<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">On 14 July 2016 at 01:07, frank <span dir="ltr"><<a href="mailto:hengjiew@uci.edu" target="_blank">hengjiew@uci.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Dave,<br>
<br>
Sorry for the late reply.<br>
Thank you so much for your detailed reply.<br>
<br>
I have a question about the estimation of the memory usage. There
are 4223139840 allocated non-zeros and 18432 MPI processes. Double
precision is used. So the memory per process is:<br>
4223139840 * 8bytes / 18432 / 1024 / 1024 = 1.74M ? <br>
Did I do sth wrong here? Because this seems too small.<br></div></blockquote><div><br></div><div>No - I totally f***ed it up. You are correct. That'll teach me for fumbling around with my iphone calculator and not using my brain. (Note that to convert to MB just divide by 1e6, not 1024^2 - although I apparently cannot convert between units correctly....)</div><div><br></div><div>From the PETSc objects associated with the solver, It looks like it _should_ run with 2GB per MPI rank. Sorry for my mistake. Possibilities are: somewhere in your usage of PETSc you've introduced a memory leak; PETSc is doing a huge over allocation (e.g. as per our discussion of MatPtAP); or in your application code there are other objects you have forgotten to log the memory for.</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
<br>
I am running this job on <a href="https://bluewaters.ncsa.illinois.edu/user-guide" target="_blank">Bluewater</a> </div></blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
I am using the 7 points FD stencil in 3D. <br></div></blockquote><div><br></div><div>I thought so on both counts.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
<br>
I apologize that I made a stupid mistake in computing the memory per
core. My settings render each core can access only 2G memory on
average instead of 8G which I mentioned in previous email. I re-run
the job with 8G memory per core on average and there is no "Out Of
Memory" error. I would do more test to see if there is still some
memory issue.<br></div></blockquote><div><br></div><div>Ok. I'd still like to know where the memory was being used since my estimates were off.</div><div><br></div><div><br></div><div>Thanks,</div><div> Dave</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
<br>
Regards,<br>
Frank<div><div class="h5"><br>
<br>
<br>
<div>On 07/11/2016 01:18 PM, Dave May wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Frank,<br>
<br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 11 July 2016 at 19:14, frank <span dir="ltr"><<a href="mailto:hengjiew@uci.edu" target="_blank">hengjiew@uci.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote">
<div> Hi Dave,<br>
<br>
I re-run the test using bjacobi as the preconditioner on
the coarse mesh of telescope. The Grid is 3072*256*768
and process mesh is 96*8*24. The petsc option file is
attached.<br>
I still got the "Out Of Memory" error. The error
occurred before the linear solver finished one step. So
I don't have the full info from ksp_view. The info from
ksp_view_pre is attached.</div>
</blockquote>
<div><br>
</div>
<div>Okay - that is essentially useless (sorry)<br>
</div>
<div> </div>
<blockquote class="gmail_quote">
<div> <br>
It seems to me that the error occurred when the
decomposition was going to be changed.<br>
</div>
</blockquote>
<div><br>
</div>
<div>Based on what information?<br>
</div>
<div>Running with -info would give us more clues, but will
create a ton of output.<br>
</div>
<div>Please try running the case which failed with -info<br>
</div>
<div> </div>
<blockquote class="gmail_quote">
<div> I had another test with a grid of 1536*128*384 and
the same process mesh as above. There was no error. The
ksp_view info is attached for comparison.<br>
Thank you.</div>
</blockquote>
<div><br>
</div>
<div><br>
[3] Here is my crude estimate of your memory usage. <br>
I'll target the biggest memory hogs only to get an order
of magnitude estimate<br>
<br>
<div>* The Fine grid operator contains 4223139840
non-zeros --> 1.8 GB per MPI rank assuming double
precision.<br>
</div>
<div>The indices for the AIJ could amount to another 0.3
GB (assuming 32 bit integers)<br>
</div>
<div><br>
* You use 5 levels of coarsening, so the other operators
should represent (collectively) <br>
2.1 / 8 + 2.1/8^2 + 2.1/8^3 + 2.1/8^4 ~ 300 MB per MPI
rank on the communicator with 18432 ranks.<br>
</div>
<div>The coarse grid should consume ~ 0.5 MB per MPI rank
on the communicator with 18432 ranks.</div>
<div><br>
* You use a reduction factor of 64, making the new
communicator with 288 MPI ranks. <br>
PCTelescope will first gather a temporary matrix
associated with your coarse level operator assuming a
comm size of 288 living on the comm with size 18432. <br>
This matrix will require approximately 0.5 * 64 = 32 MB
per core on the 288 ranks. <br>
This matrix is then used to form a new MPIAIJ matrix on
the subcomm, thus require another 32 MB per rank. <br>
The temporary matrix is now destroyed.<br>
</div>
<div><br>
* Because a DMDA is detected, a permutation matrix is
assembled. <br>
This requires 2 doubles per point in the DMDA. <br>
Your coarse DMDA contains 92 x 16 x 48 points. <br>
Thus the permutation matrix will require < 1 MB per
MPI rank on the sub-comm.<br>
<br>
</div>
<div>* Lastly, the matrix is permuted. This uses
MatPtAP(), but the resulting operator will have the same
memory footprint as the unpermuted matrix (32 MB). At
any stage in PCTelescope, only 2 operators of size 32 MB
are held in memory when the DMDA is provided.<br>
</div>
<div><br>
</div>
<div>From my rough estimates, the worst case memory foot
print for any given core, given your options is
approximately <br>
</div>
<div>2100 MB + 300 MB + 32 MB + 32 MB + 1 MB = 2465 MB<br>
</div>
<div>This is way below 8 GB.<br>
<br>
Note this estimate completely ignores:<br>
(1) the memory required for the restriction operator, <br>
(2) the potential growth in the number of non-zeros per
row due to Galerkin coarsening (I wished -ksp_view_pre
reported the output from MatView so we could see the
number of non-zeros required by the coarse level
operators)<br>
</div>
<div>(3) all temporary vectors required by the CG solver,
and those required by the smoothers.<br>
</div>
<div>(4) internal memory allocated by MatPtAP<br>
</div>
<div>(5) memory associated with IS's used within
PCTelescope<br>
</div>
<div><br>
</div>
So either I am completely off in my estimates, or you have
not carefully estimated the memory usage of your
application code. Hopefully others might examine/correct
my rough estimates<br>
</div>
<div>
<div><br>
Since I don't have your code I cannot access the latter.<br>
Since I don't have access to the same machine you are
running on, I think we need to take a step back.<br>
</div>
<br>
[1] What machine are you running on? Send me a URL if its
available<br>
</div>
<div><br>
[2] What discretization are you using? (I am guessing a
scalar 7 point FD stencil)<br>
</div>
<div>If it's a 7 point FD stencil, we should be able to
examine the memory usage of your solver configuration
using a standard, light weight existing PETSc example, run
on your machine at the same scale. <br>
</div>
<div>This would hopefully enable us to correctly evaluate
the actual memory usage required by the solver
configuration you are using.<br>
</div>
<div><br>
</div>
<div>Thanks,<br>
</div>
<div> Dave<br>
</div>
<div> </div>
<blockquote class="gmail_quote">
<div><span><br>
<br>
Frank</span>
<div>
<div><br>
<br>
<br>
<br>
<div>On 07/08/2016 10:38 PM, Dave May wrote:<br>
</div>
<blockquote type="cite"><br>
<br>
On Saturday, 9 July 2016, frank <<a></a><a href="mailto:hengjiew@uci.edu" target="_blank">hengjiew@uci.edu</a>>
wrote:<br>
<blockquote class="gmail_quote">Hi Barry and Dave,<br>
<br>
Thank both of you for the advice.<br>
<br>
@Barry<br>
I made a mistake in the file names in last
email. I attached the correct files this time.<br>
For all the three tests, 'Telescope' is used as
the coarse preconditioner.<br>
<br>
== Test1: Grid: 1536*128*384, Process Mesh:
48*4*12<br>
Part of the memory usage: Vector 125
124 3971904 0.<br>
Matrix 101 101 9462372 0<br>
<br>
== Test2: Grid: 1536*128*384, Process Mesh:
96*8*24<br>
Part of the memory usage: Vector 125
124 681672 0.<br>
Matrix 101 101 1462180 0.<br>
<br>
In theory, the memory usage in Test1 should be 8
times of Test2. In my case, it is about 6 times.<br>
<br>
== Test3: Grid: 3072*256*768, Process Mesh:
96*8*24. Sub-domain per process: 32*32*32<br>
Here I get the out of memory error.<br>
<br>
I tried to use -mg_coarse jacobi. In this way, I
don't need to set -mg_coarse_ksp_type and
-mg_coarse_pc_type explicitly, right?<br>
The linear solver didn't work in this case.
Petsc output some errors.<br>
<br>
@Dave<br>
In test3, I use only one instance of
'Telescope'. On the coarse mesh of 'Telescope',
I used LU as the preconditioner instead of SVD.<br>
If my set the levels correctly, then on the last
coarse mesh of MG where it calls 'Telescope',
the sub-domain per process is 2*2*2.<br>
On the last coarse mesh of 'Telescope', there is
only one grid point per process.<br>
I still got the OOM error. The detailed petsc
option file is attached.</blockquote>
<div><br>
</div>
<div>Do you understand the expected memory usage
for the particular parallel LU implementation
you are using? I don't (seriously). Replace LU
with bjacobi and re-run this test. My point
about solver debugging is still valid. </div>
<div><br>
</div>
<div>And please send the result of KSPView so we
can see what is actually used in the
computations</div>
<div><br>
</div>
<div>Thanks</div>
<div> Dave</div>
<div> </div>
<blockquote class="gmail_quote"> <br>
<br>
Thank you so much.<br>
<br>
Frank<br>
<br>
<br>
<br>
On 07/06/2016 02:51 PM, Barry Smith wrote:<br>
<blockquote class="gmail_quote">
<blockquote class="gmail_quote"> On Jul 6,
2016, at 4:19 PM, frank <<a href="mailto:hengjiew@uci.edu" target="_blank"></a><a href="mailto:hengjiew@uci.edu" target="_blank">hengjiew@uci.edu</a>>
wrote:<br>
<br>
Hi Barry,<br>
<br>
Thank you for you advice.<br>
I tried three test. In the 1st test, the
grid is 3072*256*768 and the process mesh is
96*8*24.<br>
The linear solver is 'cg' the preconditioner
is 'mg' and 'telescope' is used as the
preconditioner at the coarse mesh.<br>
The system gives me the "Out of Memory"
error before the linear system is completely
solved.<br>
The info from '-ksp_view_pre' is attached. I
seems to me that the error occurs when it
reaches the coarse mesh.<br>
<br>
The 2nd test uses a grid of 1536*128*384 and
process mesh is 96*8*24. The 3rd test uses
the same grid but a different process mesh
48*4*12.<br>
</blockquote>
Are you sure this is right? The total
matrix and vector memory usage goes from 2nd
test<br>
Vector 384 383
8,193,712 0.<br>
Matrix 103 103
11,508,688 0.<br>
to 3rd test<br>
Vector 384 383
1,590,520 0.<br>
Matrix 103 103
3,508,664 0.<br>
that is the memory usage got smaller but if
you have only 1/8th the processes and the same
grid it should have gotten about 8 times
bigger. Did you maybe cut the grid by a factor
of 8 also? If so that still doesn't explain it
because the memory usage changed by a factor
of 5 something for the vectors and 3 something
for the matrices.<br>
<br>
<br>
<blockquote class="gmail_quote"> The linear
solver and petsc options in 2nd and 3rd
tests are the same in 1st test. The linear
solver works fine in both test.<br>
I attached the memory usage of the 2nd and
3rd tests. The memory info is from the
option '-log_summary'. I tried to use
'-momery_info' as you suggested, but in my
case petsc treated it as an unused option.
It output nothing about the memory. Do I
need to add sth to my code so I can use
'-memory_info'?<br>
</blockquote>
Sorry, my mistake the option is
-memory_view<br>
<br>
Can you run the one case with -memory_view
and -mg_coarse jacobi -ksp_max_it 1 (just so
it doesn't iterate forever) to see how much
memory is used without the telescope? Also run
case 2 the same way.<br>
<br>
Barry<br>
<br>
<br>
<br>
<blockquote class="gmail_quote"> In both tests
the memory usage is not large.<br>
<br>
It seems to me that it might be the
'telescope' preconditioner that allocated a
lot of memory and caused the error in the
1st test.<br>
Is there is a way to show how much memory it
allocated?<br>
<br>
Frank<br>
<br>
On 07/05/2016 03:37 PM, Barry Smith wrote:<br>
<blockquote class="gmail_quote"> Frank,<br>
<br>
You can run with -ksp_view_pre to
have it "view" the KSP before the solve so
hopefully it gets that far.<br>
<br>
Please run the problem that does fit
with -memory_info when the problem
completes it will show the "high water
mark" for PETSc allocated memory and total
memory used. We first want to look at
these numbers to see if it is using more
memory than you expect. You could also run
with say half the grid spacing to see how
the memory usage scaled with the increase
in grid points. Make the runs also with
-log_view and send all the output from
these options.<br>
<br>
Barry<br>
<br>
<blockquote class="gmail_quote"> On Jul 5,
2016, at 5:23 PM, frank <<a href="mailto:hengjiew@uci.edu" target="_blank"></a><a href="mailto:hengjiew@uci.edu" target="_blank">hengjiew@uci.edu</a>>
wrote:<br>
<br>
Hi,<br>
<br>
I am using the CG ksp solver and
Multigrid preconditioner to solve a
linear system in parallel.<br>
I chose to use the 'Telescope' as the
preconditioner on the coarse mesh for
its good performance.<br>
The petsc options file is attached.<br>
<br>
The domain is a 3d box.<br>
It works well when the grid is
1536*128*384 and the process mesh is
96*8*24. When I double the size of grid
and keep the same process mesh and petsc
options, I get an "out of memory" error
from the super-cluster I am using.<br>
Each process has access to at least 8G
memory, which should be more than enough
for my application. I am sure that all
the other parts of my code( except the
linear solver ) do not use much memory.
So I doubt if there is something wrong
with the linear solver.<br>
The error occurs before the linear
system is completely solved so I don't
have the info from ksp view. I am not
able to re-produce the error with a
smaller problem either.<br>
In addition, I tried to use the block
jacobi as the preconditioner with the
same grid and same decomposition. The
linear solver runs extremely slow but
there is no memory error.<br>
<br>
How can I diagnose what exactly cause
the error?<br>
Thank you so much.<br>
<br>
Frank<br>
<petsc_options.txt><br>
</blockquote>
</blockquote>
<ksp_view_pre.txt><memory_test2.txt><memory_test3.txt><petsc_options.txt><br>
</blockquote>
</blockquote>
<br>
</blockquote>
</blockquote>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
<br>
</div></div></div>
</blockquote></div><br></div></div>