Success! Ok i figured it out. This is going to be a long one so sit back, but anyone with a similar problem, i hope this will work for you. Again I am running RetroPie on a raspberry Pi 3 with a Pi2Jamma adaptor and i ran the retropiergb mod to output to a 15khz monitor. so i figured that this was an issue with the run command, so i found a file in the /opt.retropie/configs/all, named runcommand-onend.sh . In it there is a line for HDMI timings that was different then the one in the global config.txt in the boot folder. so i added the correct timings and # out the originals and it worked! but then for some reason mame was outputting a very stretched image at 1920x240, so i went into the configuration options in the run command menu and changed the settings in the edit custom retroarch config option. In it you will see that the custom viewport is set to 1920x240, so i just added a pond symbol before the commands. Since the layout seems to be UK it is a £ instead of # for us Americans but it works just the same. and now mame defaults to the listed game resolution. I have no Idea why these options did this but I wasn't going to let this beat me. I hope this helps.

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I got it to work placing cue and bin files into the sega32x roms folder and using lr-picodrive. After launching game, hit selct-x to bring up Retroarch menu. Scroll down to "Options" and set Input device 1 to 3 button pad. and Input device 2 to "None".

@WeirdGamerAidan Like @sleve_mcdichael stated you need an OS.

My advice is here however, not to install Ubuntu since its footprint on the hardware is rather big compared to other Linux distro's.

My personal favorite is Xubuntu x64. Works perfectly with RetroPie but has a smaller footprint, thus leaving more for RetroPie to use, thus giving a better performance for emulation. N64 games run better on the same hardware with Xubuntu, compared to Ubuntu.

Nice thing about Xubuntu is that it's very flexible and performs great on older hardware, whereas Ubuntu requires more power. The biggest difference between Ubuntu and Xubuntu is the desktop interface, but that one can really consume your hardware.

I reinstalled RetroPie all over again and the joystick setup works fine now. Couldn't figure out what was causing this issue.

Answering myself, because I'm an idiot. Sorry.

In the emulator's settings (on the GUI) I had to (re-)assign a correct mapping for pause.
It had kbd.esc and two other weird keys from the controller assigned to pause.
I assigned the button behind/below the right shoulder key to pause, no idea what those are called.
Which in my case resulted to the following in controls.ini:

[ControlMapping] ... snip ... Pause = 1-111,10-197 Rewind = 1-67

So, 10-197 is the key that was missing.

@mitu thanks

@Folly Thank you friend.

@mitu
It worked! thanks a lot.
I'm using "Version: 1.4.1" for retroarch.
I just wrote a script in python to send UDP packets with this command
"READ_CORE_RAM <address> <len>"
Then I received related bytes.

@Folly I'll give that a shot.

@cmftblynu somehow I got it to work, I went into the desktop port and played with the sound settings in there. Then I went in and changed it to headphones, then changed it back it still goes to zero on the volume but works now with default, HDMI and ALSA. It is just buggy.

@yserra
ok the files are a bit tedious, but i'm happy about it, precisely because of the configuration with mouse and joypad.

the only one thing i can't running are cd32.lha games

@mitu Yes. And you are right. Unfortunatelly I did not realize each emulated system needs it's BIOS. It was indeed written in the link that was provided. I was looking for a specific controller problem and being new to the whole raspberry thing, I overlooked that information.
@aewoodall520 just happened to point out the thing I was missing.

P.S.: After updating the ES, I had to reconfigure the controlls for PSX again. It was a breeze thanks to your link, thank you.

https://retropie.org.uk/docs/EmulationStation/#gamelistxml-edits

If you use the built-in ES Scraper, your gamelist and image folders will be in ~/.emulationstation; I don't think you can change this.

If however you use another scraper (Steven Sselph's scraper or Lars Muldjord's Skyscraper) you can choose whether your scraped data goes there, or in the roms folder; if the folder is mapped to an external SSD then the scraped data will be there too, or else it will migrate along with the roms themselves by whatever other method you use (i.e. just backing up the roms folder over network shares, etc.)

Maybe this is your solution https://www.linux-projects.org/uv4l/tutorials/play-retropie-in-browser/

I tried to install it yesterday, but I run into some problems I havent figured out yet.... But I've seen people successfully installing this solution.

@BuZz Thanks a lot. In the end i went for flycast since all posts went that direction.

Solved by upgrading to newer MESA driver. Tested on same environment.

"Mar 23 21:52:24 lvl2: EmulationStation - v2.11.0rp-dev, built Mar 23 2022 - 21:34:05
Mar 23 21:52:24 lvl2: Parsing XML file "/opt/retropie/supplementary/emulationstation-dev/resources/mamenames.xml"...
Mar 23 21:52:24 lvl2: Parsing XML file "/opt/retropie/supplementary/emulationstation-dev/resources/mamebioses.xml"...
Mar 23 21:52:24 lvl2: Parsing XML file "/opt/retropie/supplementary/emulationstation-dev/resources/mamedevices.xml"...
Mar 23 21:52:24 lvl2: Creating window...
Mar 23 21:52:24 lvl2: Created window successfully.
Mar 23 21:52:24 lvl2: GL vendor: Panfrost
Mar 23 21:52:24 lvl2: GL renderer: Mali-T760 (Panfrost)
Mar 23 21:52:24 lvl2: GL version: 3.1 Mesa 22.1.0-devel
Mar 23 21:52:24 lvl2: Checking available OpenGL extensions...
Mar 23 21:52:24 lvl2: ARB_texture_non_power_of_two: ok"

Sorry for the trouble.

@CubeBox391 said in SNES config file not found:

@sleve_mcdichael how? i'm a bit new in all of these, Sorry

https://retropie.org.uk/docs/Updating-RetroPie

https://retropie.org.uk/docs/Updating-RetroPie/#updatinginstalling-individual-packages

Alright, I was able to select the second joystick in the in-game configuration - thanks for everyone who helped, it's working now!

@YFZdude
Thanks for helping
Sim

These Android geared devices are not always working with Linux/RetroPie, we got a few topics in the forum for them with issues during connection or - even after connection - not working properly.
Do you have a vendor support page with a manual/instructions on how to make them work with a PC ? Do they have a 'mode switch' between Android/PC connection mode ?