[petsc-dev] Request for comments on paper on PETSc TS

[Karl Rupp]

Hi,

thanks, that's a nice manuscript! I like the general setup and flow of 
discussion. Here are a couple of further comments; feel free to consider 
or ignore as you see fit:

Page 1: The references to MATLAB and NAG are incomplete, as they only 
show the year. Instead of "MATLAB [2014]" it should be something like 
"MATLAB [MATLAB 2014]" in order to be consistent with other references. 
Compare also with the chemkin reference on page 25.

Page 2: Consider removing the sentence "The document is organized as 
follows."

Page 3: Finish item "XXXSetUp(...) ... to be used" with a dot like for 
the other items in the list.

Page 4: (shift) is a somewhat ugly notation, because the parentheses are 
also used for mathematical expressions. Consider "[shift]" as an 
alternative.

Page 4: Swap order of the expressions (shift)F_{\dot u^n}(...) and 
F_{u^n}(...) in order to match the order used in the first line of the 
page: F_u + (shift)F_{\dot u}

Page 4: The sentence "For example, the backward Euler method \dot{u}^n = 
(u^n - u^{n-1})/\Delta t." is not a complete sentence.

Page 5/6: The code listing may benefit from more explanations, 
especially for readers who are not familiar with PETSc.

Page 7: The opening sentence "Oregonator: stiff ..." is not a full sentence.

Page 7/8: Again, a discussion of the code example is desirable.

Page 11: The table heading for Table 2 is too generic and does not 
properly explain the table content. Also, a table header like for Table 
1 should be added.

Page 12: Consider rotating Table 3 by 90 degrees and make it a full page 
table. This way the columns "Embed.", "Dense Output" and "Remarks" can 
be integrated. Also, prssp2 should have an entry in column 'SA'.

Page 14: Consider the same tweaks to Table 4 as for Table 3.

Page 13-16: The code listing is fairly heavy. Consider a reduction to 
the relevant parts. More importantly: Explain what is going on: Which 
PDE is solved ("a reaction-diffusion equation" is too vague), how are 
things discretized, etc.

Page 17: Replace "... registered vis the PETSc API." by "... registered 
via the PETSc API."

Page 17: Add blank after "estimation" in Table 5.

Page 18: Replace "... with adjoint method" by "... with the adjoint method".

Page 18: Replace "The features of PETSc adjoint solver" by "The features 
of the PETSc adjoint solver"

Page 19: "The paper [Marin et al. 2017] contains ..." is not a very 
elegant formulation. Consider to reformulate the sentence to something 
like "Details on using the infrastructure discussed here for solving 
PDE-constrained optimization problems utilizing the spectral element 
method can be found in the literature [Marin et al. 2017]."

Page 20: 'TSSetCostIntegrand()' is not formatted correctly.

Page 20: "apporach" -> "approach"

Page 21: "Figure 4 presents ..." should be supplemented by further 
explanations of the bouncing ball example, e.g.: Where does the 
event-handling kick in? What would happen without proper event handling? 
How much effort is required to set this up?
This would also convert an unpleasant one-sentence paragraph into a more 
pleasant multi-sentence paragraph.

Page 22: Consider rephrasing "Often users of ODE solver packages do not 
know ..." into "Users of ODE solver packages often do not know ..."

Page 22: Replace "... by the PETSc libraries" by "... by PETSc."

Page 23: Explain the TSView() output.

Page 25: Here I noticed the spelling "time-step". In earlier parts of 
the paper it was spelled "timestep". Please unify.

Page 26: Explain the code listing.

Page 26: A conclusion should be added, summarizing the paper and 
outlining the potential impact of having TS available for tacking 
problems in CSE.

References: Some entries contain full first names, others only the first 
letter. Please unify. Similarly, check for consistent capitalization of 
titles, e.g. "Using PETSc to Develop Scalable Applications ..." vs. 
"Evaluation of overlapping restricted additive ..."

Best regards,
Karli




On 02/19/2018 10:49 PM, Smith, Barry F. wrote:
> 
> 
>     PETSc developers,
> 
>       We have recently completed a draft manuscript on the PETSc TS 
> component, that includes discussion of adjoints and forward 
> sensitivities. It is attached. We'd appreciate any feed back on the 
> manuscript.
> 
>      Thanks
> 
>       Barry
> 
> 
> 
>