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Python libsvm core dump

I have Python code that works fine in my development environment (Ubuntu 12.04), but flushes the kernel in my production environment (Linode runs CentOS).

*** glibc detected *** python2.7: double free or corruption (out): 0x090cba60 *** ======= Backtrace: ========= /lib/i686/nosegneg/libc.so.6(+0x717b1)[0xb763d7b1] /lib/i686/nosegneg/libc.so.6(+0x73f01)[0xb763ff01] /home/michael/libsvm-3.16/python/../libsvm.so.2(svm_free_model_content+0xe2)[0xb6e0c6b2] /home/michael/libsvm-3.16/python/../libsvm.so.2(svm_free_and_destroy_model+0x2c)[0xb6e0c70c] /home/michael/lib/python2.7/lib-dynload/_ctypes.so(ffi_call_SYSV+0x17)[0xb71e375f] /home/michael/lib/python2.7/lib-dynload/_ctypes.so(ffi_call+0x5b)[0xb71e35ab] /home/michael/lib/python2.7/lib-dynload/_ctypes.so(_ctypes_callproc+0x32d)[0xb71d82ad] /home/michael/lib/python2.7/lib-dynload/_ctypes.so(+0x703e)[0xb71d003e] python2.7(PyObject_Call+0x4a)[0x805d90a] python2.7(PyEval_EvalFrameEx+0x3c0a)[0x80e04ba] python2.7(PyEval_EvalCodeEx+0x7bb)[0x80e2c1b] python2.7[0x813ee2a] python2.7(PyObject_Call+0x4a)[0x805d90a] python2.7[0x80657f1] python2.7(PyObject_Call+0x4a)[0x805d90a] python2.7(PyEval_CallObjectWithKeywords+0x42)[0x80db852] python2.7[0x80af616] python2.7[0x80a928e] python2.7[0x808e024] python2.7[0x8067c5b] python2.7[0x808c079] python2.7(PyDict_SetItem+0x87)[0x808cfa7] python2.7(_PyModule_Clear+0x123)[0x8090693] python2.7(PyImport_Cleanup+0x175)[0x80f2ca5] python2.7(Py_Finalize+0x10c)[0x80ffacc] python2.7(Py_Main+0x53d)[0x8058c1d] python2.7(main+0x1b)[0x805839b] /lib/i686/nosegneg/libc.so.6(__libc_start_main+0xe6)[0xb75e2ce6] python2.7[0x80582e1] ======= Memory map: ======== 08048000-0817d000 r-xp 00000000 ca:00 430104 /home/michael/bin/python2.7 0817d000-081ab000 rw-p 00134000 ca:00 430104 /home/michael/bin/python2.7 081ab000-081b4000 rw-p 00000000 00:00 0 ...

This happens often, but not all the time. In addition, if I delete * .pyc files in my libsvm subdirectory, it works without failures, but as soon as the * .pyc files are restored (after the first start), it will again want to reset the kernel.

Also, if I try to transfer a standard error to a file, it never fails.

Some information that may make a difference:

  • It only started when I installed Python 2.7. This did not happen with Python 2.6
  • Python2.7 is installed in my home directory (from source, since there are no python2.7 packages for CentOS)

How do I approach this problem? Where is the problem likely to be? Is this in the libsvm source or in the Python shell? I am pretty sure that this is not in my Python source, since I could not crash such an interpreter.

EDIT

I retrained models in a production environment, and the problem seems to be gone. For reference, here are the differences between dev and production environments for both models that I use.

The first header diffuser model:

 4,7c4,7 < total_sv 8858 < rho -0.500251 -0.215012 2.99972 -0.00159202 0.000223509 1.00003 < label 3 2 1 0 < nr_sv 549 6095 587 1627 --- > total_sv 8782 > rho -2.99981 0.000329574 -1.00015 -0.335094 -0.999424 -0.66958 > label 0 3 2 1 > nr_sv 1586 535 6083 578 -bash-4.1$ diff model.svm model2.svm | head -n 20 4,7c4,7 < total_sv 8858 < rho -0.500251 -0.215012 2.99972 -0.00159202 0.000223509 1.00003 < label 3 2 1 0 < nr_sv 549 6095 587 1627

Second header model:

 4,7c4,7 < total_sv 116 < rho 2.30068 -0.145028 0.169511 -1.09344 0.723723 -0.865381 < label 3 0 2 1 < nr_sv 18 32 34 32 --- > total_sv 132 > rho 0.72381 -2.00473 -0.220492 -0.962109 0.998243 -0.14499 > label 0 1 3 2 > nr_sv 43 35 18 36
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1 answer

The cause of the error is an uninitialized pointer to svm_load_model and an unverified call to free . Here's the patch:

 misha@misha-diginnos :~$ diff libsvm-3.16/svm.cpp.original libsvm-3.16/svm.cpp -p *** libsvm-3.16/svm.cpp.original 2013-03-17 17:34:00.235661297 +0900 --- libsvm-3.16/svm.cpp 2013-03-17 17:39:29.677294903 +0900 *************** svm_model *svm_load_model(const char *mo *** 2747,2752 **** --- 2747,2753 ---- model->probB = NULL; model->label = NULL; model->nSV = NULL; + model->sv_indices = NULL; char cmd[81]; while(1) *************** void svm_free_model_content(svm_model* m *** 2973,2980 **** free(model_ptr->probB); model_ptr->probB= NULL; ! free(model_ptr->sv_indices); ! model_ptr->sv_indices = NULL; free(model_ptr->nSV); model_ptr->nSV = NULL; --- 2974,2984 ---- free(model_ptr->probB); model_ptr->probB= NULL; ! if (model_ptr->sv_indices) ! { ! free(model_ptr->sv_indices); ! model_ptr->sv_indices = NULL; ! } free(model_ptr->nSV); model_ptr->nSV = NULL;

I notified the authors. They are aware of the problem and will address it in the next version.

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Source: https://habr.com/ru/post/1469282/

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