Questions tagged [hpc]
Acronym for "high performance computing"
10
questions
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views
bsub with -M and -hl a good idea?
I have been submitting my snakemake pipeline to a node-shared high performance computer (HPC) via bsub the following way:
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- 159
1
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118
views
Multiple values for memory resources shown when Snakemake is run
I am running a Snakemake (V7.14.0) pipeline on the cluster and provided resources in a resource config file like:
threads:
tool1: 4
mem_gb:
tool1: 12
Point ...
- 159
1
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answer
87
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How to get the external (cluster) job id and not internal snakemake job id in cluster log files?
Background I am using snakemake and I want to add the external (cluster) jobid to my cluster output and error log files. Below is my shell script.
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- 159
1
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0
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48
views
Load balancing numerous single-threaded processes with Snakemake on the grid
I'm familiar with running Snakemake in a DRMAA-enabled grid environment. (Most often, I write Python programs as wrappers and invoke the workflow via Snakemake's Python API.) Typically, I'm running ...
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2
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318
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Snakemake fails because it cannot create logs inside a read-only Singularity Container
I am using Snakemake from inside a Singularity container. Because of that, the directory that Snakemake wants to log to cannot be created, and I get an ...
- 131
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40
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Error while using E-utilities on slurm HPC
I keep getting the error while using E-utilities on Slurm HPC, could you suggest how I can resolve it?
SCRIPT:
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1
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2
answers
406
views
How to run Jupyter script on Slurm HPC
Now jupyter installed on the server and I am using below code to plot the rarefaction plot but I am still getting some error. could you please suggest how I can get rid of it?
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- 341
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149
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repophlan script to download bacterial genome
I am trying to donwload the microbial genome using the repophlan_get_microbes.py (https://github.com/SegataLab/repophlan) but now it is running more than 10 days and still not finished on slurm HPC.
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- 341
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2
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52
views
no result from heat map WGCNA
I have created a heat map using WGCNA using R. But the heat map command is not showing the plot and there is no error. I have a large number of modules and traits. I am not sure if that is the reason. ...
- 111
0
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1
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63
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How to run a one-time 'setup' step for amrfinder in snakemake using conda
I'm trying to add amrfinder running within conda to a snakemake workflow, working on a slurm HPC.
The first time you run amrfinder, you have to run ...
- 217