Scratch Disk?

I have 3 hard drives - 2 fast NVMEs and 1 slower SSD.

One of the NVMEs is a dedicated scratch disk so it’s mostly empty.

I’ve been putting the source video files there.

Is it quickest to also keep the exported files and MLT files there or should I put them on different drives?

Quick in the sense of exporting?
You only use SSDs and it depends on your file number as well as sizes whether there will be a substantial difference. Large files profit from the high sequential data rates but ordinary SSDs have already high rates. I would expect that a difference is only tangible if your files are dozens of GBs big; if any. (I am not an expert nor did I test this assumption.) In the end, it would be best if you use a sample project with a sizeable number of pictures, some large video files and some filters to test the performance of both drives.
I expect the CPU and/or GPU to be the bottlenecks and not different types of SSDs.

I’m asking about about exporting a video in Shotcut, not the speed of hard drives in general.

When exporting a video in Shotcut is it fast to have the source and MLT files on the same hard drive as the target export hard drive or is it faster to split them up to different hard drives?

Probably would not make much difference. The true bottleneck is CPU processing.

I don’t have NVME to test my theory though. I run everything on SSD’s, storage on HDD’s. My bottleneck is always CPU. For big exports, I restart my computer, and make sure no other programs are open.

The answer depends entirely on what your source file formats and export formats are.

If the source and export are both raw uncompressed video files, then storage bandwidth has a small chance of becoming a bottleneck.

If either source or export, or both, have any amount of compression on them at all (like H.264, ProRes, etc), then the CPU will be a bottleneck long before storage will, especially with the high-speed drives you have.

If you had magnetic HDD, then the head jumping around for read source / write export could be inefficient. But all your drives are solid state which excel at random access I/O, so you should be able to operate at the full speed of your storage. And a CPU that’s working hard to compress video has probably zero chance of saturating your storage.

If you want the highest theoretical advantages, put the source files on NVMe since you will be reading multiple files simultaneously to do your transitions. The export itself is only one file, so the slower SSD can handle the export no problem.

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