Problems with mkl_sparse_convert_csr

carvalho__rodrigo — Thu, 11 Apr 2019 11:27:11 GMT

I'm trying to use the Intel MKL Inspector/Executor Sparse BLAS library and I've been struggling with faulty memory use in the `mkl_sparse_convert_csr` subroutine. The simple program below can reproduce my problem:

program debug
use mkl_spblas
use omp_lib
use, intrinsic :: iso_c_binding, only: c_int, c_double
implicit none
integer, parameter :: DIM = 10000
integer :: stat, i
integer(kind = c_int), dimension(DIM) :: irn, jcn
real(kind = c_double), dimension(DIM) :: val
type(sparse_matrix_t) :: mat1, mat2

do i = 1, DIM
  irn(i) = i
  jcn(i) = i
  val(i) = 1.0d0
end do

call omp_set_num_threads(1)
stat = mkl_sparse_d_create_coo (A = mat1, indexing = SPARSE_INDEX_BASE_ONE, &
  rows = DIM, cols = DIM, nnz = DIM, row_indx = irn, col_indx = jcn, values = val)
if (stat /= 0) stop 'Error in mkl_sparse_d_create_coo'

stat = mkl_sparse_convert_csr (source = mat1, &
  operation = SPARSE_OPERATION_NON_TRANSPOSE, dest = mat2)
if (stat /= 0) stop 'Error in mkl_sparse_convert_csr'

stat = mkl_sparse_destroy (A = mat1)
if (stat /= 0) stop 'Error in mkl_sparse_destroy (mat1)'

stat = mkl_sparse_destroy (A = mat2)
if (stat /= 0) stop 'Error in mkl_sparse_destroy (mat2)'

call mkl_free_buffers
end program debug

When I check with Valgrind I get the following report of memory leaks:

==27267== Memcheck, a memory error detector
==27267== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==27267== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==27267== Command: ../bin/LINKS_debug
==27267== 
==27267== 
==27267== HEAP SUMMARY:
==27267==     in use at exit: 495 bytes in 6 blocks
==27267==   total heap usage: 47 allocs, 41 frees, 463,031 bytes allocated
==27267== 
==27267== 8 bytes in 1 blocks are still reachable in loss record 1 of 6
==27267==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27267==    by 0x504CA98: gomp_malloc (alloc.c:37)
==27267==    by 0x505BA56: gomp_init_num_threads (proc.c:91)
==27267==    by 0x504B06A: initialize_env (env.c:1244)
==27267==    by 0x4010732: call_init (dl-init.c:72)
==27267==    by 0x4010732: _dl_init (dl-init.c:119)
==27267==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==27267== 
==27267== 8 bytes in 1 blocks are still reachable in loss record 2 of 6
==27267==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27267==    by 0x152F22: mkl_serv_malloc (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x1261B4: mkl_sparse_d_create_coo_i4_avx2 (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x112AF8: MAIN__ (main.f90:49)
==27267==    by 0x112C07: main (main.f90:31)
==27267== 
==27267== 32 bytes in 1 blocks are still reachable in loss record 3 of 6
==27267==    at 0x4C31B25: calloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27267==    by 0x590C7E4: _dlerror_run (dlerror.c:140)
==27267==    by 0x590C050: dlopen@@GLIBC_2.2.5 (dlopen.c:87)
==27267==    by 0x150F32: mkl_serv_inspector_suppress (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x150E8C: mkl_serv_lock (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x14EFA1: mkl_serv_cpu_detect (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x112EC4: mkl_sparse_d_create_coo_i4 (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x112AF8: MAIN__ (main.f90:49)
==27267==    by 0x112C07: main (main.f90:31)
==27267== 
==27267== 47 bytes in 1 blocks are still reachable in loss record 4 of 6
==27267==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27267==    by 0x4017880: _dl_exception_create (dl-exception.c:77)
==27267==    by 0x6996250: _dl_signal_error (dl-error-skeleton.c:117)
==27267==    by 0x4009812: _dl_map_object (dl-load.c:2384)
==27267==    by 0x4014EE3: dl_open_worker (dl-open.c:235)
==27267==    by 0x69962DE: _dl_catch_exception (dl-error-skeleton.c:196)
==27267==    by 0x40147C9: _dl_open (dl-open.c:605)
==27267==    by 0x590BF95: dlopen_doit (dlopen.c:66)
==27267==    by 0x69962DE: _dl_catch_exception (dl-error-skeleton.c:196)
==27267==    by 0x699636E: _dl_catch_error (dl-error-skeleton.c:215)
==27267==    by 0x590C734: _dlerror_run (dlerror.c:162)
==27267==    by 0x590C050: dlopen@@GLIBC_2.2.5 (dlopen.c:87)
==27267== 
==27267== 192 bytes in 1 blocks are still reachable in loss record 5 of 6
==27267==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27267==    by 0x504CA98: gomp_malloc (alloc.c:37)
==27267==    by 0x5059B65: gomp_get_thread_pool (pool.h:42)
==27267==    by 0x5059B65: get_last_team (team.c:146)
==27267==    by 0x5059B65: gomp_new_team (team.c:165)
==27267==    by 0x5050DDB: GOMP_parallel_start (parallel.c:126)
==27267==    by 0x17D0A4: mkl_sparse_d_coo_csr_new_omp_i4 (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x17D4A7: mkl_sparse_d_convert_coo_to_csr_i4 (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x17D554: mkl_sparse_d_export_csr_data_i4 (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x126E68: mkl_sparse_d_convert_csr_i4_avx2 (in /home/rcarvalho/repos/debug/bin/LINKS_debug)
==27267==    by 0x112B38: MAIN__ (main.f90:52)
==27267==    by 0x112C07: main (main.f90:31)
==27267== 
==27267== 208 bytes in 1 blocks are still reachable in loss record 6 of 6
==27267==    at 0x4C2FB0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==27267==    by 0x504CA98: gomp_malloc (alloc.c:37)
==27267==    by 0x505AFFA: gomp_new_icv (team.c:968)
==27267==    by 0x504CF24: omp_set_num_threads (libgomp.h:681)
==27267==    by 0x112AB3: MAIN__ (main.f90:47)
==27267==    by 0x112C07: main (main.f90:31)
==27267== 
==27267== LEAK SUMMARY:
==27267==    definitely lost: 0 bytes in 0 blocks
==27267==    indirectly lost: 0 bytes in 0 blocks
==27267==      possibly lost: 0 bytes in 0 blocks
==27267==    still reachable: 495 bytes in 6 blocks
==27267==         suppressed: 0 bytes in 0 blocks
==27267== 
==27267== For counts of detected and suppressed errors, rerun with: -v
==27267== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

It seems that this kind of problem has been also reported before and, as suggested in https://stackoverflow.com/questions/37395541/mkl-sparse-blas-segfault-when-transposing-csr-with-100m-rows, I'm already setting the number of threads to 1 and also using the `call mkl_free_buffers` subroutine. However, the problem is still there and, in a bigger project I have, this memory leak leads leads to a program crash due to invalid writes. Any idea on how to solve this?

which version of mkl did you

Gennady_F_Intel — Fri, 12 Apr 2019 06:03:38 GMT

which version of mkl did you try?

and also, please try to check

Gennady_F_Intel — Fri, 12 Apr 2019 06:16:20 GMT

and also, please try to check the same memory problem by using Intel Inspector for Linux instead of Vlagrind? here you may take Inspector for free.

Hello,

Kirill_V_Intel — Mon, 15 Apr 2019 03:00:22 GMT

Hello,

I think this is a known issue (at least I'm sure that I know the case when such a leak can happen, for the coordinate format like in your case), and we will have it fixed in our coming releases. I'll have a look at your particular example and make an update. (confirm my guess or render it wrong)

As a workaround, I can suggest to avoid using the coordinate format for now for the input matrix to the mkl_sparse_convert_csr. It would look clumsy, of course. Or I can look whether one can use the converters from the older Sparse BLAS (not IE) and avoid the leak if this is the way you will be ok with.

Best,
Kirill

Hi all,

Kirill_V_Intel — Tue, 16 Apr 2019 18:37:00 GMT

Hi all,

Update from my side: it turned out I was thinking of a different case. Quick check showed that if there is an issue it is not the one I described above. I haven't reproduced the leak so far.

Rodrigo, could you specify the MKL version?

EDIT: Also, how do you build your program and run it?

Best,
Kirill

topic Hello, in Intel® oneAPI Math Kernel Library

Problems with mkl_sparse_convert_csr

which version of mkl did you

and also, please try to check

Hello,

Hi all,