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hca upload files using a lot of cpu/memory #358
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I'm guessing this is because the CLI is now doing client-side checksumming? @maniarathi do you stream the file while checksumming or attempt to read it into memory? Hmm looks like it is streamed in chunks |
So I did actually test the memory footprint of this a while back and the memory was 64MB which is what is expected given that it streams it in that sized chunks. |
@malloryfreeberg how much memory was consumed? Alas your Activity monitor screenshots don't show that. |
As for CPU, I expect that simultaneous checksumming of several files will be quite CPU intensive. Does it limit parallelization? It looks like it does, based on the number of cores you have There are several ways to fix this:
I realize # 3 doesn't work well with the current architecture, as client-side and server-side checksums are compared before upload starts. I wish there was a more efficient way to decide whether to upload or not. |
@sampierson @maniarathi I unfortunately did not grab memory usage during this time. I can reproduce, but I'll have to download the files to my local machine again :( Stay tuned! |
@malloryfreeberg Don't bother. I think we know what the culprit is. I think the problem is CPU not memory. |
I was using
hca upload files *
to upload about 80GB of fastq files (16 files) from my local machine to an upload area. During the transfer, I experienced significant slowdown of everything else running on my machine. I don't remember experiencing this slowdown before, although I haven't had to transfer files from a local source in a while. It looks like my machine was maxed out on CPU usage (screenshots below). Wondering if this is normal or expected behavior? It doesn't seem ideal...During transfer:
After transfer:
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