Using unique_ptr<CCfits::FITS> in omp parallel for loop results in SEG.FAULT

Question

Take the following code:

#include <omp.h>
#include <CCfits/CCfits>
#include <sys/stat.h>

int main ()
{
  std::string file ( "somefits.fits" );
  std::cout << file  << std::endl;

  // check if file exists
  struct stat bf;
  if ( stat(file.c_str(),&bf ) ) 
  { 
    std::cerr << "Error: the file: " << file << " does not exist " << std::endl;
    exit(-1);
  }

  #pragma omp parallel for schedule (dynamic)
  for ( uint i = 0; i<4; ++i )
  {
    std::unique_ptr<CCfits::FITS> fp (new CCfits::FITS (file, CCfits::Read));
    // do something
  }
  return 0;
}

The first part takes care that the file exists. Then I want to use CCfits::FITS file ( or different files ) in a for loop, that has to be parallel. Running the code without the parallelization line works perfectly.

I run the code differently, look below.

1. Why does the parallelization fail in this simple example?
2. Why is there 90% SEG. FAULT and 10% OK
3. How to fix this?
4. Can I fix this?

I. Simply running the code results in 90% SEG. FAULT 10% OK

II. Running the code with valgrind --leak-check=full ./code results in

==6654==    by 0x4EC1C11: CCfits::HDUCreator::Make(int, bool, std::vector<std::string, std::allocator<std::string> > const&) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4EB490F: CCfits::FITS::readExtensions(bool) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4EB4FA3: CCfits::FITS::FITS(std::string const&, CCfits::RWmode, bool, std::vector<std::string, std::allocator<std::string> > const&) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4013C4: main._omp_fn.0 (ccfits_omp.cpp:21)
==6654==    by 0x540C349: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==6654==    by 0x4C30E7B: ??? (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654== Other segment start (thread 2)
==6654==    at 0x4C34544: pthread_mutex_unlock (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654==    by 0x5C09DA1: fits_store_Fptr (in /usr/lib/x86_64-linux-gnu/libcfitsio.so.3.340)
==6654==    by 0x5C15042: ffopen (in /usr/lib/x86_64-linux-gnu/libcfitsio.so.3.340)
==6654==    by 0x4EB2997: CCfits::FITS::open(CCfits::RWmode) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4EB4F84: CCfits::FITS::FITS(std::string const&, CCfits::RWmode, bool, std::vector<std::string, std::allocator<std::string> > const&) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4013C4: main._omp_fn.0 (ccfits_omp.cpp:21)
==6654==    by 0x540C349: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==6654==    by 0x4C30E7B: ??? (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654==    by 0x62B5181: start_thread (pthread_create.c:312)
==6654==    by 0x5923EFC: clone (clone.S:111)
==6654== Other segment end (thread 2)
==6654==    at 0x4C338E3: pthread_mutex_lock (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654==    by 0x5C09E1E: fits_clear_Fptr (in /usr/lib/x86_64-linux-gnu/libcfitsio.so.3.340)
==6654==    by 0x5C1066E: ffclos (in /usr/lib/x86_64-linux-gnu/libcfitsio.so.3.340)
==6654==    by 0x4EB2DE5: CCfits::FITS::close() (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4EB32FD: CCfits::FITS::destroy() (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4017E7: std::default_delete<CCfits::FITS>::operator()(CCfits::FITS*) const (unique_ptr.h:67)
==6654==    by 0x401680: std::unique_ptr<CCfits::FITS, std::default_delete<CCfits::FITS> >::~unique_ptr() (unique_ptr.h:184)
==6654==    by 0x4013EB: main._omp_fn.0 (ccfits_omp.cpp:21)
==6654==    by 0x540C349: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==6654==    by 0x4C30E7B: ??? (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654==    by 0x62B5181: start_thread (pthread_create.c:312)
==6654==    by 0x5923EFC: clone (clone.S:111)
==6654== 
==6654== 
==6654== For counts of detected and suppressed errors, rerun with: -v
==6654== ERROR SUMMARY: 53 errors from 19 contexts (suppressed: 495 from 333)

III. Using valgrind --tool=drd ./code results in the following:

==6654==    by 0x4EC1C11: CCfits::HDUCreator::Make(int, bool, std::vector<std::string, std::allocator<std::string> > const&) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4EB490F: CCfits::FITS::readExtensions(bool) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4EB4FA3: CCfits::FITS::FITS(std::string const&, CCfits::RWmode, bool, std::vector<std::string, std::allocator<std::string> > const&) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4013C4: main._omp_fn.0 (ccfits_omp.cpp:21)
==6654==    by 0x540C349: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==6654==    by 0x4C30E7B: ??? (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654== Other segment start (thread 2)
==6654==    at 0x4C34544: pthread_mutex_unlock (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654==    by 0x5C09DA1: fits_store_Fptr (in /usr/lib/x86_64-linux-gnu/libcfitsio.so.3.340)
==6654==    by 0x5C15042: ffopen (in /usr/lib/x86_64-linux-gnu/libcfitsio.so.3.340)
==6654==    by 0x4EB2997: CCfits::FITS::open(CCfits::RWmode) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4EB4F84: CCfits::FITS::FITS(std::string const&, CCfits::RWmode, bool, std::vector<std::string, std::allocator<std::string> > const&) (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4013C4: main._omp_fn.0 (ccfits_omp.cpp:21)
==6654==    by 0x540C349: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==6654==    by 0x4C30E7B: ??? (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654==    by 0x62B5181: start_thread (pthread_create.c:312)
==6654==    by 0x5923EFC: clone (clone.S:111)
==6654== Other segment end (thread 2)
==6654==    at 0x4C338E3: pthread_mutex_lock (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654==    by 0x5C09E1E: fits_clear_Fptr (in /usr/lib/x86_64-linux-gnu/libcfitsio.so.3.340)
==6654==    by 0x5C1066E: ffclos (in /usr/lib/x86_64-linux-gnu/libcfitsio.so.3.340)
==6654==    by 0x4EB2DE5: CCfits::FITS::close() (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4EB32FD: CCfits::FITS::destroy() (in /usr/lib/x86_64-linux-gnu/libCCfits.so.0.0.0)
==6654==    by 0x4017E7: std::default_delete<CCfits::FITS>::operator()(CCfits::FITS*) const (unique_ptr.h:67)
==6654==    by 0x401680: std::unique_ptr<CCfits::FITS, std::default_delete<CCfits::FITS> >::~unique_ptr() (unique_ptr.h:184)
==6654==    by 0x4013EB: main._omp_fn.0 (ccfits_omp.cpp:21)
==6654==    by 0x540C349: ??? (in /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0)
==6654==    by 0x4C30E7B: ??? (in /usr/lib/valgrind/vgpreload_drd-amd64-linux.so)
==6654==    by 0x62B5181: start_thread (pthread_create.c:312)
==6654==    by 0x5923EFC: clone (clone.S:111)
==6654== 
==6654== 
==6654== For counts of detected and suppressed errors, rerun with: -v
==6654== ERROR SUMMARY: 53 errors from 19 contexts (suppressed: 495 from 333)

Answer 1

Well, you are using a lot of bad practices, and even if I don't know anythings about Fits, I can see:

• You are creating 4 threads that do the same thing: reading a file, the file is read 4 times and is the SAME file. Would not be better to read it once and share the CONST data?

• If Fits is keeping track of the already opened files (which I don't know) it is possible that is not prepared for multithreading.

  Sorry for my english.