Hello must I receive written permission to use cloud computing for example for my Gromacs output? If yes whom and what contact must I email for this request if not here? (My Laptop
M1 is taking a while for calculations.) And also which computing would be the fastest but cheapest if I am not affiliated with a Government nor University institution to use Cluster?
Thanks if you know:),
Joel🚀
Hi Joel,
from the GROMACS side you don’t need permission, because it is free software. See the GROMACS LGPL license About GROMACS — GROMACS webpage https://www.gromacs.org documentation .
If you want to know how GROMACS performs on various cloud instances, you can have a look this publication: at https://pubs.acs.org/doi/10.1021/acs.jcim.2c00044
For testing purposes most cloud providers (like Google, AWS) offer some free computing time, which can be used for trying out things.
Best,
Carsten
If you can build a workstation with a fairly powerful processor (for example 16 core processor) and a gaming GPU like rtx3080 or higher (even rtx3070, rtx2080 will be enough), definitely you would achieve enough computational power for a cheap price. I recommend you NVIDIA’s RTX3090 with 20+ threads processor if you have enough money to buy that. It will give you more than 20-fold performance gain. Cloud computing will not be cheap in the long run.
Hello Dulaj thank you for your kind update:).
This system that you recommend, what would be the total cost? And how mobile would it be i.e. if I needed to carry it somewhere, how big? Thanks:) Joel🚀
Cost;
You need just a personal desktop computer. You need a graphics card, a CPU, a motherboard, a RAM card, a hard disk, a casing, a power supply unit, a monitor, and other parts that are needed for a computer such as a keyboard and mouse. You can check the prices in your local stores or online stores like Amazon (for GPUs like RTX 2080ti/3070/3070ti/3080/3080ti/3090/4080/4090 etc. and CPUs i7 10th/11th/12 gen etc. and other parts considering the compatibility ). GPU would cost more. You can choose the GPU and CPU according to the cost and the performance trade-off. This article is about GROMACS 2022 performance on GPUs Molecular Dynamics Benchmarks GPU Roundup GROMACS NAMD2 NAMD 3alpha on 12 GPUs | Puget Systems . As I know 2023 or higher versions are optimized to run on GPUs more than previous versions also. Linux OS (Ubuntu etc.), GROMACS, and other software and drivers you need are mostly open-source and free. However, you have to pay for the electricity.
Mobility;
You would know desktop PCs are not as mobile as laptops. But you can connect to it when you go out, using SSH or using remote desktop software like ANYDESK.
If you still need a cloud computing solution https://salad.com/ would be cheap. However, I have not used it. just I have looked at their website and saw that their prices are cheaper than other services.
Hi Dulaj thank you for your kind update:).
For Salad what would you suggest i.e. price for cheapest choice for just computations?
Thanks if you know:).
Remember I haven’t used it yet. I can’t recommend it directly. You can check prices per hour for GPUs. I have seen there were somewhat powerful GPUs like RTX3070 for 0.10$/hour. Most powerful GPUs like RTX4090/3090 were at 0.30$ range. I think you could get the best cost/nanoseconds (in the MD run) ratio for mid-ranged GPUs. Also, you have to implement the MD run command to use the resources efficiently. You would not need so many vCPUs ( below 8 vCPUs). However, do not take my advice seriously as I haven’t used it. You can just try!
Hi Dulaj OK thank you for your kind and prompt update:), ill let you know for your enrichment about salad if I move forward with them.