Re: [Libmesh-users] small doc and efficiency update for ex 3 and 4

[edgar <edg...@cr...>]

On 2021-06-18 21:45, John Peterson wrote:
> Your compiler flags are definitely far more advanced/aggressive than 
> mine,

I cannot take credit for that, really. I only modified the -O2 to -O3, 
made sure that -funroll_loops was there and customised to my processor 
(amdfam10). All the other flags come directly from the Makefile provided 
by libMesh.

> which are just on the default of -O2. However, I think what we should
> conclude from your results is that there is something slower than it 
> needs
> to be with DenseMatrix::resize(), not that we should move the 
> DenseMatrix
> creation/destruction inside the loop over elements. What I tried (see
> attached patch or the "dense_matrix_resize_no_virtual" branch in my 
> fork)
> is avoiding the virtual function call to DenseMatrix::zero() which is
> currently made from DenseMatrix::resize(). In my testing, this change 
> did
> not seem to make much of a difference but I'm curious about what you 
> would
> get with your compiler args, this patch, and the unpatched ex4.

There _is_ something consistently different for sure. I only ran the 
case with `mpirun -np 4' and `-n 40'. The difference of the sums of 
times is in the order of 1 second. For five tests of this size and my 
rather limited system, I would say that your change yields marginally 
faster computation, and should be used. In which case, my modifications 
should be avoided.

In the interest of completeness, I need to say that I had to rebuild 
libMesh, because of compilation errors. I don't quite remember what 
version it is right now, but it is not the updated master branch (due to 
some issues that I am having with my Internet connection). Although this 
may not affect the comparison, it should be noted.

The results are shown below and in examples/introduction/sums.org

#+name: tbl-results
#+caption: The first two columns correspond to the (patched) original 
code. The last pair are the results with my modification (also with 
patch). In each case, the first of the columns is alive time, and the 
second one is active time. Data was copied from the .bz2 files.
| 3.65205 |   1.292 | 3.63248 | 1.31057 |
| 4.82533 | 1.76303 | 5.31107 | 1.95794 |
| 5.05955 | 1.84457 | 5.26696 |   1.964 |
| 3.86126 | 1.40952 | 3.53834 | 1.29313 |
| 3.58892 | 1.30998 |   4.369 | 1.59834 |

#+caption: calculate the sums of each column
#+begin_src python :var data=tbl-results
   ex4_alive = sum((I[0] for I in data))
   ex4_active = sum((I[1] for I in data))
   ex4_mod_alive = sum((I[2] for I in data))
   ex4_mod_active = sum((I[3] for I in data))
   return [["ex4_alive", "ex4_active", "ex4_mod_alive", 
"ex4_mod_active"],
           None,
           [ex4_alive, ex4_active, ex4_mod_alive, ex4_mod_active]]
#+end_src

#+RESULTS:
| ex4_alive |         ex4_active |      ex4_mod_alive | ex4_mod_active |
|-----------+--------------------+--------------------+----------------|
|  20.98711 | 7.6190999999999995 | 22.117849999999997 |        8.12398 |