Re: [petsc-users] Obtain the precondioned matrix

On Thu, Mar 22, 2018 at 8:29 PM, 我 wrote: > Hi all, > I want to analyze the preconditioned matrix. But the > KSPComputeExplicitOperator costs too much time to obtain the matrix. My > origin matrix is about 3000*3000 sparse one. I noticed this function is > applicable for the

[petsc-users] Obtain the precondioned matrix

Hi all, I want to analyze the preconditioned matrix. But the KSPComputeExplicitOperator costs too much time to obtain the matrix. My origin matrix is about 3000*3000 sparse one. I noticed this function is applicable for the relative small system. What's the matrix-size limitation for this

Re: [petsc-users] slepc-master does not configure correctly

Thanks, Jose, Works fine. Thanks, Fande, On Thu, Mar 22, 2018 at 2:43 AM, Jose E. Roman wrote: > Fixed > https://bitbucket.org/slepc/slepc/commits/464bcc967aa18470486aba71868e0a > e158c3fe49 > > > > El 22 mar 2018, a las 3:23, Satish Balay escribió: >

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

On Thu, Mar 22, 2018 at 2:01 PM, Smith, Barry F. wrote: > > > > On Mar 22, 2018, at 12:58 PM, Balay, Satish wrote: > > > > On Thu, 22 Mar 2018, Smith, Barry F. wrote: > > > >> > >> > >>> On Mar 22, 2018, at 10:22 AM, Klaij, Christiaan >

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

> On Mar 22, 2018, at 12:58 PM, Balay, Satish wrote: > > On Thu, 22 Mar 2018, Smith, Barry F. wrote: > >> >> >>> On Mar 22, 2018, at 10:22 AM, Klaij, Christiaan wrote: >>> >>> Well, that's a small burden. >>> >>> By the way, the option --with-cc=mpicc

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

On Thu, 22 Mar 2018, Smith, Barry F. wrote: > > > > On Mar 22, 2018, at 10:22 AM, Klaij, Christiaan wrote: > > > > Well, that's a small burden. > > > > By the way, the option --with-cc=mpicc together with export > > I_MPI_CC=icc doesn't work together with --download-hdf5,

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

> On Mar 22, 2018, at 10:22 AM, Klaij, Christiaan wrote: > > Well, that's a small burden. > > By the way, the option --with-cc=mpicc together with export > I_MPI_CC=icc doesn't work together with --download-hdf5, while it > works --with-cc=mpiicc and no export. Guess the

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

Well, that's a small burden. By the way, the option --with-cc=mpicc together with export I_MPI_CC=icc doesn't work together with --download-hdf5, while it works --with-cc=mpiicc and no export. Guess the export doesn't make it into the hdf5 configure. Any plans for adding --download-cgns and have

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

Should mention: one nice thing about --with-mpi-dir option is - it attempts to pick up related/compatible compilers - i.e MPI_DIR/bin/{mpicc,mpicxx,mpif90} When one uses --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpicxx - the burden on providing related/compatible compilers is on the user - i.e

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

Guess I shouldn't have read the intel manual :-) Lesson learned, no more guessing. And I sure appreciate all the effort you are putting into this, especially the option to configure and build other packages in a consistent way with the --download-package option. Chris dr. ir. Christiaan Klaij

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

Sure - they have so many ways of tweaking things - so one can't things will be the same across multiple users. Most users dont' set these env variables [thats extra work - and not the default behavior anyway] - so they rely on the default behavior - i.e use mpicc for gnu and mpiicc for intel

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

Fair enough. As a side note: if you want intel compilers, there's no need to specify mpiicc, intel says to export I_MPI_CC=icc, which gives $ which mpicc /opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/intel64/bin/mpicc $ mpicc -v mpiicc for the Intel(R) MPI Library 2017 Update 1 for

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

On Thu, 22 Mar 2018, Klaij, Christiaan wrote: > OK, configure works with the option --with-cc=/path/to/mpicc, > thanks! > > I'm not sure you are right about checking --with-mpi-dir/bin, There are 2 types of options to configure: - tell configure what to use - i.e do not guess [like

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

There's a bin64 symlink: $ ls -l /opt/intel/compilers_and_libraries_2017.1.132/linux/mpi total 0 drwxr-xr-x. 3 root root 16 Mar 28 2017 benchmarks lrwxrwxrwx. 1 root root 11 Mar 28 2017 bin64 -> intel64/bin drwxr-xr-x. 2 root root 41 Mar 28 2017 binding lrwxrwxrwx. 1 root root 11 Mar 28 2017

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

OK, configure works with the option --with-cc=/path/to/mpicc, thanks! I'm not sure you are right about checking --with-mpi-dir/bin, because, at least with this install, the binaries are located in --with-mpi-dir/intel64/bin: $ which mpicc

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

Added this change to balay/mpi-dir-check-warning/maint and merged to next. Satish On Thu, 22 Mar 2018, Satish Balay wrote: > The relevant change that is causing the difference is: > > https://bitbucket.org/petsc/petsc/commits/a98758b74fbc47f3dca87b526141d347301fd5eb > > Perhaps we should

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

The relevant change that is causing the difference is: https://bitbucket.org/petsc/petsc/commits/a98758b74fbc47f3dca87b526141d347301fd5eb Perhaps we should print a warning if with-mpi-dir/bin is missing. $ ./configure --with-mpi-dir=$HOME/tmp

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

On Thu, Mar 22, 2018 at 8:42 AM, Klaij, Christiaan wrote: > Matt, > > The problem must be earlier, because it should be using mpicc for > the check, not gcc. The mpi.h is found here by the 3.7.5 config: > Yes, I believe we took out the compiler finding stuff since the

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

In either case --mpi-dir=/opt/intel/compilers_and_libraries_2017.1.132/linux/mpi is the wrong option. Its a shortcut for --with-cc=/opt/intel/compilers_and_libraries_2017.1.132/linux/mpi/bin/mpicc - which you don't have. Since you have mpicc in your path - you can just use: --with-cc=mpicc

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

Matt, The problem must be earlier, because it should be using mpicc for the check, not gcc. The mpi.h is found here by the 3.7.5 config: Executing: mpicc -E -I/tmp/petsc-JIF0WC/config.setCompilers -I/tmp/petsc-JIF0WC/config.types -I/tmp/petsc-JIF0WC/config.headers

Re: [petsc-users] problem configuring 3.8.3 with intel mpi

On Thu, Mar 22, 2018 at 8:00 AM, Klaij, Christiaan wrote: > Satish, > > I'm trying to upgrade from 3.7.5 to 3.8.3. The first problem is > that my intel mpi installation, which works for 3.7.5, fails with > 3.8.3, see the attached logs. It seems that the mpi compilers are > not

Re: [petsc-users] slepc-master does not configure correctly

Fixed https://bitbucket.org/slepc/slepc/commits/464bcc967aa18470486aba71868e0ae158c3fe49 > El 22 mar 2018, a las 3:23, Satish Balay escribió: > > The primary change is - DESTDIR in petscvariables is replaced with PREFIXDIR > > i.e: > > diff --git