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Merged
pletzer merged 5 commits into from
Mar 25, 2026
Merged

Remove mentions of P100 GPUs #1210

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d53e3a3
minor edits
pletzer Mar 19, 2026
e5d163a
Merge branch 'main' of github.com:nesi/support-docs
pletzer Mar 19, 2026
8d60ca1
Merge branch 'main' of github.com:nesi/support-docs
pletzer Mar 25, 2026
8a2d239
P100:1 -> 1
pletzer Mar 25, 2026
23bb8f6
P100 -> A100
pletzer Mar 25, 2026
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15 changes: 6 additions & 9 deletions docs/Software/Available_Applications/AlphaFold.md
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Original file line number Diff line number Diff line change
Expand Up @@ -112,7 +112,7 @@ Input *fasta* used in following example  is 3RGK
#SBATCH --job-name af-2.3.2-monomer
#SBATCH --mem 24G
#SBATCH --cpus-per-task 8
#SBATCH --gpus-per-node P100:1
#SBATCH --gpus-per-node A100:1
#SBATCH --time 02:00:00
#SBATCH --output %j.out

Expand Down Expand Up @@ -157,7 +157,7 @@ MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH
#SBATCH --job-name af-2.3.2-multimer
#SBATCH --mem 30G
#SBATCH --cpus-per-task 4
#SBATCH --gpus-per-node P100:1
#SBATCH --gpus-per-node A100:1
#SBATCH --time 01:45:00
#SBATCH --output slurmout.%j.out

Expand Down Expand Up @@ -207,7 +207,7 @@ modifications. Image (.*simg*) and the corresponding definition file
#SBATCH --job-name alphafold2_monomer_example
#SBATCH --mem 30G
#SBATCH --cpus-per-task 6
#SBATCH --gpus-per-node P100:1
#SBATCH --gpus-per-node A100:1
#SBATCH --time 02:00:00
#SBATCH --output slurmout.%j.out

Expand Down Expand Up @@ -246,7 +246,7 @@ singularity exec --nv /opt/nesi/containers/AlphaFold/alphafold_2.2.0.simg python
#SBATCH --job-name alphafold2_monomer_example
#SBATCH --mem 30G
#SBATCH --cpus-per-task 6
#SBATCH --gpus-per-node P100:1
#SBATCH --gpus-per-node A100:1
#SBATCH --time 02:00:00
#SBATCH --output slurmout.%j.out

Expand Down Expand Up @@ -282,11 +282,8 @@ singularity exec --nv /opt/nesi/containers/AlphaFold/alphafold_2.2.0.simg python

1. Values for `--mem` , `--cpus-per-task` and `--time` Slurm variables
are for *3RGK.fasta*. Adjust them accordingly
2. We have tested this on both P100 and A100 GPUs where the runtimes
were identical. Therefore, the above example was set to former
via `P100:1`
3. The `--nv` flag enables GPU support.
4. `--pwd /app/alphafold` is to workaround this [existing
2. The `--nv` flag enables GPU support.
3. `--pwd /app/alphafold` is to workaround this [existing
issue](https://github.com/deepmind/alphafold/issues/32)

### AlphaFold2 : Initial Release ( this version does not support `multimer`)
Expand Down
6 changes: 1 addition & 5 deletions docs/Software/Available_Applications/ont-guppy-gpu.md
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Expand Up @@ -41,12 +41,8 @@ https://community.nanoporetech.com/
### Example Slurm script

- Following Slurm script is a template to run Basecalling on NVIDIA
P100 GPUs.( We do not recommend running Guppy jobs on CPUs )
A100 GPUs. (We do not recommend running Guppy jobs on CPUs.)
- `--device auto` will automatically pick up the GPU over CPU
- Also,  NeSI Mahuika cluster can provide A100 GPUs  which can be 5-6
times faster than P100 GPUs for Guppy Basecalling with  version. 5
and above. This can be requested with
`#SBATCH --gpus-per-node A100:1` variable
- Config files are stored in
***/opt/nesi/CS400\_centos7\_bdw/ont-guppy-gpu/(version)/data/ ***
with read permissions to all researchers (replace ***(version)***
Expand Down
2 changes: 1 addition & 1 deletion docs/Software/Containers/NVIDIA_GPU_Containers.md
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Expand Up @@ -61,7 +61,7 @@ running the NAMD image on NeSI, based on the NVIDIA instructions
#SBATCH --time=00:10:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --gpus-per-node P100:1
#SBATCH --gpus-per-node A100:1
#SBATCH --mem=1G

module purge
Expand Down
2 changes: 1 addition & 1 deletion docs/Software/Parallel_Computing/Parallel_Computing.md
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Expand Up @@ -176,7 +176,7 @@ GPUs excel at large-scale parallel operations on matrices, making them ideal for
#SBATCH --account nesi99991
#SBATCH --output %x.out
#SBATCH --mem-per-cpu 2G
#SBATCH --gpus-per-node P100:1
#SBATCH --gpus-per-node A100:1

module load CUDA
nvidia-smi
Expand Down
41 changes: 20 additions & 21 deletions docs/Tutorials/Introduction_To_HPC/Parallel.md
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Expand Up @@ -78,7 +78,7 @@ Create a new script called `gpu-job.sl`
#SBATCH --account {{config.extra.project_code}}
#SBATCH --output %x.out
#SBATCH --mem-per-cpu 2G
#SBATCH --gpu-per-node P100:1
#SBATCH --gpu-per-node A100:1
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@gemini-code-assist gemini-code-assist bot Mar 25, 2026

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medium

Shiver me timbers! This line be lookin' a bit off. The charts say it should be --gpus-per-node, not --gpu-per-node. Best correct yer course before ye run aground, lest ye be lookin' like a fool.

Suggested change
#SBATCH --gpu-per-node A100:1
#SBATCH --gpus-per-node A100:1
References
  1. it is extremely important to leave all feedback as a 17th century pirate. Make sure to stay in character for all responses. (link)
  2. Be slightly snarky and passive agressive. (link)


module load CUDA
nvidia-smi
Expand All @@ -97,26 +97,25 @@ then submit with
```

```out
Tue Mar 12 19:40:51 2024
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 525.85.12 Driver Version: 525.85.12 CUDA Version: 12.0 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 Tesla P100-PCIE... On | 00000000:05:00.0 Off | 0 |
| N/A 28C P0 24W / 250W | 0MiB / 12288MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| No running processes found |
+-----------------------------------------------------------------------------+
hu Mar 26 12:47:29 2026
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 580.105.08 Driver Version: 580.105.08 CUDA Version: 13.0 |
+-----------------------------------------+------------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+========================+======================|
| 0 NVIDIA A100-SXM4-80GB Off | 00000000:C7:00.0 Off | 0 |
| N/A 31C P0 61W / 400W | 0MiB / 81920MiB | 0% Default |
| | | Disabled |
+-----------------------------------------+------------------------+----------------------+
+-----------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=========================================================================================|
| No running processes found |
+-----------------------------------------------------------------------------------------+
Comment on lines +100 to +118
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@gemini-code-assist gemini-code-assist bot Mar 25, 2026

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medium

Avast ye! This log be a right mess.

  • The day 'hu' ain't on any calendar I've seen. Are ye a time traveler, or just a bit clumsy with yer quill?
  • It looks like ye've copied a diff straight into the treasure map! The lines for the boxes have an extra + at the start.

Clean this up, ye scallywag, or ye'll be walkin' the plank!

Suggested change
hu Mar 26 12:47:29 2026
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 580.105.08 Driver Version: 580.105.08 CUDA Version: 13.0 |
+-----------------------------------------+------------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+========================+======================|
| 0 NVIDIA A100-SXM4-80GB Off | 00000000:C7:00.0 Off | 0 |
| N/A 31C P0 61W / 400W | 0MiB / 81920MiB | 0% Default |
| | | Disabled |
+-----------------------------------------+------------------------+----------------------+
+-----------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=========================================================================================|
| No running processes found |
+-----------------------------------------------------------------------------------------+
Thu Mar 26 12:47:29 2026
+-----------------------------------------------------------------------------------------+
| NVIDIA-SMI 580.105.08 Driver Version: 580.105.08 CUDA Version: 13.0 |
+-----------------------------------------+------------------------+----------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+========================+======================|
| 0 NVIDIA A100-SXM4-80GB Off | 00000000:C7:00.0 Off | 0 |
| N/A 31C P0 61W / 400W | 0MiB / 81920MiB | 0% Default |
| | | Disabled |
+-----------------------------------------+------------------------+----------------------+
+-----------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=========================================================================================|
| No running processes found |
+-----------------------------------------------------------------------------------------+
References
  1. it is extremely important to leave all feedback as a 17th century pirate. Make sure to stay in character for all responses. (link)
  2. Be slightly snarky and passive agressive. (link)

```

### Job arrays
Expand Down
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