Presumably the error occurs after you type 'exit' from the terminal.
I'm not sure what to suggest. Having tools that break - is not ideal.
You could edit configure script - and bypass this check.
But what is your requirement wrt petsc and matlab?
Perhaps other petsc developers can guide you
Satish,
If I just run, /Applications/MATLAB_R2018a.app/bin/matlab -nojvm -nodisplay,
then Matlab can run normally in the terminal as
Scott-Grad-MBP:~ zhihui$ /Applications/MATLAB_R2018a.app/bin/matlab -nojvm
-nodisplay
< M A T L A B (R) >
If I run it directly, I got the following. But if I double click
/Applications/MATLAB_R2018a.app/bin/matlab in the folder. The matlab start
normally.
Last login: Thu Oct 25 19:38:28 on ttys002
Scott-Grad-MBP:~ zhihui$ /Applications/MATLAB_R2018a.app/bin/matlab -nojvm
-nodisplay -r
>>
Testing Matlab at /Applications/MATLAB_R2018a.app
Executing: /Applications/MATLAB_R2018a.app/bin/matlab -nojvm -nodisplay -r
"display(['Version ' version]); exit"
stdout:
< M A T L A B (R) >
Copyright 1984-2018 The MathWorks, Inc.
R2018a
1. You need to send us the complete log.
2. Also use current release - petsc-3.10 [not 3.8]
Satish
On Fri, 26 Oct 2018, avatar wrote:
> Scott-Grad-MBP:petsc-3.8.3 zhihui$ ./configure
> --with-matlab-dir=/Applications/MATLAB_R2018a.app/
>
Scott-Grad-MBP:petsc-3.8.3 zhihui$ ./configure
--with-matlab-dir=/Applications/MATLAB_R2018a.app/
===
Configuring PETSc to compile on your system
On Fri, 26 Oct 2018, avatar wrote:
> Scott-Grad-MBP:bin zhihui$ pwd
> /Applications/MATLAB_R2018a.app/bin
Sorry - you need
--with-matlab-dir=/Applications/MATLAB_R2018a.app/
Satish
When I do the following, it shows
Scott-Grad-MBP:~ zhihui$ cd Applications/
Scott-Grad-MBP:Applications zhihui$ ls
Chrome Apps.localized
Scott-Grad-MBP:Applications zhihui$
From these, we can see there is no MATALB_R2018a.app in Applications. But when
I get into bin, and do the following, it
still shows these
Scott-Grad-MBP:petsc-3.8.3 zhihui$ ./configure
--with-matlab-dir=/Users/zhihui/Applications/MATLAB_R2018a.app
===
Configuring PETSc to compile on your system
you need
--with-matlab-dir=/Users/zhihui/Applications/MATLAB_R2018a.app
Satish
On Fri, 26 Oct 2018, avatar wrote:
> Thank Satish. It worked as you said. But when I rebuild petsc using
> ./configure --with-matlab
> It prompts
>
Thank Satish. It worked as you said. But when I rebuild petsc using
./configure --with-matlab
It prompts
===
Configuring PETSc to compile on your system
On Fri, 26 Oct 2018, avatar wrote:
> Is there other way to overcome this problem? Because if I don't set TMPDIR as
> \tmp. My other project will break. And actually I don't even know where my
> project set up the TMPDIR value.
I guess you need to read up on some basic unix and system admin.
Is there other way to overcome this problem? Because if I don't set TMPDIR as
\tmp. My other project will break. And actually I don't even know where my
project set up the TMPDIR value.
-- Original --
From: "Balay, Satish";;
Date: Oct 26, 2018
To:
To clarify, I meant: remove 'code that is changing the value of TMPDIR to 'tmp'
Satish
On Thu, 25 Oct 2018, Satish Balay wrote:
> I see - you have:
>
> >>
> TMPDIR=tmp
> <<
>
> Did you set this in your ~/.bashrc or somewhere? This is wrong and is
> breaking tools.
> OSX should setup
I see - you have:
>>
TMPDIR=tmp
<<
Did you set this in your ~/.bashrc or somewhere? This is wrong and is breaking
tools.
OSX should setup something likethe following for you.
petsc-mini:~ balay$ echo $TMPDIR
/var/folders/lw/hyrlb1051p9fj96qkktfvhvmgn/T/
Remove it - and retry building
These are what I got:
Scott-Grad-MacBook-Pro:benchmarks zhihui$ echo $TMPDIR
tmp
Scott-Grad-MacBook-Pro:benchmarks zhihui$ ls -l libconf1.a
-rw-r--r-- 1 zhihui staff 1624 Oct 25 17:36 libconf1.a
Scott-Grad-MacBook-Pro:benchmarks zhihui$ /usr/bin/ar t libconf1.a
__.SYMDEF SORTED
sizeof.o
Looks like it worked.
What do you have for:
echo $TMPDIR
ls -l libconf1.a
/usr/bin/ar t libconf1.a
TMPDIR=$PWD /usr/bin/ar t libconf1.a
Satish
On Fri, 26 Oct 2018, avatar wrote:
> As follow. Then, what I should do next?
>
>
> Scott-Grad-MacBook-Pro:benchmarks zhihui$ TMPDIR=$PWD
As follow. Then, what I should do next?
Scott-Grad-MacBook-Pro:benchmarks zhihui$ TMPDIR=$PWD /usr/bin/ar cr libconf1.a
sizeof.o
Scott-Grad-MacBook-Pro:benchmarks zhihui$
-- Original --
From: "Balay, Satish";;
Date: Oct 26, 2018
To:
How about:
TMPDIR=$PWD /usr/bin/ar cr libconf1.a sizeof.o
Satish
On Fri, 26 Oct 2018, avatar wrote:
> Scott-Grad-MacBook-Pro:benchmarks zhihui$ mpicc -c sizeof.c
> Scott-Grad-MacBook-Pro:benchmarks zhihui$ ls
> Index.c PetscGetCPUTime.c PetscMemcmp.c
>
Scott-Grad-MacBook-Pro:benchmarks zhihui$ mpicc -c sizeof.c
Scott-Grad-MacBook-Pro:benchmarks zhihui$ ls
Index.c PetscGetCPUTime.c PetscMemcmp.c
PetscTime.c benchmarkExample.py sizeof.c
Index.c.htmlPetscGetCPUTime.c.html
What about:
mpicc -c sizeof.c
/usr/bin/ar cr libconf1.a sizeof.o
Satish
On Fri, 26 Oct 2018, avatar wrote:
> I could not do all things you posted below. I get these:
>
>
> Scott-Grad-MacBook-Pro:petsc-3.8.3 zhihui$ cd src
> Scott-Grad-MacBook-Pro:src zhihui$ cd benchmarks/
>
I could not do all things you posted below. I get these:
Scott-Grad-MacBook-Pro:petsc-3.8.3 zhihui$ cd src
Scott-Grad-MacBook-Pro:src zhihui$ cd benchmarks/
Scott-Grad-MacBook-Pro:benchmarks zhihui$ mpicc -c sizeof.c
Scott-Grad-MacBook-Pro:benchmarks zhihui$ ls -l sizeof.o
-rw-r--r-- 1 zhihui
On Fri, 26 Oct 2018, avatar wrote:
> Hi Satish,
>
>
> Thank you very much for your quick response.
>
>
> The log file is as follow:
>
>>
Executing: /usr/bin/ar cr /tmp/petsc-mjVUVK/config.setCompilers/libconf1.a
/tmp/petsc-mjVUVK/config.setCompilers/conf1.o
Possible ERROR while running
Its best to stick with one list - so will follow up on petsc-maint.
Satish
On Fri, 26 Oct 2018, avatar wrote:
> Hi,
>
> When I try to configure PETSc to connect Matlab with the following command
> ./petsc-3.8.3/configure ??with-matlab
> , it prompts
>
Hi,
When I try to configure PETSc to connect Matlab with the following command
./petsc-3.8.3/configure ??with-matlab
, it prompts
===
Configuring PETSc to compile on your system
>> Ahh, thanks. I was missing the option " -dm_plex_gmsh_periodic “. But using
>> this option I now generate a segmentation fault error when calling VecView()
>> on the solution vector with vtk and hdf5 viewers. Any suggestions?
>>
> Small example? VTK is deprecated. HDF5 should work,
Did you forget to attach "The nice picture attached"
Stephen
> From: "Stefano Zampini"
> To: "petsc-maint"
> Cc: "imilian hartig" , "PETSc users list"
>
> Sent: Thursday, October 25, 2018 4:47:43 PM
> Subject: Re: [petsc-users] Periodic BC in petsc DMPlex / firedrake
> Opened the PR [
>
Opened the PR
https://bitbucket.org/petsc/petsc/pull-requests/1203/fix-dump-vtk-field-with-periodic-meshes/diff
Il giorno gio 25 ott 2018 alle ore 17:44 Matthew Knepley
ha scritto:
> Good catch Stefano.
>
> Matt
>
> On Thu, Oct 25, 2018 at 9:36 AM Stefano Zampini
> wrote:
>
>> Maybe this is
Good catch Stefano.
Matt
On Thu, Oct 25, 2018 at 9:36 AM Stefano Zampini
wrote:
> Maybe this is a fix
>
> diff --git a/src/dm/impls/plex/plexvtu.c b/src/dm/impls/plex/plexvtu.c
> index acdea12c2f..1a8bbada6a 100644
> --- a/src/dm/impls/plex/plexvtu.c
> +++ b/src/dm/impls/plex/plexvtu.c
> @@
> I actually use hybridization and I was reading the preprint "Algebraic
> Hybridization and Static Condensation with Application to Scalable H(div)
> Preconditioning" by Dobrev et al. ( https://arxiv.org/abs/1801.08914 )
> and they show that multigrid is optimal for the grad-div problem
>
Right now, one to four. I am just running some tests with small matrices.
Later on, I am planning to do large scale tests hopefully up to 1024
processes. I was worried that iteration numbers may get worse.
I actually use hybridization and I was reading the preprint "Algebraic
Hybridization and
How many processes (subdomains) are you using?
I would not say the number of iterations is bad, and it also seems to
plateau.
The grad-div problem is quite hard to be solved (unless you use
hybridization), you can really benefit from the "Neumann" assembly.
I believe you are using GMRES, as the
Matt,
you can reproduce it via
$ valgrind ./ex12 -quiet -run_type test -interpolate 1 -bc_type dirichlet
-petscspace_degree 1 -vec_view vtk:test.vtu:vtk_vtu -f
${PETSC_DIR}/share/petsc/datafiles/meshes/square_periodic.msh
-dm_plex_gmsh_periodic
Long time ago I added support for viewing meshes
No, the eigenvalue is around -15. I've tried KS and the number of
iterations differs in one when I change the number of MPI processes, which
seems fine for me. So, I'll see if this method is fine for my specific goal
or not, and I'll try to use. Thanks for the help.
El mié., 24 oct. 2018 a las
El mar., 23 oct. 2018 a las 13:53, Matthew Knepley ()
escribió:
> On Tue, Oct 23, 2018 at 6:24 AM Ale Foggia wrote:
>
>> Hello,
>>
>> I'm currently using Lanczos solver (EPSLANCZOS) to get the smallest real
>> eigenvalue (EPS_SMALLEST_REAL) of a Hermitian problem (EPS_HEP). Those are
>> the only
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