BlueBrain / BlueBrain/Brion

Segfault in brain::neuron::Soma::getProfilePoints

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#308 5 comments 0 reactions 1 assignee Claimed by @chevtche View on GitHub
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Description

Backtrace is:
```backtrace
60 /nvme//spack-stage-brion-3.3.0-uhz33z2f5zwooo35gzjg54hwc7givx5x/spack-src/brain/neuron/soma.cpp: No such file or directory.
Missing separate debuginfos, use: debuginfo-install glibc-2.17-260.el7_6.6.x86_64 libicu-50.1.2-17.el7.x86_64
(gdb) bt
#0 brain::neuron::Soma::getProfilePoints (this=this@entry=0x7fffffffcd00) at /nvme/spack-stage-brion-3.3.0-uhz33z2f5zwooo35gzjg54hwc7givx5x/spack-src/brain/neuron/soma.cpp:60
#1 0x00007fffed48ef23 in brain::neuron::Soma::getMeanRadius (this=this@entry=0x7fffffffcd00) at /nvme//spack-stage-brion-3.3.0-uhz33z2f5zwooo35gzjg54hwc7givx5x/spack-src/brain/neuron/soma.cpp:65
#2 0x00007fffed6cf19c in ems::EventsLoader::_computeStaticEventGeometry(std::vector, std::allocator > > const&, std::vector, std::allocator > > const&) () at ../emSim/EventsLoader.cpp:116
#3 0x00007fffed6d0671 in ems::EventsLoader::_loadStaticEventGeometry() () at ../emSim/EventsLoader.cpp:87
#4 0x00007fffed6d0c42 in ems::EventsLoader::EventsLoader(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, glm::vec<2, float, (glm::qualifier)0> const&, float) () at ../emSim/EventsLoader.cpp:44
#5 0x00000000004160fe in process(EmsimParams const&) () at ../apps/emsimLFP/main.cpp:131
#6 0x0000000000415d55 in main () at ../apps/emsimLFP/main.cpp:176
#7 0x00007fffec447495 in __libc_start_main () from /lib64/libc.so.6
#8 0x0000000000415e8f in _start () at ../apps/emsimLFP/main.cpp:181
```

This is with the MOOC circuit (proj112/simulations/CA1.O1.mooc-circuit/LFP/full_dt05//BlueConfig); a couple things that may help with debug:
1) This uses SWC files (as determined by the BlueConfig `MorphologyType swc`), however, I see it try and access the h5 morphs first:
```
stat("CA1.O1/mooc-circuit/morphologies/swc//011127HP1_-_Scale_x1.000_y0.850_z1.000.h5", 0x7fffffffc730) = -1 ENOENT (No such file or directory)
stat("CA1.O1/mooc-circuit/morphologies/swc//011127HP1_-_Scale_x1.000_y0.850_z1.000.swc", {st_mode=S_IFREG|0664, st_size=3210557, ...}) = 0
```
2) There is an warning:
```
[Brion][Warning]Requested 18198 GIDs [1:18198] are not a subset of the 18198 GIDs in the report [0:18197[Brion][Warning]], using intersection size 18197 [1:18197]
```

So I'm wondering if it's a mismatch in GIDs; it appears that the following SONATA files are being loaded:
```
proj42/circuits/CA1.O1/mooc-circuit/sonata/nodes/nodes.h5
proj42/circuits/CA1.O1/mooc-circuit/sonata/edges/edges.h5
proj112/simulations/CA1.O1.mooc-circuit/LFP/full_dt05//AllCompartmentsIMembrane.h5
```

Any ideas?

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