On Fri, Nov 22, 2024 at 12:57 PM David Scott <[email protected]> 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 <[email protected]> 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.
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