installation of GPU code on parallelcluster

Question

I am trying to use miniconda to install OpenMM, and MD engine that utilizes GPUs. My ParallelCluster configuration is as follows:
* Head node: c5.2xlarge
* Compute nodes: g4dn.metal (T4 GPUs)
* Networked EFS storage from EC2
I can install OpenMM with miniconda on the head node, but when I run a test to see if OpenMM works, I get the following error:
```
python -m openmm.testInstallation

OpenMM Version: 8.0
Git Revision: a7800059645f4471f4b91c21e742fe5aa4513cda

There are 3 Platforms available:

1 Reference - Successfully computed forces
2 CPU - Successfully computed forces
3 CUDA - Error computing forces with CUDA platform

CUDA platform error: Error initializing CUDA: CUDA_ERROR_NO_DEVICE (100) at /home/conda/feedstock_root/build_artifacts/openmm_1675115856424/work/platforms/cuda/src/CudaContext.cpp:140

Median difference in forces between platforms:

Reference vs. CPU: 6.2955e-06

All differences are within tolerance.
```
My head node lacks a GPU, which would explain why the error CUDA_ERROR_NO_DEVICE was given. My next thought was to log in interactively into one of my GPU nodes, either using

```
salloc --time=30 --account=centos --nodes=1
salloc: Granted job allocation 5
```
or

```
srun --pty --mem=1g -n 1 --gres=gpu:1 -J modbind -p modbind /bin/bash
```
The first try with salloc, even though it shows that I'm in interactive mode, doesn't actually log me into the GPU node (the output of lspci -v is exactly the same before and after). The second try with srun simply hangs.

I've also referenced the GROMACS on AWS workshop using spack [https://catalog.workshops.aws/gromacs-on-aws-parallelcluster/en-US](), since OpenMM is included in the list of software for spack, but unfortunately the workshop only compiled GROMACS for CPU architecture, not CPU+GPU. Any help would be much appreciated.

enrico-aws · Accepted Answer

HI @blakem,

I can confirm the first issue is due to lack of GPU in the head node.
To experiment within one of the compute nodes you can submit a job, retrieve the node hostname and then when the job is Running connect to the node with SSH:

[ec2-user@ip-10-0-0-33 ~]$ sbatch --wrap "sleep 100"
    Submitted batch job 1

[ec2-user@ip-10-0-0-33 ~]$ squeue
                 JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
                     1    queue1     wrap ec2-user R       0:03      1 queue1-dy-queue1-t2medium-1

[ec2-user@ip-10-0-0-33 ~]$ ssh queue1-dy-queue1-t2medium-1
   
Once in the compute node you can try to manually install the package on it.
If it works as expected you can automate the installation by using `OnNodeConfigured` custom bootstrap action: https://docs.aws.amazon.com/parallelcluster/latest/ug/custom-bootstrap-actions-v3.html

Enrico

blakem · Answer

@enrico-aws, thanks for the quick turnaround and suggestion. I had to wait for 10+ minutes for my GPU node to finish initializing, but once it was running I was able to log into the GPU node.

installation of GPU code on parallelcluster

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