[petsc-dev] configuring hypre on batch system

Fri Jan 9 12:44:30 CST 2015

The values need to be comma separated. You can specify the affinities in different ways as described in the PetscOptionsGetIntArray docs. http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PetscOptionsGetIntArray.html.

I'll fix the docs for threadcomm.

From: Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>>
Date: Fri, 9 Jan 2015 13:28:48 -0500
To: Shri <abhyshr at mcs.anl.gov<mailto:abhyshr at mcs.anl.gov>>
Cc: barry smith <bsmith at mcs.anl.gov<mailto:bsmith at mcs.anl.gov>>, petsc-dev mailing list <petsc-dev at mcs.anl.gov<mailto:petsc-dev at mcs.anl.gov>>
Subject: Re: [petsc-dev] configuring hypre on batch system

OK, threads seem to be working as advertised but I still get this error with

-threadcomm_nthreads 8
-threadcomm_affinities 0 1 2 3 4 5 6 7

I'm guessing it must do the right thing.

Thanks again,
Mark

SOLVER_INIT: make partitioning with    2872/   3705 real vertices
[10]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[10]PETSC ERROR: Nonconforming object sizes
[10]PETSC ERROR: Must set affinities for all threads, Threads = 8, Core affinities set = 1
[10]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[10]PETSC ERROR: Petsc Development GIT revision: v3.5.2-1345-g927ffcc  GIT Date: 2015-01-08 16:04:39 -0700
[10]PETSC ERROR: ./xgc2 on a arch-titan-opt-pgi named nid02295 by adams Fri Jan  9 13:20:52 2015
[10]PETSC ERROR: Configure options --COPTFLAGS="-mp -fast" --CXXOPTFLAGS="-mp -fast" --FOPTFLAGS="-mp -fast" --with-threadcomm --with-pthreadclasses --with-openmp --download-hypre --download-metis --download-parmetis --with-cc=cc --with-clib-autodetect=0 --with-cxx=CC --with-cxxlib-autodetect=0 --with-fc=ftn --with-fortranlib-autodetect=0 --with-shared-libraries=0 --known-mpi-shared-libraries=1 --with-x=0 --with-debugging=0 PETSC_ARCH=arch-titan-opt-pgi PETSC_DIR=/lustre/atlas2/env003/scratch/adams/petsc2
[10]PETSC ERROR: #1 PetscThreadCommSetAffinities() line 431 in /lustre/atlas2/env003/scratch/adams/petsc2/src/sys/threadcomm/interface/threadcomm.c
[10]PETSC ERROR: #2 PetscThreadCommWorldInitialize() line 1231 in /lustre/atlas2/env003/scratch/adams/petsc2/src/sys/threadcomm/interface/threadcomm.c
[10]PETSC ERROR: #3 PetscGetThreadCommWorld() line 82 in /lustre/atlas2/env003/scratch/adams/petsc2/src/sys/threadcomm/interface/threadcomm.c
[10]PETSC ERROR: #4 PetscCommGetThreadComm() line 117 in /lustre/atlas2/env003/scratch/adams/petsc2/src/sys/threadcomm/interface/threadcomm.c
[10]PETSC ERROR: #5 PetscCommDuplicate() line 195 in /lustre/atlas2/env003/scratch/adams/petsc2/src/sys/objects/tagm.c
[10]PETSC ERROR: #6 PetscHeaderCreate_Private() line 59 in /lustre/atlas2/env003/scratch/adams/petsc2/src/sys/objects/inherit.c

On Fri, Jan 9, 2015 at 12:25 AM, Abhyankar, Shrirang G. <abhyshr at mcs.anl.gov<mailto:abhyshr at mcs.anl.gov>> wrote:
Mark,
  The input for -threadcomm_affinities are the processor numbers

So -threadcomm_nthreads 4
     -threadcomm_affinities 0 1 2 3

will pin the 4 threads to processors 0,1,2,3. Unfortunately, there is no standardization of processor number mapping on physical and/or logical cores (it is decided by the OS I think). For example, on one node with two quad-core CPUs (total 8 processors, no hyperthreading), the 1st CPU may have processor numbers 0,1,3,5, while the other 2,4,6,8. On another node with similar hardware, the processor numbers may be 0,1,2,3 on the 1st CPU and 4,5,6,7 on the second. Hence, tools like likwid or hwloc are very helpful for getting the hardware layout. You may also obtain this info by looking at /proc/cupinfo on linux.

Shri
From: Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>>
Date: Thu, 8 Jan 2015 21:43:30 -0500
To: barry smith <bsmith at mcs.anl.gov<mailto:bsmith at mcs.anl.gov>>
Cc: petsc-dev mailing list <petsc-dev at mcs.anl.gov<mailto:petsc-dev at mcs.anl.gov>>
Subject: Re: [petsc-dev] configuring hypre on batch system

> -threadcomm_affinities 0 1 2 3 4 5 6 7  ?????

I    don't know what the flag is here

Neither do I.  The web page http://www.mcs.anl.gov/petsc/features/threads.html says:

  *
-threadcomm_affinities <list_of_affinities>: Sets the core affinities of threads

I'm not sure what to put here ...

> -threadcomm_type openmp
>
> Then would I get threaded MatVec and other CG + MG stuff?  I know this will not be faster but I just need data to corroborate what we all know.  And I don't care about setup.

  Depends on the smoother, we don't have any threaded SOR, if you using Jacobi + Cheyby it will be threaded.

Oh right, thanks,

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20150109/ef958099/attachment.html>