tested the files on Apollo, added a setup file, added a restart file, cleaned...

### Application block ###

application "/ascldap/users/lpswile/Workbench-Linux/rte/entry.sh /ascldap/users/lpswile/Workbench-Linux/rte/nek4nuc.py -i pipe_3840.parn -e srun -v 0 -nek '/ascldap/users/lpswile/Nek5000'"

    input_file 'pipe_3840.parn'

    input_tmpl 'pipe_3840.tmpl'

### Extract block ###

# Extract friction velocity

extract_from 'pipe_3840.dragLogic/pipe_3840.frctVel.txt' find last_line 

column 1 delimiter ' '

# Compute L2 error norm between Nek5000 data and experimental data

extract_from 'pipe_3840.linePlots/pipe_3840.avg.txt' using "/ascldap/users/lpswile/Workbench-Linux/rte/entry.sh pipe_3840_postprocess.py"

extract_from 'pipe_3840.linePlots/pipe_3840.avg.txt' using "/ascldap/users/lpswile/Workbench-Linux/rte/entry.sh pipe_3840_postprocess.py pipe_3840_pipe_exp_data.txt pipe_3840.linePlots/pipe_3840.avg.txt"

### Scheduler block ###

scheduler

    header = "#!/bin/bash"

    scheduler_header = "#!/bin/bash"

                       "#SBATCH --nodes=2"

                       "#SBATCH --ntasks=72"

                       "#SBATCH --time=03:00:00"

                       "#SBATCH --account=FY200018"

             "#SBATCH --job-name=nektry"

                       "#SBATCH --job-name=DakNek"

                       "module purge"

                       "module load sparc-dev/intel"

    submit_path = '/usr/bin/sbatch'

environment

  tabular_graphics_data

    tabular_graphics_file = 'pipe_3840_tabular_output.dat'

    write_restart = "pipe_3840_restart.dat"

method

  multidim_parameter_study

    partition 2 5 2

    partitions 2 5 2

variables

  active all

    integer 2

      num_set_values 3 6 

      set_values 5 10 15 4 6 8 10 12 14

	  descriptor 'filterWeight' 'lx1'

	  descriptors 'filterWeight' 'lx1'

    real 1

      num_set_values 3 

      set_values 0.1 0.5 0.9

	  descriptor 'filterCutoffRatio'

	  descriptors 'filterCutoffRatio'

interface

  analysis_drivers = 'python dakota_driver.py'

  fork

  work_directory

    named 'pipe_3841_workdir'

    named 'pipe_3840_workdir'

    directory_tag

    directory_save

  copy_files = "pipe_3840.re2"

              "pipe_3840.tmpl"

              "pipe_3840_31000.fld"

              "pipe_3840_restart.fld"

              "dakota_driver.py"

              "pipe_3840.drive"

              "pipe_3840.txt"

responses

	response_functions = 2 

        descriptors = 'L2_error_norm' 'Friction_velocity'

        descriptors = 'Friction_velocity' 'L2_error_norm'

	no_gradients

	no_hessians

setup_properties {

    runtime_command = "/home/mxd/NEAMS+VisIt-rev67bd6a14e-Linux/rte/entry.sh /home/mxd/NEAMS+VisIt-rev67bd6a14e-Linux/rte/dakota.py"

    application_path = "/home/mxd/packages/dakota-6.10.0.Linux.x86_64/bin/dakota"

    hostname = "apollo.ornl.gov"

    username = "mxd"

    remote_execution_home = "/home/mxd"

    application_name = "dakota_nek4nuc_pipe_apollo"

    upload_patterns = ["${BASENAME}.re2", "${BASENAME}.in", "${BASENAME}.drive", "${BASENAME}.tmpl", "${BASENAME}.txt", "pipe_3840_postprocess.py", "pipe_3840_restart.fld", "pipe_3840_exp_xyz_coord.txt", "pipe_3840_pipe_exp_data.txt"]

    download_patterns = ["pipe_3840_tabular_output.dat", "pipe_3840_restart.dat"]

    version_number = "1.0.0"

    scheduler_type = single_box

}

 No newline at end of file

targetCFL = 0.8

timeStepper = bdf3

writeInterval = 1000000

startFrom = pipe_3840_31000

startFrom = "pipe_3840_restart"

filtering=hpfrt

filterWeight=<filterWeight>

filterCutoffRatio=<filterCutoffRatio>

import sys

import os

import math

import numpy as np

exp_data_file = '/ascldap/users/lpswile/Workbench-Linux/rte/full-3d/longPipeReTest.txt'

sim_data_file = 'pipe_3840.linePlots/pipe_3840.avg.txt'

# Get input arguments

exp_data_file = sys.argv[1]

sim_data_file = sys.argv[2]

#---------------------------------------------------------------#

############ post-processing Nek5000 simulation data ############

############ Post-processing Nek5000 simulation data ############

#---------------------------------------------------------------#

# Extract data from the Nek5000 line plot.

nb_head=5 # number of line to skip before reading Nek5000 data

exp_nb_head=2 # number of line to skip before reading experimental data

head=[] # list storing the head file

num_lines = sum(1 for line in open(sim_data_file, 'r')) # number of lines in the file

# read data file

data=open(sim_data_file, 'r')

for i in xrange(0,nb_head,1):

    line=data.readline()

    head.append(line.split())

# set and print information from head file

numlines = nb_points=int(head[3][0])

# declare variables to store data

t = []

head = [] # header

x = [] # x

y = [] # y

z = [] # z

vx = [] # velocity x 

vy = [] # velocity y

vz = [] # velocity z

vel_norm = [] # L2 norm of velocity 

# loop over the remaining of the file, make them float and store them

for i in xrange(0,numlines,1):

  line=data.readline()

with open(sim_data_file) as fp:

    lines = fp.readlines()

    # Extract header content

    for line in lines[0:nb_head]:

        head.append(line.split())

    # Extract numerical data

    for line in lines[nb_head:]:

        row = line.split()

        x.append(float(row[1]))

        y.append(float(row[2]))

        vz.append(float(row[6]))

# Compute norm of the velocity vector

for i in xrange(0,numlines,1):

vel_norm = [] # L2 norm of velocity

for i in xrange(0,len(x),1):

    temp1 = math.sqrt(vx[i]**2 + vy[i]**2 + vz[i]**2)

    vel_norm.append(temp1)

#---------------------------------------------------------------#

############### post-processing experimental data ###############

############### Post-processing experimental data ###############

#---------------------------------------------------------------#

# Read experimental data

# Read experimental data and store values in 'exp_vel'

exp_nb_head=2 # number of line to skip before reading experimental data

exp_vel = []

num_lines=sum(1 for line in open(exp_data_file, 'r')) # number of lines in the file

exp_data=open(exp_data_file, 'r')

for line in xrange(0, exp_nb_head, 1):

  exp_data.readline()

for line in xrange(exp_nb_head,num_lines,1):

  line=exp_data.readline()

with open(exp_data_file) as fp:

    for line in fp.readlines()[exp_nb_head:]:

        row = line.split()

        exp_vel.append(float(row[0]))

# Check experimental data consistency

if len(vel_norm) != len(exp_vel):

  print 'ERROR: the number of experimental nodes and the number of nodal velocity do not match.'

    msg = "ERROR: the number of experimental nodes and the number of nodal velocity do not match."

    print msg

    sys.exit()

res=[]

#---------------------------------------------------------------#

##################### Compute L2 error norm #####################

#---------------------------------------------------------------#

# Compute total L2 error norm

total = 0.0

for i in xrange(0,numlines,1):

for i in xrange(0,len(x),1):

    temp2 = exp_vel[i]-vel_norm[i]

  res.append(temp2)

    total += (temp2*temp2)

total = math.sqrt(total)

res_data=open("sumres.txt", 'w')

res_data.write(str(total))

# Print the total value

print total

data.close()

exp_data.close()

res_data.close()

sys.exit()