Merged branch into next for testing
> On Mar 1, 2016, at 11:18 AM, Hong Zhang <[email protected]> wrote:
>
> Hi Barry,
>
> Actually the TSTrajectory object can save both the solution and the
> corresponding time information into binary files. Although it is designed
> specifically for adjoint checkpointing, it does have the side benefit to
> assist in visualization of simulation trajectories. For adjoint
> checkpointing, not only solution is saved, but also stage values are saved.
> So I created a new TSTrajectory type particularly for visualization purpose,
> which can be access at my branch hongzh/tstrajectory_visualization.
>
> One can enable this feature using the command line options
>
> -ts_save_trajectory 1 -tstrajectory_type visualization
>
> The full trajectory will be saved into a folder with multiple files, one file
> corresponding to one time step. Then we can use a MATLAB script, such as
> PetscBinaryRead.m, to read these binary files. But the default script coming
> with PETSc needs to be modified a little bit. Because the trajectory is
> always saved as a solution vector, followed by a PetscReal variable, I
> suggest to use the following code in MATLAB:
>
> if header == 1211214 % Petsc Vec Object
> %% Read state vector
> m = double(read(fd,1,indices));
> x = zeros(m,1);
> v = read(fd,m,precision);
> x(:) = v;
> %% Read time
> t = read(fd,1,precision);
> end
>
> Shri (copied in this email) has successfully used this approach to do
> visualization. Perhaps we can include this feature in the new release if it
> is useful to some users.
>
> Hong
>
>
>> On Mar 1, 2016, at 10:32 AM, Barry Smith <[email protected]> wrote:
>>
>>>
>>> On Mar 1, 2016, at 12:39 AM, Ed Bueler <[email protected]> wrote:
>>>
>>> Barry --
>>>
>>> Will try it.
>>>
>>>> ... since, presumably, other more powerful IO tools exist that would be
>>>> used for "real" problems?
>>>
>>> I know there are tools for snapshotting from PETSc, e.g. VecView to .vtk.
>>> In fact petsc binary seems fairly convenient for that. On the other hand,
>>> I am not sure I've ever done anything "real". ;-)
>>>
>>> Anyone out there: Are there a good *convenient* tools for saving
>>> space/time-series (= movies) from PETSc TS? I want to add frames and
>>> movies from PETSc into slides, etc. I can think of NetCDF but it seems
>>> not-very-convenient, and I am worried not well-supported from PETSc. Is
>>> setting up TS with events (=TSSetEventMonitor()) and writing separate
>>> snapshot files the preferred scalable usage, despite the extra effort
>>> compared to "-ts_monitor_solution binary:foo.dat"?
>>
>> Ed,
>>
>> As I said in my previous email since we don't have a way of indicating
>> plain double precision numbers in our binary files it is not possible to put
>> both the vectors and the time steps in the same file without augmenting our
>> file format.
>>
>> Barry
>>
>>
>>
>>>
>>> Ed
>>>
>>>
>>> On Mon, Feb 29, 2016 at 8:53 PM, Barry Smith <[email protected]> wrote:
>>>
>>> Ed,
>>>
>>> I have added a branch barry/feature-ts-monitor-binary that supports
>>> -ts_monitor binary:timesteps that will store in simple binary format each
>>> of the time steps associated with each solution. This in conjugation with
>>> -ts_monitor_solution binary:solutions will give you two files you can read
>>> in. But note that timesteps is a simple binary file of double precision
>>> numbers you should read in directly in python, you cannot use
>>> PetscBinaryIO.py which is what you will use to read in the solutions file.
>>>
>>> Barry
>>>
>>> Currently PETSc has a binary file format where we can save Vec, Mat, IS,
>>> each is marked with a type id for PetscBinaryIO.py to detect, we do not
>>> have type ids for simple double precision numbers or arrays of numbers.
>>> This is why I have no way of saving the time steps in a way that
>>> PetscBinaryIO.py could read them in currently. I don't know how far we want
>>> to go in "spiffing up" the PETSc binary format to do more elaborate things
>>> since, presumably, other more power IO tools exist that would be used for
>>> "real" problems?
>>>
>>>
>>>> On Feb 29, 2016, at 3:24 PM, Ed Bueler <[email protected]> wrote:
>>>>
>>>> Dear PETSc --
>>>>
>>>> I have a short C ode code that uses TS to solve y' = g(t,y) where y(t)
>>>> is a 2-dim'l vector. My code defaults to -ts_type rk so it does adaptive
>>>> time-stepping; thus using -ts_monitor shows times at stdout:
>>>>
>>>> $ ./ode -ts_monitor
>>>> solving from t0 = 0.000 with initial time step dt = 0.10000 ...
>>>> 0 TS dt 0.1 time 0.
>>>> 1 TS dt 0.170141 time 0.1
>>>> 2 TS dt 0.169917 time 0.270141
>>>> 3 TS dt 0.171145 time 0.440058
>>>> 4 TS dt 0.173931 time 0.611203
>>>> 5 TS dt 0.178719 time 0.785134
>>>> 6 TS dt 0.0361473 time 0.963853
>>>> 7 TS dt 0.188252 time 1.
>>>> error at tf = 1.000 : |y-y_exact|_inf = 0.000144484
>>>>
>>>> I want to output the trajectory in PETSc binary and plot it in python
>>>> using bin/PetscBinaryIO.py. Clearly I need the times shown above to do
>>>> that.
>>>>
>>>> Note "-ts_monitor_solution binary:XX" gives me a binary file with only y
>>>> values in it, but not the corresponding times.
>>>>
>>>> My question is, how to get those times in either the same binary file
>>>> (preferred) or separate binary files? I have tried
>>>>
>>>> $ ./ode -ts_monitor binary:foo.dat # invalid
>>>> $ ./ode -ts_monitor_solution binary:bar.dat # no t in file
>>>> $ ./ode -ts_monitor_solution binary:baz.dat -ts_save_trajectory # no t
>>>> in file
>>>>
>>>> without success. (I am not sure what the boolean option
>>>> -ts_save_trajectory does, by the way.)
>>>>
>>>> Thanks!
>>>>
>>>> Ed
>>>>
>>>> PS Sorry if this is a "RTFM" question, but so far I can't find the
>>>> documentation.
>>>>
>>>>
>>>> --
>>>> Ed Bueler
>>>> Dept of Math and Stat and Geophysical Institute
>>>> University of Alaska Fairbanks
>>>> Fairbanks, AK 99775-6660
>>>> 301C Chapman and 410D Elvey
>>>> 907 474-7693 and 907 474-7199 (fax 907 474-5394)
>>>
>>>
>>>
>>>
>>> --
>>> Ed Bueler
>>> Dept of Math and Stat and Geophysical Institute
>>> University of Alaska Fairbanks
>>> Fairbanks, AK 99775-6660
>>> 301C Chapman and 410D Elvey
>>> 907 474-7693 and 907 474-7199 (fax 907 474-5394)
>
