OpneMP segmentation fault using reduction on a big array

Question

I've a problem with OpenMP. I'm trying to parallelize the first step of the Counting Sort algorithm: counting the frequencies of all the possibile values (in this case I'm counting the number of neighbors of all vertices of a graph). When I run this code on a small array (e.g. num_vertices = 100k) it works fine. Instead, when the row_ptr array is big (e.g. num_vertices = 1M) i get segmentation fault (or sometimes zsh: bus error).

PS: it works fine also with high number of iteration (e.g. num_edges = 50M) and size(e_list) = num_edges.

#pragma omp parallel for reduction(+: row_ptr[:num_vertices + 2])
    for (uint64_t i = 0; i < num_edges; i++)
        row_ptr[std::get<0>(e_list[i]) + 1]++;

The problem could be the available RAM of the machine or could be something else? Thank you

Laci · Answer 1 · 2022-06-20T15:25:12.843

0

Arrays used in reduction are reserved on the stack. So, the most probable cause of your problem is that your stack is too small and you have an overflow. Try increasing it by setting the OMP_STACKSIZE environmental variable. If it does not solve your problem, please provide a minimal reproducible example.

edited Jun 20 '22 at 15:25

answered Jun 20 '22 at 15:19

Laci

2,738
1
13
22

How i can do this? – gabrielekarra Jun 20 '22 at 16:06
Which OS do you use? – Laci Jun 20 '22 at 16:07
windows 11 with wsl (ubuntu) – gabrielekarra Jun 20 '22 at 16:08
e.g. `setenv OMP_STACKSIZE 50M` – Laci Jun 20 '22 at 16:09
on terminal? or on code? – gabrielekarra Jun 20 '22 at 16:10
on terminal before you run your code – Laci Jun 20 '22 at 16:11
How `row_ptr` is allocated? On stack or on the heap? – Laci Jun 20 '22 at 16:13
setenv "command not found" so i used export OMP_STACKSIZE=50M – gabrielekarra Jun 20 '22 at 16:14
and it not run, return "segmentation fault" – gabrielekarra Jun 20 '22 at 16:16
row ptr on the heap – gabrielekarra Jun 20 '22 at 16:18
How big is `num_vertices`? – Laci Jun 20 '22 at 16:20
around 2394385 uint64_t – gabrielekarra Jun 20 '22 at 16:21
try `ulimit -s 90000`, if it does not help post a [mre] – Laci Jun 20 '22 at 16:23

OpneMP segmentation fault using reduction on a big array

1 Answers1