segmentation fault on exit of openmp code - c++

Question

I have a CPP code which uses openmp. It is linked to a fortran90 code. If run with one thread, everything is fine. If run with any number of threads different from 1, I get a segmentation fault when exiting the cpp part. The result of the code is exact, no errors whatsoever. It runs smoothly, until it's time to exit. The part of the code related to openmp is:
#pragma omp parallel for shared(even_phi,odd_phi,odd_divisor,odd_start_index,odd_iter_index) private(ii,jj,kk,cc,io,pp,f1,f2,f3,f4,f5,f6,ff,tmp_phi) schedule(static)
for (kk=1; kk<nz-1; kk++)
{
cc = (kk-1)*(ny-2);
for (jj=1; jj<ny-1; jj++)
{
io = odd_start_index[cc];
pp = odd_iter_index[cc++];
for (ii=io; ii<maxElem; ii++)
{
f1 = even_phi[pp-odown];
f2 = even_phi[pp-oright];
f3 = even_phi[pp];
tmp_phi = odd_phi[pp];
f4 = even_phi[pp+1];
f5 = even_phi[pp+oleft];
f6 = even_phi[pp+oup];
ff = f1+f2+f3+f4+f5+f6;
odd_phi[pp] = odd_divisor[pp]*ff + c2*tmp_phi;
pp++;
}
}
}
it's a standard numerical solver code. Which also works perfectly without openmp, and with OMP_NUM_THREADS=1. If executed with more threads, after an almost complete normal execution, Valgrinds says:
==23723== Thread 20:
==23723== Jump to the invalid address stated on the next line
==23723== at 0x2A6EBBB8: ???
==23723== by 0x2A6EA515: ???
==23723== Address 0x2a6ebbb8 is not stack'd, malloc'd or (recently) free'd
==23723==
==23723==
==23723== Process terminating with default action of signal 11 (SIGSEGV)
==23723== Access not within mapped region at address 0x2A6EBBB8
==23723== at 0x2A6EBBB8: ???
==23723== by 0x2A6EA515: ???
==23723== If you believe this happened as a result of a stack
==23723== overflow in your program's main thread (unlikely but
==23723== possible), you can try to increase the size of the
==23723== main thread stack using the --main-stacksize= flag.
==23723== The main thread stack size used in this run was 1048576.
==23723==
==23723== HEAP SUMMARY:
==23723== in use at exit: 632,995,339 bytes in 101 blocks
==23723== total heap usage: 10,071 allocs, 9,970 frees, 1,257,933,743 bytes allocated
==23723==
==23723== Thread 1:
==23723== 6,992 bytes in 23 blocks are possibly lost in loss record 47 of 74
==23723== at 0x4A04A28: calloc (vg_replace_malloc.c:467)
==23723== by 0x35A0E11812: _dl_allocate_tls (dl-tls.c:300)
==23723== by 0x35A1E07068: pthread_create##GLIBC_2.2.5 (allocatestack.c:571)
==23723== by 0x2A6EA981: ???
==23723== by 0x2A4C666E: ???
==23723== by 0x4C8DB7: solvermodule (in /home/tom/bin/solver)
==23723== by 0x4C6794: MAIN__ (qdiff4v.f90:749)
==23723== by 0x4C8DF9: main (in /home/tom/bin/solver)
==23723==
==23723== 30,276 bytes in 1 blocks are definitely lost in loss record 50 of 74
==23723== at 0x4A0674C: operator new[](unsigned long) (vg_replace_malloc.c:305)
==23723== by 0x2A4C6394: ???
==23723== by 0x4C8DB7: solvermodule (in /home/tom/bin/solver)
==23723== by 0x4C6794: MAIN__ (qdiff4v.f90:749)
==23723== by 0x4C8DF9: main (in /home/tom/bin/solver)
==23723==
==23723== 30,276 bytes in 1 blocks are definitely lost in loss record 51 of 74
==23723== at 0x4A0674C: operator new[](unsigned long) (vg_replace_malloc.c:305)
==23723== by 0x2A4C63BF: ???
==23723== by 0x4C8DB7: solvermodule (in /home/tom/bin/solver)
==23723== by 0x4C6794: MAIN__ (qdiff4v.f90:749)
==23723== by 0x4C8DF9: main (in /home/tom/bin/solver)
==23723==
==23723== 30,276 bytes in 1 blocks are definitely lost in loss record 52 of 74
==23723== at 0x4A0674C: operator new[](unsigned long) (vg_replace_malloc.c:305)
==23723== by 0x2A4C63EA: ???
==23723== by 0x4C8DB7: solvermodule (in /home/tom/bin/solver)
==23723== by 0x4C6794: MAIN__ (qdiff4v.f90:749)
==23723== by 0x4C8DF9: main (in /home/tom/bin/solver)
==23723==
==23723== 30,276 bytes in 1 blocks are definitely lost in loss record 53 of 74
==23723== at 0x4A0674C: operator new[](unsigned long) (vg_replace_malloc.c:305)
==23723== by 0x2A4C6415: ???
==23723== by 0x4C8DB7: solvermodule (in /home/tom/bin/solver)
==23723== by 0x4C6794: MAIN__ (qdiff4v.f90:749)
==23723== by 0x4C8DF9: main (in /home/tom/bin/solver)
==23723==
==23723== 39,232 bytes in 1 blocks are definitely lost in loss record 57 of 74
==23723== at 0x4A0674C: operator new[](unsigned long) (vg_replace_malloc.c:305)
==23723== by 0x2A4C6369: ???
==23723== by 0x4C8DB7: solvermodule (in /home/tom/bin/solver)
==23723== by 0x4C6794: MAIN__ (qdiff4v.f90:749)
==23723== by 0x4C8DF9: main (in /home/tom/bin/solver)
==23723==
==23723== LEAK SUMMARY:
==23723== definitely lost: 160,336 bytes in 5 blocks
==23723== indirectly lost: 0 bytes in 0 blocks
==23723== possibly lost: 6,992 bytes in 23 blocks
==23723== still reachable: 632,828,011 bytes in 73 blocks
==23723== suppressed: 0 bytes in 0 blocks
==23723== Reachable blocks (those to which a pointer was found) are not shown.
==23723== To see them, rerun with: --leak-check=full --show-reachable=yes
==23723==
==23723== For counts of detected and suppressed errors, rerun with: -v
==23723== ERROR SUMMARY: 7 errors from 7 contexts (suppressed: 6 from 6)
gdb says:
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7ffff5a04700 (LWP 23837)]
0x00007ffff7024bc2 in ?? ()
Missing separate debuginfos, use: debuginfo-install libgcc-4.4.6-4.el6.x86_64 libgfortran-4.4.6-4.el6.x86_64 libgomp-4.4.6-4.el6.x86_64 libstdc++-4.4.6-4.el6.x86_64
which clearly doesn't help. I've been playing with GOMP_STACKSIZE and the number of threads,
thinking that I may have a stack size problem, but to no avail.
I'm missing something. Maybe something stupid. And cannot find it.

Answer 1

This is a bug in GCC. I found a bug reported on GCC about problems related to the use of openmp and the iso_c_binding module. After that I Compiled and executed the code using the intel compiler with no problem whatsoever.
My code is quite long, and have no idea how to isolate the problematic part to reproduce the bug and make a report. Will do my best to do that.
I'm using gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4), CentOS release 6.3 (Final).
I'll mark this as the answer, and if I find anything more usefull later I'll post it here because it may be usefull to others.