This is a test version of Biostars. For the public version, visit https://www.biostars.org.
SLURM: running equilibration steps for MD simulation

sbatch: error: Batch job submission failed: Invalid node name specified

How can I solve this?

slurm md simulation sbatch
• 2,329 views • link
written by asma.nounna • asma.nounna

This is something you need to take up with your local IT support. Sounds like you used a node name that is invalid.

• 0 views • link
written by GenoMax GenoMax

Agreed, contact the administrator. You could type pestat to get a list of all available nodes with their names, number of CPUs, memory etc.

• 0 views • link
written by ATpoint ATpoint

@genomax @ATpoint Thank you for your prompt reply. yes, I did contact them and they solved this issue.

• 0 views • link
written by asma.nounna • asma.nounna

Thank you. what about this error:

FATAL ERROR: CUDA error cudaGetDeviceCount(&deviceCount) in file src/DeviceCUDA.C, function initialize, line 135 on Pe 18 helios3.helios.calculquebec.ca):no CUDA-capable device is detected

Thank you

• 0 views • link
written by asma.nounna • asma.nounna

You do not appear to have any Video card/node(s) that are capable of running CUDA code (which runs on Graphics processor units).

• 0 views • link
written by GenoMax GenoMax

Please contact your cluster administrator. This is nothing we can help with from remote. CUDA requires a GPU. Please ask the admin if you have nodes that are equiped with GPUs.

• 0 views • link
written by ATpoint ATpoint

@ATpoint Thank you. Yes, I contacted them. it was because I was using login node instead of compute node

• 0 views • link
written by asma.nounna • asma.nounna

1 answer

@genomax Thank you. Yes, the error was because I was running the job from login node instead of the compute node.

• 0 views • link
written by asma.nounna • asma.nounna

Log in to answer this question.

More posts like this