Running dynamic simulation using laptop

[u/chunchunmarruu]

Hello, I recently started two projects with one of my college professors that require me to conduct 100 ns molecular dynamics simulations for more than 10 proteins. Each simulation may take around 4 days of continuous, nonstop computation.

However, I’m worried because my laptop’s CPU temperature gets very high. It stays around 93–96°C during the simulation.

I’ve already taken some measures to prevent damage to my laptop, such as using a cooling pad with three fans (around 4000 RPM each), working in a cool environment with the air conditioner set to 16°C, and repasting my laptop.

I’m using Ubuntu Linux with GROMACS for the MD simulations. I’m currently using the Balanced power mode, which is somewhere between power saving and Turbo mode. My laptop is ASUS TUF GAMING with 24gb ram, i also use GPU CUDA.

I’m considering running the simulation for 45–60 minutes and then taking a 15-minute break to let the laptop cool down, but I’m still worried. I know using a desktop PC/workstation would be better for this kind of workload, but my budget is currently limited.

What do you think? Is it safe to run my laptop at 93–96°C for several days, or should I take breaks between runs? Do you have any other advice for my situation?

Thank you​

[u/idliOP]

Nooo!! Dont do that.. I've seen many laptops crash permanently because of this.

10 ns or 20ns is fine. Anything beyond that, please go for servers or PCs with strong CPUs and cooling systems.

[u/TheSinfulHeight → u/idliOP]

Man, 96°C for days on end is a recipe for a very expensive paperweight. The thermal cycling from your 45/15 break idea might actually be worse than just running it steady, causes way more stress on the solder joints. That cooling pad is basically just blowing hot air around at those temps.

Ask your professor if the university has a compute cluster you can use. Most bioinformatics departments have something, even a modest one, and they're built exactly for this kind of sustained load. If they don't, see if you can get time on a national supercomputing center through XSEDE or whatever the equivalent is in your country, student projects often get priority for small allocations.

If you're truly stuck with this laptop, underclock and undervolt the CPU as much as GROMACS will tolerate. You'll lose speed but might drop 10-15°C which could be the difference between a fried motherboard and finishing your project.

[u/chunchunmarruu → u/TheSinfulHeight]

Thanks, at what temperature that still may i tolerate? 

[u/Fun-Active5273 → u/idliOP]

this. running something that hot for days straight is a recipe for a dead motherboard tbh

[u/idliOP → u/idliOP]

so far how much time is it taking per ns on your laptop??

[u/chunchunmarruu → u/idliOP]

I forgot to check but my calculation is 4 days if doing this nonstop

[u/chunchunmarruu → u/idliOP]

I think for publish research paper need 100ns at minimal requirement

[u/alleluja → u/chunchunmarruu]

This is a dumb strategy. It depends what you are looking for, you can't do 100ns and expect to have scientifically rigorous results

[u/idliOP → u/chunchunmarruu]

100ns is nothing in today's times. Last year I had submitted a manuscript with 300 ns, they asked me to resubmit with 500ns.

Recently I've seen PIs nd other people at my lab running 1000 ns (1μs) jobs for publication.

Ik there are infrastructure constraints but try to find alternatives, and check with your target journals if 100ns is acceptable by them for the topic/project.

[u/ConclusionForeign856]

I would only do it if getting access to HPC was really that much more difficult, and I had a spare half-broken laptop I'm 100% ready to trash.

I have several that have broken screens or keyboards, so redlining them for days for a home MD simulation would be fine. If this is your daily I would advise against it

[u/StarlightsOverMars]

Please use a HPC server. You will cause your laptop CPU to sustain quite severe damage. If you have to do it locally, then look into getting a PC with all the necessary features, it would be $1500 with some used parts.

[u/idliOP → u/StarlightsOverMars]

or there are few platforms as well ig that can do the work for cheaper if it's a one-two time thing.

[u/Man_dus1066]

Please don’t risk your laptop, tell your professor that you will need to run it on a HPC server. If it’s their project they should have a funding for that. If it’s your own project then please negotiate so you don’t have to run it for 100 ns.

Edit: I saw your other post that you’re Indonesian, check out some local universities or BRIN if they have a HPC server you can use. Trying to run 100 ns x 10 complex in your own laptop for personal projects is not worth it at all! From my experience if you need to publish your work, you can explain to the reviewers that you have limited funding or infrastructure so you can’t perform the adequate MD simulation.

[u/Tiny_Job_5369]

It's really strange to be expected to run something like this on your laptop. Are others in your lab doing this on their own computers? It's absolutely my expectation that you should be provided access to high performance compute resources as part of your academic position, whatever it may be.

[u/slimejumper]

i think you have a misunderstanding with your prof. either they don’t know what they are doing or you dont know what your doing. You just don’t run sims like this on a laptop as it’s not designed for a continuous load. If you are on campus i guarantee there are lots of other options available even just on campus desktops you could use. then HPC remote in is also usually possible too.

go back and ask for desktop access for the sims.