OK.
I had started to wonder if that was the case. I'll do some further
investigation.
Thanks,
David
On 22/11/2024 22:10, Matthew Knepley wrote:
This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain that
the email is genuine and the content is safe.
On Fri, Nov 22, 2024 at 12:57 PM David Scott <d.sc...@epcc.ed.ac.uk>
wrote:
Matt,
Thanks for the quick response.
Yes 1) is trivially true.
With regard to 2), from the SLURM output:
[0] Maximum memory PetscMalloc()ed 29552 maximum size of entire
process 4312375296
[1] Maximum memory PetscMalloc()ed 29552 maximum size of entire
process 4311990272
Yes only 29KB was malloced but the total figure was 4GB per process.
Looking at
mem0 = 16420864.000000000
mem0 = 16117760.000000000
mem1 = 4311490560.0000000
mem1 = 4311826432.0000000
mem2 = 4311490560.0000000
mem2 = 4311826432.0000000
mem0 is written after PetscInitialize.
mem1 is written roughly half way through the options being read.
mem2 is written on completion of the options being read.
The code does very little other than read configuration options.
Why is so much memory used?
This is not due to options processing, as that would fall under Petsc
malloc allocations. I believe we are measuring this
using RSS which includes the binary, all shared libraries which are
paged in, and stack/heap allocations. I think you are
seeing the shared libraries come in. You might be able to see all the
libraries that come in using strace.
Thanks,
Matt
I do not understand what is going on and I may have expressed
myself badly but I do have a problem as I certainly cannot use
anywhere near 128 processes on a node with 128GB of RAM before I
get an OOM error. (The code runs successfully on 32 processes but
not 64.)
Regards,
David
On 22/11/2024 16:53, Matthew Knepley wrote:
This email was sent to you by someone outside the University.
You should only click on links or attachments if you are certain
that the email is genuine and the content is safe.
On Fri, Nov 22, 2024 at 11:36 AM David Scott
<d.sc...@epcc.ed.ac.uk> wrote:
Hello,
I am using the options mechanism of PETSc to configure my CFD
code. I
have introduced options describing the size of the domain
etc. I have
noticed that this consumes a lot of memory. I have found that
the amount
of memory used scales linearly with the number of MPI
processes used.
This restricts the number of MPI processes that I can use.
There are two statements:
1) The memory scales linearly with P
2) This uses a lot of memory
Let's deal with 1) first. This seems to be trivially true. If I
want every process to have
access to a given option value, that option value must be in the
memory of every process.
The only alternative would be to communicate with some process in
order to get values.
Few codes seem to be willing to make this tradeoff, and we do not
offer it.
Now 2). Looking at the source, for each option we store
a PetscOptionItem, which I count
as having size 37 bytes (12 pointers/ints and a char). However,
there is data behind every
pointer, like the name, help text, available values (sometimes),
I could see it being as large
as 4K. Suppose it is. If I had 256 options, that would be 1M. Is
this a large amount of memory?
The way I read the SLURM output, 29K was malloced. Is this a
large amount of memory?
I am trying to get an idea of the scale.
Thanks,
Matt
Is there anything that I can do about this or do I need to
configure my
code in a different way?
I have attached some code extracted from my application which
demonstrates this along with the output from a running it on
2 MPI
processes.
Best wishes,
David Scott
The University of Edinburgh is a charitable body, registered
in Scotland, with registration number SC005336. Is e
buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann,
clàraichte an Alba, àireamh clàraidh SC005336.
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to
which their experiments lead.
-- Norbert Wiener
https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cH8SjJvsuVEK1zv8noUjNUJC0VnHFqems68PjB2E94pqxc3q55YprX1q2JXFvPAzXJkh40J1-erXPWdIvc-xrLkRIgg$
<https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cH8SjJvsuVEK1zv8noUjNUJC0VnHFqems68PjB2E94pqxc3q55YprX1q2JXFvPAzXJkh40J1-erXPWdIvc-xGybRwKU$ >
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which
their experiments lead.
-- Norbert Wiener
https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cH8SjJvsuVEK1zv8noUjNUJC0VnHFqems68PjB2E94pqxc3q55YprX1q2JXFvPAzXJkh40J1-erXPWdIvc-xrLkRIgg$
<https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!cH8SjJvsuVEK1zv8noUjNUJC0VnHFqems68PjB2E94pqxc3q55YprX1q2JXFvPAzXJkh40J1-erXPWdIvc-xGybRwKU$ >
