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Problems.txt
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Following Errormessages were produced by using a h5py without parallel support:
submitBulkTissue.py
thierry3000@dema3000:/localdisk/output$ python2 /localdisk/tc_install/py/krebsjobs/submitBulkTissue.py prez3 vessels-q2d_mini_test_Pdefault-typeI-13x5L130-sample00.h5
EPETRA_MPI flag is set!
omp num threads <- 1
generating tumor run with
vessel: vessels-q2d_mini_test_Pdefault-typeI-13x5L130-sample00.h5
output: /media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/output/tum-q2d_mini_test_Pdefault-typeI-sample00-prez3.h5
paramset: prez3
Traceback (most recent call last):
File "/localdisk/tc_install/py/krebsjobs/submitBulkTissue.py", line 209, in <module>
run_with_vessels(fn, goodArguments.tumParamSet, factory, '1GB', 2.)
File "/localdisk/tc_install/py/krebsjobs/submitBulkTissue.py", line 142, in run_with_vessels
config_ = set_lattice_size(config_, vessel_fn)
File "/localdisk/tc_install/py/krebsjobs/submitBulkTissue.py", line 131, in set_lattice_size
sx, sy, sz = vess_size_to_tum_size(vesselfilename, c['lattice_scale'])
File "/localdisk/tc_install/py/krebsjobs/submitBulkTissue.py", line 54, in vess_size_to_tum_size
ld = krebsutils.read_lattice_data_from_hdf(krebsutils.find_lattice_group_(vesselgroup))
RuntimeError: initialization of Object with invalid handle. Error Stack:
thierry3000@dema3000:/localdisk/output$ python2 /localdisk/tc_install/py/krebsjobs/submitDetailedO2.py default vessels-q2d_mini_test_Pdefault-typeI-13x5L130-sample00.h5 vessels
EPETRA_MPI flag is set!
omp num threads <- 1
submitting ... default
solubility_plasma 3.1e-05
rd_tum 50.0
conductivity_coeff1 8.0
conductivity_coeff2 4.7
conductivity_coeff3 0.0
rd_norm 150.0
po2init_r0 55.0
rd_necro 150.0
c0 0.5
S_n 2.7
num_threads 4
solubility_tissue 2.8e-05
debug_zero_o2field false
name "default"
S_p50 27.0
massTransferCoefficientModelNumber 1
grid_lattice_const 50.0
po2init_dr 1.0
axial_integration_step_factor 0.25
calcflow {
viscosityPlasma 1.2e-06
rheology "RheologySecomb2005"
includePhaseSeparationEffect true
inletHematocrit 0.45
}
D_tissue 2000.0
po2init_cutoff 100.0
max_iter 50
for files ['vessels-q2d_mini_test_Pdefault-typeI-13x5L130-sample00.h5']
and resolved groups therein: vessels
detailedo2 on vessels-q2d_mini_test_Pdefault-typeI-13x5L130-sample00.h5 / vessels
omp num threads <- 4
Traceback (most recent call last):
File "/localdisk/tc_install/py/krebsjobs/submitDetailedO2.py", line 172, in <module>
run(goodArguments.o2params, filenames, goodArguments.grp_pattern, systemsize)
File "/localdisk/tc_install/py/krebsjobs/submitDetailedO2.py", line 112, in run
change_cwd = True)
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../qsub.py", line 412, in submit
submit_qsub(obj, prog, **qsubopts)
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../qsub.py", line 356, in submit_qsub
return submit_(obj.interpreter, submission_program, f.getvalue())
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../qsub.py", line 203, in submit_
exec script in dict(), dict()
File "<string>", line 20, in <module>
File "/localdisk/tc_install/py/krebsjobs/submitDetailedO2.py", line 46, in worker_on_client
o2_refs = detailedo2.doit(fn, pattern, (o2params, o2params['name']))
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../krebs/detailedo2/__init__.py", line 275, in doit
ref = computePO2(f, group_path, parameters, cachelocation)
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../krebs/detailedo2/__init__.py", line 234, in computePO2
new_flow_data_ref = myutils.hdf_data_caching(read1, write1, fm, ('recomputed_flow', cachelocation[1]), (0, 1))
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../myutils.py", line 461, in hdf_data_caching
ret = hdf_data_caching(read, write, g, path[1:], versions[1:])
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../myutils.py", line 448, in hdf_data_caching
write(f, p)
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../krebs/detailedo2/__init__.py", line 229, in write1
copyVesselnetworkAndComputeFlow(gdst, vesselgroup1, parameters.get("calcflow"))
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../krebs/detailedo2/__init__.py", line 99, in copyVesselnetworkAndComputeFlow
pressure, flow, shearforce, hematocrit, flags = krebsutils.calc_vessel_hydrodynamics(gv, return_flags = True, bloodflowparams = bloodflowparams)
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../krebsutils/__init__.py", line 506, in calc_vessel_hydrodynamics
return calc_vessel_hydrodynamics_(vesselgroup, calc_hematocrit, return_flags, override_hematocrit, bloodflowparams )
File "/media/thierry3000/276f915f-9344-48ef-9da2-6a32cbe67da6/tc_install/py/krebsjobs/../krebsutils/__init__.py", line 529, in calc_vessel_hydrodynamics_
return calc_vessel_hydrodynamics_Ccode(vesselgroup, return_flags, bloodflowparams, simple)
RuntimeError: initialization of Object with invalid handle. Error Stack: