Re: [petsc-users] HPCToolKit/HPCViewer on OS X

On Jan 13, 2016, at 9:17 PM, Griffith, Boyce Eugene mailto:boy...@email.unc.edu>> wrote: I see one hot spot: Here is with opt build *** WIDEN YOUR WINDOW TO 12

Re: [petsc-users] HPCToolKit/HPCViewer on OS X

Thanks! That worked for me. On Jan 13, 2016, at 10:05 PM, Justin Chang mailto:jychan...@gmail.com>> wrote: HPCToolkit for MacOSX doesn't require any installation. Just go to: http://hpctoolkit.org/download/hpcviewer/ and download this file: hpctraceviewer-5.4.2-r20160111-macosx.cocoa.x86_64.

Re: [petsc-users] Why use MATMPIBAIJ?

Okay that makes sense, thanks On Wed, Jan 13, 2016 at 10:12 PM, Barry Smith wrote: > > > On Jan 13, 2016, at 10:24 PM, Justin Chang wrote: > > > > Thanks Barry, > > > > 1) So for block matrices, the ja array is smaller. But what's the > "hardware" explanation for this performance improvement? D

Re: [petsc-users] HPCToolKit/HPCViewer on OS X

HPCToolkit for MacOSX doesn't require any installation. Just go to: http://hpctoolkit.org/download/hpcviewer/ and download this file: hpctraceviewer-5.4.2-r20160111-macosx.cocoa.x86_64.zip Important note: be sure to unzip the file via the terminal, not with Finder. It may screw up the GUI. On

[petsc-users] undefined reference error in make test

I’ve written a fortan code (F90) for domain decomposition.* I've specified **the paths of include files and libraries, but the compiler/linker still * *complained about undefined references.undefined reference to `vectorset_'undefined reference to `dmdagetlocalinfo_'*I’m attaching makefile and

Re: [petsc-users] osx configuration error

Thanks Satish, this worked. On Wed, Jan 13, 2016 at 9:49 AM, Satish Balay wrote: > > Executing: mpif90 -o > /var/folders/sw/67cq0mmx43g93vrb5xkf1j7cgn/T/petsc-2z06LS/config.setCompilers/conftest > > /var/folders/sw/67cq0mmx43g93vrb5xkf1j7cgn/T/petsc-2z06LS/config.setCompilers/c

Re: [petsc-users] HPCToolKit/HPCViewer on OS X

I see one hot spot: On Jan 14, 2016, at 12:12 AM, Bhalla, Amneet Pal S mailto:amne...@live.unc.edu>> wrote: ## ## # WARNING!!!

Re: [petsc-users] Why use MATMPIBAIJ?

> On Jan 13, 2016, at 10:24 PM, Justin Chang wrote: > > Thanks Barry, > > 1) So for block matrices, the ja array is smaller. But what's the "hardware" > explanation for this performance improvement? Does it have to do with spatial > locality where you are more likely to reuse data in that ja

Re: [petsc-users] HPCToolKit/HPCViewer on OS X

On Jan 13, 2016, at 6:22 PM, Matthew Knepley mailto:knep...@gmail.com>> wrote: Can you mail us a -log_summary for a rough cut? Sometimes its hard to interpret the data avalanche from one of those tools without a simple map. Does this indicate some hot spots? *

Re: [petsc-users] compiler error

On Wed, 13 Jan 2016, Gideon Simpson wrote: > I haven’t seen this before: > > /mnt/HA/opt/openmpi/intel/2015/1.8.1-mlnx-ofed/bin/mpicc -o fixed_batch.o -c > -fPIC -wd1572 -g -I/home/simpson/software/petsc/include > -I/home/simpson/software/petsc/arch-linux2-c-debug/include > -I/mnt/HA/opt/op

[petsc-users] compiler error

I haven’t seen this before: /mnt/HA/opt/openmpi/intel/2015/1.8.1-mlnx-ofed/bin/mpicc -o fixed_batch.o -c -fPIC -wd1572 -g -I/home/simpson/software/petsc/include -I/home/simpson/software/petsc/arch-linux2-c-debug/include -I/mnt/HA/opt/openmpi/intel/2015/1.8.1-mlnx-ofed/include -Wall `pwd`/

Re: [petsc-users] Why use MATMPIBAIJ?

Thanks Barry, 1) So for block matrices, the ja array is smaller. But what's the "hardware" explanation for this performance improvement? Does it have to do with spatial locality where you are more likely to reuse data in that ja array, or does it have to do with the fact that loading/storing small

Re: [petsc-users] Why use MATMPIBAIJ?

> On Jan 13, 2016, at 9:57 PM, Justin Chang wrote: > > Hi all, > > 1) I am guessing MATMPIBAIJ could theoretically have better performance than > simply using MATMPIAIJ. Why is that? Is it similar to the reasoning that > block (dense) matrix-vector multiply is "faster" than simple matrix-vect

[petsc-users] Why use MATMPIBAIJ?

Hi all, 1) I am guessing MATMPIBAIJ could theoretically have better performance than simply using MATMPIAIJ. Why is that? Is it similar to the reasoning that block (dense) matrix-vector multiply is "faster" than simple matrix-vector? 2) I am looking through the manual and online documentation and

Re: [petsc-users] Difference between Block Jacobi and ILU?

Thanks Satish, And yes I meant sequentially. On Wed, Jan 13, 2016 at 8:26 PM, Satish Balay wrote: > On Wed, 13 Jan 2016, Justin Chang wrote: > > > Hi all, > > > > What exactly is the difference between these two preconditioners? When I > > use them to solve a Galerkin finite element poisson pro

Re: [petsc-users] Difference between Block Jacobi and ILU?

On Wed, 13 Jan 2016, Justin Chang wrote: > Hi all, > > What exactly is the difference between these two preconditioners? When I > use them to solve a Galerkin finite element poisson problem, I get the > exact same performance (iterations, wall-clock time, etc). you mean - when you run sequential

[petsc-users] Difference between Block Jacobi and ILU?

Hi all, What exactly is the difference between these two preconditioners? When I use them to solve a Galerkin finite element poisson problem, I get the exact same performance (iterations, wall-clock time, etc). Only thing is I can't seem to use ILU in parallel though. Thanks, Justin

Re: [petsc-users] [petsc-maint] HPCToolKit/HPCViewer on OS X

The Instruments tool on the Mac, part of Xcode is trivial to use (you don't need to use Xcode GUI to build) and seems to provide useful information. Barry > On Jan 13, 2016, at 8:22 PM, Matthew Knepley wrote: > > On Wed, Jan 13, 2016 at 8:01 PM, Bhalla, Amneet Pal S > wrote: > > Hi Fo

Re: [petsc-users] HPCToolKit/HPCViewer on OS X

On Wed, Jan 13, 2016 at 8:01 PM, Bhalla, Amneet Pal S wrote: > > Hi Folks, > > I am trying to profile my application code that uses a lot of PETSc > solvers. I am running applications on OS X - Yosemite. I am thinking > of using HPCToolKit for the purpose, but could not find a dmg package for > t

[petsc-users] HPCToolKit/HPCViewer on OS X

Hi Folks, I am trying to profile my application code that uses a lot of PETSc solvers. I am running applications on OS X - Yosemite. I am thinking of using HPCToolKit for the purpose, but could not find a dmg package for that. I have access to a remote linux machine that has HPCToolkit and HPCV

Re: [petsc-users] SNES NEWTONLS serial vs. parallel

OK, will do, thanks. David On Wed, Jan 13, 2016 at 4:05 PM, Barry Smith wrote: > > Since you are using a direct solver almost for sure a bug in your > parallel function or parallel Jacobian. > >Try -snes_mf_operator try -snes_fdtry -snes_type test as three > different approaches

Re: [petsc-users] SNES NEWTONLS serial vs. parallel

Since you are using a direct solver almost for sure a bug in your parallel function or parallel Jacobian. Try -snes_mf_operator try -snes_fdtry -snes_type test as three different approaches to see what is going on. Barry > On Jan 13, 2016, at 2:51 PM, David Knezevic > wrote:

Re: [petsc-users] SNES NEWTONLS serial vs. parallel

Oops! I pasted the wrong text for the serial case. The correct text is below: *Serial case:* NL step 0, |residual|_2 = 4.714515e-02 Line search: gnorm after quadratic fit 7.862867755130e-02 Line search: Cubically determined step, current gnorm 4.663945044088e-02 lambda=1.42765492233

[petsc-users] SNES NEWTONLS serial vs. parallel

I'm using NEWTONLS (with mumps for the linear solves) to do a nonlinear PDE solve. It converges well when I use 1 core. When I use 2 or more cores, the line search stagnates. I've pasted the output of -snes_linesearch_monitor below in these two cases. I was wondering if this implies that I must ha

Re: [petsc-users] ODE Solver on multiple cores

If x is just a scalar, it would not be a surprise that the code does not run in parallel. If x is a vector, you need a DM object to handle the decomposition. Hong On Jan 13, 2016, at 1:13 PM, Hasan, Fahad wrote: > Hello, > > I have written a code to solve a simple differential equation (x’’

Re: [petsc-users] ODE Solver on multiple cores

Likely there is something wrong with the IFunction or RHSFunction or their Jacobians that you provide in parallel. For the example you are running the easiest way to manage the parallelism of the data is with a DMDACreate1d(). Otherwise you need to manage the ghost point communication yourse

Re: [petsc-users] ODE Solver on multiple cores

Fahad: Run your code with '-ts_view' to see what solvers being used for sequential and parallel runs. Hong Hello, > > > > I have written a code to solve a simple differential equation (x’’+x’+6x=0 > with initial values, x(0)=2, x’(0)=3). It works well on a single core and > produces result close

[petsc-users] ODE Solver on multiple cores

Hello, I have written a code to solve a simple differential equation (x''+x'+6x=0 with initial values, x(0)=2, x'(0)=3). It works well on a single core and produces result close to theoretical answer but whenever I am trying to run the same code on multiple cores, I am getting incorrect results

Re: [petsc-users] osx configuration error

Executing: mpif90 -o /var/folders/sw/67cq0mmx43g93vrb5xkf1j7cgn/T/petsc-2z06LS/config.setCompilers/conftest /var/folders/sw/67cq0mmx43g93vrb5xkf1j7cgn/T/petsc-2z06LS/config.setCompilers/conftest.o Testing executable /var/folders/sw/67cq0mmx43g93vrb5xkf1j7cgn/T/petsc-2z0

[petsc-users] The 7th Annual Scientific Software Days Conference

The 7th Annual Scientific Software Days Conference (SSD) targets users and developers of scientific software. The conference will be held at the University of Texas at Austin Thursday Feb 25 - Friday Feb 26, 2016 and focuses on two themes: a) sharing best practices acr

Re: [petsc-users] error on MatZeroRowsColumns

On Wed, Jan 13, 2016 at 3:34 AM, Hoang Giang Bui wrote: > Dear PETSc developers > > I got an error with MatZeroRowsColumns, which said there was one missing > diagonal entries > > This is the full log message that I got: > > Mat Object: 2 MPI processes > type: mpiaij > rows=41064, cols=41064,

Re: [petsc-users] osx configuration error

On Tue, Jan 12, 2016 at 6:31 PM, Satish Balay wrote: > > 'file' object has no attribute 'getvalue' File > "/Users/markadams/Codes/petsc/config/configure.py", line 363, in > petsc_configure > > Hm - have to figure this one out - but the primary issue is: > > > stderr: > > gfortran: warning: could

[petsc-users] error on MatZeroRowsColumns

Dear PETSc developers I got an error with MatZeroRowsColumns, which said there was one missing diagonal entries This is the full log message that I got: Mat Object: 2 MPI processes type: mpiaij rows=41064, cols=41064, bs=4 total: nonzeros=5.66069e+06, allocated nonzeros=1.28112e+07 total