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icommands

Last modified by hajaalin@helsinki_fi on 2024/01/24 07:07

Login to lmu-ida.biocenter.helsinki.fi.

Create a virtual machine for connecting to Ida.

 

Locate your data on LMU1 or LMU2.

[hajaalin@lmu-ida ~]$ ls /mnt/biotek-ad/biotek-groups/LMU1/users/harri
analysis_htj.py              CAM-ImageJ_Intelligent_Scan.zip  CAMScriptHighRes.txt         

Locate your folder in Ida.

[hajaalin@lmu-ida ~]$ ils /ida/hy/hy7004
/ida/hy/hy7004:
  collectionMetadataTemplate
  testi.txt
  C- /ida/hy/hy7004/Jernvall
  C- /ida/hy/hy7004/Lappalainen
  C- /ida/hy/hy7004/LMU-staff
  C- /ida/hy/hy7004/Mäkelä
  C- /ida/hy/hy7004/published
  C- /ida/hy/hy7004/Thesleff
  C- /ida/hy/hy7004/Vartiainen
[hajaalin@lmu-ida ~]$ ils /ida/hy/hy7004/LMU-staff
/ida/hy/hy7004/LMU-staff:
  C- /ida/hy/hy7004/LMU-staff/hajaalin
  C- /ida/hy/hy7004/LMU-staff/mcrivaro
  C- /ida/hy/hy7004/LMU-staff/mikmolin
  C- /ida/hy/hy7004/LMU-staff/tanhuanp[hajaalin@lmu-ida ~]$ ils /ida/hy/hy7004/LMU-staff/hajaalin
/ida/hy/hy7004/LMU-staff/hajaalin:
  C- /ida/hy/hy7004/LMU-staff/hajaalin/CAM_study
  C- /ida/hy/hy7004/LMU-staff/hajaalin/MyNewProject
  C- /ida/hy/hy7004/LMU-staff/hajaalin/testing

Create a new folder in Ida.

[hajaalin@lmu-ida ~]$ imkdir /ida/hy/hy7004/LMU-staff/hajaalin/LMU1
[hajaalin@lmu-ida ~]$ ils /ida/hy/hy7004/LMU-staff/hajaalin
/ida/hy/hy7004/LMU-staff/hajaalin:
  C- /ida/hy/hy7004/LMU-staff/hajaalin/CAM_study
  C- /ida/hy/hy7004/LMU-staff/hajaalin/LMU1
  C- /ida/hy/hy7004/LMU-staff/hajaalin/MyNewProject
  C- /ida/hy/hy7004/LMU-staff/hajaalin/testing

Synchronize AD folder and Ida folder.

[hajaalin@lmu-ida ~]$ nohup irsync -VKr /mnt/biotek-ad/biotek-groups/LMU1/users/harri i:/ida/hy/hy7004/LMU-staff/hajaalin/LMU1 >& ida_irsync_harri_lmu1.log&
  • nohup: run the command in the background, the process will not stop even if you close the terminal
  • irsync: the command the does the transfer
  • -V: very verbose logging
  • -K: calculate and compare checksums
  • -r: recursive

  • /mnt/biotek-ad/biotek-groups/LMU1/users/harri: the folder you want to copy to Ida

  • i: indicates the folder is in Ida
  • /ida/hy/hy7004/LMU-staff/hajaalin/LMU1: the Ida folder
  • >& direct output to log file
  • ida_rsync_harri_lmu1.log: the log file
  • &: run in background (together with nohup)

Check that everything arrived.

irsync -rls /mnt/biotek-ad/biotek-groups/LMU1/users/harri i:/ida/hy/hy7004/LMU-staff/hajaalin/LMU1
  • l = don't move data, only check if there are differences
  • s = compare file sizes (not checksums)

When run like this, the command does not print anything, if all files are present in the destination folder in Ida, and the file sizes match.