On 12/18/23 16:41, Jisca Huisman wrote:
Hello Ivan & Tomas,

Thank you for your time and helpful suggestions!

The finer details of memory use and heap vs stack are still outside my comfort zone, but some trial and error shows that using an allocatable does indeed solve the issue. When using the largest value I expect users to use before running into Out Of Memory issues at other points in the code, I get

==3154== Warning: set address range perms: large range [0xd0ff3070, 0x14834c470) (undefined) ==3154== Warning: set address range perms: large range [0x14834d040, 0x1bf6a6440) (undefined) ==3154== Warning: set address range perms: large range [0x14834d028, 0x1bf6a6458) (noaccess)

but no valgrind errors. So I'm happy with this fairly straightforward solution, thanks Ivan!



You might perhaps submit a bug report for flang-new, asking whether their heuristics for these cases are as intended, showing that they differ from gfortran.
Will do; I suspect gfortran may have some trick to make it work somehow.
Thanks.

You might get more help on mailing lists discussing Fortran language, specifically - this is not an R issue.

Since the original error was "segfault from C stack overflow" I was not convinced that this was a Fortran issue, but thanks for the suggestion - I will try to find those for future issues.

The segfault handler belongs to R, but it is triggered by the overflow in the fortran function. If you ran the example outside R, it would use the default segfault handler, which would simply terminate the program (possibly creating a core dump, depending on the OS/setup).

Best
Tomas



But in practice, yes, using "allocatable" should work much better for large arrays.

Good to know!



Best
Tomas

Thanks,

Jisca



On 18-12-2023 16:06, Tomas Kalibera wrote:

On 12/18/23 15:09, Ivan Krylov wrote:
В Mon, 18 Dec 2023 11:06:16 +0100
Jisca Huisman <jisca.huis...@gmail.com> пишет:

I isolated the problem in a minimal working example available here:
https://github.com/JiscaH/flang_segfault_min_example . All that does
is pass a vector of length N*N back and forth between R and Fortran.
It works fine for very long vectors (tested up to length 5e8), but
throws a segfault when I reshape a large array in Fortran to a vector
to pass to R, both when using RESHAPE() and when using loops.
You've done an impressive amount of investigative work. Thank you for
reducing your problem to such a small example! My eyes are drawn to
these two lines:

  integer, intent(IN) :: N
  integer :: M(N,N)
If this was C, such a declaration would mean a variable-length array
that would have to be placed on the (limited-size) stack and eventually
overflow it. gfortran places the array on the heap, so the program
works:

   integer, intent(IN) :: N
   integer, intent(INOUT) :: V(N*N)
   integer :: M(N,N)
     1205:       48 63 db                movslq %ebx,%rbx
     1208:       b8 00 00 00 00          mov    $0x0,%eax
     120d:       48 85 db                test   %rbx,%rbx
     1210:       49 89 c4                mov    %rax,%r12
     1213:       4c 0f 49 e3             cmovns %rbx,%r12
     1217:       48 89 df                mov    %rbx,%rdi
     121a:       49 0f af fc             imul   %r12,%rdi
     121e:       48 85 ff                test   %rdi,%rdi
     1221:       48 0f 48 f8             cmovs  %rax,%rdi
     1225:       48 c1 e7 02             shl    $0x2,%rdi
     1229:       b8 01 00 00 00          mov    $0x1,%eax
     122e:       48 0f 44 f8             cmove  %rax,%rdi
     1232:       e8 19 fe ff ff          callq  1050 <malloc@plt>
     1237:       48 89 c5                mov    %rax,%rbp
     123a:       4c 89 e7                mov    %r12,%rdi
     123d:       48 f7 d7                not    %rdi

(Looking at the address of M in GDB and comparing it with the output
of info proc mappings, I can confirm that it lives on the heap.)

flang-new makes M into a C-style VLA:

   integer, intent(IN) :: N
   integer, intent(INOUT) :: V(N*N)
   integer :: M(N,N)
     74ec:       48 63 17                movslq (%rdi),%rdx
     74ef:       89 d1                   mov    %edx,%ecx
     74f1:       31 c0                   xor    %eax,%eax
     74f3:       48 85 d2                test   %rdx,%rdx
     74f6:       48 0f 49 c2             cmovns %rdx,%rax
     74fa:       48 89 85 b0 fe ff ff    mov %rax,-0x150(%rbp)
     7501:       48 89 c2                mov    %rax,%rdx
     7504:       48 0f af d2             imul   %rdx,%rdx
     7508:       48 8d 34 95 0f 00 00    lea 0xf(,%rdx,4),%rsi
     750f:       00
     7510:       48 83 e6 f0             and $0xfffffffffffffff0,%rsi
     7514:       48 89 e2                mov    %rsp,%rdx
     7517:       48 29 f2                sub    %rsi,%rdx
     751a:       48 89 95 b8 fe ff ff    mov %rdx,-0x148(%rbp)
     7521:       48 89 d4                mov    %rdx,%rsp

(Looking at the value of the stack pointer in GDB after M(N,N) is
declared, I can see it way below the end of the stack and the loaded
shared libraries according to info proc mappings. GDB doesn't let me
see the address of M. The program crashes in `M = 42`, trying to
overwrite the code from the C standard library.)

Are Fortran processors allowed to place such "automatic data objects"
like integer :: M(N,N) on the stack?

From my reading, yes, they are allowed to do that. Local arrays can be put on the stack or the heap. Even the "allocatable" could be placed on the stack. But I am not a fortran expert.

Allocating on the stack has the problem that it is not possible to have a portable test whether there is enough space, hence the crash when it isn't. This is not specific to fortran. Some systems try to still detect such cases (like R), but it is not portable. There are OS-specific ways to increase the stack size limit, but that cannot be relied on with R, it would be rather too much asking R users to do that.

You might perhaps submit a bug report for flang-new, asking whether their heuristics for these cases are as intended, showing that they differ from gfortran.

You might get more help on mailing lists discussing Fortran language, specifically - this is not an R issue.

But in practice, yes, using "allocatable" should work much better for large arrays.

Best
Tomas


The Fortran standard doesn't seem
to give an answer to this question, but if you make your M allocatable,
you won't have to worry about stack usage:

subroutine dostuff(N,V)
   implicit none

   integer, intent(IN) :: N
   integer, intent(INOUT) :: V(N*N)
   integer, allocatable :: M(:,:) ! <-- here

   allocate(M(N,N))               ! <-- and here
   M = 42
   V = RESHAPE(M, (/N*N/))
end subroutine dostuff

No leaks or crashes observed with these two changes and either
compiler. The Fortran standard requires that local allocatable unsaved
arrays (except for the function result) are deallocated at the end of
procedures.


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