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Hi,
Our hpc runs 2 slurm clusters, this requires us to provide the -M or --cluster option to most slurm related commands like sbatch, squeue and scancel. This option is unsupported in snakemake 8+ …
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@yingyisong
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Dear Kate,
I am trying to run squish.o but it crashed after hashing. I tries it on both computing cluster and Mac, and the error is the same.
```
/immunopeptidogenomics/squish.o -d file1_transc…
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**Preconditions** (Any important steps we need to know)
Redis cluster created on slurm.
**Steps to reproduce** (How to reproduce what you found step by step)
1) Create cluster nodes
```bash
sru…
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- [ ] mv important parts of bianca specifics from slurm_on_bianca_details.md to slurm_on_bianca.md
- [ ] mv important parts of cluster agnostics from slurm_details.md to slurm.md
- [ ] populate sl…
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Hi, I was following the guide on https://aws.amazon.com/blogs/hpc/leveraging-slurm-accounting-in-aws-parallelcluster/ and encountered the following error:
```
[execute] sacctmgr: error: slurm_persis…
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2: Traceback (most recent call last):
2: File "/workspace/NeMo/examples/nlp/language_modeling/tuning/megatron_gpt_finetuning.py", line 64, in main
2: model = MegatronGPTSFTModel.restore_from(cfg.mod…
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There are hardcoded paths and slurm loaded modules, these need to be provided as separate scripts -- that the user can override from its home directory, such that we can run on any slurm cluster
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I came across this when trying to export data from some years.
But its not related to running over a long time period because it fails the same way even when I have history-start the day this issue …
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**Software Versions**
Snakemake 8.16.0
snakemake-executor-plugin-slurm 0.9.0
slurm 23.11.7
**Describe the bug**
I have recently moved to Snakemake v8.16 and have been trying to execute…