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Updated coupled FTX UQ example #25

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Updated coupled FTX UQ example #25

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41219d7
Updated coupled FTX UQ example
Oct 9, 2022
9dd0be1
Several edits for new bubble bursting model / PISCES
Jan 20, 2023
461ea54
Added ts_adapt_clip option again
Jan 23, 2023
2696b35
Added time decimal as an option
Jun 13, 2023
ea11c7c
test
Jun 13, 2023
0fbb92f
Undo README changes
Jun 13, 2023
9eb515c
Added default configuration file (set to perlmutter)
Jul 13, 2023
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2 changes: 1 addition & 1 deletion iterative-xolotlFT-UQ/README
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
For running this test, copy the content to a folder in $SCRATCH. Otherwise there might be issues with netcdf when running GITR.
The test should easily be completed in 30min (debug queue), using 2 nodes.

A.L., 03/21/2022
A.L., 03/21/2022
41 changes: 41 additions & 0 deletions iterative-xolotlFT-UQ/conf.ips
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@@ -0,0 +1,41 @@
HOST = perlmutter
MPIRUN = srun #mpirun

PORTAL_URL = http://lb.ipsportal.production.svc.spin.nersc.org

#######################################
# resource detection method
#######################################
NODE_DETECTION = slurm_env # checkjob | qstat | pbs_env | slurm_env

#######################################
# manual allocation description
#######################################
TOTAL_PROCS = 128
NODES = 1

PROCS_PER_NODE = 128

#######################################
# node topology description
#######################################
CORES_PER_NODE = 128
SOCKETS_PER_NODE = 1

#######################################
# framework setting for node allocation
#######################################
# THE FOLLOWING ENTRIES MUST ADHERE TO THE PLATFORM'S CAPABILITIES
#
# NODE_ALLOCATION_MODE
# * EXCLUSIVE : only one task per node
# * SHARED : multiple tasks may share a node
# For single node jobs, this can be overridden allowing multiple
# tasks per node.
#
# USE_ACCURATE_NODES
# * ON : use accurate nodes if detected properly
# * OFF : DO NOT use accurate nodes even if detected properly
NODE_ALLOCATION_MODE = EXCLUSIVE # SHARED | EXCLUSIVE
USE_ACCURATE_NODES = ON # ON | OFF
#USE_ACCURATE_NODES = OFF # ON | OFF
8 changes: 4 additions & 4 deletions iterative-xolotlFT-UQ/conf.ips.cori
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@@ -1,7 +1,7 @@
HOST = cori
MPIRUN = srun #mpirun

PORTAL_URL = http://lb.ipsportal.production.svc.spin.nersc.org
PORTAL_URL = #http://lb.ipsportal.production.svc.spin.nersc.org

#######################################
# resource detection method
Expand All @@ -11,10 +11,10 @@ NODE_DETECTION = slurm_env # checkjob | qstat | pbs_env | slurm_env
#######################################
# manual allocation description
#######################################
TOTAL_PROCS = 136
NODES = 2
#TOTAL_PROCS = 136
#NODES = 2

PROCS_PER_NODE = 68
#PROCS_PER_NODE = 68

#######################################
# node topology description
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4 changes: 2 additions & 2 deletions iterative-xolotlFT-UQ/conf.ips.perlmutter
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Expand Up @@ -19,8 +19,8 @@ PROCS_PER_NODE = 128
#######################################
# node topology description
#######################################
CORES_PER_NODE = 64
SOCKETS_PER_NODE = 2
CORES_PER_NODE = 128
SOCKETS_PER_NODE = 1

#######################################
# framework setting for node allocation
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23 changes: 12 additions & 11 deletions iterative-xolotlFT-UQ/ips.ftx.config
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Expand Up @@ -18,22 +18,21 @@ RUN_COMMENT = F-Tridyn-Xolotl UQ run
TOKAMAK_ID = ANY
SHOT_NUMBER = 12345

SIM_NAME = ftx_Sim
SIM_NAME = {SIM_NAME}
SIM_ROOT = {SIM_ROOT}
SIM_INPUT_DIR= $SIM_ROOT/_inputs

OUTPUT_PREFIX =
LOG_FILE = log.warning
LOG_FILE = $SIM_ROOT/log.warning
LOG_LEVEL = INFO # DEBUG | INFO | WARN | ERROR | CRITICAL

SIM_ROOT = $PWD
SIM_INPUT_DIR= $PWD/_inputs

SIMULATION_MODE = NORMAL # NORMAL or RESTART
RESTART_TIME = LATEST # Float or LATEST
RESTART_ROOT = $SIM_ROOT

#option of running multiple IPS simulations, each from a different directory
CASE_PATH=$PWD
INPUT_DIR=$CASE_PATH
CASE_PATH=$SIM_ROOT
INPUT_DIR=$SIM_ROOT

# ======================================================================
# PLASMA STATE SECTION
Expand Down Expand Up @@ -135,7 +134,7 @@ PLASMA_STATE_FILES = $FT_PWD_PATH #$XFT_TRANSFER_FILE $XOLOTL_INPUT_FILES $XOLOT
NPROC = {NPROC} #TEST VALUE: for testing request just 32 ; for full runs change to 128 #ideally: NPROC/task_ppn = number of nodes
task_ppn={task_ppn}
THREADS_PER_TASK=1 #OMP_NUM_THREADS
BIN_PATH = $ATOM_CORI/xolotl/xolotl-bursting-UQ-gnu/xolotl/
BIN_PATH = $ATOM_{MACHINE}/xolotl/xolotl-bursting-UQ-gnu/xolotl/
XOLOTL_EXE = $BIN_PATH/xolotl
INPUT_DIR = #$BIN_PATH
INPUT_FILES = #$INPUT_DIR/param.template
Expand All @@ -153,16 +152,16 @@ PLASMA_STATE_FILES = $FT_PWD_PATH #$XFT_TRANSFER_FILE $XOLOTL_INPUT_FILES $XOLOT
SUB_CLASS =
NAME = ftridynWorker
NPROC = 1
BIN_PATH = $FTRIDYN_PATH/src
BIN_PATH = $ATOM_{MACHINE}/fractal-tridyn/src
FTRIDYN_EXE = $BIN_PATH/shell_Ftridyn.sh
INPUT_DIR = #/Users/tqd/Code/hi_input
INPUT_FILES = #$INPUT_DIR/example.txt
OUTPUT_FILES = output.txt
PWD_PATH= $FT_PWD_PATH
MODULE = ips_xolotlFT.ftridyn_comp
SCRIPT =
FTMPI_EXEC = $GITR_PATH/python/runFTexec_vEdison.py
FTMPI_NODES = 2 #TEST VALUE: for testing request just 1 ; for full runs change to 4
FTMPI_EXEC = $ATOM_{MACHINE}/GITR/python/runFTexec_vEdison.py
FTMPI_NODES = {FTMPI_NODES} #TEST VALUE: for testing request just 1 ; for full runs change to 4
FTMPI_PPN = {FTMPI_PPN}
THREADS_PER_TASK=1 #OMP_NUM_THREADS
STATE_FILES = $TRIDYN_DAT_FILE $SP_YIELDS_FILE $ALL_SPYIELDS_FILE $LAY_FILES $FT_PWD_PATH $LAST_TRIDYN #$PLASMA_STATE_FILES
Expand All @@ -184,6 +183,7 @@ PLASMA_STATE_FILES = $FT_PWD_PATH #$XFT_TRANSFER_FILE $XOLOTL_INPUT_FILES $XOLOT
LOG_FILE=$CASE_PATH/log.ftx
PRINT_TEST='on' #on = print test lines (for devel / debug) ; off = print the std running output
STATE_FILES = $FT_PWD_PATH $XFT_TRANSFER_FILE $XOLOTL_INPUT_FILES $XOLOTL_CURRENT_FILES $RESTART_FILES #$PLASMA_STATE_FILES
time_decimal={time_decimal}

##### FILES ####
## IEADs:
Expand Down Expand Up @@ -353,6 +353,7 @@ PLASMA_STATE_FILES = $FT_PWD_PATH #$XFT_TRANSFER_FILE $XOLOTL_INPUT_FILES $XOLOT
-ts_atol={ts_atol}
-ts_rtol={ts_rtol}
-tridyn='False'
-ts_adapt_clip={ts_adapt_clip}

### F-TRIDYN RELATED PARAMETERS ###
[[FTRIDYN_INPUT_PARAMETERS]]
Expand Down
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