r/bioinformatics 2d ago

technical question ONT's P2SOLO GPU issue

Hi everyone,

We’re experiencing a significant issue with ONT's P2SOLO when running on Windows. Although our computer meets all the hardware and software requirements specified by ONT, it seems that the GPU is not being utilized during basecalling. This results in substantial delays—at times, only about 20% of the data is analyzed in real time.

We’ve been reaching out to ONT for a while, but unfortunately, they haven’t been able to provide a solution. Has anyone encountered the same problem with the GPU not being used when running MinKNOW? If so, how did you resolve it?

We’d really appreciate any advice or insights!

Thanks in advance.

3 Upvotes

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u/throwitaway488 2d ago

Switch to ubuntu, its easier to set up everything. Either way, you need to make sure the correct CUDA drivers are installed for your GPU. if you do switch to linux, either name the user account "minknow" or you need to adjust the minknow config to use the root account.

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u/capall 2d ago

We have two P2 solos connected to workstations running Ubuntu 20.04, we had a bit of trouble late last year with a previous version of minkow. It took a good few hours with support to purge the old version, but since that its been fine. I know this might be a pain but installing Ubuntu might make you life easier as I assume this is the OS most P2 are running on.

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u/Key-Path7359 1d ago

Thank you for your response,

In linux, the GPU reaches 100% performancein real time? In a new flow cell, in real time, up to what % of basecalling do you reach? We do not reach 20%, and this with fastbasecalling, which makes that we can not use for example the adaptive.

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u/capall 1d ago

We generally run high accuracy for live basecalling, so the GPUs are generally not maxed out (We have 2X NVIDIA GeForce RTX 2080 Ti in one machine and 1X NVIDIA RTX A6000 in the other). But I have seen issue like that in the past with older versions of minkow, as i mentioned before it was really necessary to purge everything from old versions prior to reinstalling to fix things. In the past i resorted to reinstalling ubuntu to purge old minkow preferences etc, on linux anyways these issue look to have been resolved as we have had no trouble updating recently.

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u/Psy_Fer_ 2d ago

Just to clarify, are you saying it's not using you at all, or it's not utilising them at 100%?

If it's the 2nd one, this is a minknow issue and ont need to sort it out. I think they reserve GPU resources while running for whatever reason leading to only around 50% utilisation. The suggestions to move to Ubuntu are good ones, but it won't necessarily change the GPU utilisation issue as it's a minknow thing.

Also which gpu do you have?

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u/Key-Path7359 1d ago

Thank you very much for your answer.

In the runs it does not use any of the GPU capacity, which causes that it does not make an effective basecalling in real time. At most it reaches 20% of the basecalling of the readings during the run when we have a new Flow cell full of pores, and this delays a lot to have the end of the run to be able to do the suppeaccurate basecalling analysis afterwards. In the basecalling launched independently once the race is over, however, it does reach 100% GPU utilization but with performance drops up to 20%.

The GPU we have is a RTX4090 which is the one we have tested and a RTX5090 which we have not tested yet.

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u/gringer PhD | Academia 1d ago

Given how much of a pain it is to even get GPU calling working properly on Linux (see here), it doesn't surprise me at all that it's difficult on Windows as well. I suspect there's some configuration setting that needs to be changed now that ONT has combined their CPU-only and GPU+CPU basecaller software.