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More fixes for the run_acme script #1458

Merged
merged 8 commits into from
Apr 27, 2017
Merged

More fixes for the run_acme script #1458

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5ef0514
Remove run_name from the list of configuration variables
mfdeakin-sandia Apr 26, 2017
697583f
Fix issues with checking whether a variables is defined
mfdeakin-sandia Apr 26, 2017
c4a21d6
Change handle-preexisting-dirs to use the existing ones rather than a…
mfdeakin-sandia Apr 26, 2017
24eb0b7
Add vowels to 'bld'
mfdeakin-sandia Apr 26, 2017
bddd8e1
Rename case_root_dir to acme_simulations_dir
mfdeakin-sandia Apr 26, 2017
5bbab97
Fix usage of xmlchange for the customknl configuration
mfdeakin-sandia Apr 26, 2017
41a4a24
Give project a default value, in which case CIME will determine the p…
mfdeakin-sandia Apr 26, 2017
c6d7018
Update the script version and the update notes
mfdeakin-sandia Apr 27, 2017
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152 changes: 105 additions & 47 deletions run_acme.template.csh
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
###===================================================================

### BASIC INFO ABOUT RUN
set run_name = run_acme.template
set job_name = A_WCYCL1850_template
set compset = A_WCYCL1850
set resolution = ne4np4_oQU240
Expand Down Expand Up @@ -40,14 +39,15 @@ set submit_run = true
set debug_queue = true

### PROCESSOR CONFIGURATION
set processor_config = S
set processor_config = M

### STARTUP TYPE
set model_start_type = initial
set restart_files_dir = none

### DIRECTORIES
set code_root_dir = default
set acme_simulations_dir = default
set case_build_dir = default
set case_run_dir = default
set short_term_archive_root_dir = default
Expand All @@ -64,6 +64,7 @@ set do_long_term_archiving = false
### SIMULATION OPTIONS
set atm_output_freq = -24
set records_per_atm_output_file = 40
set start_date = default

### COUPLER HISTORY FILES
set do_cpl_hist = true
Expand All @@ -76,8 +77,6 @@ set cpl_hist_num = 1

### BASIC INFO ABOUT RUN (1)

#run_name: the run will be named: ${tag_name}.${compset}.${resolution}.${run_name}. run_name is to explain the
# purpose of the run (e.g. run_name=ParallelPhysDyn) or just to ensure the run name is unique (e.g. run_name=test1).
#job_name: This is only used to name the job in the batch system. The problem is that batch systems often only
# provide the first few letters of the job name when reporting on jobs inthe queue, which may not be enough
# to distinguish simultaneous jobs.
Expand Down Expand Up @@ -182,6 +181,7 @@ set cpl_hist_num = 1
#NOTE: If there will be more than one 'history tape' defined in the atm namelist, then
# atm_output_freq and records_per_atm_output_file should be a comma-separated list of numbers
# (specifying the option for each history tape).
#start_date: The day that the simulation starts

### GENERAL NOTES:

Expand Down Expand Up @@ -267,25 +267,20 @@ endif

if ( `lowercase $old_executable` == true ) then
if ( $seconds_before_delete_source_dir >= 0 ) then
acme_newline
acme_print 'ERROR: It is unlikely that you want to delete the source code and then use the existing compiled executable.'
acme_print ' Hence, this script will abort to avoid making a mistake.'
acme_print ' $seconds_before_delete_source_dir = '$seconds_before_delete_source_dir' $old_executable = '$old_executable
exit 11
endif

if ( $seconds_before_delete_bld_dir >= 0 ) then
acme_newline
acme_print 'ERROR: It makes no sense to delete the source-compiled code and then use the existing compiled executable.'
acme_print ' Hence, this script will abort to avoid making a mistake.'
acme_print ' $seconds_before_delete_bld_dir = '$seconds_before_delete_bld_dir' $old_executable = '$old_executable
exit 12
endif

if ( `lowercase $case_build_dir` == default ) then
acme_print 'WARNING: run_acme must be run interactively when using the default build directory and old executables'
acme_print ' To remedy this, either set $case_build_dir to the path of the executables'
acme_print ' If this is an interactive shell, deactivate this test'
exit 13
endif
endif

if ( `lowercase $case_build_dir` == default && $seconds_before_delete_bld_dir >= 0 ) then
Expand Down Expand Up @@ -383,16 +378,41 @@ endif
acme_newline
acme_print '$case_name = '$case_name

#============================================
# DETERMINE THE SCRATCH DIRECTORY TO USE
#============================================

if ( $acme_simulations_dir == default ) then
### NOTE: csh doesn't short-circuit; so we can't check whether $SCRATCH exists or whether it's empty in the same condition
if ( ! $?SCRATCH ) then
acme_newline
acme_print 'WARNING: Performing science runs while storing run output in your home directory is likely to exceed your quota'
acme_print ' To avoid any issues, set $acme_simulations_dir to a scratch filesystem'
set acme_simulations_dir = ${HOME}/acme_simulations
else
### Verify that $SCRATCH is not an empty string
if ( "${SCRATCH}" == "" ) then
set acme_simulations_dir = ${HOME}/acme_simulations
acme_newline
acme_print 'WARNING: Performing science runs while storing run output in your home directory is likely to exceed your quota'
acme_print ' To avoid any issues, set $acme_simulations_dir to a scratch filesystem'
else
set acme_simulations_dir = ${SCRATCH}/acme_simulations
endif
endif
endif

#============================================
# DELETE PREVIOUS DIRECTORIES (IF REQUESTED)
#============================================
### Determine the case_scripts directory
### Remove existing case_scripts directory (so it doesn't have to be done manually every time)
### Note: This script causes create_newcase to generate a temporary directory (part of a workaround to put the case_name into the script names)
### If something goes wrong, this temporary directory is sometimes left behind, so we need to delete it too.
### Note: To turn off the deletion, set $num_seconds_until_delete to be negative.
### To delete immediately, set $num_seconds_until_delete to be zero.

set case_scripts_dir = `pwd -P`/$case_name
set case_scripts_dir = ${acme_simulations_dir}/${case_name}/case_scripts

if ( -d $case_scripts_dir ) then
if ( ${seconds_before_delete_case_dir} >= 0 ) then
Expand Down Expand Up @@ -524,27 +544,55 @@ else # No vers
endif

#=============================================================
# CREATE CASE_SCRIPTS DIRECTORY AND POPULATE WITH NEEDED FILES
# DETERMINE THE OPTIONS FOR CREATE_NEWCASE
#=============================================================

set configure_options = "--case ${case_name} --compset ${compset} --res ${resolution} --project ${project} --pecount ${std_proc_configuration}"
set configure_options = "--case ${case_scripts_dir} --compset ${compset} --res ${resolution} --project ${project} --pecount ${std_proc_configuration} --handle-preexisting-dirs u"

if ( `lowercase $machine` != default ) then
set configure_options = "$configure_options --mach ${machine}"
set configure_options = "${configure_options} --mach ${machine}"
endif

if ( `lowercase $case_build_dir` == default ) then
set case_build_dir = ${acme_simulations_dir}/${case_name}/build
endif

if ( `lowercase $case_run_dir` == default ) then
set case_run_dir = ${acme_simulations_dir}/${case_name}/run
endif

mkdir -p ${case_build_dir}
set build_root = `cd ${case_build_dir}/..; pwd -P`
mkdir -p ${case_run_dir}
set run_root = `cd ${case_run_dir}/..; pwd -P`

if ( ${build_root} == ${run_root} ) then
set configure_options = "${configure_options} --output-root ${build_root}"
endif

#=============================================================
# CREATE CASE_SCRIPTS DIRECTORY AND POPULATE WITH NEEDED FILES
#=============================================================

acme_newline
acme_print '-------- Starting create_newcase --------'
acme_newline

acme_print $create_newcase_exe $configure_options
$create_newcase_exe $configure_options
cd ${case_name}

cd ${case_scripts_dir}

acme_newline
acme_print '-------- Finished create_newcase --------'
acme_newline

#================================================
# CORRECT THE CASE NAME FOR THE OUTPUT FILES
#================================================

${xmlchange_exe} --id CASE --val ${case_name}

#================================================
# UPDATE VARIABLES WHICH REQUIRE A CASE TO BE SET
#================================================
Expand All @@ -553,11 +601,14 @@ if ( `lowercase $machine` == default ) then
set machine = `$xmlquery_exe MACH --value`
endif
if ( `lowercase $case_build_dir` == default ) then
set case_build_dir = `$xmlquery_exe EXEROOT --value`
set case_build_dir = ${acme_simulations_dir}/${case_name}/bld
endif
${xmlchange_exe} EXEROOT=${case_build_dir}

if ( `lowercase $case_run_dir` == default ) then
set case_run_dir = `$xmlquery_exe RUNDIR --value`
set case_run_dir = ${case_scripts_dir}/${case_name}/run
endif
${xmlchange_exe} RUNDIR=${case_run_dir}

#================================
# SET WALLTIME FOR CREATE_NEWCASE
Expand All @@ -578,6 +629,14 @@ endif
# Allow the user to specify how long the job taks
$xmlchange_exe JOB_WALLCLOCK_TIME=$walltime

#================================
# SET THE STARTDATE FOR THE SIMULATION
#================================

if ( `lowercase $start_date` != 'default' ) then
$xmlchange_exe RUN_STARTDATE=$start_date
endif

#NOTE: Details of the configuration setup by create_newcase are in $case_scripts_dir/env_case.xml, which should NOT be edited.
# It will be used by cesm_setup (formerly 'configure -case').
#NOTE: To get verbose output from create_newcase, add '-v' to the argument list.
Expand Down Expand Up @@ -622,7 +681,6 @@ endif

if ( `lowercase $processor_config` == '1' ) then

# NOTE: xmlchange won't work with shell variables for the id, so we have to write it out in full.
set ntasks = 1
set nthrds = 1
set sequential_or_concurrent = 'sequential'
Expand All @@ -646,41 +704,41 @@ else if ( `lowercase $processor_config` == 'customknl' ) then

acme_print 'using custom layout for cori-knl because $processor_config = '$processor_config

./xmlchange MAX_TASKS_PER_NODE="64"
./xmlchange PES_PER_NODE="256"
${xmlchange_exe} MAX_TASKS_PER_NODE="64"
${xmlchange_exe} PES_PER_NODE="256"

./xmlchange NTASKS_ATM="5400"
./xmlchange ROOTPE_ATM="0"
${xmlchange_exe} NTASKS_ATM="5400"
${xmlchange_exe} ROOTPE_ATM="0"

./xmlchange NTASKS_LND="320"
./xmlchange ROOTPE_LND="5120"
${xmlchange_exe} NTASKS_LND="320"
${xmlchange_exe} ROOTPE_LND="5120"

./xmlchange NTASKS_ICE="5120"
./xmlchange ROOTPE_ICE="0"
${xmlchange_exe} NTASKS_ICE="5120"
${xmlchange_exe} ROOTPE_ICE="0"

./xmlchange NTASKS_OCN="3840"
./xmlchange ROOTPE_OCN="5440"
${xmlchange_exe} NTASKS_OCN="3840"
${xmlchange_exe} ROOTPE_OCN="5440"

./xmlchange NTASKS_CPL="5120"
./xmlchange ROOTPE_CPL="0"
${xmlchange_exe} NTASKS_CPL="5120"
${xmlchange_exe} ROOTPE_CPL="0"

./xmlchange NTASKS_GLC="320"
./xmlchange ROOTPE_GLC="5120"
${xmlchange_exe} NTASKS_GLC="320"
${xmlchange_exe} ROOTPE_GLC="5120"

./xmlchange NTASKS_ROF="320"
./xmlchange ROOTPE_ROF="5120"
${xmlchange_exe} NTASKS_ROF="320"
${xmlchange_exe} ROOTPE_ROF="5120"

./xmlchange NTASKS_WAV="5120"
./xmlchange ROOTPE_WAV="0"
${xmlchange_exe} NTASKS_WAV="5120"
${xmlchange_exe} ROOTPE_WAV="0"

./xmlchange NTHRDS_ATM="1"
./xmlchange NTHRDS_LND="1"
./xmlchange NTHRDS_ICE="1"
./xmlchange NTHRDS_OCN="1"
./xmlchange NTHRDS_CPL="1"
./xmlchange NTHRDS_GLC="1"
./xmlchange NTHRDS_ROF="1"
./xmlchange NTHRDS_WAV="1"
${xmlchange_exe} NTHRDS_ATM="1"
${xmlchange_exe} NTHRDS_LND="1"
${xmlchange_exe} NTHRDS_ICE="1"
${xmlchange_exe} NTHRDS_OCN="1"
${xmlchange_exe} NTHRDS_CPL="1"
${xmlchange_exe} NTHRDS_GLC="1"
${xmlchange_exe} NTHRDS_ROF="1"
${xmlchange_exe} NTHRDS_WAV="1"

endif

Expand Down Expand Up @@ -767,9 +825,9 @@ acme_newline
acme_print '-------- Starting case.setup --------'
acme_newline

acme_print $case_setup_exe
acme_print ${case_setup_exe}

$case_setup_exe --reset
${case_setup_exe} --reset

acme_newline
acme_print '-------- Finished case.setup --------'
Expand Down