Lakeflow Input

Build and Run Commands

Local or EC2 (Docker)

git clone https://github.com/SWOT-Confluence/LakeFlow_Confluence/tree/travis_dev

cd Lakeflow_Confluence

docker build -t lakeflow_input -f Dockerfile_input .

docker run -v /mnt/input/lakeflow:/data/input -v /mnt/input/sword:/data/sword/ lakeflow_input -c /data/input/reaches_of_interest.json -w 1 -i /data/input

HPC (Singularity)

docker -t lakeflow_input travissimmons/lakeflow_input:latest

docker push travissimmons/lakeflow_input:latest

singularity build lakeflow_input.simg docker://travissimmons/lakeflow_input

singularity run –bind /mnt/input/lakeflow:/data/input,/mnt/input/sword:/data/sword lakeflow_input.sif -c /data/input/reaches_of_interest.json -w 1 -i /data/input

Dev notes….

/mnt/input/sword should have a the relevant sword for your continent /mnt/input/lakeflow (-i flag) should have all of your auxilary input data like below

updated_pld = fread(file.path(indir,”/SWORDv16_PLDv103_wo_ghost_rch.csv”)) et = fread(file.path(indir, ‘/ancillary/et.csv’)) tributary = fread(file.path(indir,’/ancillary/tributaries.csv’)) sword_geoglows = fread(file.path(indir,’/ancillary/sword_geoglows.csv’)) dir.create(file.path(indir, “/clean”), showWarnings = FALSE)

Lakeflow Deploy

Build and Run Commands

Local or EC2 (Docker)

git clone https://github.com/SWOT-Confluence/LakeFlow_Confluence/tree/travis_dev

cd Lakeflow_Confluence

docker build -t lakeflow_deploy -f Dockerfile_deploy .

docker run -v /mnt/input/lakeflow:/data/input -v /mnt/input/sos:/sos/input lakeflow_deploy -c /data/input/viable/viable_locations-255.csv -s /sos/input -w 1 -i /data/input -o /data/input/out –index 2

HPC (Singularity)

docker -t lakeflow_deploy travissimmons/lakeflow_deploy:latest

docker push travissimmons/lakeflow_deploy:latest

singularity build lakeflow_deploy.simg docker://travissimmons/lakeflow_deploy

singularity run –bind /mnt/input/lakeflow:/data/input,/mnt/input/sos:/sos/input lakeflow_deploy.sif -c /data/input/viable/viable_locations-255.csv -s /sos/input -w 1 -i /data/input -o /data/input/out –index 2

Dev notes….

/mnt/input/sos (-s flag) should ahve the SOS file for the relevant continent

## Here is a link to an empty mount with an sos and a copy of sword https://drive.google.com/file/d/1xRltFZ1gyP_nvwHMJW-rIgClzXx8CSLC/view?usp=sharing

Here is a link to my last delivery notes, reading through the lakeflow sections may be helpful https://umass-my.sharepoint.com/:w:/g/personal/tsimmons_umass_edu/EQXh6_zLNVRMjxdkHHI1PW0BSlifSnKlEiFuoLK_UA85-w?rtime=-U2lf–U3Ug