title: SegFault file.c not found (Works on other computers)
body: <p>I have a really odd problem with Cython. </p>
  
  <p>I've tested my package on Mac OS and Arch Linux without failure. </p>
  
  <p>Now when I test my package on CentOS I get a Segmentation Fault</p>
  
  <p>Here's the gdb trace</p>
  
  <pre><code>Program received signal SIGSEGV, Segmentation fault.
  __Pyx_GetItemInt_Fast (o=0x2aaac56d3b90, i=2, boundscheck=0, wraparound=0, is_list=0) at myprog/Snv.c:10678
  10678   myprog/Snv.c: No such file or directory.
  
  (gdb) where
  
  
  #0  __Pyx_GetItemInt_Fast (o=0x2aaac56d3b90, i=2, boundscheck=0, wraparound=0, is_list=0) at myprog/Snv.c:10678
  #1  0x00002aaabe7a8b76 in __pyx_f_3sv2_3Snv_tokenize_vcf (__pyx_v_Bam=&lt;optimized out&gt;, __pyx_v_Variant=&lt;optimized out&gt;, __pyx_optional_args=&lt;optimized out&gt;) at myprog/Snv.c:6685
  #2  0x00002aaabe7ac6a2 in __pyx_pf_3sv2_3Snv_6c_preprocess_snv (__pyx_self=&lt;optimized out&gt;, __pyx_v_masked=&lt;optimized out&gt;, __pyx_v_Bam=&lt;optimized out&gt;) at myprog/Snv.c:5374
  #3  __pyx_pw_3sv2_3Snv_7c_preprocess_snv (__pyx_self=0x2aaac56d3b90, __pyx_args=0x2aaaab221870, __pyx_kwds=0x2aaab712d690 &lt;__pyx_pw_5pysam_9libctabix_13TabixIterator_5__next__&gt;) at myprog/Snv.c:4916
  #4  0x00002aaabe7b7ca1 in __Pyx_PyObject_Call (kw=&lt;optimized out&gt;, arg=&lt;optimized out&gt;, func=&lt;optimized out&gt;) at myprog/Snv.c:10555
  #5  __pyx_pf_3sv2_3Snv_2preprocess_snv (__pyx_self=&lt;optimized out&gt;, __pyx_v_masked=&lt;optimized out&gt;, __pyx_v_Bam=&lt;optimized out&gt;) at myprog/Snv.c:2994
  #6  __pyx_pw_3sv2_3Snv_3preprocess_snv (__pyx_self=0x2aaac56d3b90, __pyx_args=0x2aaabe4f2f38, __pyx_kwds=0x2aaaaab41240 &lt;PyCFunction_Call&gt;) at myprog/Snv.c:2935
  #7  0x00002aaabe579680 in __Pyx_PyObject_Call (kw=0x0, arg=&lt;optimized out&gt;, func=0x2aaabe4f2d40) at myprog/Preprocess.c:9226
  #8  __pyx_f_3sv2_10Preprocess_sv2_preprocess (__pyx_v_Bam=0x2aaac56d3dd0, __pyx_v_ofh=0x2aaac56d22d0, __pyx_v_seed=0x619558, __pyx_v_gen=0x2aaaab23b150, __pyx_v_tmp_dir=0x2aaac5ce6bb8) at myprog/Preprocess.c:3527
  #9  0x00002aaabe591307 in __pyx_pf_3sv2_10Preprocess_preprocess (__pyx_self=&lt;optimized out&gt;, __pyx_v_tmp_dir=&lt;optimized out&gt;, __pyx_v_gen=&lt;optimized out&gt;, __pyx_v_seed=&lt;optimized out&gt;, 
  __pyx_v_ofh=&lt;optimized out&gt;, __pyx_v_Bam=&lt;optimized out&gt;) at myprog/Preprocess.c:2837
  #10 __pyx_pw_3sv2_10Preprocess_1preprocess (__pyx_self=0x2aaac56d3b90, __pyx_args=0x2aaac55fc1e0, __pyx_kwds=0x2aaaaae61270 &lt;_Py_NoneStruct&gt;) at myprog/Preprocess.c:2700
  #11 0x00002aaaaabab1e5 in call_function (oparg=&lt;optimized out&gt;, pp_stack=0x7fffffffb908) at Python/ceval.c:4352
  #12 PyEval_EvalFrameEx (f=&lt;optimized out&gt;, throwflag=&lt;optimized out&gt;) at Python/ceval.c:2989
  #13 0x00002aaaaabac345 in fast_function (nk=&lt;optimized out&gt;, na=&lt;optimized out&gt;, n=&lt;optimized out&gt;, pp_stack=0x7fffffffba78, func=0x2aaac56ccc08) at Python/ceval.c:4437
  #14 call_function (oparg=&lt;optimized out&gt;, pp_stack=0x7fffffffba78) at Python/ceval.c:4372
  #15 PyEval_EvalFrameEx (f=&lt;optimized out&gt;, throwflag=&lt;optimized out&gt;) at Python/ceval.c:2989
  #16 0x00002aaaaabacc3e in PyEval_EvalCodeEx (co=0x2aaaab222a30, globals=&lt;optimized out&gt;, locals=&lt;optimized out&gt;, args=&lt;optimized out&gt;, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0)
  at Python/ceval.c:3584
  #17 0x00002aaaaabacd52 in PyEval_EvalCode (co=&lt;optimized out&gt;, globals=&lt;optimized out&gt;, locals=&lt;optimized out&gt;) at Python/ceval.c:669
  #18 0x00002aaaaabcd450 in run_mod (arena=0x617e10, flags=0x7fffffffbd70, locals=0x2aaaaaf1b168, globals=0x2aaaaaf1b168, filename=&lt;optimized out&gt;, mod=0x6aaa70) at Python/pythonrun.c:1376
  #19 PyRun_FileExFlags (fp=0x638fc0, filename=&lt;optimized out&gt;, start=&lt;optimized out&gt;, globals=0x2aaaaaf1b168, locals=0x2aaaaaf1b168, closeit=1, flags=0x7fffffffbd70) at Python/pythonrun.c:1362
  #20 0x00002aaaaabcd62f in PyRun_SimpleFileExFlags (fp=0x638fc0, filename=0x7fffffffc47f "/home/me/anaconda/bin/myprog", closeit=1, flags=0x7fffffffbd70) at Python/pythonrun.c:948
  #21 0x00002aaaaabe2fd4 in Py_Main (argc=&lt;optimized out&gt;, argv=&lt;optimized out&gt;) at Modules/main.c:645
  #22 0x00000033b881ed1d in __libc_start_main () from /lib64/libc.so.6
  #23 0x0000000000400729 in _start ()
  
  $ head -n 10678 /home/me/myprog_dist/versions/1.4.0/myprog-1.4.0/myprog/Snv.c | tail -n 1
  PyThreadState *tstate = __Pyx_PyThreadState_Current;
  </code></pre>
  
  <p>I'm running python Python 2.7.13 :: Anaconda custom (64-bit)</p>
  
  <p>I have no idea why this SegFault is happening. This package works on Arch Linux and MacOS. So why does it fail with CentOS? </p>