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thierry3000 / tumorcode

Simulation of Vascularized Tumors including Angiogenesis, Oxygen, Drugs and Interstitial Fluid
http://www.uni-saarland.de/fak7/rieger/homepage/research/tumor/tumor.html
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Segmentation fault on running submitVesselgeneration (default case, Tutorial A) #7

Closed ceserthen closed 6 years ago

ceserthen commented 6 years ago

While working through tutorial A during the vessel generation step. I first encountered an error with running submitVesselgeneration -p default giving a default number of points (4) giving the following error

This width might be a little small!

For the time being I modified line 169 of tumorcode/py/krebs/krebsjobs/submitVesselgeneration.py to if nums_points<4: to remove this error on the default case. I then ran the submitVesselgeneration -p default and was given the following output:

EPETRA_MPI flag is set!
setting nums_points: 4
lattice_size "<4, 5, 5>"
lattice_spacing 130.000000
lattice_type "fcc"
seed 3718951843
message "default-typeI"
out_fn "vessels-default-typeI-7x9L130"
full_debug_output false
max_num_iter 500
num_threads 4
num_hierarchical_iterations 1
max_sprout_radius_artery 8.0
max_sprout_radius_vein 8.0
radius_vein 3.8
radius_capi 2.5
radius_artery 2.5
capillariesUntilLevel 0
changeRateThreshold 0.001000
murray_alpha_vein 3.0
murray_alpha_artery 3.0
ensemble_index 0
generate_more_capillaries 0
o2 {
  diffusion_range 300.0
}
calcflow {
  viscosityPlasma 1.2e-06
  rheology RheologySecomb2005
  inletHematocrit 0.37
  includePhaseSeparationEffect True
}
roots {
}

submitting vessels-default-typeI-7x9L130-sample00, estimated runtime 0.000111 h, 500 iters
{'mem': '2000MB', 'num_cpus': 4, 'name': 'job_vessels-default-typeI-7x9L130-sample00', 'days': 4.6296296296296296e-06}
goodArgumentsQueue
Namespace(days=None, memory=None, mpi=False, numThreads=None, q_dry=False, q_local=False, q_verbose=False)
Warning: no supported queueing system found -> run locally
run this on client: donald-X551MA
invoked by: run_vesselgen_client
cwd: /home/donald
vesselgen init ...
  size <4,5,5> scale 130
  seed 3718951843
field lattice:  [LatticeDataQuad3d 
  box:    [-1,11]x[-1,11]x[-1,9]
  size:   <13,13,11> x 50
  stride: <1,13,169>
  offset: 0
  cell-centering: <1,1,1>
  world-offset of <0,0,0>: <-65,0,0>
  world-box: [-115,535]x[-50,600]x[-50,500]
]
[donald-X551MA:10269] *** Process received signal ***
[donald-X551MA:10269] Signal: Segmentation fault (11)
[donald-X551MA:10269] Signal code:  (128)
[donald-X551MA:10269] Failing at address: (nil)
[donald-X551MA:10269] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7f70dde72390]
[donald-X551MA:10269] [ 1] /lib/libepetra.so.12(+0xe1761)[0x7f70c361e761]
[donald-X551MA:10269] [ 2] /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x3f)[0x7f70c00c0d9f]
[donald-X551MA:10269] [ 3] /lib/libepetra.so.12(_ZN18Epetra_MultiVector5ScaleEd+0x6a)[0x7f70c362850a]
[donald-X551MA:10269] [ 4] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN6Linsys11end_fillingERKN5boost9unordered13unordered_mapIi6FlowBCNS0_4hashIiEESt8equal_toIiESaISt4pairIKiS3_EEEE+0x209)[0x7f70c4856129]
[donald-X551MA:10269] [ 5] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_Z14CalcFlowSimpleR12VesselList3dRK19BloodFlowParametersb+0x612)[0x7f70c484a982]
[donald-X551MA:10269] [ 6] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_Z8CalcFlowR12VesselList3dRK19BloodFlowParameters+0x46)[0x7f70c484da86]
[donald-X551MA:10269] [ 7] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN6Grower8CalcFlowEv+0x13)[0x7f70c495ff33]
[donald-X551MA:10269] [ 8] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN6Grower3RunERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_EEENS0_9function1IbRKS_EE+0x16a)[0x7f70c496d45a]
[donald-X551MA:10269] [ 9] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN10VessGenApp3runERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_EEE+0x89d)[0x7f70c4949c4d]
[donald-X551MA:10269] [10] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN15VesselGenerator3runERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_EEE+0x3a)[0x7f70c494a46a]
[donald-X551MA:10269] [11] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_Z13run_vesselgenRKN5boost6python3strE+0xa1)[0x7f70c481e111]
[donald-X551MA:10269] [12] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN5boost6python7objects23caller_py_function_implINS0_6detail6callerIPFvRKNS0_3strEENS0_21default_call_policiesENS_3mpl7vector2IvS7_EEEEEclEP7_objectSH_+0x3b)[0x7f70c481e7ab]
[donald-X551MA:10269] [13] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(_ZNK5boost6python7objects8function4callEP7_objectS4_+0x26d)[0x7f70c40105cd]
[donald-X551MA:10269] [14] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(+0x297c8)[0x7f70c40107c8]
[donald-X551MA:10269] [15] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(_ZN5boost6python21handle_exception_implENS_9function0IvEE+0x73)[0x7f70c4018613]
[donald-X551MA:10269] [16] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(+0x26999)[0x7f70c400d999]
[donald-X551MA:10269] [17] python2(PyObject_Call+0x43)[0x4b0cb3]
[donald-X551MA:10269] [18] python2(PyEval_EvalFrameEx+0x5faf)[0x4c9faf]
[donald-X551MA:10269] [19] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10269] [20] python2[0x4de8b8]
[donald-X551MA:10269] [21] python2(PyObject_Call+0x43)[0x4b0cb3]
[donald-X551MA:10269] [22] python2(PyEval_EvalFrameEx+0x2ad1)[0x4c6ad1]
[donald-X551MA:10269] [23] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10269] [24] python2(PyEval_EvalCode+0x19)[0x4c2509]
[donald-X551MA:10269] [25] python2(PyRun_StringFlags+0x76)[0x521186]
[donald-X551MA:10269] [26] python2(PyEval_EvalFrameEx+0x9d0f)[0x4cdd0f]
[donald-X551MA:10269] [27] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10269] [28] python2(PyEval_EvalFrameEx+0x68d1)[0x4ca8d1]
[donald-X551MA:10269] [29] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10269] *** End of error message ***
Segmentation fault (core dumped)

I then ran valgrind to look for any issues by running valgrind mpirun submitVesselgeneration -p default and received the following output

`==10171== Memcheck, a memory error detector
==10171== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==10171== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info
==10171== Command: mpirun submitVesselgeneration -p default
==10171== 
==10173== Warning: invalid file descriptor 1024 in syscall close()
==10173== Warning: invalid file descriptor 1025 in syscall close()
==10173== Warning: invalid file descriptor 1026 in syscall close()
==10173== Warning: invalid file descriptor 1027 in syscall close()
==10173==    Use --log-fd=<number> to select an alternative log fd.
==10173== Warning: invalid file descriptor 1028 in syscall close()
==10173== Warning: invalid file descriptor 1029 in syscall close()
==10173== Warning: invalid file descriptor 1030 in syscall close()
==10174== Warning: invalid file descriptor 1024 in syscall close()
==10174== Warning: invalid file descriptor 1025 in syscall close()
==10174== Warning: invalid file descriptor 1026 in syscall close()
==10174== Warning: invalid file descriptor 1027 in syscall close()
==10174==    Use --log-fd=<number> to select an alternative log fd.
==10174== Warning: invalid file descriptor 1028 in syscall close()
==10174== Warning: invalid file descriptor 1029 in syscall close()

EPETRA_MPI flag is set!

EPETRA_MPI flag is set!
setting nums_points: 4
lattice_size "<4, 5, 5>"
lattice_spacing 130.000000
lattice_type "fcc"
seed 3718951843
message "default-typeI"
out_fn "vessels-default-typeI-7x9L130"
full_debug_output false
max_num_iter 500
num_threads 4
num_hierarchical_iterations 1
max_sprout_radius_artery 8.0
max_sprout_radius_vein 8.0
radius_vein 3.8
radius_capi 2.5
radius_artery 2.5
capillariesUntilLevel 0
changeRateThreshold 0.001000
murray_alpha_vein 3.0
murray_alpha_artery 3.0
ensemble_index 0
generate_more_capillaries 0
o2 {
  diffusion_range 300.0
}
calcflow {
  viscosityPlasma 1.2e-06
  rheology RheologySecomb2005
  inletHematocrit 0.37
  includePhaseSeparationEffect True
}
roots {
}

submitting vessels-default-typeI-7x9L130-sample00, estimated runtime 0.000111 h, 500 iters
{'mem': '2000MB', 'num_cpus': 4, 'name': 'job_vessels-default-typeI-7x9L130-sample00', 'days': 4.6296296296296296e-06}
goodArgumentsQueue
Namespace(days=None, memory=None, mpi=False, numThreads=None, q_dry=False, q_local=False, q_verbose=False)
setting nums_points: 4
lattice_size "<4, 5, 5>"
lattice_spacing 130.000000
lattice_type "fcc"
seed 3718951843
message "default-typeI"
out_fn "vessels-default-typeI-7x9L130"
full_debug_output false
max_num_iter 500
num_threads 4
num_hierarchical_iterations 1
max_sprout_radius_artery 8.0
max_sprout_radius_vein 8.0
radius_vein 3.8
radius_capi 2.5
radius_artery 2.5
capillariesUntilLevel 0
changeRateThreshold 0.001000
murray_alpha_vein 3.0
murray_alpha_artery 3.0
ensemble_index 0
generate_more_capillaries 0
o2 {
  diffusion_range 300.0
}
calcflow {
  viscosityPlasma 1.2e-06
  rheology RheologySecomb2005
  inletHematocrit 0.37
  includePhaseSeparationEffect True
}
roots {
}

submitting vessels-default-typeI-7x9L130-sample00, estimated runtime 0.000111 h, 500 iters
{'mem': '2000MB', 'num_cpus': 4, 'name': 'job_vessels-default-typeI-7x9L130-sample00', 'days': 4.6296296296296296e-06}
goodArgumentsQueue
Namespace(days=None, memory=None, mpi=False, numThreads=None, q_dry=False, q_local=False, q_verbose=False)
Warning: no supported queueing system found -> run locally
Warning: no supported queueing system found -> run locally
run this on client: donald-X551MA
invoked by: run_vesselgen_client
cwd: /home/donald
run this on client: donald-X551MA
invoked by: run_vesselgen_client
cwd: /home/donald
vesselgen init ...
  size <4,5,5> scale 130
  seed 3718951843
field lattice:  [LatticeDataQuad3d 
  box:    [-1,11]x[-1,11]x[-1,9]
  size:   <13,13,11> x 50
  stride: <1,13,169>
  offset: 0
  cell-centering: <1,1,1>
  world-offset of <0,0,0>: <-65,0,0>
  world-box: [-115,535]x[-50,600]x[-50,500]
]
[donald-X551MA:10174] *** Process received signal ***
vesselgen init ...
[donald-X551MA:10174] Signal: Segmentation fault (11)
[donald-X551MA:10174] Signal code:  (128)
[donald-X551MA:10174] Failing at address: (nil)
[donald-X551MA:10174] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7f6367eca390]
[donald-X551MA:10174] [ 1] /lib/libepetra.so.12(+0xe1761)[0x7f6344a54761]
[donald-X551MA:10174] [ 2] /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x3f)[0x7f63414f6d9f]
[donald-X551MA:10174] [ 3]   size <4,5,5> scale 130
  seed 3718951843
field lattice:  [LatticeDataQuad3d 
  box:    [-1,11]x[-1,11]x[-1,9]
  size:   <13,13,11> x 50
  stride: <1,13,169>
  offset: 0
  cell-centering: <1,1,1>
  world-offset of <0,0,0>: <-65,0,0>
  world-box: [-115,535]x[-50,600]x[-50,500]
]
/lib/libepetra.so.12(_ZN18Epetra_MultiVector5ScaleEd+0x6a)[0x7f6344a5e50a]
[donald-X551MA:10174] [ 4] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN6Linsys11end_fillingERKN5boost9unordered13unordered_mapIi6FlowBCNS0_4hashIiEESt8equal_toIiESaISt4pairIKiS3_EEEE+0x209)[0x7f6345c8c129]
[donald-X551MA:10174] [ 5] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_Z14CalcFlowSimpleR12VesselList3dRK19BloodFlowParametersb+0x612)[0x7f6345c80982]
[donald-X551MA:10174] [ 6] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_Z8CalcFlowR12VesselList3dRK19BloodFlowParameters+0x46)[0x7f6345c83a86]
[donald-X551MA:10174] [ 7] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN6Grower8CalcFlowEv+0x13)[0x7f6345d95f33]
[donald-X551MA:10174] [ 8] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN6Grower3RunERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_EEENS0_9function1IbRKS_EE+0x16a)[0x7f6345da345a]
[donald-X551MA:10174] [ 9] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN10VessGenApp3runERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_EEE+0x89d)[0x7f6345d7fc4d]
[donald-X551MA:10174] [10] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN15VesselGenerator3runERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_EEE+0x3a)[0x7f6345d8046a]
[donald-X551MA:10174] [11] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_Z13run_vesselgenRKN5boost6python3strE+0xa1)[0x7f6345c54111]
[donald-X551MA:10174] [12] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN5boost6python7objects23caller_py_function_implINS0_6detail6callerIPFvRKNS0_3strEENS0_21default_call_policiesENS_3mpl7vector2IvS7_EEEEEclEP7_objectSH_+0x3b)[0x7f6345c547ab]
[donald-X551MA:10174] [13] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(_ZNK5boost6python7objects8function4callEP7_objectS4_+0x26d)[0x7f63454465cd]
[donald-X551MA:10174] [14] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(+0x297c8)[0x7f63454467c8]
[donald-X551MA:10174] [15] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(_ZN5boost6python21handle_exception_implENS_9function0IvEE+0x73)[0x7f634544e613]
[donald-X551MA:10174] [16] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(+0x26999)[0x7f6345443999]
[donald-X551MA:10174] [17] python2(PyObject_Call+0x43)[0x4b0cb3]
[donald-X551MA:10174] [18] python2(PyEval_EvalFrameEx+0x5faf)[0x4c9faf]
[donald-X551MA:10174] [19] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10174] [20] python2[0x4de8b8]
[donald-X551MA:10174] [21] python2(PyObject_Call+0x43)[0x4b0cb3]
[donald-X551MA:10174] [22] python2(PyEval_EvalFrameEx+0x2ad1)[0x4c6ad1]
[donald-X551MA:10174] [23] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10174] [24] python2(PyEval_EvalCode+0x19)[0x4c2509]
[donald-X551MA:10174] [25] python2(PyRun_StringFlags+0x76)[0x521186]
[donald-X551MA:10174] [26] python2(PyEval_EvalFrameEx+0x9d0f)[0x4cdd0f]
[donald-X551MA:10174] [27] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10174] [28] python2(PyEval_EvalFrameEx+0x68d1)[0x4ca8d1]
[donald-X551MA:10174] [29] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10174] *** End of error message ***
[donald-X551MA:10173] *** Process received signal ***
[donald-X551MA:10173] Signal: Segmentation fault (11)
[donald-X551MA:10173] Signal code:  (128)
[donald-X551MA:10173] Failing at address: (nil)
[donald-X551MA:10173] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7f44eb90d390]
[donald-X551MA:10173] [ 1] /lib/libepetra.so.12(+0xe1761)[0x7f44c848d761]
[donald-X551MA:10173] [ 2] /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x3f)[0x7f44c4f2fd9f]
[donald-X551MA:10173] [ 3] /lib/libepetra.so.12(_ZN18Epetra_MultiVector5ScaleEd+0x6a)[0x7f44c849750a]
[donald-X551MA:10173] [ 4] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN6Linsys11end_fillingERKN5boost9unordered13unordered_mapIi6FlowBCNS0_4hashIiEESt8equal_toIiESaISt4pairIKiS3_EEEE+0x209)[0x7f44c96c5129]
[donald-X551MA:10173] [ 5] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_Z14CalcFlowSimpleR12VesselList3dRK19BloodFlowParametersb+0x612)[0x7f44c96b9982]
[donald-X551MA:10173] [ 6] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_Z8CalcFlowR12VesselList3dRK19BloodFlowParameters+0x46)[0x7f44c96bca86]
[donald-X551MA:10173] [ 7] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN6Grower8CalcFlowEv+0x13)[0x7f44c97cef33]
[donald-X551MA:10173] [ 8] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN6Grower3RunERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_EEENS0_9function1IbRKS_EE+0x16a)[0x7f44c97dc45a]
[donald-X551MA:10173] [ 9] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN10VessGenApp3runERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_EEE+0x89d)[0x7f44c97b8c4d]
[donald-X551MA:10173] [10] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN15VesselGenerator3runERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_EEE+0x3a)[0x7f44c97b946a]
[donald-X551MA:10173] [11] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_Z13run_vesselgenRKN5boost6python3strE+0xa1)[0x7f44c968d111]
[donald-X551MA:10173] [12] /home/donald/tc_install/py/krebsutils/../../lib/libkrebs_.so(_ZN5boost6python7objects23caller_py_function_implINS0_6detail6callerIPFvRKNS0_3strEENS0_21default_call_policiesENS_3mpl7vector2IvS7_EEEEEclEP7_objectSH_+0x3b)[0x7f44c968d7ab]
[donald-X551MA:10173] [13] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(_ZNK5boost6python7objects8function4callEP7_objectS4_+0x26d)[0x7f44c8e7f5cd]
[donald-X551MA:10173] [14] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(+0x297c8)[0x7f44c8e7f7c8]
[donald-X551MA:10173] [15] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(_ZN5boost6python21handle_exception_implENS_9function0IvEE+0x73)[0x7f44c8e87613]
[donald-X551MA:10173] [16] /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0(+0x26999)[0x7f44c8e7c999]
[donald-X551MA:10173] [17] python2(PyObject_Call+0x43)[0x4b0cb3]
[donald-X551MA:10173] [18] python2(PyEval_EvalFrameEx+0x5faf)[0x4c9faf]
[donald-X551MA:10173] [19] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10173] [20] python2[0x4de8b8]
[donald-X551MA:10173] [21] python2(PyObject_Call+0x43)[0x4b0cb3]
[donald-X551MA:10173] [22] python2(PyEval_EvalFrameEx+0x2ad1)[0x4c6ad1]
[donald-X551MA:10173] [23] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10173] [24] python2(PyEval_EvalCode+0x19)[0x4c2509]
[donald-X551MA:10173] [25] python2(PyRun_StringFlags+0x76)[0x521186]
[donald-X551MA:10173] [26] python2(PyEval_EvalFrameEx+0x9d0f)[0x4cdd0f]
[donald-X551MA:10173] [27] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10173] [28] python2(PyEval_EvalFrameEx+0x68d1)[0x4ca8d1]
[donald-X551MA:10173] [29] python2(PyEval_EvalCodeEx+0x255)[0x4c2765]
[donald-X551MA:10173] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 10173 on node donald-X551MA exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
==10171== Syscall param write(buf) points to uninitialised byte(s)
==10171==    at 0x53614BD: ??? (syscall-template.S:84)
==10171==    by 0xCEC6FC8: ??? (in /usr/lib/openmpi/lib/openmpi/mca_oob_tcp.so)
==10171==    by 0x4E7DD6B: ??? (in /usr/lib/openmpi/lib/libopen-rte.so.12.0.2)
==10171==    by 0x50F603E: mca_base_framework_close (in /usr/lib/openmpi/lib/libopen-pal.so.13.0.2)
==10171==    by 0x79A747C: ??? (in /usr/lib/openmpi/lib/openmpi/mca_ess_hnp.so)
==10171==    by 0x4E4E439: orte_finalize (in /usr/lib/openmpi/lib/libopen-rte.so.12.0.2)
==10171==    by 0x404F97: ??? (in /usr/bin/orterun)
==10171==    by 0x403615: ??? (in /usr/bin/orterun)
==10171==    by 0x558E82F: (below main) (libc-start.c:291)
==10171==  Address 0xffefffa24 is on thread 1's stack
==10171== 
==10171== 
==10171== HEAP SUMMARY:
==10171==     in use at exit: 665,053 bytes in 7,638 blocks
==10171==   total heap usage: 30,037 allocs, 22,399 frees, 807,015,880 bytes allocated
==10171== 
==10171== LEAK SUMMARY:
==10171==    definitely lost: 940 bytes in 18 blocks
==10171==    indirectly lost: 1,419 bytes in 13 blocks
==10171==      possibly lost: 3,224 bytes in 26 blocks
==10171==    still reachable: 659,470 bytes in 7,581 blocks
==10171==         suppressed: 0 bytes in 0 blocks
==10171== Rerun with --leak-check=full to see details of leaked memory
==10171== 
==10171== For counts of detected and suppressed errors, rerun with: -v
==10171== Use --track-origins=yes to see where uninitialised values come from
==10171== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)

Any help resolving this issue is appreciated.

thierry3000 commented 6 years ago

For the time being I modified line 169 of tumorcode/py/krebs/krebsjobs/submitVesselgeneration.py to if nums_points<4: to remove this error on the default case.

This is a bad idea since too small systems will crash the algorithm. In the release build this is checked only in python to speed things up. In order to obtain nicer c++ debug information build the code in the "DEBUG" version.

For this special issue increase the system size in order to obtain enough discretization points. This is also done by the exact command in the supplemental S1_example.pdf

s u b m i t V e s s e l g e n e r a t i o n −t 8 −p d e f a u l t −w 2000 − i 1 −e 1

I will also change this in the wiki now! Thanks for reporting.

ceserthen commented 6 years ago

Approach: fresh install In a fresh install of ubuntu 16.04 without updates I was able to get submitVesselgeneration -t 8 -p defulat -w 2000 -i 1 -e working using a Release cmake build. On that system I am able to run submitVesselgeneration, submitFakeTum, and submitBulkTissue without any problems but am still unable to run submitDetailedO2 as described in tutorial A.

Approach: original machine Unfortunately on the original machine i am still unable to get the submitVesslgeneration to run. I used the submitVesselgeneration -p default -t 8 -w 2000 command with the num_points check restored to < 5. submitVesselgeneration was able to run, but still met returned the same segfault as before. I recompiled the code in debug mode (-DCMAKE_BUILD_TYPE=Debug). Upon running the code I now receive the following traceback ImportError:

Traceback (most recent call last):
  File "/home/donald/tc_install/bin/submitVesselgeneration", line 30, in <module>
    import krebsutils
  File "/home/donald/tc_install/py/krebsjobs/../krebsutils/__init__.py", line 43, in <module>
    libkrebs = __import__('libkrebs_', globals(), locals())
ImportError: No module named libkrebs_

I'm clearing the cmake cache and respective directories and hoping that a new install will work for the second machine. Hopefuly I can find a simple fix to this problem.

ceserthen commented 6 years ago

Clearing the cache and simplifying the cmake script to the following appears to have solved the problem on the original machine. I also found a small issue with the submitDetailedO2 command referenced in Tutrorial A. submitDetailedO2 default vessels-default-typeI-15x19L130-sample00.h5 vessels should instead be submitDetailedO2 default_o2 vessels-default-typeI-15x19L130-sample00.h5 vessels to match paramterSetsO2.py

thierry3000 commented 6 years ago

Again, I can only say thank your for taking the time to go thoroughly go trough the instructions and help to improve them. Yes, at some point I rename "default" to "default_o2" since I did not want so many defaults. The ImportError: is hopefully not as severe as it appears since you probably have a library called "libkrebs_d.so" in your lib dir when compilling in debug mode. Sorry, but the debug options are not yet documented. The release "submit" scripts which are python wrappers do not yet support that. According to the python specs (see python -h) you do have to invoke debug mode by adding python -d flag. In your case this should be python2 -d /home/donald/tc_install/py/krebsjobs/submitVesselgeneration.py -t 8 -p defulat -w 2000 -i 1 With the other scripts this works accordingly. The "-d" tells python to use the c++ library compilled with debug informations.

Since we work with the code across multiple linux distributions and also plan other architectures , the cmake has to be that elaborated.