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APSIM-HPC
Deploy APSIM (Agricultural Production Systems sIMulator - https://www.apsim.info/) on high performance computing clusters.
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Updating branch
#58
Ollehar
closed
4 hours ago
0
Snakefile : combined Snakefile for both Process txt and Process apsimx is ignoring the latter which is the second rule
#57
DininduSenanayake
opened
1 day ago
0
shell script to launch Snakefiles in order
#56
DininduSenanayake
closed
1 day ago
0
add db_sorter rule to Snakefile_apsimx
#55
DininduSenanayake
closed
1 day ago
0
add two separate Snakefiles for txt-apsimx & apsimx-db for testing
#54
DininduSenanayake
closed
1 day ago
0
Snakefile 1 - First Production level Snakefile for 06-slurm-array/array_create_db_files.sl
#53
DininduSenanayake
closed
1 day ago
2
change directory numbering scheme to avoid 10 being above 2
#52
DininduSenanayake
closed
3 days ago
0
add Slurm profiling figures to main directory structure
#51
DininduSenanayake
closed
3 days ago
0
Update generate_apsim_configs.R
#50
Ollehar
closed
4 days ago
0
Restart script for timedout/failed jobs while creating .apsimx and .db placeholder files
#49
DininduSenanayake
closed
1 week ago
0
reliable & clean "restart" method for jobs which "timed out" while creating .apsimx ( and .db placeholder) files.
#48
DininduSenanayake
closed
1 week ago
1
change directory structure to address issue #42
#47
DininduSenanayake
closed
1 week ago
0
create slurmlogs directory within each of the set-x directoties as part of the split script
#46
DininduSenanayake
closed
1 week ago
0
add YYYY-MM-DD to apsim-simulations directory name
#45
DininduSenanayake
closed
1 week ago
0
When did we create the apsim-simulations directory ? . Record the date with apsim-simulations-$(date +"%Y%m%d")
#44
DininduSenanayake
closed
1 week ago
0
add `mkdir -p set-x/slurmlogs` to split_configfiles_to_sets.sh as Slurm < 23.0.0 can not automatically create dir in `#SBATCH --output dir/...`
#43
DininduSenanayake
closed
1 week ago
0
move split_configfiles_to_sets.sh out of 8-misc-scripts to a higher level
#42
DininduSenanayake
closed
1 week ago
0
add split starting message to split config shell script
#41
DininduSenanayake
closed
1 week ago
0
split_configfiles_to_sets.sh needs a confirmation at the start to say the "splitting is in progress"
#40
DininduSenanayake
closed
1 week ago
1
copy .met and .apsimx files from current working directory to set-x d…
#39
DininduSenanayake
closed
1 week ago
0
Direct split_configfiles_to_sets.sh to make a copy of .met and .apsimx files from current working directory to each `set-x`
#38
DininduSenanayake
closed
1 week ago
1
add a README to misc scripts
#37
DininduSenanayake
closed
1 week ago
0
misc-scripts and "skip failed and hop" apsimx generate script
#36
DininduSenanayake
closed
1 week ago
0
4-create-apsimx-files: Allow the for loop to continue for 10 ( arbitrary number) consecutive input failures while moving the failed .txt files to a separate directory AND implement a reliable restart method
#35
DininduSenanayake
closed
3 days ago
4
Running create_apsimx.sl to create .apsimx files and .db place holder files require a progress bar
#34
DininduSenanayake
opened
2 weeks ago
3
New array script
#33
DininduSenanayake
closed
2 weeks ago
0
Create apsimx
#32
DininduSenanayake
closed
2 weeks ago
0
creating .apsimx files in parallel while all Config files and master .apsix files are on the same directory triggers System.IO.FileNotFoundException
#31
DininduSenanayake
closed
2 weeks ago
1
R script for generating *.txt Config files with the use of ExampleConfig.txt template
#30
DininduSenanayake
closed
2 weeks ago
0
*.db size sorter - Split *.db files to PASSED and FAILED based on file size ( current threshold is <1MB failed)
#29
DininduSenanayake
closed
2 weeks ago
0
create mock .db files with varying sizes for file sorter validation
#28
DininduSenanayake
closed
1 week ago
2
*.db file verification : Add a sanity check to verify the .db files based on file size ( define the threshold to be >1MB)
#27
DininduSenanayake
closed
2 weeks ago
2
Record runtime information with CPU:Memory efficiency to find the optimal resource request
#26
DininduSenanayake
closed
3 days ago
3
Investigate the use --cpu-count flag with `Models` and `Models --apply`
#25
DininduSenanayake
closed
2 weeks ago
3
Run `Models --apply` and `Models` interactively for few samples
#24
DininduSenanayake
closed
2 weeks ago
1
investigate weather file deadlocking ?
#23
DininduSenanayake
closed
2 weeks ago
2
add version verfication command to slurm script
#22
DininduSenanayake
closed
3 weeks ago
0
Exclude MasterSoil and LargeExample *.apsimx files from ${APSIMX_FILES}
#21
DininduSenanayake
closed
2 weeks ago
2
Exclude "ExampleConfig.txt" from ${CONFIG_FILES}
#20
DininduSenanayake
closed
2 weeks ago
3
print container image path
#19
DininduSenanayake
closed
4 weeks ago
0
fix recursive concatenation
#18
DininduSenanayake
closed
1 month ago
0
update_readme.py : Recursive concatenation is not the desirable behaviour
#17
DininduSenanayake
closed
1 month ago
1
fix item one indexing error: first item on the CSV was getting excluded
#16
DininduSenanayake
closed
3 weeks ago
2
possible indexing issue : First sample ID from CSV being ignored
#15
DininduSenanayake
closed
3 weeks ago
1
database_list.txt registers .db names based on Slurm state which included failed sample IDs
#14
DininduSenanayake
closed
1 month ago
1
Introduce better error handling for failed jobs as Slurm state was marked as "COMPLETED" for failed jobs
#13
DininduSenanayake
closed
1 month ago
1
Snakemake rule to confirm the ".apsimx" files required for the "current" simulation is in the same path as config files AND the submission script
#12
DininduSenanayake
closed
1 day ago
1
Run a version verification after the container build with `Models` command
#11
DininduSenanayake
closed
3 weeks ago
2
Document Slurm array throttling
#10
DininduSenanayake
closed
4 weeks ago
1
Add example config
#9
DininduSenanayake
closed
1 month ago
0
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