/' `
Expand All @@ -41,16 +41,16 @@ if ("X$runt_secs" == "X") set runt_secs = 0
cat > $run/Walltime.Remaining <<EOF1
$remaining $sample_interval
EOF1
/bin/cp -p $run/cesm.log.$lid $dir/cesm.log.$lid.$remaining
/bin/cp --preserve=timestamps $run/acme.log.$lid $dir/acme.log.$lid.$remaining

while ($remaining > 0)
grep -a -i -e "nstep" -e "model date" $run/*atm.log.$lid | tail > $dir/atm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/cesm.log.$lid | tail > $dir/cesm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/acme.log.$lid | tail > $dir/acme.log.$lid.nstep.$remaining
grep -a -i -e "timestep" -e "model date" $run/*lnd.log.$lid | tail > $dir/lnd.log.$lid.timestep.$remaining
grep -a -i -e "timestep" -e "Step number" -e "model date" $run/*ocn.log.$lid | tail > $dir/ocn.log.$lid.stepnum.$remaining
grep -a -i -e "timestep" -e "istep" -e "model date" $run/*ice.log.$lid | tail > $dir/ice.log.$lid.istep.$remaining
grep -a -i "model date" $run/*cpl.log.$lid | tail > $dir/cpl.log.$lid.modeldata.$remaining
cp -p -u $timing/* $dir
/bin/cp --preserve=timestamps -p -u $timing/* $dir
# xtnodestat > $dir/xtnodestat.$lid.$remaining
sqs -w -a > $dir/sqsw.$lid.$remaining
chmod a+r $dir/*
Expand Down
10 changes: 5 additions & 5 deletions cime/cime_config/acme/machines/syslog.mira
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Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,11 @@ set timing = $5
set dir = $6

# wait until output file is nonempty before checking remaining time
# (note that calling script 'touch'es the cesm log file before spawning this script, so that 'wc' does not fail)
# (note that calling script 'touch'es the acme log file before spawning this script, so that 'wc' does not fail)
set outlth = 0
while ($outlth < 1)
sleep 10
set outlth = `wc \-l $run/cesm.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
set outlth = `wc \-l $run/acme.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
end

set TimeRemaining = `qstat -lf $jid | grep TimeRemaining | sed 's/^ *TimeRemaining *: *\([0-9]*:[0-9]*:[0-9]*\) */\1/' `
Expand All @@ -29,16 +29,16 @@ if ("X$rem_secs" == "X") set rem_secs = 0
cat > $run/Walltime.Remaining <<EOF1
$remaining $sample_interval
EOF1
/bin/cp -p $run/cesm.log.$lid $dir/cesm.log.$lid.$remaining
/bin/cp --preserve=timestamps $run/acme.log.$lid $dir/acme.log.$lid.$remaining

while ($remaining > 0)
grep -a -i -e "nstep" -e "model date" $run/*atm.log.$lid | tail > $dir/atm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/cesm.log.$lid | tail > $dir/cesm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/acme.log.$lid | tail > $dir/acme.log.$lid.nstep.$remaining
grep -a -i -e "timestep" -e "model date" $run/*lnd.log.$lid | tail > $dir/lnd.log.$lid.timestep.$remaining
grep -a -i -e "timestep" -e "Step number" -e "model date" $run/*ocn.log.$lid | tail > $dir/ocn.log.$lid.stepnum.$remaining
grep -a -i -e "timestep" -e "istep" -e "model date" $run/*ice.log.$lid | tail > $dir/ice.log.$lid.istep.$remaining
grep -a -i "model date" $run/*cpl.log.$lid | tail > $dir/cpl.log.$lid.modeldata.$remaining
cp -p -u $timing/* $dir
/bin/cp --preserve=timestamps -u $timing/* $dir
chmod a+r $dir/*
sleep $sample_interval
set TimeRemaining = `qstat -lf $jid | grep TimeRemaining | sed 's/^ *TimeRemaining *: *\([0-9]*:[0-9]*:[0-9]*\) */\1/' `
Expand Down
10 changes: 5 additions & 5 deletions cime/cime_config/acme/machines/syslog.titan
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Original file line number Diff line number Diff line change
Expand Up @@ -11,27 +11,27 @@ set timing = $5
set dir = $6

# wait until job mapping information is output before saving output file
# (note that calling script 'touch'es the cesm log file before spawning this script, so that 'wc' does not fail)
# (note that calling script 'touch'es the acme log file before spawning this script, so that 'wc' does not fail)
set nnodes = `qstat -f $jid | grep Resource_List.nodes | sed 's/ *Resource_List.nodes = *\([0-9]*\):ppn=*\([0-9]*\) */\1/' `
set outlth = 0
while ($outlth < $nnodes)
sleep 10
set outlth = `wc \-l $run/cesm.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
set outlth = `wc \-l $run/acme.log.$lid | sed 's/ *\([0-9]*\) *.*/\1/' `
end
set remaining = `qstat -f $jid | grep Walltime.Remaining | sed 's/ *Walltime.Remaining = *\([0-9]*\) */\1/' `
cat > $run/Walltime.Remaining <<EOF1
$remaining $sample_interval
EOF1
/bin/cp -p $run/cesm.log.$lid $dir/cesm.log.$lid.$remaining
/bin/cp --preserve=timestamps $run/acme.log.$lid $dir/acme.log.$lid.$remaining

while ($remaining > 0)
grep -a -i -e "nstep" -e "model date" $run/*atm.log.$lid | tail > $dir/atm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/cesm.log.$lid | tail > $dir/cesm.log.$lid.nstep.$remaining
# grep -a -i "nstep" $run/acme.log.$lid | tail > $dir/acme.log.$lid.nstep.$remaining
grep -a -i -e "timestep" -e "model date" $run/*lnd.log.$lid | tail > $dir/lnd.log.$lid.timestep.$remaining
grep -a -i -e "timestep" -e "Step number" -e "model date" $run/*ocn.log.$lid | tail > $dir/ocn.log.$lid.stepnum.$remaining
grep -a -i -e "timestep" -e "istep" -e "model date" $run/*ice.log.$lid | tail > $dir/ice.log.$lid.istep.$remaining
grep -a -i "model date" $run/*cpl.log.$lid | tail > $dir/cpl.log.$lid.modeldata.$remaining
cp -p -u $timing/* $dir
/bin/cp --preserve=timestamps -u $timing/* $dir
xtnodestat > $dir/xtnodestat.$lid.$remaining
showq > $dir/showq.$lid.$remaining
chmod a+r $dir/*
Expand Down
1 change: 1 addition & 0 deletions cime/driver_cpl/cime_config/buildnml
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,7 @@ def _main_func():
% (grid, atm_grid, lnd_grid, rof_grid, ocn_grid, wav_grid)

rc, out, err = run_cmd(cmd, from_dir=confdir)
logger.info(out)
expect(rc==0,"Command %s failed rc=%d\nout=%s\nerr=%s"%(cmd,rc,out,err))

# copy drv_in, drv_flds_in, seq_maps.rc and all *modio* files to rundir
Expand Down
9 changes: 8 additions & 1 deletion cime/utils/python/CIME/case.py
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Original file line number Diff line number Diff line change
Expand Up @@ -688,6 +688,7 @@ def _set_pio_xml(self):
def _create_caseroot_tools(self):
machines_dir = os.path.abspath(self.get_value("MACHDIR"))
toolsdir = os.path.join(self.get_value("CIMEROOT"),"scripts","Tools")
casetools = os.path.join(self._caseroot, "Tools")
# setup executable files in caseroot/
exefiles = (os.path.join(toolsdir, "case.setup"),
os.path.join(toolsdir, "case.build"),
Expand Down Expand Up @@ -721,7 +722,7 @@ def _create_caseroot_tools(self):
toolfiles.append( os.path.join(toolsdir,"mdiag_reduce.pl") )

for toolfile in toolfiles:
destfile = os.path.join(self._caseroot,"Tools",os.path.basename(toolfile))
destfile = os.path.join(casetools, os.path.basename(toolfile))
expect(os.path.isfile(toolfile)," File %s does not exist"%toolfile)
try:
os.symlink(toolfile, destfile)
Expand Down Expand Up @@ -764,6 +765,12 @@ def _create_caseroot_tools(self):
# except Exception as e:
# logger.warning("FAILED to set up infofiles: %s" % str(e))

if get_model() == "acme":
if os.path.exists(os.path.join(machines_dir, "syslog.%s" % machine)):
shutil.copy(os.path.join(machines_dir, "syslog.%s" % machine), os.path.join(casetools, "mach_syslog"))
else:
shutil.copy(os.path.join(machines_dir, "syslog.noop"), os.path.join(casetools, "mach_syslog"))

def _create_caseroot_sourcemods(self):
components = self.get_compset_components()
for component in components:
Expand Down
6 changes: 3 additions & 3 deletions cime/utils/python/CIME/get_timing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@

from CIME.XML.standard_module_setup import *

import datetime, shutil, re, gzip
import datetime, shutil, re

logger = logging.getLogger(__name__)

Expand Down Expand Up @@ -160,7 +160,7 @@ def getTiming(self):
finfilename = os.path.join(self.caseroot, "timing",
"%s_timing_stats.%s" % (cime_model, self.lid))
foutfilename = os.path.join(self.caseroot, "timing",
"%s_timing.%s.%s.gz" % (cime_model, caseid, self.lid))
"%s_timing.%s.%s" % (cime_model, caseid, self.lid))

timingDir = os.path.join(self.caseroot, "timing")
if not os.path.isdir(timingDir):
Expand Down Expand Up @@ -215,7 +215,7 @@ def getTiming(self):
m.offset = int((maxoffset*m.rootpe)/peminmax) + extraoff
cpl.offset = 0
try:
self.fout = gzip.open(foutfilename, "wb")
self.fout = open(foutfilename, "w")
except Exception, e:
logger.critical("Could not open file for writing: %s"
% foutfilename)
Expand Down
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