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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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submitVesselgeneration error #18

Closed lopezmarinn closed 5 years ago

lopezmarinn commented 5 years ago

When running "submitVesselgeneration -h" I get this error:

Traceback (most recent call last): File "./submitVesselgeneration", line 30, in import krebsutils File "/home/vdd/nelia/tumorcode/py/krebsjobs/../krebsutils/init.py", line 50, in libkrebs = import('libkrebs', globals(), locals()) ImportError: dynamic module does not define init function (initlibkrebs)

thierry3000 commented 5 years ago

Have you installed in a non-default location? In this case you have to set your PYTHONPATH environment variable to point to the new python library "libkrebs". It looks like installed into the source directory, right? Please follow the instruction in the wiki and let me know whether you succeeded.

lopezmarinn commented 5 years ago

Thanks Thierry, I solved the issue compiling everything again from the beginning with the Debug option and the program run successfully. But running submitBulkTissue with tutorial options I got this error:

python2: /home/vdd/nelia/tumorcode-master/src/common/simple_oxygen_model.cpp:192: Assertion `v->maturation > 0.' failed. [vdd:08118] Process received signal [vdd:08118] Signal: Aborted (6) [vdd:08118] Signal code: (-6) [vdd:08118] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x41100)[0x7f08884c0100] [vdd:08118] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f08884c0077] [vdd:08118] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x121)[0x7f08884a1535] [vdd:08118] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2240f)[0x7f08884a140f] [vdd:08118] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x32142)[0x7f08884b1142] [vdd:08118] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x321cb)[0x7f08884b11cb] [vdd:08118] [ 6] /home/vdd/nelia/tumorcode/py/krebsutils/../../lib/libtumors_d.so(_Z12_HasDebuggerv+0x0)[0x7f087f289a70] [vdd:08118] [ 7] /home/vdd/nelia/tumorcode/py/krebsutils/../../lib/libtumors_d.so(_ZN7O2Model21AddSourceDistributionERK5BBoxdIiLi3EERK17Lattic eDataQuad3di7Array3dIfES8_RKN23polymorphic_latticedata11LatticeDataERK8DynArrayIPK6VesselERKN5boost13property_tree11basic_ptreeINSt7__cxx1112b asic_stringIcSt11char_traitsIcESaIcEEESS_St4lessISS_EEE+0x312)[0x7f087f18b546] [vdd:08118] [ 8] /home/vdd/nelia/tumorcode/py/krebsutils/../../lib/libtumors_d.so(+0x3c9603)[0x7f087f063603] [vdd:08118] [ 9] /usr/lib/x86_64-linux-gnu/libgomp.so.1(+0x16b2e)[0x7f088101ab2e] [vdd:08118] [10] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8164)[0x7f0888466164] [vdd:08118] [11] /lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7f0888599def] [vdd:08118] End of error message Aborted (core dumped)

Any help?

thierry3000 commented 5 years ago

I build a vessel network with latest "dev_fredrich" branch and the options: python2 submitVesselgeneration.py -t 8 -p default -w 2000 -i 1 -e 1

Then I ran python2 submitBulkTissue.py bulktissue_tutorial vessels-default-typeI-15x19L130-sample00.h5

Your error code indicates a runtime error. Maybe your vesselnetwork was too small or too big? Did the error appear immediately after start or after a while? Sorry, I could not reproduce the issue.

lopezmarinn commented 5 years ago

I ran: submitVesselgeneration.py -t 8 -p default -w 2000 -i 1 -e 1 submitBulkTissue.py bulktissue_tutorial vessels-default-typeI-15x19L130-sample00.h5

after some simulation time I got the output:

454: ves:finished can sprout 454: ves:!dst_vc happend 454: ves:!dst_vc happend 454: ves:collapse called 454: ves:Nothing to KILL! 454: ves:collapse ened 454: ves:integrity ended 454: ves:enlarge ended 454: ves:smooth ended 454: ves:maturate ended enter ComputeCirculatedComponents!exit ComputeCirculatedComponents!enter ComputeCirculatedComponents!exit ComputeCirculatedComponents! 454: ves:ComputeCirculatedComponents called first: 3747, second: 5.751792 first: 3743, second: 5.649776 first: 3741, second: 6.403641 first: 3739, second: 5.606359 first: 3736, second: 5.586980 first: 3759, second: 5.458482 first: 3757, second: 2.929903 first: 3755, second: 5.593495 first: 3752, second: 3.687399 first: 3749, second: 2.943366 first: 3768, second: 3.146209 first: 2220, second: 3.240108 first: 3767, second: 5.730170 first: 3761, second: 3.346633 first: 3745, second: 5.778083 first: 3762, second: 5.649776 first: 3765, second: 3.127659 454: ves:Linsys constructor called bcs.size(): 17 first: 3747, second: 5.751792 first: 3743, second: 5.649776 first: 3741, second: 6.403641 first: 3739, second: 5.606359 first: 3736, second: 5.586980 first: 3759, second: 5.458482 first: 3757, second: 2.929903 first: 3755, second: 5.593495 first: 3752, second: 3.687399 first: 3749, second: 2.943366 first: 3768, second: 3.146209 first: 2220, second: 3.240108 first: 3767, second: 5.730170 first: 3761, second: 3.346633 first: 3745, second: 5.778083 first: 3762, second: 5.649776 first: 3765, second: 3.127659 454: ves:default constructor called called 454: ves:EllipticEquationSolver::init 454: ves:multigrid selected 454: ves:before asking 454: ves: 454: ves:Belos::StatusTestGeneralOutput: Failed 454: ves: (Num calls,Mod test,State test): (1, 10, Passed Failed Undefined) 454: ves: Failed.......OR Combination -> 454: ves: OK...........Number of Iterations = 0 < 1000 454: ves: Unconverged..(2-Norm Imp Res Vec) / (2-Norm Res0) 454: ves: residual [ 0 ] = 1 > 1e-05 454: ves: 454: ves:================================================================================ 454: ves: 454: ves: TimeMonitor results over 1 processor 454: ves: 454: ves:Timer Name Global time (num calls)
454: ves:-------------------------------------------------------------------------------- 454: ves:Belos: BiCGStabSolMgr total solve time 63.47 (133)
454: ves:Belos: Operation Opx 3.455 (1117)
454: ves:Belos: Operation Precx 57.31 (984)
454: ves:Epetra_CrsMatrix::Multiply(TransA,X,Y) 3.449 (1117)
454: ves:Epetra_CrsMatrix::Multiply(TransA,x,y) 31.27 (8310)
454: ves:================================================================================ 454: ves:after asking 454: ves:EllipticEquationSolver destructor called 454: ves:boundary node id: 3747, value = 5.751792 454: ves:boundary node id: 3743, value = 5.649776 454: ves:boundary node id: 3741, value = 6.403641 454: ves:boundary node id: 3739, value = 5.606359 454: ves:boundary node id: 3736, value = 5.586980 454: ves:boundary node id: 3759, value = 5.458482 454: ves:boundary node id: 3757, value = 2.929903 454: ves:boundary node id: 3755, value = 5.593495 454: ves:boundary node id: 3752, value = 3.687399 454: ves:boundary node id: 3749, value = 2.943366 454: ves:boundary node id: 3768, value = 3.146209 454: ves:boundary node id: 2220, value = 3.240108 454: ves:boundary node id: 3767, value = 5.730170 454: ves:boundary node id: 3761, value = 3.346633 454: ves:boundary node id: 3745, value = 5.778083 454: ves:boundary node id: 3762, value = 5.649776 454: ves:boundary node id: 3765, value = 3.127659 454: ves:Linsys destructor called 454: ves:CalcFlow done 454: ves:t = 65.000000, dt = 1.000000 454: adavanceVesselState done 454: chemicals done 454: master t = 64.159891, dt = 0.159891 454: stopFlag0 455: tum:ves:volume fraction and o2 sources update! 455: tum:ves:sort vessel into mt boxes: 219.153ms python2: /home/vdd/nelia/tumorcode-master/src/common/simple_oxygen_model.cpp:192: Assertion `v->maturation > 0.' failed. [vdd:03693] Process received signal [vdd:03693] Signal: Aborted (6) [vdd:03693] Signal code: (-6) [vdd:03693] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x41100)[0x7f33eb58d100] [vdd:03693] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f33eb58d077] [vdd:03693] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x121)[0x7f33eb56e535] [vdd:03693] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x2240f)[0x7f33eb56e40f] [vdd:03693] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x32142)[0x7f33eb57e142] [vdd:03693] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x321cb)[0x7f33eb57e1cb] [vdd:03693] [ 6] /home/vdd/nelia/tumorcode/py/krebsutils/../../lib/libtumors_d.so(_Z12_HasDebuggerv+0x0)[0x7f33e2356a70] [vdd:03693] [ 7] /home/vdd/nelia/tumorcode/py/krebsutils/../../lib/libtumors_d.so(_ZN7O2Model21AddSourceDistributionERK5BBoxdIiLi3EERK17LatticeDataQuad3di7Array3dIfES8_RKN23polymorphic_latticedata11LatticeDataERK8DynArrayIPK6VesselERKN5boost13property_tree11basic_ptreeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESS_St4lessISS_EEE+0x312)[0x7f33e2258546] [vdd:03693] [ 8] /home/vdd/nelia/tumorcode/py/krebsutils/../../lib/libtumors_d.so(+0x3c9603)[0x7f33e2130603] [vdd:03693] [ 9] /usr/lib/x86_64-linux-gnu/libgomp.so.1(+0x16b2e)[0x7f33e40e7b2e] [vdd:03693] [10] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8164)[0x7f33eb533164] [vdd:03693] [11] /lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7f33eb666def] [vdd:03693] End of error message Aborted (core dumped)

thierry3000 commented 5 years ago

Unfortunately this is a runtime error and it is hard to tell what's the reason without further information. Is it reproducible? Does it also happen if your build in the Release mode?

lopezmarinn commented 5 years ago

It is reproducible, even changing the size of the vesselnetwork. I will try in the release mode

lopezmarinn commented 5 years ago

If I compile in the Release mode I get the following error:

vdd@vdd:~/nelia/tumorcode-master$ ../tumorcode/bin/submitVesselgeneration -h Traceback (most recent call last): File "../tumorcode/bin/submitVesselgeneration", line 30, in import krebsutils File "/home/vdd/nelia/tumorcode/py/krebsjobs/../krebsutils/init.py", line 50, in libkrebs = import('libkrebs', globals(), locals()) ImportError: dynamic module does not define init function (initlibkrebs)

thierry3000 commented 5 years ago

How did you solve the problem initially? Just by compiling in debug mode? That would be strange. Try to set you PYTHONPATH to the correct location and use: python2 .../../what/ever/install/path/of/tumorcode/py/krebsjobs/submitVesselgeneration.py -h Does it work?

lopezmarinn commented 5 years ago

Hi Thierry, Finally I was able to run the programs using -DCMAKE_BUILD_TYPE=Release in the cmake. If I deleted the error appears. Really strange.