deepconsensus: Running deepconsensus results in "free(): invalid pointer" error

I installed deepconsensus via pip in a virtualenv like this:

virtualenv /apps/deepconsensus/1.0.0/python-3.8.2_cpu
source /apps/deepconsensus/1.0.0/python-3.8.2_cpu/bin/activate
pip install pyyaml==5.4.1 'deepconsensus[cpu]==1.0.0'

I used pyyaml==5.4.1 since tf-models-official 2.10.0 requires pyyaml<6.0,>=5.1. I’m using Python 3.8.2.

When I run deepconsensus, even just for the help message, it fails–deepconsensus -h resulted in this error message:

2022-11-10 12:51:17.016037: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
*** Error in `/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python': free(): invalid pointer: 0x00007f075c296c80 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x7f078b91d329]
/lib64/libstdc++.so.6(_ZNSt6locale5_Impl16_M_install_facetEPKNS_2idEPKNS_5facetE+0x142)[0x7f075c000192]
/lib64/libstdc++.so.6(_ZNSt6locale5_ImplC1Em+0x1e3)[0x7f075c0005e3]
/lib64/libstdc++.so.6(+0x71555)[0x7f075c001555]
/lib64/libpthread.so.0(+0x620b)[0x7f078c37920b]
/lib64/libstdc++.so.6(+0x715a1)[0x7f075c0015a1]
/lib64/libstdc++.so.6(_ZNSt6localeC2Ev+0x13)[0x7f075c0015e3]
/lib64/libstdc++.so.6(_ZNSt8ios_base4InitC2Ev+0xbc)[0x7f075bffe43c]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/lib/python3.8/site-packages/google/protobuf/pyext/_message.cpython-38-x86_64-linux-gnu.so(+0xb1150)[0x7f075bdd0150]
/lib64/ld-linux-x86-64.so.2(+0xf9c3)[0x7f078c7d59c3]
/lib64/ld-linux-x86-64.so.2(+0x1459e)[0x7f078c7da59e]
/lib64/ld-linux-x86-64.so.2(+0xf7d4)[0x7f078c7d57d4]
/lib64/ld-linux-x86-64.so.2(+0x13b8b)[0x7f078c7d9b8b]
/lib64/libdl.so.2(+0xfab)[0x7f078c16ffab]
/lib64/ld-linux-x86-64.so.2(+0xf7d4)[0x7f078c7d57d4]
/lib64/libdl.so.2(+0x15ad)[0x7f078c1705ad]
/lib64/libdl.so.2(dlopen+0x31)[0x7f078c170041]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyImport_FindSharedFuncptr+0x16b)[0x539abb]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyImport_LoadDynamicModuleWithSpec+0x159)[0x503e69]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x501a23]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x46f563]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(PyVectorcall_Call+0x5c)[0x439d8c]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x76d8)[0x42a308]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalCodeWithName+0xadf)[0x4e171f]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyFunction_Vectorcall+0x90)[0x438570]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x422821]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x5f91)[0x428bc1]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x421571]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x422821]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x1fb5)[0x424be5]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x421571]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x422821]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x15af)[0x4241df]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x421571]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x422821]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x15af)[0x4241df]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x421571]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x422821]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x15af)[0x4241df]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x421571]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x437f74]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyObject_CallMethodIdObjArgs+0xf1)[0x439831]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(PyImport_ImportModuleLevelObject+0x3fd)[0x502c8d]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x5ee426]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x437c24]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x76d8)[0x42a308]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalCodeWithName+0xadf)[0x4e171f]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyFunction_Vectorcall+0x90)[0x438570]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x422821]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x15af)[0x4241df]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalCodeWithName+0xadf)[0x4e171f]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyFunction_Vectorcall+0x90)[0x438570]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x437f74]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyObject_CallMethodIdObjArgs+0xf1)[0x439831]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(PyImport_ImportModuleLevelObject+0x4e6)[0x502d76]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x6e78)[0x429aa8]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalCodeWithName+0xadf)[0x4e171f]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(PyEval_EvalCode+0x23)[0x4e1b43]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x5efe34]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python[0x46f563]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(PyVectorcall_Call+0x5c)[0x439d8c]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalFrameDefault+0x76d8)[0x42a308]
/zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/bin/python(_PyEval_EvalCodeWithName+0xadf)[0x4e171f]
======= Memory map: ========
00400000-006f3000 r-xp 00000000 00:31 37327427                           /zapps7/python/3.8.2/gcc-9.2.0/bin/python3.8
008f2000-008f3000 r--p 002f2000 00:31 37327427                           /zapps7/python/3.8.2/gcc-9.2.0/bin/python3.8
008f3000-0092b000 rw-p 002f3000 00:31 37327427                           /zapps7/python/3.8.2/gcc-9.2.0/bin/python3.8
0092b000-0094c000 rw-p 00000000 00:00 0 
01dd2000-03209000 rw-p 00000000 00:00 0                                  [heap]
7f0754000000-7f0754021000 rw-p 00000000 00:00 0 
7f0754021000-7f0758000000 ---p 00000000 00:00 0 
7f075bd1f000-7f075bdbc000 r--p 00000000 00:31 77736144                   /zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/lib/python3.8/site-packages/google/protobuf/pyext/_message.cpython-38-x86_64-linux-gnu.so
7f075bdbc000-7f075bf0b000 r-xp 0009d000 00:31 77736144                   /zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/lib/python3.8/site-packages/google/protobuf/pyext/_message.cpython-38-x86_64-linux-gnu.so
7f075bf0b000-7f075bf7f000 r--p 001ec000 00:31 77736144                   /zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/lib/python3.8/site-packages/google/protobuf/pyext/_message.cpython-38-x86_64-linux-gnu.so
7f075bf7f000-7f075bf80000 ---p 00260000 00:31 77736144                   /zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/lib/python3.8/site-packages/google/protobuf/pyext/_message.cpython-38-x86_64-linux-gnu.so
7f075bf80000-7f075bf85000 r--p 00260000 00:31 77736144                   /zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/lib/python3.8/site-packages/google/protobuf/pyext/_message.cpython-38-x86_64-linux-gnu.so
7f075bf85000-7f075bf8f000 rw-p 00265000 00:31 77736144                   /zapps7/deepconsensus/1.0.0/python-3.8.2_cpu/lib/python3.8/site-packages/google/protobuf/pyext/_message.cpython-38-x86_64-linux-gnu.sozsh: abort      deepconsensus -h

Is there something different I should have done when installing?

About this issue

  • Original URL
  • State: closed
  • Created 2 years ago
  • Comments: 15

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Most upvoted comments

Thanks for the updates @mjg0 ! Glad that it worked. I’ll close this issue now. Feel free to open another one if you encounter any other issues.

OK, one more update. Here is what my requirements.txt currently looks like. Not finalize yet because I’m still testing. But sharing in advance in case @mjg0 you want to test out on your end:

numpy==1.20.3
pandas==1.5.1
tf-models-official==2.9.2
pyyaml==5.4.1  # because of tf-models-official
ml_collections==0.1.1
absl-py==1.0.0
keras==2.9.0
pysam==0.19.0

(and setup.py should also pin:

    'cpu': ['intel-tensorflow==2.9.1'],
    'gpu': ['tensorflow-gpu==2.9.1']

)