Cannot clone Github repo to Raven

[sr320]

Trying

get

>> /usr/bin/git clone --progress https://github.com/epigeneticstoocean/2018_L18-adult-methylation.git 2018_L18-adult-methylation
Cloning into '2018_L18-adult-methylation'...
error: chmod on /media/8TB_ext_HDD01/sr320/github/2018_L18-adult-methylation/.git/config.lock failed: Operation not permitted
fatal: could not set 'core.filemode' to 'false'

[kubu4]

Oh boy...

Annoying workaround would be to clone repo to one of the other HDDs and then move the entire repo to the 8TB HDD.

The "real" fix is to reformat that drive and change it to a different file system that is compatible with Unix permissions...

[sr320]

actually will try cp

[kubu4]

Ah! For the rsync command, you won't be able to use the -a option with that drive... Another annoying "nuance" with the file system set for that HDD...

[sr320]

rsync without the -a does not move anything... trying cp -r now.

[sr320]

re rsync

sr320@raven:/media/8TB_ext_HDD01/sr320/github$ rsync -vz /home/sr320/github/2018_L18-adult-methylation/ 2018_L18-adult-methylation/
skipping directory .

sent 16 bytes  received 12 bytes  56.00 bytes/sec
total size is 0  speedup is 0.00
sr320@raven:/media/8TB_ext_HDD01/sr320/github$ rsync -vz /home/sr320/github/2018_L18-adult-methylation/* 2018_L18-adult-methylation/
skipping directory analyses
skipping directory bg_data
skipping directory code
skipping directory data
2018_L18-adult-methylation.Rproj
README.md

sent 469 bytes  received 54 bytes  1,046.00 bytes/sec
total size is 383  speedup is 0.73
sr320@raven:/media/8TB_ext_HDD01/sr320/github$ rsync -vz /home/sr320/github/2018_L18-adult-methylation .
skipping directory 2018_L18-adult-methylation

sent 16 bytes  received 12 bytes  56.00 bytes/sec
total size is 0  speedup is 0.00

[kubu4]

I think you need to add -r to put it into recursive mode (which is part of what the -a option does).

[sr320]

Stepping back for a minute- the HD is not a solution to the problem of no space on raven.

I use raven for Rstudio / Github... I need to be able to work in external HD

[kubu4]

I don't think I follow...

[sr320]

Reason for the external hard drives is to free up space on raven proper.
I cannot work on external hard drive because drive format does not let me clone github repos to...

[sr320]

I suppose I could maybe start new repo on external HD? then work (commit/pull).. (cannot test right now as I am using Rstudio ATM)

But presume pull would not work.

[kubu4]

The 8TB external HDD attached to my computer is formatted in a Linux-friendly format (ext4). This means that permission changes and timestamp changes can be manipulated via traditional commands (e.g. chmod, chown, chgrp, etc) which would probably simplify our usage if we swapped this for the one currently attached to Raven.

If you'd like to do this, I've already "unmounted" the HDD attached to my computer, so you can just pull it out of the toaster without worry. Along those lines, we should unmount the 8TB external attached to Raven prior to removal. I'm guessing you could do this via the GUI. Otherwise, let me know and I can unmount it remotely.

[kubu4]

Ha! Well, that went just as smoothly as it's been going for the past week. Rebooted and now can't get in (again)...

[kubu4]

Believe it or not, the 8TB external HDD on Raven is up and running!!!!!! There shouldn't be any permission issues or rsync issues!

Please test and report back!

[sr320]

No permissions issue... (unless you try to clone a repo - https://d.pr/i/hosUFw)

[kubu4]

I'm in the same boat as well. Can't make a directory (again)...

[kubu4]

I have unmounted the 8TB HDD and am currently running sudo fsck.ext4 -fy on that drive. This looks for and attempts to fix any errors. It has found numerous errors (crazy stuff about inodes, "imagic flag", timestamps...) and is supposedly fixing them. We'll see...

[kubu4]

Hallelujah! I think I've done it! Seriously. I moved the 8TB HDD to an internal drive bay. I've even upped the game by adding a second 8TB HDD and an additional internal 1TB HDD!

Here're the details (I'll get these added to the Handbook shortly).

List of all HDDs and the locations (this list does not include the primary 1TB boot drive):

/dev/sde1       916G  407G  464G  47% /media/1TB_ext_SSD01
/dev/sdf1       916G   77M  870G   1% /media/1TB_ext_SSD02
/dev/sdc1       7.3T  519M  6.9T   1% /home/shared/8TB_HDD_01
/dev/sdd1       7.3T   93M  6.9T   1% /home/shared/8TB_HDD_02
/dev/sdb1       916G   77M  870G   1% /home/shared/1TB_HDD02

I've briefly tested by successfully cloning the RobertsLab/resources repo to the three internal HDDs and the computer didn't lock up!

Please try things out and let me know how it goes...

🙏