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cleanup homes directory #1461

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ala-ebi opened this issue Oct 15, 2024 · 0 comments
Open
10 tasks

cleanup homes directory #1461

ala-ebi opened this issue Oct 15, 2024 · 0 comments
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@ala-ebi
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ala-ebi commented Oct 15, 2024

make sure all the scheduled slurm jobs in scrontab have an error and output dir instead of using sportbot home dir by default.
among those jobs:

  • FTP SYNC (prod, dev)

/hps/software/users/parkinso/spot/gwas/prod/scripts/cron/ftp_sync_wrapper_slurm.sh
/hps/software/users/parkinso/spot/gwas/dev/scripts/cron/ftp_sync_wrapper_slurm.sh
Although the sbatch inside scrontab has defined --output and --error, there logs in the homes dir indicating another job is created, probably because the original sbatch starts another sbatch (although I cant see it in the file, maybe from the .py script that's called)

  • GENERATE YAML (DEV)

/hps/software/users/parkinso/spot/gwas/dev/scripts/cron/sumstats_service/submit_yaml_generation.sh

  • GENERATE YAML (PROD)

/hps/software/users/parkinso/spot/gwas/prod/scripts/cron/sumstats_service/submit_yaml_generation.sh

  • Stop RabbitMQ consuming messages for publication added in Depo curation

/hps/software/users/parkinso/spot/gwas/prod/sw/gwas-rabbitmq-listener/cancel-slurm-publication-import.sh

  • Start RabbitMQ to consume messages for publication added in Depo curation

/hps/software/users/parkinso/spot/gwas/prod/sw/gwas-rabbitmq-listener/run-slurm-publication-import.sh

  • SEND YAML GEN FAILURES (DEV)

/hps/software/users/parkinso/spot/gwas/dev/scripts/cron/sumstats_service/submit_agg_email.sh

  • SEND YAML GEN FAILURES (PROD)

/hps/software/users/parkinso/spot/gwas/prod/scripts/cron/sumstats_service/submit_agg_email.sh

  • /hps/software/users/parkinso/spot/gwas/prod/sw/deposition_sync/run-slurm-sync-wrapper.sh

  • /hps/software/users/parkinso/spot/gwas/prod/sw/deposition_sync/run-slurm-sync-wrapper.sh unpublished

  • /hps/software/users/parkinso/spot/gwas/prod/sw/mapping-pipeline/run-slurm-scheduled-mapping.sh

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