topic Hi, in Intel® oneAPI Math Kernel Library

ifort with mkl and function mkl_sparse_d_mv

watanabe__renato — Wed, 22 Aug 2018 16:07:10 GMT

I compile my program and it gives the following error:

forrtl: severe (174): SIGSEGV, segmentation fault occurred

I isolated the problem and it is occurring at the call of the mkl_sparse_d_mv function of the following function:

function dVdt(self, t, V)
class(MotorUnitPool), intent(inout) :: self
real(wp), intent(in) :: t
real(wp), intent(in) :: V(:)
real(wp), dimension(self%totalNumberOfCompartments) :: dVdt
integer :: i, j, stat
real(wp), dimension(:), allocatable :: matInt

allocate(matInt(self%totalNumberOfCompartments))

do i = 1, self%MUnumber
do j = 1, self%unit(i)%compNumber
self%iIonic((i-1)*self%unit(i)%compNumber+j) = self%unit(i)%Compartments(j)%computeCurrent(t, V((i-1)*self%unit(i)%compNumber+j))
end do
end do

stat = mkl_sparse_d_mv(self%spOperation, &
self%spAlpha, &
self%GSp, &
self%spDescr, &
V, &
self%spBeta, &
matInt)

dVdt = (self%iIonic + matInt + self%iInjected + self%EqCurrent_nA) * self%capacitanceInv
end function

I compile with gfortran without any problems. As compiler options to the ifort compiler i tried to use the option -heap_arrays, whith no success.

This function is part of a bigger program, with some files. If you want to see the whole software, you can find it in https://github.com/rnwatanabe/projectFR .

Thanks in advance,

Renato Watanabe

could you isolate the case in

Gennady_F_Intel — Fri, 24 Aug 2018 04:43:48 GMT

could you isolate the case in the form of standalone example whicj we may compile and execute on our side w/o extracted the code from your project!

Thank you for your answer

watanabe__renato — Fri, 24 Aug 2018 15:28:00 GMT

Thank you for your answer Gennady.

I isolated the problem in one file. It has a run-time segmentation fault with ifort and not with gfortran:

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Image PC Routine Line Source
spTest 0000000000860BAD Unknown Unknown Unknown
libpthread-2.23.s 00007FBA1A709390 Unknown Unknown Unknown
spTest 0000000000545E88 Unknown Unknown Unknown
spTest 00000000004090B0 Unknown Unknown Unknown
spTest 0000000000406DAA Unknown Unknown Unknown
spTest 000000000040484C Unknown Unknown Unknown
spTest 000000000040332E Unknown Unknown Unknown
libc-2.23.so 00007FBA19E41830 __libc_start_main Unknown Unknown
spTest 0000000000403229 Unknown Unknown Unknown

The file is attached.

could you please show the

Gennady_F_Intel — Mon, 27 Aug 2018 10:42:41 GMT

could you please show the linking line

The whole command line I used

watanabe__renato — Mon, 27 Aug 2018 14:38:09 GMT

The whole command line I used is :

ifort -c $MKLROOT/include/mkl_spblas.f90 & ifort spTest.f90 -o spTest -O3 -Wl,--start-group $MKLROOT/lib/intel64/libmkl_intel_lp64.a $MKLROOT/lib/intel64/libmkl_sequential.a $MKLROOT/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm -ldl -I$MKLROOT/include

The Linux version is:

Linux 4.15.0-33-generic #36-Ubuntu x86_64 x86_64 x86_64 GNU/Linux

No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.1 LTS
Release: 18.04
Codename: bionic

The ifort version is:

ifort (IFORT) 18.0.3 20180410

The MKL version is the version released in May 2018.

Thank you,

Renato

I found a way to solve the

watanabe__renato — Tue, 25 Sep 2018 22:04:31 GMT

I found a way to solve the issue. If I create the sparse matrix every step of the simulation, it works fine, both with gfortran and ifort. The code is attached. The problem now is that there is a memory leak. on the creation of the sparse matrix. Any idea of why?

Hi,

MariaZh — Tue, 25 Sep 2018 22:44:58 GMT

Hi,

I don't see a call to the mkl_sparse_destroy() routine.
(please, refer to https://software.intel.com/en-us/mkl-developer-reference-fortran-mkl-sparse-destroy)
I guess this can be a root cause for the memory leak in your implementation.

Please, let me know what you find out!
Best regards,
Maria

Thank you Maria! Now it

watanabe__renato — Wed, 26 Sep 2018 16:16:46 GMT

Thank you Maria! Now it worked.

Renato