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Ingvord edited this page Mar 23, 2020
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Rebuild node-hdf5:
node-gyp rebuild --debug --hdf5_home_linux=/usr/lib/x86_64-linux-gnu/hdf5/serial
Run mongodb:
docker run -p 27017:27017 --rm --name mongodb -d mongo
Mount gpfs-core
mount -o nfsvers=4.0,sec=krb5,hard asap3.desy.de:/asap3/petra3/gpfs /asap3/petra3/gpfs
Build docker:
docker build -t ingvord/beamtimedb-utils .
Push docker:
docker push ingvord/beamtimedb-utils:latest
Pull docker:
docker pull ingvord/beamtimedb-utils:latest
Run docker:
docker run --env-file .beamtimedb-utils.env -v /asap3/petra3/gpfs:/gpfs -it ingvord/beamtimedb-utils:latest /bin/bash
Trim .txt to .json
head -n -2 /gpfs/p05/2019/data/11008939/beamtime-metadata-11008939.txt | tail -n +4 > beamtime-metadata-11008939.json
Run import
node /usr/src/app/js/import_beamtime.js --doorBeamtimeJson beamtime-metadata-11008939.json
Run walk gpfs
node /usr/src/app/js/walk_gpfs.js --gpfsBeamtimeDataRoot=/gpfs/p05/2019
Run walk gpfs detached:
docker run --env-file .beamtimedb-utils.env -v /asap3/petra3/gpfs:/gpfs -d ingvord/beamtimedb-utils:latest /usr/local/bin/node /usr/src/app/js/walk_gpfs.js --gpfsBeamtimeDataRoot=/gpfs/p05/2019