diff --git a/wetb/prepost/Simulations.py b/wetb/prepost/Simulations.py
index fa55cdccdbcab0915d37d27ba0fb7f414d63e4f2..c93dc79d8b273e82451197b80aaad27152a7f9f7 100755
--- a/wetb/prepost/Simulations.py
+++ b/wetb/prepost/Simulations.py
@@ -1046,7 +1046,7 @@ def launch(cases, runmethod='local', verbose=False, copyback_turb=True,
msg = 'unsupported runmethod, valid options: local, thyra, gorm or opt'
raise ValueError(msg)
-def post_launch(cases, save_iter=False):
+def post_launch(cases, save_iter=False, silent=False):
"""
Do some basics checks: do all launched cases have a result and LOG file
and are there any errors in the LOG files?
@@ -1101,8 +1101,9 @@ def post_launch(cases, save_iter=False):
nr_tot = len(cases)
tmp = list(cases.keys())[0]
- print('checking logs, path (from a random item in cases):')
- print(os.path.join(run_dir, log_dir))
+ if not silent:
+ print('checking logs, path (from a random item in cases):')
+ print(os.path.join(run_dir, log_dir))
for k in sorted(cases.keys()):
# a case could not have a result, but a log file might still exist
@@ -1117,12 +1118,15 @@ def post_launch(cases, save_iter=False):
errorlogs.PathToLogs = os.path.join(run_dir, log_dir, kk)
try:
errorlogs.check(save_iter=save_iter)
- print('checking logfile progress: ' + str(nr) + '/' + str(nr_tot))
+ if not silent:
+ print('checking logfile progress: % 6i/% 6i' % (nr, nr_tot))
except IOError:
- print(' no logfile for: %s' % (errorlogs.PathToLogs))
+ if not silent:
+ print(' no logfile for: %s' % (errorlogs.PathToLogs))
except Exception as e:
- print(' log analysis failed for: %s' % kk)
- print(e)
+ if not silent:
+ print(' log analysis failed for: %s' % kk)
+ print(e)
nr += 1
# if simulation did not ended correctly, put it on the fail list
@@ -1161,18 +1165,27 @@ def post_launch(cases, save_iter=False):
return cases_fail
-def copy_pbs_in_failedcases(cases_fail, pbs_fail='pbs_in_fail'):
+
+def copy_pbs_in_failedcases(cases_fail, pbs_fail='pbs_in_fail', silent=True):
"""
Copy all the pbs_in files from failed cases to a new directory so it
is easy to re-launch them
"""
-
+ if not silent:
+ print('Following failed cases pbs_in files are copied:')
for cname in cases_fail.keys():
case = cases_fail[cname]
pbs_in_fname = '%s.p' % (case['[case_id]'])
- pbs_in_dir = case['[pbs_in_dir]'].replace('pbs_in', pbs_fail)
run_dir = case['[run_dir]']
- fname = os.path.join(run_dir, pbs_in_dir, pbs_in_fname)
+
+ src = os.path.join(run_dir, case['[pbs_in_dir]'], pbs_in_fname)
+
+ pbs_in_dir_fail = case['[pbs_in_dir]'].replace('pbs_in', pbs_fail)
+ dst = os.path.join(run_dir, pbs_in_dir_fail, pbs_in_fname)
+
+ if not silent:
+ print(dst)
+ shutil.copy2(src, dst)
def logcheck_case(errorlogs, cases, case, silent=False):
@@ -3470,7 +3483,7 @@ class Cases(object):
launch(self.cases, runmethod=runmethod, verbose=verbose, silent=silent,
check_log=check_log, copyback_turb=copyback_turb)
- def post_launch(self, save_iter=False):
+ def post_launch(self, save_iter=False, copy_pbs_failed=True):
"""
Post Launching Maintenance
@@ -3480,6 +3493,10 @@ class Cases(object):
# TODO: integrate global post_launch in here
self.cases_fail = post_launch(self.cases, save_iter=save_iter)
+ if copy_pbs_failed:
+ copy_pbs_in_failedcases(self.cases_fail, pbs_in_fail='pbs_in_fail',
+ silent=self.silent)
+
if self.rem_failed:
self.remove_failed()
@@ -5089,37 +5106,57 @@ class Results(object):
return M_x_equiv
-class ManTurb64(object):
+class ManTurb64(prepost.prepost.PBSScript):
"""
alfaeps, L, gamma, seed, nr_u, nr_v, nr_w, du, dv, dw high_freq_comp
mann_turb_x64.exe fname 1.0 29.4 3.0 1209 256 32 32 2.0 5 5 true
"""
def __init__(self):
- self.man64_exe = 'mann_turb_x64.exe'
- self.wine = 'WINEARCH=win64 WINEPREFIX=~/.wine64 wine'
-
- def run():
- pass
+ super(ManTurb64, self).__init__()
+ self.exe = 'time wine mann_turb_x64.exe'
+ # PBS configuration
+ self.umask = '003'
+ self.walltime = '00:59:59'
+ self.queue = 'workq'
+ self.lnodes = '1'
+ self.ppn = '1'
- def gen_pbs(cases):
+ def gen_pbs(self, cases):
case0 = cases[list(cases.keys())[0]]
- pbs = prepost.PBSScript()
- # make sure the path's end with a trailing separator
- pbs.pbsworkdir = os.path.join(case0['[run_dir]'], '')
- pbs.path_pbs_e = os.path.join(case0['[pbs_out_dir]'], '')
- pbs.path_pbs_o = os.path.join(case0['[pbs_out_dir]'], '')
- pbs.path_pbs_i = os.path.join(case0['[pbs_in_dir]'], '')
- pbs.check_dirs()
+ # make sure the path's end with a trailing separator, why??
+ self.pbsworkdir = os.path.join(case0['[run_dir]'], '')
+# pbs.path_pbs_e = os.path.join(case0['[pbs_out_dir]'], '')
+# pbs.path_pbs_o = os.path.join(case0['[pbs_out_dir]'], '')
+# pbs.path_pbs_i = os.path.join(case0['[pbs_in_dir]'], '')
+# pbs.check_dirs()
for cname, case in cases.items():
- base = case['[case_id]']
- pbs.path_pbs_e = os.path.join(case['[pbs_out_dir]'], base + '.err')
- pbs.path_pbs_o = os.path.join(case['[pbs_out_dir]'], base + '.out')
- pbs.path_pbs_i = os.path.join(case['[pbs_in_dir]'], base + '.pbs')
+ base = case['[Turb base name]']
+ self.path_pbs_e = os.path.join(case['[pbs_out_dir]'], base + '.err')
+ self.path_pbs_o = os.path.join(case['[pbs_out_dir]'], base + '.out')
+ self.path_pbs_i = os.path.join(case['[pbs_turb_dir]'], base + '.pbs')
- pbs.execute()
- pbs.create()
+ if case['[turb_db_dir]'] is not None:
+ self.prelude = 'cd %s' % case['[turb_db_dir]']
+ else:
+ self.prelude = 'cd %s' % case['[turb_dir]']
+
+ # alfaeps, L, gamma, seed, nr_u, nr_v, nr_w, du, dv, dw high_freq_comp
+ rpl = (case['[AlfaEpsilon]'],
+ case['[L_mann]'],
+ case['[Gamma]'],
+ case['[tu_seed]'],
+ case['[turb_nr_u]'],
+ case['[turb_nr_v]'],
+ case['[turb_nr_w]'],
+ case['[turb_dx]'],
+ case['[turb_dy]'],
+ case['[turb_dz]'].
+ case['[high_freq_comp]'])
+ params = '%1.6f %1.6f %1.6f %i %i %i %i %1.4 %1.4 %1.4f %i' % rpl
+ self.execution = '%s %s %s' % (self.exe, base, params)
+ self.create(check_dirs=True)
def eigenbody(cases, debug=False):
diff --git a/wetb/prepost/prepost.py b/wetb/prepost/prepost.py
index bb6a864633a2f837c53622ea8b5793f2a0395367..c706aa79cb69e6f97edcc2a9e50cc8763c5a3a8b 100644
--- a/wetb/prepost/prepost.py
+++ b/wetb/prepost/prepost.py
@@ -12,9 +12,6 @@ from io import open
from future import standard_library
standard_library.install_aliases()
-
-
-
import os
import copy
@@ -37,6 +34,9 @@ class PBSScript(object):
### Queue name
#PBS -q [queue]
+### #PBS -a [start_time]
+### #PBS -W depend=afterany:[job_id]
+
### Browse to current working dir
echo ""
cd $PBS_O_WORKDIR
@@ -75,13 +75,13 @@ exit
def __init__(self):
# PBS configuration
- self.jobname = None
+ self.jobname = 'no_name_job'
# relative paths with respect to PBS working directory
self.path_pbs_o = 'pbs_out/dummy.out'
self.path_pbs_e = 'pbs_out/dummy.err'
self.path_pbs_i = 'pbs_in/dummy.pbs'
# absolute path of the PBS working directory
- self.pbsworkdir = None
+ self.pbsworkdir = './'
self.umask = '003'
self.walltime = '00:59:59'
self.queue = 'workq'