Fix memory allocations in sparse_graph.pyx

[jdemeyer]

1. Use checking allocation functions from cysignals to avoid a crash when running out of memory.

2. A malloc(n) followed by a memset(..., 0, n) should be a calloc().

CC: @jm58660

Component: cython

Author: Jeroen Demeyer

Branch/Commit: 5d1b42e

Reviewer: Marc Mezzarobba

Issue created by migration from https://trac.sagemath.org/ticket/21720

[jdemeyer]

Branch: u/jdemeyer/fix_some_memory_allocations_in_sparse_graph_pyx

[jdemeyer]

Commit: 5d1b42e

[jdemeyer]

New commits:

5d1b42e

Fix memory allocations

[jm58660]

comment:8

I don't know enough cython to review this, but at least it seems to work. With /proc/sys/vm/overcommit_memory as 0 or 1 it ends with MemoryError: failed to allocate 18446744072098938880 * 8 bytes, with 2 the error message is MemoryError: failed to allocate 1342177280 * 8 bytes.

[jm58660]

comment:9

Btw, is there same problem for example in src/sage/combinat/degree_sequences.pyx

    sig_on()
    seq = <unsigned char *> sig_malloc((n+1)*sizeof(unsigned char))
    memset(seq,0,(n+1)*sizeof(unsigned char))
    sig_off()

?

[jdemeyer]

comment:10

I can't fix all problems in Sage...

[jm58660]

comment:11

Replying to @jdemeyer:

I can't fix all problems in Sage...

I know... But will it help someone if I open a ticket and search other uses of unnecessay memset?

[jdemeyer]

comment:12

Replying to @jm58660:

Replying to @jdemeyer:

I can't fix all problems in Sage...

I know... But will it help someone if I open a ticket and search other uses of unnecessay memset?

To be honest... unless you plan to fix it yourself, there is probably not much point.

[jdemeyer]

comment:13

Replying to @jm58660:

With /proc/sys/vm/overcommit_memory as 0 or 1 it ends with MemoryError: failed to allocate 18446744072098938880 * 8 bytes

What is "it" in the sentence above?

[jm58660]

comment:14

Replying to @jdemeyer:

Replying to @jm58660:

With /proc/sys/vm/overcommit_memory as 0 or 1 it ends with MemoryError: failed to allocate 18446744072098938880 * 8 bytes

What is "it" in the sentence above?

Error message.

[jdemeyer]

comment:15

Replying to @jm58660:

Replying to @jdemeyer:

Replying to @jm58660:

With /proc/sys/vm/overcommit_memory as 0 or 1 it ends with MemoryError: failed to allocate 18446744072098938880 * 8 bytes

What is "it" in the sentence above?

Error message.

The error message when doing what?

[jm58660]

comment:16

Uh, sorry. I tested Graph(10^10), but wrote that only in sage-devel, not here.

[jdemeyer]

comment:17

Replying to @jdemeyer:

Replying to @jm58660:

With /proc/sys/vm/overcommit_memory as 0 or 1 it ends with MemoryError: failed to allocate 18446744072098938880 * 8 bytes

By the way, this number shows that some integer overflow is happening also (a different issue from this ticket).

The number 18446744072098938880 equals <size_t><int>(10 << 28) where the correct value would be just <size_t>(10 << 28) = 2684354560.

[jdemeyer]

comment:18

Please review...

[mezzarobba]

Reviewer: Marc Mezzarobba

[vbraun]

Changed branch from u/jdemeyer/fix_some_memory_allocations_in_sparse_graph_pyx to 5d1b42e