def get_versioninfo(obj,outputdir):
'''
Get version (svn) information of directories and return a list of strings.
'''
try:
my_sys.my_system(os.path.join("../../tools/sliksvn/bin","svn") + " info " + str(obj) + " 1> " +\
os.path.join(outputdir,"tempuit1.txt") + " 2> " +\
os.path.join(outputdir,"tempuit.err"),fatal=1)
my_sys.my_system(os.path.join("../../tools","grep") + " Rev " +\
os.path.join(outputdir,"tempuit1.txt") + " 1> " +\
os.path.join(outputdir,"tempuit.txt") + " 2> " +\
os.path.join(outputdir,"tempuit.err"),fatal=1)
list = my_sys.my_readfile(os.path.join(outputdir,"tempuit.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit1.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit.err"))
list.insert(0,"Directory " +str(obj))
except (MyError,OSError):
try:
#Try another time but with the assumption that the system has svn installed.
my_sys.my_system("svn info " + str(obj) + " 1> " +\
os.path.join(outputdir,"tempuit1.txt") + " 2> " +\
os.path.join(outputdir,"tempuit.err"),fatal=1)
my_sys.my_system("grep Rev " +\
os.path.join(outputdir,"tempuit1.txt") + " 1> " +\
os.path.join(outputdir,"tempuit.txt") + " 2> " +\
os.path.join(outputdir,"tempuit.err"),fatal=1)
list = my_sys.my_readfile(os.path.join(outputdir,"tempuit.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit1.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit.err"))
list.insert(0,"Directory " +str(obj))
except (MyError,OSError):
list = []
list.append("Directory "+str(obj) + " has no version info.")
# Remove temporary files which are created here
if (os.path.isfile(os.path.join(outputdir,"tempuit.txt"))):
my_sys.my_removefile(os.path.join(outputdir,"tempuit.txt"))
if (os.path.isfile(os.path.join(outputdir,"tempuit1.txt"))):
my_sys.my_removefile(os.path.join(outputdir,"tempuit1.txt"))
if (os.path.isfile(os.path.join(outputdir,"tempuit.err"))):
my_sys.my_removefile(os.path.join(outputdir,"tempuit.err"))
return list
def get_versioninfo(obj,outputdir):
'''
Get version (svn) information of directories and return a list of strings.
'''
try:
my_sys.my_system(os.path.join("../../tools/sliksvn/bin","svn") + " info " + str(obj) + " 1> " +\
os.path.join(outputdir,"tempuit1.txt") + " 2> " +\
os.path.join(outputdir,"tempuit.err"),fatal=1)
my_sys.my_system(os.path.join("../../tools","grep") + " Rev " +\
os.path.join(outputdir,"tempuit1.txt") + " 1> " +\
os.path.join(outputdir,"tempuit.txt") + " 2> " +\
os.path.join(outputdir,"tempuit.err"),fatal=1)
list = my_sys.my_readfile(os.path.join(outputdir,"tempuit.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit1.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit.err"))
list.insert(0,"Directory " +str(obj))
except (MyError,OSError):
try:
#Try another time but with the assumption that the system has svn installed.
my_sys.my_system("svn info " + str(obj) + " 1> " +\
os.path.join(outputdir,"tempuit1.txt") + " 2> " +\
os.path.join(outputdir,"tempuit.err"),fatal=1)
my_sys.my_system("grep Rev " +\
os.path.join(outputdir,"tempuit1.txt") + " 1> " +\
os.path.join(outputdir,"tempuit.txt") + " 2> " +\
os.path.join(outputdir,"tempuit.err"),fatal=1)
list = my_sys.my_readfile(os.path.join(outputdir,"tempuit.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit1.txt"))
my_sys.my_removefile(os.path.join(outputdir,"tempuit.err"))
list.insert(0,"Directory " +str(obj))
except (MyError,OSError):
list = []
list.append("Directory "+str(obj) + " has no version info.")
# Remove temporary files which are created here
if (os.path.isfile(os.path.join(outputdir,"tempuit.txt"))):
my_sys.my_removefile(os.path.join(outputdir,"tempuit.txt"))
if (os.path.isfile(os.path.join(outputdir,"tempuit1.txt"))):
my_sys.my_removefile(os.path.join(outputdir,"tempuit1.txt"))
if (os.path.isfile(os.path.join(outputdir,"tempuit.err"))):
my_sys.my_removefile(os.path.join(outputdir,"tempuit.err"))
return list
import sys
import os
import ascraster
import my_sys
# Read input file
grid = ascraster.Asciigrid(ascii_file=sys.argv[1])
grid.save_as_bitmap("qq.jpeg",minV=0,maxV=5,mode="RGB",color=(1,0,0))
my_sys.my_system("display qq.jpeg")
my_sys.my_removefile("qq.jpeg")
def run_dgnm(args):
'''
Run DGNM model main routine
args: list of arguments passed trough command-line or other script
'''
# Parse command-line arguments and set parameters for script
# Startup logging and runtime start
params, log, s = general_startup.general_startup(args)
# Read mask of the input grids.
# The mask takes care to do the calculations on an efficient way.
# Only the grid cells which are in the mask are calculated and stored.
if (params.lmask):
# Global
#mask = ascraster.create_mask(params.file_mask, 0,'GT',numtype=float)
# General formulation in the ini file.
mask = ascraster.create_mask(params.file_mask,
params.maskid,
params.mask_bool_operator,
numtype=int)
if (params.ldebug):
print("MASK: ", params.file_mask + " has been read.")
log.write_and_print(s.interval("Reading mask."))
else:
mask = None
log.write_and_print(s.interval("No mask is used for this simulation."))
# Read species file, conservative variables, sources and processes file
species, sources, proc, params_local = read_parameter.readfile(
params.species_ini)
# Add all params_local to params.
for iname in params_local.names:
setattr(params, iname, params_local.get_val(iname))
del params_local
# Make an indexnumber in the species list with the name of the species.
# For example: params.io2 = general_func.find_spec(species,"O2")
make_index_species.make_index_species(params, species, proc)
# Make the photosythesis for each species which needs it.
# Calculate this for each day and for just 1 year.
# Calculation is only done if no photosynthesis input file is provided.
make_photo.make_photosyn(params, species)
# Define characteristics of low Strahler orders if constant.
if (not params.lstrahlergrids): #LV 28-02-2018
define_subgrid_streamorder.define_subgrid_streamorder_constant(params)
# Delete all the locking files on the output directory
file_locking.clean_locks(params)
# Read river basin map
basin = ascraster.Asciigrid(ascii_file=params.basin,
mask=mask,
numtype=int)
if (params.ldebug):
print(params.basin + " has been read.")
# Create the information of the mask to an output file to be able to read the output files.
fp_out = open(os.path.join(params.outputdir, "mask.pkl"), "wb")
pickle.dump(basin, fp_out, -1)
pickle.dump(params, fp_out, -1)
fp_out.close()
# Make a list of all the riverbasins that have to be calculated.
list_riverid = list(set(basin.values))
list_riverid.sort()
# Creation of pickle file with fixed initial concentrations (read in ini file).
if (params.lspinup == -1):
general_func.make_header(
os.path.join(params.pkl_outputdir, "start_fixed_conc.pkl"),
species, params.starttime)
elif (params.lspinup == 0):
# Check the startup file
general_func.check_header(params.startup_file, species,
params.starttime)
elif (params.lspinup == 1):
# Make empty output files where all the processes can add their information.
create_outfiles.create_outfiles(params, species, proc,
params.starttime)
# Make all output files.
year = params.starttime + params.outputtime
timeperiod = -1
while (year < params.endtime):
timeperiod += 1
# Make all restart files.
lrestart = ((timeperiod + 1) % iround(params.restartnumber) == 0)
create_outfiles.create_outfiles(params,
species,
proc,
year,
lrestart=lrestart)
year += params.outputtime
# Make output files for last time
year = params.endtime
create_outfiles.create_outfiles(params, species, proc, year)
# Determine the number of cells per riverbasin, to avoid too small portions.
riverid_num = {}
for icell in range(basin.length):
id = basin.get_data(icell)
if (id != None):
try:
riverid_num[id] += 1
except KeyError:
riverid_num[id] = 1
# Store the objects that are needed in the dgnm_river.
# Write these objects to file, so dgnm_river can read this file.
# Here the general data is accessible for all subprocesses.
fp_out = open(os.path.join(params.outputdir, "general_objects.pkl"), "wb")
pickle.dump(params, fp_out, -1)
pickle.dump(species, fp_out, -1)
pickle.dump(proc, fp_out, -1)
pickle.dump(sources, fp_out, -1)
fp_out.close()
# Prepare for multitasking.
if (params.llocal):
# Use the local processing power and use the multiprocessing module of python.
import multiprocessing as mp
# Define a lock to regulate the access of shared objects over all the processes.
lock = mp.Lock()
# Set the number of cpu that will be used.
number_of_cpu = min(mp.cpu_count(), params.ncpu)
# Create list with jobs.
jobs = []
# Start with submitting the jobs
item = 0
jobnum = 1
while (item < len(list_riverid)):
try:
total_cells = riverid_num[list_riverid[item]]
except KeyError:
item += 1
continue
numbers = [list_riverid[item]]
while (total_cells < params.minimal_number_of_cells):
item += 1
if (item > len(list_riverid) - 1):
# Last riverbasin, so no more cells.
break
else:
total_cells += riverid_num[list_riverid[item]]
numbers.append(list_riverid[item])
if (params.llocal):
# Define the process with riverid "num", return value p is process "handler"
p = mp.Process(target=dgnm_river.calculate,
args=(numbers, lock, params, species, proc,
sources))
# Add the process handler to the jobs list.
jobs.append(p)
# Start the process
general_func.start_process(p, jobs, number_of_cpu)
else:
# Distribute the work over the nodes of the EEJIT cluster with sbatch
# Make command string to execute on the cluster
cmd = make_cluster_cmd.make_cluster_cmd(params, jobnum, numbers,
total_cells)
# Submit the job.
my_sys.my_system(cmd)
time.sleep(2)
item += 1
jobnum += 1
# Wait until all jobs are finished.
if (params.llocal):
for p in jobs:
p.join()
print("All processes are ready.")
log.write_and_print(s.total("Total run"))
del log
# ******************************************************
## Revision "$LastChangedDate: 2018-06-01 15:05:44 +0200 (Fri, 01 Jun 2018) $"
## Date "$LastChangedRevision: 1 $"
## Author "$LastChangedBy: arthurbeusen $"
## URL "$HeadURL: https://pbl.sliksvn.com/generalcode/trunk/showimage.py $"
## Copyright 2017, PBL Netherlands Environmental Assessment Agency and Utrecht University.
## Reuse permitted under Gnu Public License, GPL v3.
# ******************************************************
import sys
import os
import ascraster
import my_sys
# Read input file
grid = ascraster.Asciigrid(ascii_file=sys.argv[1])
grid.save_as_bitmap("qq.jpeg", minV=0, maxV=5, mode="RGB", color=(1, 0, 0))
my_sys.my_system("display qq.jpeg")
my_sys.my_removefile("qq.jpeg")