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DHI / mikeio

Read, write and manipulate dfs0, dfs1, dfs2, dfs3, dfsu and mesh files.
https://dhi.github.io/mikeio
BSD 3-Clause "New" or "Revised" License
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DFSU.read() very slow on AMD CPU or linux #709

Open bhlevca opened 3 months ago

bhlevca commented 3 months ago

Describe the bug A clear and concise description of what the bug is. I am expecting some differences but not 30x.

There is something in the read algorithm that may be favoured by Intel CPU.

I have a code 

dfs = Dfsu(filename)
dsp = dfs.read(x=x, y=y)

The dfsu file is large ~ 52 GB. The same read operation takes 17-18 sec on an Intel i7 CPU laptop running Windows 10 and 420 sec on a powerful AMD Ryzen 3950X desktop running Linux.

To Reproduce Steps to reproduce the behavior:

Get a large DFSU file and use read (x,y)

System information:

jsmariegaard commented 2 months ago

@JesperGr - this most be related to MIKE Core ...

bhlevca commented 2 months ago

@JesperGr - this most be related to MIKE Core ...

Is there anything we can do about it? It may be related to what you do in the read function. Is it using pandas in the underlying code? I know that pandas code is slower on AMD platforms.

jsmariegaard commented 2 months ago

@bhlevca could you try with a profiler - I hear Scalene is great https://github.com/plasma-umass/scalene :-)

bhlevca commented 2 months ago

I guess that I need to use the mikeio source files to do useful profiling

jsmariegaard commented 2 months ago

You get those when you install MIKE IO (pure python)

bhlevca commented 2 months ago

Usually, When I debug, I point Pythonpath to the git folder From what you're saying, it will be enough to use the pip installed mikeio for the profiling purposes

bhlevca commented 1 month ago

I used Scalene but i didn't get extra information other than the read() function take minutes on an AMD CPU whether is Linux or Windows. Scalene did not get inside theread() function. I looked at mikecore source files but it is complex and it would be easier for you to determine the problem if you have access to an AMD CPU.

I tested on an AMD computer with dual boot:

- on Windows on an Intel CPU   -  16 sec
- on  Windows on an AMD CPU    -  85 sec
- on Linux on the same AMS CPU - 442 sec

If you don't have the time please give me some instruction where to look, what files and what is calling what and how I can debug this thing.. Thanks

jsmariegaard commented 4 weeks ago

@JesperGr do you know anything about read speed of dfsu files on AMD using MIKE Core?

bhlevca commented 4 weeks ago

I don't, but if you give some guidance on how to do it, I will try to test the MIKE CORE read()

JesperGr commented 4 weeks ago

I am not aware of any performance differences when reading DFS files for AMD compared to Intel processors. Common performance issues are usually related to disc performance and not processor performance.

To test that, you could try run a raw MIKE-Core Python read test, i.e. not involving mikeio at all. Something similar to the ReadingDfs2File method in:

https://github.com/DHI/mikecore-python/blob/master/tests/examples_dfs2.py

which loops over all items and time steps.

bhlevca commented 4 weeks ago

There is a known problem with Pandas performance on AMD processors when compared with Intel processors because of the MKL library.

I assumed that a 3D DFSU has the same issue because I thought that some calculations are needed to decrypt when reading the file.

I am going to put the file on a SSD to test your assumption. Also, I am going to try your suggestions on the Intel laptop and on the big AMD workstation on the current disks

On Mon, Oct 28, 2024, 06:56 Jesper Grooss @.***> wrote:

I am not aware of any performance differences when reading DFS files for AMD compared to Intel processors. Common performance issues are usually related to disc performance and not processor performance.

To test that, you could try run a raw MIKE-Core Python read test, i.e. not involving mikeio at all. Something similar to the ReadingDfs2File method in:

https://github.com/DHI/mikecore-python/blob/master/tests/examples_dfs2.py

which loops over all items and time steps.

— Reply to this email directly, view it on GitHub https://github.com/DHI/mikeio/issues/709#issuecomment-2441254701, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABMRXVVNEKHSOP472ANPYDZ5YC6HAVCNFSM6AAAAABLZSLYZGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINBRGI2TINZQGE . You are receiving this because you were mentioned.Message ID: @.***>

bhlevca commented 3 weeks ago

You are right. The disk transfer speed is the main problem. I tested on various disks, including SDD, and the read() function time varies wildly.
Closing.