[3dem] Installing Relion on a GPU cluster

[Dr. Clara Cai]

Hi, Sayan

Our suggestions:
1. You can actually install CUDA on the headnode (you will not be able to
run the program without the driver but compiling should be fine). Make sure
that all nodes have the same CUDA installed and for compute nodes, NVIDIA
driver is installed properly.

2. Then compile and make RELION into a module that can be loaded on all
nodes.

3. Set up a job submission template for RELION. We typically use SLURM
scheduler, but it really depends on your cluster setup.

Good luck!

Best regards,

-Clara
SingleParticle.com


On Wed, Oct 24, 2018 at 12:41 PM Sayan Bhakta <19sayanbhakta89 at gmail.com>
wrote:

> Hi,
> I am using a cluster with 4 blades. One is the master node without any
> graphics card. Other three have CUDA compatible high end graphics card. In
> the master node CUDA was installed without any graphics driver and in the
> three slave nodes CUDA was installed with appropriate graphics driver. All
> the four nodes has similar architecture and CUDA installation paths are
> same on each blades.
>
> I was going to compile relion with cmake in the master node and I got
> stuck how to source the paths of CUDA and Nvidia driver environments from
> different nodes while compiling with cmake. As on the master node there are
> no graphics driver, cmake will not be able to compile the GPU version of
> relion.
>
> My plan was as below.
>
> First, making a module with CUDA environment variables and loading it
> before relion compilation. But I don't know how to make the module with
> CUDA from different nodes. If any guidance is there would be very helpful.
>
> Secondly, after successful installation, making a module for relion with
> all CUDA and other necessary (like openmpi,  ctffind, gctf,
> mitioncorrection, etc) environment variables and loading it while
> submitting the job. But in this case also I don't know how to specify GPU
> from different nodes in the module file.
>
> Please help and ask for further information if needed.
>
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