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feedback on steps up to training #5

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feedback on steps up to training #5

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8b5a14e
feedback on steps up to training
sfmig May 19, 2023
0462d90
replaced my email with generic email address)
niksirbi Jun 15, 2023
fee389c
moved details about SLEAP module in troubleshooting
niksirbi Jun 15, 2023
9aa8914
added appendices
niksirbi Aug 9, 2023
437a696
add graph describing HPC access
niksirbi Aug 10, 2023
22f9cb3
try embedding mermaid graph with img link
niksirbi Aug 10, 2023
dc51819
include the flowchart image in the repo
niksirbi Aug 10, 2023
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333 changes: 254 additions & 79 deletions SLEAP/HowTo.md
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1,218 changes: 369 additions & 849 deletions SLEAP/presentation/presentation.html
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8 changes: 4 additions & 4 deletions SLEAP/presentation/presentation.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -227,7 +227,7 @@ cat train_script.sbatch
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
#SBATCH --mail-type=ALL
#SBATCH --mail-user=[email protected]
#SBATCH --mail-user=[email protected]

# Load the SLEAP module
module load SLEAP
Expand Down Expand Up @@ -309,7 +309,7 @@ training_log.csv
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
#SBATCH --mail-type=ALL
#SBATCH --mail-user=n.sirmpilatze@@ucl.ac.uk
#SBATCH --mail-user=[email protected]

# Load the SLEAP module
module load SLEAP
Expand Down Expand Up @@ -432,7 +432,7 @@ if __name__ == "__main__":
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
#SBATCH --mail-type=ALL
#SBATCH --mail-user=[email protected]
#SBATCH --mail-user=[email protected]

# Load the SLEAP module
module load SLEAP
Expand Down Expand Up @@ -475,7 +475,7 @@ What if we want to run the previous script for multiple batch sizes?
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
#SBATCH --mail-type=ALL
#SBATCH --mail-user=[email protected]
#SBATCH --mail-user=[email protected]
#SBATCH --array=0-2

# Load the SLEAP module
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2 changes: 1 addition & 1 deletion SLEAP/scripts/infer_script.sbatch
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Expand Up @@ -9,7 +9,7 @@
#SBATCH -o slurm.%N.%j.out # write STDOUT
#SBATCH -e slurm.%N.%j.err # write STDERR
#SBATCH --mail-type=ALL
#SBATCH --mail-user=[email protected]
#SBATCH --mail-user=[email protected]

# Load the SLEAP module
module load SLEAP
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2 changes: 1 addition & 1 deletion SLEAP/scripts/train_script.sbatch
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Expand Up @@ -9,7 +9,7 @@
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
#SBATCH --mail-type=ALL
#SBATCH --mail-user=[email protected]
#SBATCH --mail-user=[email protected]

# Load the SLEAP module
module load SLEAP
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2 changes: 1 addition & 1 deletion SLEAP/scripts/train_script_python.sbatch
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
#SBATCH --mail-type=ALL
#SBATCH --mail-user=[email protected]
#SBATCH --mail-user=[email protected]

# Load the SLEAP module
module load SLEAP
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2 changes: 1 addition & 1 deletion SLEAP/scripts/train_script_python_array.sbatch
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Expand Up @@ -9,7 +9,7 @@
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
#SBATCH --mail-type=ALL
#SBATCH --mail-user=[email protected]
#SBATCH --mail-user=[email protected]
#SBATCH --array=0-2

# Load the SLEAP module
Expand Down
Binary file added img/swc_hpc_access_flowchart.png
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