A customer involved in the research and development of adhesive materials asked us about a machine for conducting large-scale molecular dynamics calculations.
We mainly use LAMMPS and GROMACS, and we plan to use quantum chemical calculations (Density Functional Theory: DFT) as necessary.
Also, in order to perform calculations with GPGPU, we also requested the installation of CUDA.
The specific conditions are as follows.
・The model is Mac Pro
Based on the above, we have proposed the following specifications.
|CPU||AMD Ryzen ThreadripperPRO 5995WX (2.70GHz 64 cores)|
|Storage 1||480GB SSD S-ATA|
|Storage 2||4TB HDD S-ATA|
|network||on board (1GbE x1 10GBase-T x1)|
|Housing + power supply||Tower type chassis + 1000W (redundant power supply)|
|GPU||NVIDIA A100 80GB PCI-E|
This configuration assumes large-scale molecular dynamics calculations with LAMMPS and GROMACS.
The points to consider are as follows.
Cooling method needs to be considered for configurations with AMD ThreadripperPRO and NVIDIA A100
Since AMD ThreadripperPRO comes standard with a water-cooled CPU cooler, the chassis side does not come standard with a fan that can cool the NVIDIA A100.Therefore, the cooling of the NVIDIA A100 is supported by adding a case fan dedicated to GPU cooling.Also, by attaching a dummy cover to the empty PCI-E slot, we are trying to improve the cooling efficiency of the NVIDIA A100.
When using LAMMPS and GROMACS, if you do not perform double precision calculations on the GPU, you can reduce the cost by changing the GPU to a general product.
The configuration of this case study is based on the conditions given by the customer.
Please feel free to contact us even if you are considering different conditions from what is posted.
・What is LAMMPS?
reference:LAMMPS Molecular Dynamics Simulator *Jumps to an external site
・What is GROMACS?
reference:GROMACS *Jumps to an external site
・What is NVIDIA A100?
reference:NVIDIA A100 Tensor Core GPU (NVIDIA) *Jumps to an external site
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