/usr/people... home directory masks /usr in Singularity image

[Peter van Heusden]

Hi there

The home directories on our cluster are /usr/people/<username>. This causes chaos with Singularity images, as /usr ends up containing simply /usr/people/<username> and /usr/bin, /usr/local, etc go missing.

I cannot seem to change this behaviour, no matter what combination of -c, -H and other flags I use. This is with singularity 2.2.

Any ideas how to work around this?

Thanks,

Peter

[Gregory M. Kurtzer]

Hi Peter,

There is a workaround you can do in 2.2 (but we will need to come up with a better fix for that for 2.3). 

Try the option:

 -H /usr/people/username:/home/username 

And if that works export that out in an environment variable in /etc/singularity/init as:

SINGULARITY_HOME=...

export SINGULARITY_HOME

Hopefully that works! Good luck. 

Greg

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[Peter van Heusden]

Hi Greg

Thanks, this works, but only with "sudo singularity". Otherwise I get:

ERROR  : Home directory ownership incorrect: /usr/people/pvh:/home/pvh

ABORT  : Retval = 255

And here is partial debug output:

DEBUG   [U=1124,P=542]     mount-util.c:42:check_mounted()            : Opening /proc/mounts

DEBUG   [U=1124,P=542]     mount-util.c:48:check_mounted()            : Iterating through /proc/mounts

DEBUG   [U=1124,P=542]     util/util.c:102:envar_path()               : Checking environment variable is valid path: 'SINGULARITY_HOME'

VERBOSE [U=1124,P=542]     util/util.c:50:envar()                     : Checking input from environment: 'SINGULARITY_HOME'

DEBUG   [U=1124,P=542]     util/util.c:52:envar()                     : Checking environment variable is defined: SINGULARITY_HOME

DEBUG   [U=1124,P=542]     util/util.c:58:envar()                     : Checking environment variable length (<= 4096): SINGULARITY_HOME

DEBUG   [U=1124,P=542]     util/util.c:64:envar()                     : Checking environment variable has allowed characters: SINGULARITY_HOME

VERBOSE [U=1124,P=542]     util/util.c:87:envar()                     : Obtained input from environment 'SINGULARITY_HOME' = '/usr/people/pvh:/home/pvh'

DEBUG   [U=1124,P=542]     config_parser.c:62:singularity_config_rewind(): Rewinding configuration file

DEBUG   [U=1124,P=542]     config_parser.c:107:singularity_config_get_bool(): Called singularity_config_get_bool(user bind control, 1)

DEBUG   [U=1124,P=542]     config_parser.c:80:singularity_config_get_value(): Called singularity_config_get_value(user bind control)

VERBOSE [U=1124,P=542]     config_parser.c:91:singularity_config_get_value(): Got config key user bind control (= 'yes')

DEBUG   [U=1124,P=542]     config_parser.c:113:singularity_config_get_bool(): Return singularity_config_get_bool(user bind control, 1) = 1

VERBOSE [U=1124,P=542]     home.c:86:singularity_mount_home()         : Set the home directory source (via envar) to: /usr/people/pvh:/home/pvh

DEBUG   [U=1124,P=542]     util/file.c:247:s_mkpath()                 : Creating directory: /tmp/.singularity-session-1124.2050.8814447/usr

DEBUG   [U=1124,P=542]     util/file.c:247:s_mkpath()                 : Creating directory: /tmp/.singularity-session-1124.2050.8814447/usr/people

DEBUG   [U=1124,P=542]     util/file.c:247:s_mkpath()                 : Creating directory: /tmp/.singularity-session-1124.2050.8814447/usr/people/pvh

DEBUG   [U=1124,P=542]     home.c:129:singularity_mount_home()        : Checking permissions on home directory: /usr/people/pvh:/home/pvh

DEBUG   [U=1124,P=542]     util/file.c:180:is_owner()                 : Checking ownership on /usr/people/pvh:/home/pvh

ERROR   [U=1124,P=542]     home.c:131:singularity_mount_home()        : Home directory ownership incorrect: /usr/people/pvh:/home/pvh

ABORT   [U=1124,P=542]     home.c:132:singularity_mount_home()        : Retval = 255

That "Checking ownership on" message is an extra debug message I put in is_owner. It looks like it is checking ownership on the whole /usr/people/pvh:/home/pvh thing rather than /usr/people/pvh ? I might be reading this wrong though.

Peter

[Gregory M. Kurtzer]

I think this was fixed in the 2.2 branch of Github. Will you test that, and confirm?

Thanks!

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Gregory M. Kurtzer

HPC Systems Architect and Technology Developer

Lawrence Berkeley National Laboratory HPCS
University of California Berkeley Research IT
Singularity Linux Containers (http://singularity.lbl.gov/)

Warewulf Cluster Management (http://warewulf.lbl.gov/)

GitHub: https://github.com/gmkurtzer, Twitter: https://twitter.com/gmkurtzer

[Nekel-Seyew]

I've tried this, using the released 2.2, but it still says that the /real/path in  --home /real/path:/container_path has permission denied.

-Kyle

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[Gregory M. Kurtzer]

Hi Kyle,

Opps, I meant the 2.x branch in github. Sorry for the confusion.

Greg

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