Hi Barry,
Another strange problem:
Currently I have PETSc-3.4.2 MPI version and PETSc-dev OpenMP version on
my computer, with different environment variable of PETSC_ARCH and
PETSC_DIR. Before installation of PETSc-dev OpenMP version, the
PETSc-3.4.2 MPI version works fine. But after installation of PETSc-dev
OpenMP version, the same problem exist in PETSc-3.4.2 MPI version if run
with 1 processor, but no problem with 2 or more processors.
Thanks,
Danyang
On 23/09/2013 12:01 PM, Danyang Su wrote:
Hi Barry,
Sorry I forgot the message in the previous email. It is still slow
when run without the "-threadcomm_type openmp -threadcomm_nthreads 1"
Thanks,
Danyang
On 23/09/2013 11:43 AM, Barry Smith wrote:
You did not answer my question from yesterday:
If you run the Openmp compiled version WITHOUT the
-threadcomm_nthreads 1
-threadcomm_type openmp
command line options is it still slow?
On Sep 23, 2013, at 1:33 PM, Danyang Su <[email protected]> wrote:
Hi Shri,
It seems that the problem does not result from the affinities
setting for threads. I have tried several settings, the threads are
set to different cores, but there is no improvement.
Here is the information of package, core and thread maps
OMP: Info #204: KMP_AFFINITY: decoding x2APIC ids.
OMP: Info #202: KMP_AFFINITY: Affinity capable, using global cpuid
leaf 11 info
OMP: Info #154: KMP_AFFINITY: Initial OS proc set respected:
{0,1,2,3,4,5,6,7,8,9,10,11}
OMP: Info #156: KMP_AFFINITY: 12 available OS procs
OMP: Info #157: KMP_AFFINITY: Uniform topology
OMP: Info #179: KMP_AFFINITY: 1 packages x 6 cores/pkg x 2
threads/core (6 total cores)
OMP: Info #206: KMP_AFFINITY: OS proc to physical thread map:
OMP: Info #171: KMP_AFFINITY: OS proc 0 maps to package 0 core 0
thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 1 maps to package 0 core 0
thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 2 maps to package 0 core 1
thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 3 maps to package 0 core 1
thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 4 maps to package 0 core 2
thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 5 maps to package 0 core 2
thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 6 maps to package 0 core 3
thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 7 maps to package 0 core 3
thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 8 maps to package 0 core 4
thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 9 maps to package 0 core 4
thread 1
OMP: Info #171: KMP_AFFINITY: OS proc 10 maps to package 0 core 5
thread 0
OMP: Info #171: KMP_AFFINITY: OS proc 11 maps to package 0 core 5
thread 1
OMP: Info #144: KMP_AFFINITY: Threads may migrate across 1 innermost
levels of machine
And here is the internal thread bounding with different kmp_affinity
settings:
1. KMP_AFFINITY=verbose,granularity=thread,compact
OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set
{0}
OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set
{1}
OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set
{2}
OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set
{3}
2. KMP_AFFINITY=verbose,granularity=fine,compact
OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set
{0}
OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set
{1}
OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set
{2}
OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set
{3}
3. KMP_AFFINITY=verbose,granularity=fine,compact,1,0
OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set
{0}
OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set
{2}
OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set
{4}
OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set
{6}
4. KMP_AFFINITY=verbose,scatter
OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set
{0,1}
OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set
{2,3}
OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set
{4,5}
OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set
{6,7}
5. KMP_AFFINITY=verbose,compact (For this setting, two threads are
assigned to the same core)
OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set
{0,1}
OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set
{0,1}
OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set
{2,3}
OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set
{2,3}
6. KMP_AFFINITY=verbose,granularity=core,compact (For this setting,
two threads are assigned to the same core)
OMP: Info #147: KMP_AFFINITY: Internal thread 0 bound to OS proc set
{0,1}
OMP: Info #147: KMP_AFFINITY: Internal thread 1 bound to OS proc set
{0,1}
OMP: Info #147: KMP_AFFINITY: Internal thread 2 bound to OS proc set
{2,3}
OMP: Info #147: KMP_AFFINITY: Internal thread 3 bound to OS proc set
{2,3}
The first 4 settings can assign threads to a distinct core, but the
problem is not solved.
Thanks,
Danyang
On 22/09/2013 8:00 PM, Shri wrote:
I think this is definitely an issue with setting the affinities for
threads, i.e., the assignment of threads to cores. Ideally each
thread should be assigned to a distinct core but in your case all
the 4 threads are getting pinned to the same core resulting in such
a massive slowdown. Unfortunately, the thread affinities for OpenMP
are set through environment variables. For Intel's OpenMP one needs
to define the thread affinities through the environment variable
KMP_AFFINITY. See this document here
http://software.intel.com/sites/products/documentation/studio/composer/en-us/2011Update/compiler_c/optaps/common/optaps_openmp_thread_affinity.htm.
Try setting the affinities via KMP_AFFINITY and let us know if it
works.
Shri
On Sep 21, 2013, at 11:06 PM, Danyang Su wrote:
Hi Shri,
Thanks for your info. It can work with the option -threadcomm_type
openmp. But another problem arises, as described as follows.
The sparse matrix is 53760*53760 with 1067392 non-zero entries.
If the codes is compiled using PETSc-3.4.2, it works fine, the
equations can be solved quickly and I can see the speedup. But if
the code is compiled using PETSc-dev with OpenMP option, it takes
a long time in solving the equations and I cannot see any speedup
when more processors are used.
For PETSc-3.4.2, run by "mpiexec -n 4 ksp_inhm_d -log_summary
log_mpi4_petsc3.4.2.log", the iteration and runtime are:
Iterations 6 time_assembly 0.4137E-01 time_ksp 0.9296E-01
For PETSc-dev, run by "mpiexec -n 1 ksp_inhm_d -threadcomm_type
openmp -threadcomm_nthreads 4 -log_summary
log_openmp_petsc_dev.log", the iteration and runtime are:
Iterations 6 time_assembly 0.3595E+03 time_ksp 0.2907E+00
Most of the time 'time_assembly 0.3595E+03' is spent on the
following codes
do i = istart, iend - 1
ii = ia_in(i+1)
jj = ia_in(i+2)
call MatSetValues(a, ione, i, jj-ii,
ja_in(ii:jj-1)-1, a_in(ii:jj-1), Insert_Values, ierr)
end do
The log files for both PETSc-3.4.2 and PETSc-dev are attached.
Is there anything wrong with my codes or with running option? The
above codes works fine when using MPICH.
Thanks and regards,
Danyang
On 21/09/2013 2:09 PM, Shri wrote:
There are three thread communicator types in PETSc. The default
is "no thread" which is basically a non-threaded version. The
other two types are "openmp" and "pthread". If you want to use
OpenMP then use the option -threadcomm_type openmp.
Shri
On Sep 21, 2013, at 3:46 PM, Danyang Su <[email protected]>
wrote:
Hi Barry,
Thanks for the quick reply.
After changing
#if defined(PETSC_HAVE_PTHREADCLASSES) || defined
(PETSC_HAVE_OPENMP)
to
#if defined(PETSC_HAVE_PTHREADCLASSES)
and comment out
#elif defined(PETSC_HAVE_OPENMP)
PETSC_EXTERN PetscStack *petscstack;
It can be compiled and validated with "make test".
But I still have questions on running the examples. After
rebuild the codes (e.g., ksp_ex2f.f), I can run it with "mpiexec
-n 1 ksp_ex2f", or "mpiexec -n 4 ksp_ex2f", or "mpiexec -n 1
ksp_ex2f -threadcomm_nthreads 1", but if I run it with "mpiexec
-n 1 ksp_ex2f -threadcomm_nthreads 4", there will be a lot of
error information (attached).
The codes is not modified and there is no OpenMP routines in it.
For the current development in my project, I want to keep the
OpenMP codes in calculating matrix values, but want to solve it
with PETSc (OpenMP). Is it possible?
Thanks and regards,
Danyang
On 21/09/2013 7:26 AM, Barry Smith wrote:
Danyang,
I don't think the || defined (PETSC_HAVE_OPENMP)
belongs in the code below.
/* Linux functions CPU_SET and others don't work if sched.h is
not included before
including pthread.h. Also, these functions are active only
if either _GNU_SOURCE
or __USE_GNU is not set (see /usr/include/sched.h and
/usr/include/features.h), hence
set these first.
*/
#if defined(PETSC_HAVE_PTHREADCLASSES) || defined
(PETSC_HAVE_OPENMP)
Edit include/petscerror.h and locate these lines and remove
that part and then rerun make all. Let us know if it works or
not.
Barry
i.e. replace
#if defined(PETSC_HAVE_PTHREADCLASSES) || defined
(PETSC_HAVE_OPENMP)
with
#if defined(PETSC_HAVE_PTHREADCLASSES)
On Sep 21, 2013, at 6:53 AM, Matthew Knepley
<[email protected]>
wrote:
On Sat, Sep 21, 2013 at 12:18 AM, Danyang Su
<[email protected]>
wrote:
Hi All,
I got error information in compiling petsc-dev with openmp in
cygwin. Before, I have successfully compiled petsc-3.4.2 and
it works fine.
The log files have been attached.
The OpenMP configure test is wrong. It clearly fails to find
pthread.h, but the test passes. Then in petscerror.h
we guard pthread.h using PETSC_HAVE_OPENMP. Can someone who
knows OpenMP fix this?
Matt
Thanks,
Danyang
--
What most experimenters take for granted before they begin
their experiments is infinitely more interesting than any
results to which their experiments lead.
-- Norbert Wiener
<error.txt>
<log_mpi4_petsc3.4.2.log><log_openmp_petsc_dev.log>
