Re: [petsc-users] Problem with BLASdot in 3.19.4
Just FYI, with the configuration below, PETSc 3.19.5 works fine with Visual Studio 2022, statically linked to MS MPI and Intel MKL 2023. Thuc -Original Message- From: petsc-users [mailto:petsc-users-boun...@mcs.anl.gov] On Behalf Of Thuc Bui Sent: Tuesday, September 19, 2023 11:24 PM To: 'petsc-users' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Correction! The MKL library mkl_rt.lib was mistakenly included in the configure below. It is not needed to build PETSc, but the app requires to link to it and petsc.lib. Thuc -Original Message- From: petsc-users [mailto:petsc-users-boun...@mcs.anl.gov] On Behalf Of Thuc Bui Sent: Tuesday, September 19, 2023 11:10 PM To: 'petsc-users' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Hi Satish and Barry, Thank you very for getting back to me with the suggestion of the OMP_NUM_THREADS environmental variable and how to set the option no_signal_handler per Barry's suggestion. Yes, I am using threaded Intel MKL. So, I first set the environmental variable OMP_NUM_THREADS=1, and run the Visual Studio debugger. It still crashes at the same place with the same errors. I then set the PETSC_OPTIONS=-no_signal_handler, the debugger refuses to pass through the access exception, and I have to stop the debugger; consequently no PETSc errors were reported. I know there is an option somewhere in the VS debugger to bypass this access exception, but I didn't pursue further. Finally, I removed Intel MKL 2000 (to uninstall it requires a 3rd party software!), and use Intel oneAPI MKL (2023) with PETSc 3.18.6 and Visual Studio 2022. Now my code with 1, 2 or 4 cores work! I will try 3.19.4 next and will keep you posted. Thank you again for your help, Thuc Bui // ./configure --with-cc='win32fe cl' --with-fc=0 --with-cxx='win32fe cl' --with-openmp \ --with-mpi-include='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include:/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include/x64' \ --with-mpi-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpi.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpifec.lib] \ --with-blas-lapack-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_lp64.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_core.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_thread.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_rt.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/libiomp5md.lib] \ --with-mpiexec='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/bin/x64/mpiexec' \ --with-shared-libraries=0 /// -Original Message- From: Satish Balay [mailto:ba...@mcs.anl.gov] Sent: Tuesday, September 19, 2023 10:01 AM To: Thuc Bui Cc: 'Barry Smith'; 'PETSc users list' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Its a run time option to petsc (application) binary. So you can either specify it via command line - at run time - or add it to env variable "PETSC_OPTIONS" - or add it to $HOME/.petscrc file Satish On Tue, 19 Sep 2023, Thuc Bui wrote: > Hi Barry, > > > > Thanks for getting back to me. The diagnostics were generated when tracing > under the VS debugger. To use the option –no_signal_handler, I believe I will > need to reconfigure PETSc with this additional option. I will try it now. > > > > Thuc > > > > > > From: Barry Smith [mailto:bsm...@petsc.dev] > Sent: Tuesday, September 19, 2023 8:24 AM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Can you run in the Microsoft Visual Studio debugger? Use the additional > PETSc option -no_signal_handler > > > > > > It won't show exactly where the SEGV happens but might focus in a bit on > it. For example it may be ddot() or ddot_(). > > > > Barry > > > > > > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with > VS 2022 also crashes at the same place. The same errors are shown below. I > don’t remember for sure, but I don’t think I was able to configure Petsc > 3.19.4 with VS 2019. However, I will still try that next. > &
Re: [petsc-users] Problem with BLASdot in 3.19.4
Correction! The MKL library mkl_rt.lib was mistakenly included in the configure below. It is not needed to build PETSc, but the app requires to link to it and petsc.lib. Thuc -Original Message- From: petsc-users [mailto:petsc-users-boun...@mcs.anl.gov] On Behalf Of Thuc Bui Sent: Tuesday, September 19, 2023 11:10 PM To: 'petsc-users' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Hi Satish and Barry, Thank you very for getting back to me with the suggestion of the OMP_NUM_THREADS environmental variable and how to set the option no_signal_handler per Barry's suggestion. Yes, I am using threaded Intel MKL. So, I first set the environmental variable OMP_NUM_THREADS=1, and run the Visual Studio debugger. It still crashes at the same place with the same errors. I then set the PETSC_OPTIONS=-no_signal_handler, the debugger refuses to pass through the access exception, and I have to stop the debugger; consequently no PETSc errors were reported. I know there is an option somewhere in the VS debugger to bypass this access exception, but I didn't pursue further. Finally, I removed Intel MKL 2000 (to uninstall it requires a 3rd party software!), and use Intel oneAPI MKL (2023) with PETSc 3.18.6 and Visual Studio 2022. Now my code with 1, 2 or 4 cores work! I will try 3.19.4 next and will keep you posted. Thank you again for your help, Thuc Bui // ./configure --with-cc='win32fe cl' --with-fc=0 --with-cxx='win32fe cl' --with-openmp \ --with-mpi-include='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include:/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include/x64' \ --with-mpi-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpi.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpifec.lib] \ --with-blas-lapack-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_lp64.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_core.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_thread.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_rt.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/libiomp5md.lib] \ --with-mpiexec='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/bin/x64/mpiexec' \ --with-shared-libraries=0 /// -Original Message- From: Satish Balay [mailto:ba...@mcs.anl.gov] Sent: Tuesday, September 19, 2023 10:01 AM To: Thuc Bui Cc: 'Barry Smith'; 'PETSc users list' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Its a run time option to petsc (application) binary. So you can either specify it via command line - at run time - or add it to env variable "PETSC_OPTIONS" - or add it to $HOME/.petscrc file Satish On Tue, 19 Sep 2023, Thuc Bui wrote: > Hi Barry, > > > > Thanks for getting back to me. The diagnostics were generated when tracing > under the VS debugger. To use the option –no_signal_handler, I believe I will > need to reconfigure PETSc with this additional option. I will try it now. > > > > Thuc > > > > > > From: Barry Smith [mailto:bsm...@petsc.dev] > Sent: Tuesday, September 19, 2023 8:24 AM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Can you run in the Microsoft Visual Studio debugger? Use the additional > PETSc option -no_signal_handler > > > > > > It won't show exactly where the SEGV happens but might focus in a bit on > it. For example it may be ddot() or ddot_(). > > > > Barry > > > > > > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with > VS 2022 also crashes at the same place. The same errors are shown below. I > don’t remember for sure, but I don’t think I was able to configure Petsc > 3.19.4 with VS 2019. However, I will still try that next. > > > > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debug
Re: [petsc-users] Problem with BLASdot in 3.19.4
Hi Satish and Barry, Thank you very for getting back to me with the suggestion of the OMP_NUM_THREADS environmental variable and how to set the option no_signal_handler per Barry's suggestion. Yes, I am using threaded Intel MKL. So, I first set the environmental variable OMP_NUM_THREADS=1, and run the Visual Studio debugger. It still crashes at the same place with the same errors. I then set the PETSC_OPTIONS=-no_signal_handler, the debugger refuses to pass through the access exception, and I have to stop the debugger; consequently no PETSc errors were reported. I know there is an option somewhere in the VS debugger to bypass this access exception, but I didn't pursue further. Finally, I removed Intel MKL 2000 (to uninstall it requires a 3rd party software!), and use Intel oneAPI MKL (2023) with PETSc 3.18.6 and Visual Studio 2022. Now my code with 1, 2 or 4 cores work! I will try 3.19.4 next and will keep you posted. Thank you again for your help, Thuc Bui // ./configure --with-cc='win32fe cl' --with-fc=0 --with-cxx='win32fe cl' --with-openmp \ --with-mpi-include='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include:/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include/x64' \ --with-mpi-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpi.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpifec.lib] \ --with-blas-lapack-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_lp64.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_core.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_thread.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_rt.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/libiomp5md.lib] \ --with-mpiexec='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/bin/x64/mpiexec' \ --with-shared-libraries=0 /// -Original Message- From: Satish Balay [mailto:ba...@mcs.anl.gov] Sent: Tuesday, September 19, 2023 10:01 AM To: Thuc Bui Cc: 'Barry Smith'; 'PETSc users list' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Its a run time option to petsc (application) binary. So you can either specify it via command line - at run time - or add it to env variable "PETSC_OPTIONS" - or add it to $HOME/.petscrc file Satish On Tue, 19 Sep 2023, Thuc Bui wrote: > Hi Barry, > > > > Thanks for getting back to me. The diagnostics were generated when tracing > under the VS debugger. To use the option –no_signal_handler, I believe I will > need to reconfigure PETSc with this additional option. I will try it now. > > > > Thuc > > > > > > From: Barry Smith [mailto:bsm...@petsc.dev] > Sent: Tuesday, September 19, 2023 8:24 AM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Can you run in the Microsoft Visual Studio debugger? Use the additional > PETSc option -no_signal_handler > > > > > > It won't show exactly where the SEGV happens but might focus in a bit on > it. For example it may be ddot() or ddot_(). > > > > Barry > > > > > > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with > VS 2022 also crashes at the same place. The same errors are shown below. I > don’t remember for sure, but I don’t think I was able to configure Petsc > 3.19.4 with VS 2019. However, I will still try that next. > > > > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see <https://petsc.org/release/faq/#valgrind> > https://petsc.org/release/faq/#valgrind and <https://petsc.org/release/faq/> > https://petsc.org/release/faq/ > > [0]PETSC ERROR: - Stack Frames > > > [0]PETSC ERROR: The line numbers in the error traceback are not always
Re: [petsc-users] Problem with BLASdot in 3.19.4
Its a run time option to petsc (application) binary. So you can either specify it via command line - at run time - or add it to env variable "PETSC_OPTIONS" - or add it to $HOME/.petscrc file Satish On Tue, 19 Sep 2023, Thuc Bui wrote: > Hi Barry, > > > > Thanks for getting back to me. The diagnostics were generated when tracing > under the VS debugger. To use the option –no_signal_handler, I believe I will > need to reconfigure PETSc with this additional option. I will try it now. > > > > Thuc > > > > > > From: Barry Smith [mailto:bsm...@petsc.dev] > Sent: Tuesday, September 19, 2023 8:24 AM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Can you run in the Microsoft Visual Studio debugger? Use the additional > PETSc option -no_signal_handler > > > > > > It won't show exactly where the SEGV happens but might focus in a bit on > it. For example it may be ddot() or ddot_(). > > > > Barry > > > > > > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with > VS 2022 also crashes at the same place. The same errors are shown below. I > don’t remember for sure, but I don’t think I was able to configure Petsc > 3.19.4 with VS 2019. However, I will still try that next. > > > > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see <https://petsc.org/release/faq/#valgrind> > https://petsc.org/release/faq/#valgrind and <https://petsc.org/release/faq/> > https://petsc.org/release/faq/ > > [0]PETSC ERROR: - Stack Frames > > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > [0]PETSC ERROR: #3 VecNorm() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > [0]PETSC ERROR: #7 KSPSolve_Private() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > [0]PETSC ERROR: #8 KSPSolve() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x4400), error 59, comm rank 0 > > > > > > > > From: petsc-users [ <mailto:petsc-users-boun...@mcs.anl.gov> > mailto:petsc-users-boun...@mcs.anl.gov] On Behalf Of Thuc Bui > Sent: Monday, September 18, 2023 4:24 PM > To: 'Barry Smith' > Cc: 'PETSc users list' > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > Thanks a lot Barry, for getting back to me. Will do what you have suggested, > and get back with the results. > > > > Best regards, > > Thuc > > > > From: Barry Smith [ <mailto:bsm...@petsc.dev> mailto:bsm...@petsc.dev] > Sent: Monday, September 18, 2023 3:43 PM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Ok, two things are being changed at the same time: the version of PETSc > and the version of Visual Studio. > > > > Could you please try with the new Visual Studio version but the same older > PETSc version? If that works could you try with the old Visual Studio version > but the new PETSc version? > > > > Barry > > > > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui < <mailto:b...@calcreek.com> > b...@calcreek.com> wrote: > > > > Dear Petsc users and exp
Re: [petsc-users] Problem with BLASdot in 3.19.4
Hi Barry,
Thanks for getting back to me. The diagnostics were generated when tracing
under the VS debugger. To use the option –no_signal_handler, I believe I will
need to reconfigure PETSc with this additional option. I will try it now.
Thuc
From: Barry Smith [mailto:bsm...@petsc.dev]
Sent: Tuesday, September 19, 2023 8:24 AM
To: Thuc Bui
Cc: PETSc users list
Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4
Can you run in the Microsoft Visual Studio debugger? Use the additional PETSc
option -no_signal_handler
It won't show exactly where the SEGV happens but might focus in a bit on it.
For example it may be ddot() or ddot_().
Barry
On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote:
Hi Barry,
Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with
VS 2022 also crashes at the same place. The same errors are shown below. I
don’t remember for sure, but I don’t think I was able to configure Petsc 3.19.4
with VS 2019. However, I will still try that next.
Thanks for your help,
Thuc
[0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see <https://petsc.org/release/faq/#valgrind>
https://petsc.org/release/faq/#valgrind and <https://petsc.org/release/faq/>
https://petsc.org/release/faq/
[0]PETSC ERROR: - Stack Frames
[0]PETSC ERROR: The line numbers in the error traceback are not always exact.
[0]PETSC ERROR: #1 BLASdot()
[0]PETSC ERROR: #2 VecNorm_Seq() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216
[0]PETSC ERROR: #3 VecNorm() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237
[0]PETSC ERROR: #4 VecNormalize() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318
[0]PETSC ERROR: #5 KSPGMRESCycle() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111
[0]PETSC ERROR: #6 KSPSolve_GMRES() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228
[0]PETSC ERROR: #7 KSPSolve_Private() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899
[0]PETSC ERROR: #8 KSPSolve() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071
job aborted:
[ranks] message
[0] application aborted
aborting MPI_COMM_WORLD (comm=0x4400), error 59, comm rank 0
From: petsc-users [ <mailto:petsc-users-boun...@mcs.anl.gov>
mailto:petsc-users-boun...@mcs.anl.gov] On Behalf Of Thuc Bui
Sent: Monday, September 18, 2023 4:24 PM
To: 'Barry Smith'
Cc: 'PETSc users list'
Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4
Thanks a lot Barry, for getting back to me. Will do what you have suggested,
and get back with the results.
Best regards,
Thuc
From: Barry Smith [ <mailto:bsm...@petsc.dev> mailto:bsm...@petsc.dev]
Sent: Monday, September 18, 2023 3:43 PM
To: Thuc Bui
Cc: PETSc users list
Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4
Ok, two things are being changed at the same time: the version of PETSc and
the version of Visual Studio.
Could you please try with the new Visual Studio version but the same older
PETSc version? If that works could you try with the old Visual Studio version
but the new PETSc version?
Barry
On Sep 18, 2023, at 6:26 PM, Thuc Bui < <mailto:b...@calcreek.com>
b...@calcreek.com> wrote:
Dear Petsc users and experts,
If someone can direct me how to track this bug, I would really appreciate it.
The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio
2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code
works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL,
and built with Visual Studio 2019.
When my code calls PetscCall(KSPSolve(...)), it gets to
PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), )),
PetscCall(VecNorm(x, NORM_2, )) and then crashes in VecNorm_Seq() at:
PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] =
PetscSqrtReal(PetscRealPart(BLASdot_(, xx, , xx, ;
I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to
Intel MKL, and its library does not contain debug information. After the code
exits, the errors are shown below the hash line.
Should I install the latest Intel MKL to work with Petsc 3.19.4?
Many thanks in advance for your help,
Thuc Bui
Senior R Engineer
Calabazas Creek Research, Inc
(650) 948-5361
Re: [petsc-users] Problem with BLASdot in 3.19.4
BTW: Can check if you are using threaded MKL? We default to: Libraries: -L/cygdrive/c/PROGRA~2/Intel/oneAPI/mkl/2022.1.0/lib/intel64 mkl_intel_lp64_dll.lib mkl_sequential_dll.lib mkl_core_dll.lib If using threaded MKL - try using env variable "OMP_NUM_THREADS=1" and see that makes a difference Satish On Tue, 19 Sep 2023, Barry Smith wrote: > > Can you run in the Microsoft Visual Studio debugger? Use the additional > PETSc option -no_signal_handler > > > It won't show exactly where the SEGV happens but might focus in a bit on > it. For example it may be ddot() or ddot_(). > > Barry > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built > > with VS 2022 also crashes at the same place. The same errors are shown > > below. I don’t remember for sure, but I don’t think I was able to configure > > Petsc 3.19.4 with VS 2019. However, I will still try that next. > > > > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: > > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > > probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and > > https://petsc.org/release/faq/ > > [0]PETSC ERROR: - Stack Frames > > > > [0]PETSC ERROR: The line numbers in the error traceback are not always > > exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > [0]PETSC ERROR: #3 VecNorm() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > [0]PETSC ERROR: #7 KSPSolve_Private() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > [0]PETSC ERROR: #8 KSPSolve() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x4400), error 59, comm rank 0 > > > > > > > > From: petsc-users [mailto:petsc-users-boun...@mcs.anl.gov] On Behalf Of > > Thuc Bui > > Sent: Monday, September 18, 2023 4:24 PM > > To: 'Barry Smith' > > Cc: 'PETSc users list' > > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > Thanks a lot Barry, for getting back to me. Will do what you have > > suggested, and get back with the results. > > > > Best regards, > > Thuc > > > > From: Barry Smith [mailto:bsm...@petsc.dev] > > Sent: Monday, September 18, 2023 3:43 PM > > To: Thuc Bui > > Cc: PETSc users list > > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Ok, two things are being changed at the same time: the version of PETSc > > and the version of Visual Studio. > > > > Could you please try with the new Visual Studio version but the same > > older PETSc version? If that works could you try with the old Visual Studio > > version but the new PETSc version? > > > > Barry > > > > > > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui > <mailto:b...@calcreek.com>> wrote: > > > > Dear Petsc users and experts, > > > > If someone can direct me how to track this bug, I would really appreciate > > it. > > > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual > > Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The > > same code works fine with Petsc 3.18.6 using the same versions of MS MPI > > and Intel MKL, and built with Visual Studio 2019. > > > > When my code calls PetscCall(KSPSolve(...)), it gets to > > PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), )), > > PetscCall(Vec
Re: [petsc-users] Problem with BLASdot in 3.19.4
Can you run in the Microsoft Visual Studio debugger? Use the additional PETSc
option -no_signal_handler
It won't show exactly where the SEGV happens but might focus in a bit on it.
For example it may be ddot() or ddot_().
Barry
> On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote:
>
> Hi Barry,
>
> Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with
> VS 2022 also crashes at the same place. The same errors are shown below. I
> don’t remember for sure, but I don’t think I was able to configure Petsc
> 3.19.4 with VS 2019. However, I will still try that next.
>
> Thanks for your help,
> Thuc
>
> [0]PETSC ERROR:
>
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and
> https://petsc.org/release/faq/
> [0]PETSC ERROR: - Stack Frames
>
> [0]PETSC ERROR: The line numbers in the error traceback are not always exact.
> [0]PETSC ERROR: #1 BLASdot()
> [0]PETSC ERROR: #2 VecNorm_Seq() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216
> [0]PETSC ERROR: #3 VecNorm() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237
> [0]PETSC ERROR: #4 VecNormalize() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318
> [0]PETSC ERROR: #5 KSPGMRESCycle() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111
> [0]PETSC ERROR: #6 KSPSolve_GMRES() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228
> [0]PETSC ERROR: #7 KSPSolve_Private() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899
> [0]PETSC ERROR: #8 KSPSolve() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071
>
> job aborted:
> [ranks] message
>
> [0] application aborted
> aborting MPI_COMM_WORLD (comm=0x4400), error 59, comm rank 0
>
>
>
> From: petsc-users [mailto:petsc-users-boun...@mcs.anl.gov] On Behalf Of Thuc
> Bui
> Sent: Monday, September 18, 2023 4:24 PM
> To: 'Barry Smith'
> Cc: 'PETSc users list'
> Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4
>
> Thanks a lot Barry, for getting back to me. Will do what you have suggested,
> and get back with the results.
>
> Best regards,
> Thuc
>
> From: Barry Smith [mailto:bsm...@petsc.dev]
> Sent: Monday, September 18, 2023 3:43 PM
> To: Thuc Bui
> Cc: PETSc users list
> Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4
>
>
> Ok, two things are being changed at the same time: the version of PETSc
> and the version of Visual Studio.
>
> Could you please try with the new Visual Studio version but the same older
> PETSc version? If that works could you try with the old Visual Studio version
> but the new PETSc version?
>
> Barry
>
>
>
>
> On Sep 18, 2023, at 6:26 PM, Thuc Bui <mailto:b...@calcreek.com>> wrote:
>
> Dear Petsc users and experts,
>
> If someone can direct me how to track this bug, I would really appreciate it.
>
> The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual
> Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same
> code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel
> MKL, and built with Visual Studio 2019.
>
> When my code calls PetscCall(KSPSolve(...)), it gets to
> PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), )),
> PetscCall(VecNorm(x, NORM_2, )) and then crashes in VecNorm_Seq() at:
>
> PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] =
> PetscSqrtReal(PetscRealPart(BLASdot_(, xx, , xx, ;
>
> I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to
> Intel MKL, and its library does not contain debug information. After the code
> exits, the errors are shown below the hash line.
>
> Should I install the latest Intel MKL to work with Petsc 3.19.4?
>
> Many thanks in advance for your help,
> Thuc Bui
> Senior R Engineer
> Calabazas Creek Research, Inc
> (650) 948-5361
>
>
> ###
>
> [0]PETSC ERROR:
>
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
Re: [petsc-users] Problem with BLASdot in 3.19.4
On Tue, 19 Sep 2023, Matthew Knepley wrote: > On Tue, Sep 19, 2023 at 7:04 AM Thuc Bui wrote: > > > Hi Barry, > > > > > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built > > with VS 2022 also crashes at the same place. The same errors are shown > > below. I don’t remember for sure, but I don’t think I was able to configure > > Petsc 3.19.4 with VS 2019. However, I will still try that next. > > > > It is so easy to hate VS. This suggests that VS is secretly linking to > another BLAS, perhaps with different calling semantics. There could be multiple issues: - code bugs - that show up in different settings - Intel Compilers/OneAPI are have tight dependency on native compilers [on linux and windows] So perhaps the current install is over VS19 - and not VS22. If this is the case - a reinstall [of Intel Compilers] over VS22 might help? Or there could be different compiler dlls in VS vs Intel installs - and one of them is misbehaving.. [so reorder PATH location for Intel/MS?] - MLK bugs that show up in some setups? [here using alternate blas - aka fblaslapack might help?] - Latest VS with latest OneAPI might help? [however our test setup is with older versions of these compilers.. >>> Compilers: C Compiler: /cygdrive/e/svcpetsc/builds/Cw-cvdV3/0/petsc/petsc/lib/petsc/bin/win32fe/win_cl -GF -MD -wd4996 -Zc:preprocessor -O2 Version: Win32 Development Tool Front End, version 1.11.4 Fri, Sep 10, 2021 6:33:40 PM\nMicrosoft (R) C/C++ Optimizing Compiler Version 19.32.31329 for x64 C++ Compiler: /cygdrive/e/svcpetsc/builds/Cw-cvdV3/0/petsc/petsc/lib/petsc/bin/win32fe/win_cl -GF -MD -GR -EHsc -Zc:preprocessor -Zc:__cplusplus -O2 -Zm200 -std:c++20 -TP Version: Win32 Development Tool Front End, version 1.11.4 Fri, Sep 10, 2021 6:33:40 PM\nMicrosoft (R) C/C++ Optimizing Compiler Version 19.32.31329 for x64 Fortran Compiler: /cygdrive/e/svcpetsc/builds/Cw-cvdV3/0/petsc/petsc/lib/petsc/bin/win32fe/win_ifort -MD -O3 -fpp Version: Win32 Development Tool Front End, version 1.11.4 Fri, Sep 10, 2021 6:33:40 PM\nIntel(R) Fortran Intel(R) 64 Compiler Classic for applications running on Intel(R) 64, Version 2021.6.0 Build 20220226_00 <<< Satish > > Thanks, > > Matt > > > > Thanks for your help, > > > > Thuc > > > > > > > > [0]PETSC ERROR: > > > > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > > probably memory access out of range > > > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and > > https://petsc.org/release/faq/ > > > > [0]PETSC ERROR: - Stack Frames > > > > > > [0]PETSC ERROR: The line numbers in the error traceback are not always > > exact. > > > > [0]PETSC ERROR: #1 BLASdot() > > > > [0]PETSC ERROR: #2 VecNorm_Seq() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > > > [0]PETSC ERROR: #3 VecNorm() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > > > [0]PETSC ERROR: #4 VecNormalize() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > > > [0]PETSC ERROR: #5 KSPGMRESCycle() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > > > [0]PETSC ERROR: #7 KSPSolve_Private() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > > > [0]PETSC ERROR: #8 KSPSolve() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > > > > > job aborted: > > > > [ranks] message > > > > > > > > [0] application aborted > > > > aborting MPI_COMM_WORLD (comm=0x4400), error 59, comm rank 0 > > > > > > > > > > > > > > > > *From:* petsc-users [mailto:petsc-users-boun...@mcs.anl.gov] *On Behalf > > Of *Thuc Bui > > *Sent:* Monday, September 18, 2023 4:24 PM > > *To:* 'Barry Smith' > > *Cc:* 'PETSc users list' > > *Subject:* Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > > > Thanks a lot Barry, for getting back to me. Will do what you hav
Re: [petsc-users] Problem with BLASdot in 3.19.4
On Tue, Sep 19, 2023 at 7:04 AM Thuc Bui wrote:
> Hi Barry,
>
>
>
> Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built
> with VS 2022 also crashes at the same place. The same errors are shown
> below. I don’t remember for sure, but I don’t think I was able to configure
> Petsc 3.19.4 with VS 2019. However, I will still try that next.
>
It is so easy to hate VS. This suggests that VS is secretly linking to
another BLAS, perhaps with different calling semantics.
Thanks,
Matt
> Thanks for your help,
>
> Thuc
>
>
>
> [0]PETSC ERROR:
>
>
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
>
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and
> https://petsc.org/release/faq/
>
> [0]PETSC ERROR: - Stack Frames
>
>
> [0]PETSC ERROR: The line numbers in the error traceback are not always
> exact.
>
> [0]PETSC ERROR: #1 BLASdot()
>
> [0]PETSC ERROR: #2 VecNorm_Seq() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216
>
> [0]PETSC ERROR: #3 VecNorm() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237
>
> [0]PETSC ERROR: #4 VecNormalize() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318
>
> [0]PETSC ERROR: #5 KSPGMRESCycle() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111
>
> [0]PETSC ERROR: #6 KSPSolve_GMRES() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228
>
> [0]PETSC ERROR: #7 KSPSolve_Private() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899
>
> [0]PETSC ERROR: #8 KSPSolve() at
> D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071
>
>
>
> job aborted:
>
> [ranks] message
>
>
>
> [0] application aborted
>
> aborting MPI_COMM_WORLD (comm=0x4400), error 59, comm rank 0
>
>
>
>
>
>
>
> *From:* petsc-users [mailto:petsc-users-boun...@mcs.anl.gov] *On Behalf
> Of *Thuc Bui
> *Sent:* Monday, September 18, 2023 4:24 PM
> *To:* 'Barry Smith'
> *Cc:* 'PETSc users list'
> *Subject:* Re: [petsc-users] Problem with BLASdot in 3.19.4
>
>
>
> Thanks a lot Barry, for getting back to me. Will do what you have
> suggested, and get back with the results.
>
>
>
> Best regards,
>
> Thuc
>
>
>
> *From:* Barry Smith [mailto:bsm...@petsc.dev]
> *Sent:* Monday, September 18, 2023 3:43 PM
> *To:* Thuc Bui
> *Cc:* PETSc users list
> *Subject:* Re: [petsc-users] Problem with BLASdot in 3.19.4
>
>
>
>
>
> Ok, two things are being changed at the same time: the version of PETSc
> and the version of Visual Studio.
>
>
>
> Could you please try with the new Visual Studio version but the same
> older PETSc version? If that works could you try with the old Visual Studio
> version but the new PETSc version?
>
>
>
> Barry
>
>
>
>
>
>
>
> On Sep 18, 2023, at 6:26 PM, Thuc Bui wrote:
>
>
>
> Dear Petsc users and experts,
>
>
>
> If someone can direct me how to track this bug, I would really appreciate
> it.
>
>
>
> The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual
> Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The
> same code works fine with Petsc 3.18.6 using the same versions of MS MPI
> and Intel MKL, and built with Visual Studio 2019.
>
>
>
> When my code calls PetscCall(KSPSolve(...)), it gets to
> PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), )),
> PetscCall(VecNorm(x, NORM_2, )) and then crashes in VecNorm_Seq() at:
>
>
>
> PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] =
> PetscSqrtReal(PetscRealPart(BLASdot_(, xx, , xx, ;
>
>
>
> I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong
> to Intel MKL, and its library does not contain debug information. After the
> code exits, the errors are shown below the hash line.
>
>
>
> Should I install the latest Intel MKL to work with Petsc 3.19.4?
>
>
>
> Many thanks in advance for your help,
>
> Thuc Bui
>
> Senior R Engineer
>
> Calabazas Creek Research, Inc
>
> (650) 948-5361
>
>
>
>
>
> ###
>
>
>
> [0]PETSC ERROR:
Re: [petsc-users] Problem with BLASdot in 3.19.4
Hi Barry,
Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built
with VS 2022 also crashes at the same place. The same errors are shown
below. I don't remember for sure, but I don't think I was able to configure
Petsc 3.19.4 with VS 2019. However, I will still try that next.
Thanks for your help,
Thuc
[0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and
https://petsc.org/release/faq/
[0]PETSC ERROR: - Stack Frames
[0]PETSC ERROR: The line numbers in the error traceback are not always
exact.
[0]PETSC ERROR: #1 BLASdot()
[0]PETSC ERROR: #2 VecNorm_Seq() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.
c:216
[0]PETSC ERROR: #3 VecNorm() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvecto
r.c:237
[0]PETSC ERROR: #4 VecNormalize() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvecto
r.c:318
[0]PETSC ERROR: #5 KSPGMRESCycle() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmre
s.c:111
[0]PETSC ERROR: #6 KSPSolve_GMRES() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmre
s.c:228
[0]PETSC ERROR: #7 KSPSolve_Private() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc
.c:899
[0]PETSC ERROR: #8 KSPSolve() at
D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc
.c:1071
job aborted:
[ranks] message
[0] application aborted
aborting MPI_COMM_WORLD (comm=0x4400), error 59, comm rank 0
From: petsc-users [mailto:petsc-users-boun...@mcs.anl.gov] On Behalf Of Thuc
Bui
Sent: Monday, September 18, 2023 4:24 PM
To: 'Barry Smith'
Cc: 'PETSc users list'
Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4
Thanks a lot Barry, for getting back to me. Will do what you have suggested,
and get back with the results.
Best regards,
Thuc
From: Barry Smith [mailto:bsm...@petsc.dev]
Sent: Monday, September 18, 2023 3:43 PM
To: Thuc Bui
Cc: PETSc users list
Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4
Ok, two things are being changed at the same time: the version of PETSc
and the version of Visual Studio.
Could you please try with the new Visual Studio version but the same older
PETSc version? If that works could you try with the old Visual Studio
version but the new PETSc version?
Barry
On Sep 18, 2023, at 6:26 PM, Thuc Bui wrote:
Dear Petsc users and experts,
If someone can direct me how to track this bug, I would really appreciate
it.
The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual
Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The
same code works fine with Petsc 3.18.6 using the same versions of MS MPI and
Intel MKL, and built with Visual Studio 2019.
When my code calls PetscCall(KSPSolve(...)), it gets to
PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), )),
PetscCall(VecNorm(x, NORM_2, )) and then crashes in VecNorm_Seq() at:
PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] =
PetscSqrtReal(PetscRealPart(BLASdot_(, xx, , xx, ;
I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong
to Intel MKL, and its library does not contain debug information. After the
code exits, the errors are shown below the hash line.
Should I install the latest Intel MKL to work with Petsc 3.19.4?
Many thanks in advance for your help,
Thuc Bui
Senior R Engineer
Calabazas Creek Research, Inc
(650) 948-5361
###
[0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see <https://petsc.org/release/faq/#valgrind>
https://petsc.org/release/faq/#valgrind and
<https://petsc.org/release/faq/> https://petsc.org/release/faq/
[0]PETSC ERROR: - Stack Frames
[0]PETSC ERROR: The line numbers in the error traceback are not always
exact.
[0]PETSC ERROR: #1 BLASdot()
[0]PETSC ERROR: #2 VecNorm_Seq() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213
[0]PETSC ERROR: #3 VecNorm() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:23
7
[0]PETSC ERROR: #4 VecNormalize() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:31
Re: [petsc-users] Problem with BLASdot in 3.19.4
Thanks a lot Barry, for getting back to me. Will do what you have suggested,
and get back with the results.
Best regards,
Thuc
From: Barry Smith [mailto:bsm...@petsc.dev]
Sent: Monday, September 18, 2023 3:43 PM
To: Thuc Bui
Cc: PETSc users list
Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4
Ok, two things are being changed at the same time: the version of PETSc
and the version of Visual Studio.
Could you please try with the new Visual Studio version but the same older
PETSc version? If that works could you try with the old Visual Studio
version but the new PETSc version?
Barry
On Sep 18, 2023, at 6:26 PM, Thuc Bui wrote:
Dear Petsc users and experts,
If someone can direct me how to track this bug, I would really appreciate
it.
The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual
Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The
same code works fine with Petsc 3.18.6 using the same versions of MS MPI and
Intel MKL, and built with Visual Studio 2019.
When my code calls PetscCall(KSPSolve(...)), it gets to
PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), )),
PetscCall(VecNorm(x, NORM_2, )) and then crashes in VecNorm_Seq() at:
PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] =
PetscSqrtReal(PetscRealPart(BLASdot_(, xx, , xx, ;
I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong
to Intel MKL, and its library does not contain debug information. After the
code exits, the errors are shown below the hash line.
Should I install the latest Intel MKL to work with Petsc 3.19.4?
Many thanks in advance for your help,
Thuc Bui
Senior R Engineer
Calabazas Creek Research, Inc
(650) 948-5361
###
[0]PETSC ERROR:
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see <https://petsc.org/release/faq/#valgrind>
https://petsc.org/release/faq/#valgrind and
<https://petsc.org/release/faq/> https://petsc.org/release/faq/
[0]PETSC ERROR: - Stack Frames
[0]PETSC ERROR: The line numbers in the error traceback are not always
exact.
[0]PETSC ERROR: #1 BLASdot()
[0]PETSC ERROR: #2 VecNorm_Seq() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213
[0]PETSC ERROR: #3 VecNorm() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:23
7
[0]PETSC ERROR: #4 VecNormalize() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:31
8
[0]PETSC ERROR: #5 KSPGMRESCycle() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:11
0
[0]PETSC ERROR: #6 KSPSolve_GMRES() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:22
7
[0]PETSC ERROR: #7 KSPSolve_Private() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898
[0]PETSC ERROR: #8 KSPSolve() at
D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:107
0
job aborted:
[ranks] message
[0] application aborted
aborting MPI_COMM_WORLD (comm=0x4400), error 59, comm rank 0
Re: [petsc-users] Problem with BLASdot in 3.19.4
Ok, two things are being changed at the same time: the version of PETSc and
the version of Visual Studio.
Could you please try with the new Visual Studio version but the same older
PETSc version? If that works could you try with the old Visual Studio version
but the new PETSc version?
Barry
> On Sep 18, 2023, at 6:26 PM, Thuc Bui wrote:
>
> Dear Petsc users and experts,
>
> If someone can direct me how to track this bug, I would really appreciate it.
>
> The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual
> Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same
> code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel
> MKL, and built with Visual Studio 2019.
>
> When my code calls PetscCall(KSPSolve(...)), it gets to
> PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), )),
> PetscCall(VecNorm(x, NORM_2, )) and then crashes in VecNorm_Seq() at:
>
> PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] =
> PetscSqrtReal(PetscRealPart(BLASdot_(, xx, , xx, ;
>
> I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to
> Intel MKL, and its library does not contain debug information. After the code
> exits, the errors are shown below the hash line.
>
> Should I install the latest Intel MKL to work with Petsc 3.19.4?
>
> Many thanks in advance for your help,
> Thuc Bui
> Senior R Engineer
> Calabazas Creek Research, Inc
> (650) 948-5361
>
>
> ###
>
> [0]PETSC ERROR:
>
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and
> https://petsc.org/release/faq/
> [0]PETSC ERROR: - Stack Frames
>
> [0]PETSC ERROR: The line numbers in the error traceback are not always exact.
> [0]PETSC ERROR: #1 BLASdot()
> [0]PETSC ERROR: #2 VecNorm_Seq() at
> D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213
> [0]PETSC ERROR: #3 VecNorm() at
> D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237
> [0]PETSC ERROR: #4 VecNormalize() at
> D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318
> [0]PETSC ERROR: #5 KSPGMRESCycle() at
> D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110
> [0]PETSC ERROR: #6 KSPSolve_GMRES() at
> D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227
> [0]PETSC ERROR: #7 KSPSolve_Private() at
> D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898
> [0]PETSC ERROR: #8 KSPSolve() at
> D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070
>
> job aborted:
> [ranks] message
>
> [0] application aborted
> aborting MPI_COMM_WORLD (comm=0x4400), error 59, comm rank 0
