<br><br>On Thursday, 15 September 2016, frank <<a href="mailto:hengjiew@uci.edu">hengjiew@uci.edu</a>> 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, <br>
<br>
I write a simple code to re-produce the error. I hope this can help
to diagnose the problem.<br>
The code just solves a 3d poisson equation. </div></blockquote><div><br></div><div>Why is the stencil width a runtime parameter?? And why is the default value 2? For 7-pnt FD Laplace, you only need a stencil width of 1. </div><div><br></div><div>Was this choice made to mimic something in the real application code?</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 run the code on a 1024^3 mesh. The process partition is 32 * 32 *
32. That's when I re-produce the OOM error. Each core has about 2G
memory.<br>
I also run the code on a 512^3 mesh with 16 * 16 * 16 processes. The
ksp solver works fine. <br>
I attached the code, ksp_view_pre's output and my petsc option file.<br>
<br>
Thank you.<br>
Frank<br>
<div><br>
On 09/09/2016 06:38 PM, Hengjie Wang wrote:<br>
</div>
<blockquote type="cite">Hi Barry,
<div><br>
</div>
<div>I checked. On the supercomputer, I had the option
"-ksp_view_pre" but it is not in file I sent you. I am sorry for
the confusion.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Frank<span></span><br>
<br>
On Friday, September 9, 2016, Barry Smith <<a href="javascript:_e(%7B%7D,'cvml','bsmith@mcs.anl.gov');" target="_blank">bsmith@mcs.anl.gov</a>>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
> On Sep 9, 2016, at 3:11 PM, frank <<a>hengjiew@uci.edu</a>>
wrote:<br>
><br>
> Hi Barry,<br>
><br>
> I think the first KSP view output is from -ksp_view_pre.
Before I submitted the test, I was not sure whether there
would be OOM error or not. So I added both -ksp_view_pre and
-ksp_view.<br>
<br>
But the options file you sent specifically does NOT list the
-ksp_view_pre so how could it be from that?<br>
<br>
Sorry to be pedantic but I've spent too much time in the
past trying to debug from incorrect information and want to
make sure that the information I have is correct before
thinking. Please recheck exactly what happened. Rerun with the
exact input file you emailed if that is needed.<br>
<br>
Barry<br>
<br>
><br>
> Frank<br>
><br>
><br>
> On 09/09/2016 12:38 PM, Barry Smith wrote:<br>
>> Why does ksp_view2.txt have two KSP views in it
while ksp_view1.txt has only one KSPView in it? Did you run
two different solves in the 2 case but not the one?<br>
>><br>
>> Barry<br>
>><br>
>><br>
>><br>
>>> On Sep 9, 2016, at 10:56 AM, frank <<a>hengjiew@uci.edu</a>>
wrote:<br>
>>><br>
>>> Hi,<br>
>>><br>
>>> I want to continue digging into the memory
problem here.<br>
>>> I did find a work around in the past, which is to
use less cores per node so that each core has 8G memory.
However this is deficient and expensive. I hope to locate the
place that uses the most memory.<br>
>>><br>
>>> Here is a brief summary of the tests I did in
past:<br>
>>>> Test1: Mesh 1536*128*384 | Process Mesh
48*4*12<br>
>>> Maximum (over computational time) process
memory: total 7.0727e+08<br>
>>> Current process memory:
total 7.0727e+08<br>
>>> Maximum (over computational time) space
PetscMalloc()ed: total 6.3908e+11<br>
>>> Current space PetscMalloc()ed:
total 1.8275e+09<br>
>>><br>
>>>> Test2: Mesh 1536*128*384 | Process Mesh
96*8*24<br>
>>> Maximum (over computational time) process
memory: total 5.9431e+09<br>
>>> Current process memory:
total 5.9431e+09<br>
>>> Maximum (over computational time) space
PetscMalloc()ed: total 5.3202e+12<br>
>>> Current space PetscMalloc()ed:
total 5.4844e+09<br>
>>><br>
>>>> Test3: Mesh 3072*256*768 | Process Mesh
96*8*24<br>
>>> OOM( Out Of Memory ) killer of the
supercomputer terminated the job during "KSPSolve".<br>
>>><br>
>>> I attached the output of ksp_view( the third
test's output is from ksp_view_pre ), memory_view and also the
petsc options.<br>
>>><br>
>>> In all the tests, each core can access about 2G
memory. In test3, there are 4223139840 non-zeros in the
matrix. This will consume about 1.74M, using double precision.
Considering some extra memory used to store integer index, 2G
memory should still be way enough.<br>
>>><br>
>>> Is there a way to find out which part of KSPSolve
uses the most memory?<br>
>>> Thank you so much.<br>
>>><br>
>>> BTW, there are 4 options remains unused and I
don't understand why they are omitted:<br>
>>> -mg_coarse_telescope_mg_coarse<wbr>_ksp_type
value: preonly<br>
>>> -mg_coarse_telescope_mg_coarse<wbr>_pc_type
value: bjacobi<br>
>>> -mg_coarse_telescope_mg_levels<wbr>_ksp_max_it
value: 1<br>
>>> -mg_coarse_telescope_mg_levels<wbr>_ksp_type
value: richardson<br>
>>><br>
>>><br>
>>> Regards,<br>
>>> Frank<br>
>>><br>
>>> On 07/13/2016 05:47 PM, Dave May wrote:<br>
>>>><br>
>>>> On 14 July 2016 at 01:07, frank <<a>hengjiew@uci.edu</a>>
wrote:<br>
>>>> 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>
>>>><br>
>>>> 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....)<br>
>>>><br>
>>>> 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.<br>
>>>><br>
>>>><br>
>>>><br>
>>>> I am running this job on Bluewater<br>
>>>> I am using the 7 points FD stencil in 3D.<br>
>>>><br>
>>>> I thought so on both counts.<br>
>>>><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>
>>>><br>
>>>> Ok. I'd still like to know where the memory
was being used since my estimates were off.<br>
>>>><br>
>>>><br>
>>>> Thanks,<br>
>>>> Dave<br>
>>>><br>
>>>> Regards,<br>
>>>> Frank<br>
>>>><br>
>>>><br>
>>>><br>
>>>> On 07/11/2016 01:18 PM, Dave May wrote:<br>
>>>>> Hi Frank,<br>
>>>>><br>
>>>>><br>
>>>>> On 11 July 2016 at 19:14, frank <<a>hengjiew@uci.edu</a>>
wrote:<br>
>>>>> 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.<br>
>>>>><br>
>>>>> Okay - that is essentially useless
(sorry)<br>
>>>>><br>
>>>>> It seems to me that the error occurred
when the decomposition was going to be changed.<br>
>>>>><br>
>>>>> Based on what information?<br>
>>>>> Running with -info would give us more
clues, but will create a ton of output.<br>
>>>>> Please try running the case which failed
with -info<br>
>>>>> 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.<br>
>>>>><br>
>>>>><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>
>>>>> * The Fine grid operator contains
4223139840 non-zeros --> 1.8 GB per MPI rank assuming
double precision.<br>
>>>>> The indices for the AIJ could amount to
another 0.3 GB (assuming 32 bit integers)<br>
>>>>><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>
>>>>> The coarse grid should consume ~ 0.5 MB
per MPI rank on the communicator with 18432 ranks.<br>
>>>>><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>
>>>>><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>
>>>>> * 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>
>>>>><br>
>>>>> From my rough estimates, the worst case
memory foot print for any given core, given your options is
approximately<br>
>>>>> 2100 MB + 300 MB + 32 MB + 32 MB + 1 MB
= 2465 MB<br>
>>>>> 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>
>>>>> (3) all temporary vectors required by the
CG solver, and those required by the smoothers.<br>
>>>>> (4) internal memory allocated by MatPtAP<br>
>>>>> (5) memory associated with IS's used
within PCTelescope<br>
>>>>><br>
>>>>> 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>
>>>>><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>
>>>>><br>
>>>>> [1] What machine are you running on? Send
me a URL if its available<br>
>>>>><br>
>>>>> [2] What discretization are you using? (I
am guessing a scalar 7 point FD stencil)<br>
>>>>> 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>
>>>>> This would hopefully enable us to
correctly evaluate the actual memory usage required by the
solver configuration you are using.<br>
>>>>><br>
>>>>> Thanks,<br>
>>>>> Dave<br>
>>>>><br>
>>>>><br>
>>>>> Frank<br>
>>>>><br>
>>>>><br>
>>>>><br>
>>>>><br>
>>>>> On 07/08/2016 10:38 PM, Dave May wrote:<br>
>>>>>><br>
>>>>>> On Saturday, 9 July 2016, frank <<a>hengjiew@uci.edu</a>>
wrote:<br>
>>>>>> 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.<br>
>>>>>><br>
>>>>>> 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.<br>
>>>>>><br>
>>>>>> And please send the result of KSPView
so we can see what is actually used in the computations<br>
>>>>>><br>
>>>>>> Thanks<br>
>>>>>> Dave<br>
>>>>>><br>
>>>>>><br>
>>>>>> Thank you so much.<br>
>>>>>><br>
>>>>>> Frank<br>
>>>>>><br>
>>>>>><br>
>>>>>><br>
>>>>>> On 07/06/2016 02:51 PM, Barry Smith
wrote:<br>
>>>>>> On Jul 6, 2016, at 4:19 PM, frank
<<a>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>
>>>>>> 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>
>>>>>> 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>
>>>>>> 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>
>>>>>> 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>
>>>>>> 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>
>>>>>> On Jul 5, 2016, at 5:23 PM, frank
<<a>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>
>>>>>> <ksp_view_pre.txt><memory_test<wbr>2.txt><memory_test3.txt><petsc<wbr>_options.txt><br>
>>>>>><br>
>>>>><br>
>>>><br>
>>> <ksp_view1.txt><ksp_view2.txt><wbr><ksp_view3.txt><memory1.txt><m<wbr>emory2.txt><petsc_options1.txt<wbr>><petsc_options2.txt><petsc_<wbr>options3.txt><br>
><br>
<br>
</blockquote>
</div>
</blockquote>
<br>
</div></blockquote><div> </div>