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Error in 'python -m bohrium classifyMRELBY.py': free(): invalid pointer: 0x00007f16e0f85c00 #636

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OscarVanL opened this issue Feb 24, 2020 · 2 comments
Open

Error in 'python -m bohrium classifyMRELBY.py': free(): invalid pointer: 0x00007f16e0f85c00 #636

OscarVanL opened this issue Feb 24, 2020 · 2 comments

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@OscarVanL
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OscarVanL commented Feb 24, 2020 •
edited
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Hi,

I'm getting an invalid pointer error after taking a (working) script utilising numpy and running it with -m bohrium.

Full error 
*** Error in `python -m bohrium classifyMRELBP.py -l -a': free(): invalid pointer: 0x00007f16e0f85c00 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x816b9)[0x7f171310d6b9]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/./.libs/libbh_ve_openmp.so(create+0x9a)[0x7                                                                                                                            f16c6c2172a]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/.libs/libbh-2bcae67d.so(_ZN7bohrium9compone                                                                                                                            nt13ComponentFaceC1ERKSsi+0x8d)[0x7f16e0c3005d]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/./.libs/libbh_vem_node.so(create+0x11f)[0x7                                                                                                                            f16c6e42cef]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/.libs/libbh-2bcae67d.so(_ZN7bohrium9compone                                                                                                                            nt13ComponentFaceC1ERKSsi+0x8d)[0x7f16e0c3005d]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/./.libs/libbh_filter_bccon.so(create+0x2ed)                                                                                                                            [0x7f16c705cfdd]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/.libs/libbh-2bcae67d.so(_ZN7bohrium9compone                                                                                                                            nt13ComponentFaceC1ERKSsi+0x8d)[0x7f16e0c3005d]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/./.libs/libbh_filter_bcexp.so(create+0x27d)                                                                                                                            [0x7f16c728255d]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/.libs/libbh-2bcae67d.so(_ZN7bohrium9compone                                                                                                                            nt13ComponentFaceC1ERKSsi+0x8d)[0x7f16e0c3005d]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/.libs/libbhxx-4473dd8d.so(_ZN4bhxx7RuntimeC                                                                                                                            1Ev+0x95)[0x7f16e067f9b5]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/.libs/libbhc-6ad8b2e7.so(_ZN4bhxx7Runtime8i                                                                                                                            nstanceEv+0x43)[0x7f16e10d1da3]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/.libs/libbhxx-4473dd8d.so(_ZN4bhxx5rangeERN                                                                                                                            S_7BhArrayImEE+0x134)[0x7f16e07ac514]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium/_bh.cpython-37m-x86_64-linux-gnu.so(array_op+0x                                                                                                                            3b3)[0x7f17097811d3]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium/_bh.cpython-37m-x86_64-linux-gnu.so(PyArrayOp+0                                                                                                                            x65)[0x7f17097812d5]
python -m bohrium classifyMRELBP.py -l -a (_PyMethodDef_RawFastCallKeywords+0x264)[0x55e5038df114]
python -m bohrium classifyMRELBP.py -l -a (_PyCFunction_FastCallKeywords+0x21)[0x55e5038df231]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x4e9d)[0x55e503943a5d]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x2f9)[0x55e5038986f9]
python -m bohrium classifyMRELBP.py -l -a (_PyFunction_FastCallDict+0x400)[0x55e503899a30]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium/bhary.cpython-37m-x86_64-linux-gnu.so(+0x8c9a)[                                                                                                                            0x7f170984cc9a]
python -m bohrium classifyMRELBP.py -l -a (_PyObject_FastCallKeywords+0x48b)[0x55e5038f418b]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x5817)[0x55e5039443d7]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x2f9)[0x55e5038986f9]
python -m bohrium classifyMRELBP.py -l -a (_PyFunction_FastCallDict+0x1d5)[0x55e503899805]
/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium/bhary.cpython-37m-x86_64-linux-gnu.so(+0x8c9a)[                                                                                                                            0x7f170984cc9a]
python -m bohrium classifyMRELBP.py -l -a (_PyObject_FastCallKeywords+0x48b)[0x55e5038f418b]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x52cf)[0x55e503943e8f]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x2f9)[0x55e5038986f9]
python -m bohrium classifyMRELBP.py -l -a (_PyFunction_FastCallDict+0x400)[0x55e503899a30]
python -m bohrium classifyMRELBP.py -l -a (_PyObject_Call_Prepend+0x63)[0x55e5038b4943]
python -m bohrium classifyMRELBP.py -l -a (+0x17506a)[0x55e5038f306a]
python -m bohrium classifyMRELBP.py -l -a (_PyObject_FastCallKeywords+0x128)[0x55e5038f3e28]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x5817)[0x55e5039443d7]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x2f9)[0x55e5038986f9]
python -m bohrium classifyMRELBP.py -l -a (PyEval_EvalCodeEx+0x44)[0x55e5038995f4]
python -m bohrium classifyMRELBP.py -l -a (PyEval_EvalCode+0x1c)[0x55e50389961c]
python -m bohrium classifyMRELBP.py -l -a (+0x1d07b1)[0x55e50394e7b1]
python -m bohrium classifyMRELBP.py -l -a (_PyMethodDef_RawFastCallKeywords+0xe9)[0x55e5038def99]
python -m bohrium classifyMRELBP.py -l -a (_PyCFunction_FastCallKeywords+0x21)[0x55e5038df231]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x4764)[0x55e503943324]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x2f9)[0x55e5038986f9]
python -m bohrium classifyMRELBP.py -l -a (_PyFunction_FastCallKeywords+0x325)[0x55e5038de8b5]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x416)[0x55e50393efd6]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x2f9)[0x55e5038986f9]
python -m bohrium classifyMRELBP.py -l -a (_PyFunction_FastCallKeywords+0x387)[0x55e5038de917]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x14e6)[0x55e5039400a6]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x2f9)[0x55e5038986f9]
python -m bohrium classifyMRELBP.py -l -a (_PyFunction_FastCallKeywords+0x387)[0x55e5038de917]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x14e6)[0x55e5039400a6]
python -m bohrium classifyMRELBP.py -l -a (_PyFunction_FastCallDict+0x10b)[0x55e50389973b]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x1e35)[0x55e5039409f5]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x5da)[0x55e5038989da]
python -m bohrium classifyMRELBP.py -l -a (_PyFunction_FastCallKeywords+0x387)[0x55e5038de917]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x416)[0x55e50393efd6]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x2f9)[0x55e5038986f9]
python -m bohrium classifyMRELBP.py -l -a (PyEval_EvalCodeEx+0x44)[0x55e5038995f4]
python -m bohrium classifyMRELBP.py -l -a (PyEval_EvalCode+0x1c)[0x55e50389961c]
python -m bohrium classifyMRELBP.py -l -a (+0x1d08bd)[0x55e50394e8bd]
python -m bohrium classifyMRELBP.py -l -a (_PyMethodDef_RawFastCallKeywords+0xe9)[0x55e5038def99]
python -m bohrium classifyMRELBP.py -l -a (_PyCFunction_FastCallKeywords+0x21)[0x55e5038df231]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalFrameDefault+0x4764)[0x55e503943324]
python -m bohrium classifyMRELBP.py -l -a (_PyEval_EvalCodeWithName+0x2f9)[0x55e5038986f9]
python -m bohrium classifyMRELBP.py -l -a (_PyFunction_FastCallKeywords+0x325)[0x55e5038de8b5]
======= Memory map: ========
55e50377e000-55e5037d9000 r--p 00000000 00:38 9766622500                 /home/ojvl1g17/.conda/envs/IP/bin/python                                                                                                                            3.7
55e5037d9000-55e5039a7000 r-xp 0005b000 00:38 9766622500                 /home/ojvl1g17/.conda/envs/IP/bin/python                                                                                                                            3.7ls
python -m bohrium --info 
----
Bohrium version: 0.11.0.post54
----
Bohrium API version: 0.11.0.post54
Installed through PyPI: True
Config file: /home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/config.ini
Header dir: /home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/include
Backend stack:
----
OpenMP:
  Main memory: 128847 MB
  Hardware threads: 16
  Malloc cache limit: 19101 MB (80% of unused memory)
  Cache dir: "/home/ojvl1g17/.bohrium/cache"
  Temp dir: "/tmp/bh_4c96_e4cc8"
  Codegen flags:
    OpenMP: true
    OpenMP+SIMD: false
    Index-as-var: true
    Strides-as-var: true
    Const-as-var: true
  JIT Command: "gcc -x c -fPIC -shared  -std=gnu99  -O3 -march=native -Werror -fopenmp -I/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/include {IN} -o {OUT}"
----
Note: in order to activate and retrieve GPU info, set the `BH_STACK=opencl` or `BH_STACK=cuda` environment variable.

Sanity Check: "import bohrium as bh; import numpy as np; assert((bh.arange(10) == np.arange(10)).all())" - success!
BH_STACK=cuda python -m bohrium --info 
----
Bohrium version: 0.11.0.post54
----
Bohrium API version: 0.11.0.post54
Installed through PyPI: True
Config file: /home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/config.ini
Header dir: /home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/include
Backend stack:
----
OpenMP:
  Main memory: 128847 MB
  Hardware threads: 16
  Malloc cache limit: 19101 MB (80% of unused memory)
  Cache dir: "/home/ojvl1g17/.bohrium/cache"
  Temp dir: "/tmp/bh_4c96_e4cc8"
  Codegen flags:
    OpenMP: true
    OpenMP+SIMD: false
    Index-as-var: true
    Strides-as-var: true
    Const-as-var: true
  JIT Command: "gcc -x c -fPIC -shared  -std=gnu99  -O3 -march=native -Werror -fopenmp -I/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/include {IN} -o {OUT}"
----
Note: in order to activate and retrieve GPU info, set the `BH_STACK=opencl` or `BH_STACK=cuda` environment variable.

Sanity Check: "import bohrium as bh; import numpy as np; assert((bh.arange(10) == np.arange(10)).all())" - success!
(IP) [ojvl1g17@srv02441 Documents]$ python -m bohrium --info^C
(IP) [ojvl1g17@srv02441 Documents]$ BH_STACK=cuda python -m bohrium --info
----
Bohrium version: 0.11.0.post54
----
Bohrium API version: 0.11.0.post54
Installed through PyPI: True
Config file: /home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/config.ini
Header dir: /home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/include
Backend stack:
----
CUDA:
  Device: GeForce GTX 1080 Ti (SM 6.1 compute capability)"
  Memory: 11178 MB
  Malloc cache limit: 10060 MB (90%)
  JIT Command: /usr/local/cuda/bin/nvcc --cubin -m64 -arch=sm_61 -O3 --disable-warnings -I/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/include {IN} -o {OUT}
  Cache dir: "/home/ojvl1g17/.bohrium/cache"
  Temp dir: "/tmp/bh_4e43_590c0"
  Codegen flags:
    Index-as-var: true
    Strides-as-var: true
    const-as-var: true
----
OpenMP:
  Main memory: 128847 MB
  Hardware threads: 16
  Malloc cache limit: 19115 MB (80% of unused memory)
  Cache dir: "/home/ojvl1g17/.bohrium/cache"
  Temp dir: "/tmp/bh_4e43_b851e"
  Codegen flags:
    OpenMP: true
    OpenMP+SIMD: false
    Index-as-var: true
    Strides-as-var: true
    Const-as-var: true
  JIT Command: "gcc -x c -fPIC -shared  -std=gnu99  -O3 -march=native -Werror -fopenmp -I/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/include {IN} -o {OUT}"
----

Sanity Check: "import bohrium as bh; import numpy as np; assert((bh.arange(10) == np.arange(10)).all())" - success!
BH_STACK=opencl python -m bohrium --info 

----
Bohrium version: 0.11.0.post54
----
Bohrium API version: 0.11.0.post54
Installed through PyPI: True
Config file: /home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/config.ini
Header dir: /home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/include
Backend stack:
----
OpenCL:
  Device[0]: NVIDIA CUDA / GeForce GTX 1080 Ti (OpenCL C 1.2 )
  Available devices:
[0] NVIDIA CUDA / GeForce GTX 1080 Ti (OpenCL C 1.2 )
[1] NVIDIA CUDA / GeForce GTX 1080 Ti (OpenCL C 1.2 )
[2] NVIDIA CUDA / GeForce GTX 1080 Ti (OpenCL C 1.2 )
[3] NVIDIA CUDA / GeForce GTX 1080 Ti (OpenCL C 1.2 )
  Memory:         11178 MB
  Malloc cache limit: 1117 MB (90%)
  Cache dir: "/home/ojvl1g17/.bohrium/cache"
  Temp dir: "/tmp/bh_44fe_11462"
  Codegen flags:
    Index-as-var: true
    Strides-as-var: true
    const-as-var: true
----
OpenMP:
  Main memory: 128847 MB
  Hardware threads: 16
  Malloc cache limit: 15578 MB (80% of unused memory)
  Cache dir: "/home/ojvl1g17/.bohrium/cache"
  Temp dir: "/tmp/bh_44fe_9d964"
  Codegen flags:
    OpenMP: true
    OpenMP+SIMD: false
    Index-as-var: true
    Strides-as-var: true
    Const-as-var: true
  JIT Command: "gcc -x c -fPIC -shared  -std=gnu99  -O3 -march=native -Werror -fopenmp -I/home/ojvl1g17/.conda/envs/IP/lib/python3.7/site-packages/bohrium_api/include {IN} -o {OUT}"
----
Sanity Check: "import bohrium as bh; import numpy as np; assert((bh.arange(10) == np.arange(10)).all())" - success!

Other Info:

  • python --version: Python 3.7.6
  • Linux flavour: Red Hat Enterprise Linux Server 7.7 (Maipo)

Any ideas?
@OscarVanL
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OK I've been tracing at what point in my code this free(): invalid pointer error occurs.

I seem to have traced it to this line within my class init function:

        print("Debug setting radial angles")
        self.radial_angles = np.arange(0, self.p) * -(2 * math.pi) / self.p
        print("Debug completed radial angles")

As you can see from my new output:

Debug setting radial angles
free(): invalid pointer
./startProjAsHost.sh: line 6:   235 Aborted

It seems to have failed on this line.

The self.p variable is set to 8, so there's nothing edge-case about that.

@OscarVanL
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OscarVanL commented Feb 24, 2020 •
edited
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This is odd.

If I change the following line:

self.radial_angles = np.linspace(0, p) * - (2 * np.pi) / p)

into:

self.radial_angles = [(x * - (2 * np.pi) / p) for x in range (0, p)]

It fixes the error.

After fixing this error, later lines of code in my project result in the same error. Another line this happened on was:

filtered_image = np.zeros((width, height), dtype=np.float32)

I'm rather confused by these arbitrary seeming errors, so I'm hoping you know what might be causing this.

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