# lamenvfile.write(lamSuffix)
# lamenvfile.flush()
# lamenvfile.close()
# return lamSuffix
## Starting. First, the very first run.
issue_echo('starting', tmpDir)
# NCPU, MAX_NUM_PROCS = set_defaults_lam(tmpDir)
try:
counterApplications.add_to_counter_log('ADaCGH2', tmpDir, socket.gethostname())
except:
None
issue_echo('at 2', tmpDir)
# lamSuffix = generate_lam_suffix(tmpDir)
issue_echo('at 3', tmpDir)
time.sleep(random.uniform(0.1, 15)) ## Break ties if starting at identical times
check_room = my_queue(MAX_adacgh, MAX_DURATION_TRY = MAX_DURATION_TRY_ADaCGH)
issue_echo('after check_room', tmpDir)
if check_room == 'Failed':
## The following does not work. We would need to caputer the output
## from ps, and then get substring with -sessionsuffix and the number = lamSuffix.
## But killing lam kills all slaves and the main process
## lamdpid = os.popen('ps --ppid ' + str(lampid) + ' -o "%p" --no-headers').readline()
## time.sleep(0.5)
## general cleaning
# buried = os.system("/http/mpi.log/buryThem2.py")
# killedlamandr = os.system('/http/mpi.log/killOldLamAllMachines.py')
# cleaned_dirs = os.system('/http/mpi.log/delete_old_dirs.py')
try:
counterApplications.add_to_counter_log(application, tmpDir, socket.gethostname())
except:
None
startedOK = False
time.sleep(random.uniform(0, 1)) ## to prevent truly simultaneous from crashing MPI
for i in range(int(numtries)):
os.system('touch ' + tmpDir + '/numtries_' + str(i)) ## debug
# lamSuffix = str(int(time.time())) + str(os.getpid()) + \
# str(random.randint(10, 999999))
# lamenvfile = open(tmpDir + '/lamSuffix', mode = 'w')
# lamenvfile.write(lamSuffix)
# lamenvfile.flush()
# lamenvfile.close()
# lamenv = os.putenv('LAM_MPI_SESSION_SUFFIX', lamSuffix)
###################################################################
###################################################################
issue_echo('pomelo_run2.py pid = '+ str(os.getpid()), tmpDir)
## killedlamandr = os.system('/http/mpi.log/killOldLam.py')
# os.system("cd " + tmpDir + "; touch about_to_call_buryPom")
# os.system("cd " + tmpDir + "; /http/mpi.log/buryPom.py; touch just_called_buryPom")
try:
counterApplications.add_to_counter_log('PomeloII-' + test_type,
tmpDir, socket.gethostname())
except:
None
count_mpi_crash = 0
if test_type in limma_tests:
R_launch = R_pomelo_bin + " CMD BATCH --no-restore --no-readline --no-save -q limma_functions.R"
fullPomelocommand = "cd " + tmpDir + "; " + R_launch
issue_echo(' about to do fullPomelocommand', tmpDir)
os.system(fullPomelocommand)
issue_echo(' just did fullPomelocommand', tmpDir)
else: ## we use MPI
startedOK = False
issue_echo('starting else loop', tmpDir)