Linux fs recommendations

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Hi

I’m puzzling through a filesystem related performance issue on a new Ubuntu Dell SSD workstation, which is showing abysmal performance for some I/O intensive steps. For example, using the -stride option on mrconvert on an HCP diffusion dataset takes half an hour, while less than a minute on a MacBookPro (the latter has an nvme disk, but that doesn’t account for a 30x difference).

mrconvert reports (with -debug) that it’s memory-mapping the output file, and using indirect IO. iostat reports many threads saturating write bandwidth on the disk.

So, I’m left poking around in filesystem options (I’m using ext4 mounted with noatime,date=writeback), and I’m wondering if you have some recommendations here. OTOH if this sounds strange, maybe I need to try a newer or non-Dell kernel.

Thanks,
Marmaduke

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I guess I’m answering my question, but it looks like an aberrant kernel or linux thing: I popped in a vanilla CentOS 7 Live CD and the strided conversion runs faster than the MacBookPro now.

Hopefully this thread will at least be useful if others run into similar issues.

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Thanks for the info! We have had issues on Ubuntu 14.04 which can be mostly solved by tweaking the buffer cache settings.

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Just thought I’d add that I’ve been looking into these issues recently, there are ways to avoid these issues. But it’ll require a fair bit of work to implement, it may take a while for me to find the time to work on this…