Re: [petsc-users] Direct PETSc to use MCDRAM on KNL and other optimizations for KNL

For LCRC, it is better to follow the example on their website (http://www.lcrc.anl.gov/for-users/using-lcrc/running-jobs/running-jobs-on-bebop/) #!/bin/bash #SBATCH -J mympijobname #SBATCH -A myaccount #SBATCH -p knlall #SBATCH -C knl,quad,cache #SBATCH -N 2 #SBATCH --ntasks-per-node=64 #SBATCH

Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed

Ok, will do that. Thanks a lot! Get Outlook for iOS From: Zhang, Junchao Sent: Wednesday, February 27, 2019 8:27:17 PM To: Yuyun Yang Cc: Matthew Knepley; petsc-users@mcs.anl.gov Subject: Re: [petsc-users] AddressSanitizer: attempting free o

Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed

Try the following to see if you can catch the bug easily: 1) Get error code for each petsc function and check it with CHKERRQ; 2) Link your code with a petsc library with debugging enabled (configured with --with-debugging=1); 3) Run your code with valgrind --Junchao Zhang On Wed, Feb 27, 201

Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed

Hi Junchao, This code actually involves a lot of classes and is pretty big. Might be an overkill for me to send everything to you. I'd like to know if I see this sort of error message, which points to this domain file, is it possible that the problem happens in another file (whose operations ar

Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed

Could you provide a compilable and runnable test so I can try it? --Junchao Zhang On Wed, Feb 27, 2019 at 7:34 PM Yuyun Yang mailto:yyan...@stanford.edu>> wrote: Thanks, I fixed that, but I’m not actually calling the testScatters() function in my implementation (in the constructor, the only fun

Re: [petsc-users] Direct PETSc to use MCDRAM on KNL and other optimizations for KNL

On Wed, Feb 27, 2019 at 7:03 PM Sajid Ali mailto:sajidsyed2...@u.northwestern.edu>> wrote: Hi Junchao, I’m confused with the syntax. If I submit the following as my job script, I get an error : #!/bin/bash #SBATCH --job-name=petsc_test #SBATCH -N 1 #SBATCH -C knl,quad,flat #SBATCH -p apsxr

Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed

Thanks, I fixed that, but I’m not actually calling the testScatters() function in my implementation (in the constructor, the only functions I called are setFields and setScatters). So the problem couldn’t have been that? Best, Yuyun From: Zhang, Junchao Sent: Wednesday, February 27, 2019 10:50

Re: [petsc-users] Error with petsc on OSX with libpng

On Wed, 27 Feb 2019, Amneet Pal Bhalla via petsc-users wrote: > Ah, I see. I will try to make sure that my Xcode is working. Did you try to > update XCode yet. Hm - currently petsc is tested with: balay@ipro^~ $ xcodebuild -version Xcode 10.1 Build version 10B61 balay@ipro^~ $ clang --versi

Re: [petsc-users] Error with petsc on OSX with libpng

On Thu, 28 Feb 2019, Balay, Satish via petsc-users wrote: > For some reason your xcode compiler is giving these warnings during linktime > - and I don't know why. These warnings are confusing petsc configure. > > >>> > ld: warning: text-based stub file > /System/Library/Frameworks//OpenCL.f

Re: [petsc-users] Error with petsc on OSX with libpng

Ah, I see. I will try to make sure that my Xcode is working. Did you try to update XCode yet. On Wed, Feb 27, 2019 at 5:12 PM Balay, Satish wrote: > Can you try the following and see if it makes a difference? > > ./configure --CC=mpicc --CXX=mpicxx --FC=mpif90 --PETSC_ARCH=sierra-dbg > --with-de

Re: [petsc-users] Error with petsc on OSX with libpng

Can you try the following and see if it makes a difference? ./configure --CC=mpicc --CXX=mpicxx --FC=mpif90 --PETSC_ARCH=sierra-dbg --with-debugging=1 --download-hypre=1 --with-x=0 LIBS='-L/usr/local/Cellar/mpich/3.3/lib -lmpifort -L/usr/local/Cellar/gcc/8.3.0/lib/gcc/8 -lgfortran' For some re

Re: [petsc-users] Direct PETSc to use MCDRAM on KNL and other optimizations for KNL

Hi Junchao, I’m confused with the syntax. If I submit the following as my job script, I get an error : #!/bin/bash #SBATCH --job-name=petsc_test #SBATCH -N 1 #SBATCH -C knl,quad,flat #SBATCH -p apsxrmd #SBATCH --time=1:00:00 module load intel/18.0.3-d6gtsxs module load intel-parallel-studio/clus

Re: [petsc-users] (no subject)

Can you send configure.log from this build? Satish On Thu, 28 Feb 2019, DAFNAKIS PANAGIOTIS via petsc-users wrote: > Hi everybody, > > I am trying to install PETSc version 3.10.3 on OSX Sierra 10.13.6 with the > following configure options > ./configure --CC=mpicc --CXX=mpicxx --FC=mpif90 --P

[petsc-users] (no subject)

Hi everybody, I am trying to install PETSc version 3.10.3 on OSX Sierra 10.13.6 with the following configure options ./configure --CC=mpicc --CXX=mpicxx --FC=mpif90 --PETSC_ARCH=sierra-dbg --with-debugging=1 --download-hypre=1 --with-x=0 however I am getting the following error messages when

Re: [petsc-users] Nonconforming object sizes in axpy

Here is the error message and please find an example attached.  thanks for the efforts !   [0]PETSC ERROR: - Error Message -- [0]PETSC ERROR: No support for this operation for this object type [0]PETSC ERROR: Mat ty

Re: [petsc-users] Direct PETSc to use MCDRAM on KNL and other optimizations for KNL

Use srun numactl -m 1 ./app OR srun numactl -p 1 ./app See bottom of https://www.nersc.gov/users/computational-systems/cori/configuration/knl-processor-modes/ --Junchao Zhang On Wed, Feb 27, 2019 at 4:16 PM Sajid Ali via petsc-users mailto:petsc-users@mcs.anl.gov>> wrote: Hi, I ran a TS in

Re: [petsc-users] Nonconforming object sizes in axpy

> On Feb 27, 2019, at 3:25 PM, Marius Buerkle wrote: > > Ok. I also tried without openmp which gave the same error. > The segfault left aside, is MatAXPY supposed to work when Y is of type > ELEMENTAL and X of type MATMPIAIJ ? It worked before but now it stops with > mat elemental not suppo

Re: [petsc-users] Nonconforming object sizes in axpy

Ok. I also tried without openmp which gave the same error. The segfault left aside, is MatAXPY supposed to work when Y is of type ELEMENTAL and X of type MATMPIAIJ ? It worked before but now it stops with mat elemental not supported. > Von: "Stefano Zampini" > An: "Marius Buerkle" > Cc: "Mat

Re: [petsc-users] Fwd: PETSC installation issues

On Wed, 27 Feb 2019, Alexander Lindsay wrote: > Is this part of the log relevant? Here is the relevant part. Do not need to rebuild FBLASLAPACK <<< Here configure thinks FBLASLAPACK is already built. > TEST checkLib from config.packages.BlasLapack(/home/ryan/projects/moos

Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed

On Wed, Feb 27, 2019 at 10:41 AM Yuyun Yang via petsc-users mailto:petsc-users@mcs.anl.gov>> wrote: I called VecDestroy() in the destructor for this object – is that not the right way to do it? In Domain::testScatters(), you have many VecDuplicate(,&out), You need to VecDestroy(&out) before doi

Re: [petsc-users] Fwd: PETSC installation issues

>>> stderr: /usr/bin/ld: cannot find -lfblas <<< Looks like a broken/incomplete build - that configure thinks is successful. Suggest doing a fresh build after 'rm -rf /home/ryan/projects/moose/petsc/linux-c-opt' Also if using threads - might want to use --download-openblas [or MKL] Satish On

Re: [petsc-users] Nonconforming object sizes in axpy

If you check ALL ERROR CODES by doing ierr = _AnyPetscCall_();CHKERRQ(ierr); The code will stop at the first error I see you are using openmp. Probably this is causing the problem, I don’t know what to say without a MWE. > On Feb 25, 2019, at 10:50 PM, Marius Buerkle wrote: > >

Re: [petsc-users] AddressSanitizer: attempting free on address which was not malloc()-ed

I called VecDestroy() in the destructor for this object – is that not the right way to do it? How do I implement CHECK ALL RETURN CODES? From: Matthew Knepley Sent: Wednesday, February 27, 2019 7:24 AM To: Yuyun Yang Cc: petsc-users@mcs.anl.gov Subject: Re: [petsc-users] AddressSanitizer: attem