Backups¶
As explained in the Structure section, there are different partitions with different levels of backups. Basically, there are two options of backup:
- Snapshots : It is the state of the system at a particular point in time. It is usefull for human mistakes, ie. if you delete or edit the wrong file. For HW errors or big catastrophes (e.g. a fire) (unlikely) is not useful, because the backup data is stored in the same disk/location. We can recover the data by ourselves.
- Standard backup : Useful for human mistakes and HW/catastrophes. To recover the data from a backup, we need to contact IT and it could take a few days for recovering.
Depending the partition, the safety level is different:
home/: Snapshots: 3 per day last 1.5 days, one for each of the last 5 days and one for each of the last 4 weeks. medium-high safe.projects/: Standard backups and snapshots. Backup: every day during the last 15 days and every week during the last 12 weeks. Snapshots: 3 per day last 5 days, one for each of the last 15 days and one for each of the last 12 weeks. high safe.datasets/: Standard backups. Backup: every Sunday, replaced every week. medium safe.datasafe/: Snapshots: 3 per day last 5 days, one for each of the last 15 days and one for each of the last 12 weeks. medium-high safe.nobackup//nobackup2/: No backup at all...
Example of recovering data¶
Let's say we have deleted or edited by mistake a file in a partition with snapshots (e.g. /workspace/projects/). If we check the content of the .snapshot/ folder:
mgrau@login01:/workspace/projects$ ls /workspace/projects/.snapshot/
daily_at_23_noSun.2023-06-05_2300 daily_at_23_noSun.2023-06-15_2300 hourly_mon2fri_11_15_19.2023-06-16_1900 hourly_mon2fri_11_15_19.2023-06-21_1900 Sun_at_23.2023-05-14_2300
daily_at_23_noSun.2023-06-06_2300 daily_at_23_noSun.2023-06-16_2300 hourly_mon2fri_11_15_19.2023-06-19_1100 hourly_mon2fri_11_15_19.2023-06-22_1100 Sun_at_23.2023-05-21_2300
daily_at_23_noSun.2023-06-07_2300 daily_at_23_noSun.2023-06-17_2300 hourly_mon2fri_11_15_19.2023-06-19_1500 hourly_mon2fri_11_15_19.2023-06-22_1500 Sun_at_23.2023-05-28_2300
daily_at_23_noSun.2023-06-08_2300 daily_at_23_noSun.2023-06-19_2300 hourly_mon2fri_11_15_19.2023-06-19_1900 Sun_at_23.2023-04-02_2300 Sun_at_23.2023-06-04_2300
daily_at_23_noSun.2023-06-09_2300 daily_at_23_noSun.2023-06-20_2300 hourly_mon2fri_11_15_19.2023-06-20_1100 Sun_at_23.2023-04-09_2300 Sun_at_23.2023-06-11_2300
daily_at_23_noSun.2023-06-10_2300 daily_at_23_noSun.2023-06-21_2300 hourly_mon2fri_11_15_19.2023-06-20_1500 Sun_at_23.2023-04-16_2300 Sun_at_23.2023-06-18_2300
daily_at_23_noSun.2023-06-12_2300 hourly_mon2fri_11_15_19.2023-06-15_1900 hourly_mon2fri_11_15_19.2023-06-20_1900 Sun_at_23.2023-04-23_2300
daily_at_23_noSun.2023-06-13_2300 hourly_mon2fri_11_15_19.2023-06-16_1100 hourly_mon2fri_11_15_19.2023-06-21_1100 Sun_at_23.2023-04-30_2300
daily_at_23_noSun.2023-06-14_2300 hourly_mon2fri_11_15_19.2023-06-16_1500 hourly_mon2fri_11_15_19.2023-06-21_1500 Sun_at_23.2023-05-07_2300
We can see a daily snapshot at 23.00h during the last 15 days (daily_at_23_noSun.2023-06-XX_2300). Then we have 3 snapshots per day (at 11h,15h and 19h) during the last 5 working-days (hourly_mon2fri_11_15_19.2023-06-XX_XX00) and then we have one snapshot weekly (sunday at 23h) during the last 12 weeks (Sun_at_23.2023-0X-XX_2300).
Inside every snapshot, we can see the same file structure of projects:
mgrau@login01:/workspace/projects$ ls /workspace/projects/.snapshot/daily_at_23_noSun.2023-06-05_2300
all_aecc clustering_3d diskusage20200511.txt healthy_chemo nanopore regulatory_regions small_collaborations_ines
all_aecc_pediatric cndrivers diskusage20200619.txt hotmaps_signatures neoantigen repair_states stjude
alphafold_features colorectal_apoe diskusage20200725.txt immune_biomarkers new_oncodrivemut replication_timing st_jude_life
bgframework courses diskusage20200926.txt immune_pheno_hartwig noncoding_regions reverse_calling stockholm_ai
bladder_ts cptac_analysis diskusage20201011.txt intogen nonsense_cptac rhabdoid_tumors structural_variants
blca_eduardporta damage_maps diskusage_20211119.txt intogen_2017 olivia sample_specific_features test_folder_delete
boostdm dde diskusage.txt intogen_plus oncodrive sample_specific_profiles tf_mutations
boostdm_ch degrons driver_potential Liver_Mouse oncodrive3d samuels_hmf translation_fidelity
boostdm_germline_sensitivity diskusage20200104.txt exemple_test meso_exomes oncodriveclustl sars_cov_2 ubiquitins
breakpoints diskusage20200115.txt expression_signatures methyl_predictors oriol_aml_intogen scell_tall worms
build_table.py diskusage20200201.txt genomewide_mmr miguel_nanopore pagerank_combination service zfp36l1
cgi diskusage20200215.txt genomewide_MMR mutfootprints pancreas_meritxell sherlock
cgi_clinics diskusage20200319.txt genomic_regions mutfootprints_code_review pepe_clustering signature_sensitivity
chemogenomics diskusage20200330.txt hairpins mutograph periodicity signet
chemotrans diskusage20200421.txt hartwig mut_region_profile pileup_mappability simuclones
clonalhemato_ukb diskusage20200427.txt hartwig_signatures_id mut_risk prominent sjd_pediatric_tumors
We can then copy back the file deleted to the original location.
Reference¶
- Miguel Grau
- Jordi Deu-Pons