can't run singularity exec as a regular user

[toufique]

Hi, 

I am sure this has been discussed in this forum.

I have a container that I have setup as 'root' . Now when I go about using that container to get (even) a 'shell' off the container, I get the error below:

./singularity shell /tmp/singularity_containers/debian_latest.img                          

ERROR  : Singularity is not running with appropriate privileges!

ERROR  : Check installation path is not mounted with 'nosuid', and/or consult manual.

ABORT  : Retval = 255

How do I fix this so, I can install containers as a 'root' user but still be able to run -  'exec' , 'run', 'shell' commands as a regular user?

Thanks for your help!

[vanessa s]

Could you show the exact commands you used to install singularity, and on what host?

Best,

Vanessa

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[Imam Toufique]

Hi Vanessa, 

the following is what i did to create the image, and bootstrap the image.

Installed singularity from source code in my NFS disk as user 'root'.  Version is 2.3.1 . 

(as root)

to create the container: 

singularity -v create --size 30000 /nfs/singularity_containers/debian_jessie_tvb.img

(as root)

to bootstrap the container:

singularity -v bootstrap \

/nfs/singularity_containers/containers/debian_jessie_tvb.img \

/nfs/apps/singularity/2.3.1/container_templates/ubuntu/Singularity

Should I have created the container and bootstrapped as a regular user?

thanks.

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Regards,

Imam Toufique

213-700-5485

[vanessa s]

Hey Imam,

I would try the following:

1. install as sudo: check, you did this

2. as a user: create (doesn't need sudo)

3. as a user: bootstrap (does need sudo, so the command above would be "sudo singularity bootstrap"

Could you try those things, and when you hit the bug, please share the output of sudo singularity --debug bootstrap ... Then we can better help!

Best,

Vanessa

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Regards,

Imam Toufique

213-700-5485

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Vanessa Villamia Sochat
Stanford University '16

(603) 321-0676

[Imam Toufique]

yeah, I was thinking about the same thing, create/bootstrap as a user and then retry using the container as a user.

are there any restrictions that a container created by one user can't be used by another user?  if the container is group writable in the host file-system, can all users in the group able to modify the container (let's say...) to place files? 

thanks.

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Vanessa Villamia Sochat
Stanford University '16

(603) 321-0676

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Regards,

Imam Toufique

213-700-5485

[vanessa s]

The user permissions inside the container are the same as the user permissions outside. A container is akin to a file, so whomever has permission to read, execute, etc, can use the container. 

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[Gregory M. Kurtzer]

What is the installation prefix/path?

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Gregory M. Kurtzer

CEO, SingularityWare, LLC.

Senior Architect, RStor

Computational Science Advisor, Lawrence Berkeley National Laboratory

[Chris Hines]

Hi Imam

I haven't tried 2.3.1 but certainly in the 2.2 series you should find a file libexec/sexec-suid that must be SUID (i.e. permissions -rwsr-xr-x). I don't know how your nfs is mounted. Its certainly possible for singularity to work when the secec-suid is on NFS, but its also common to have nfs "root-squashed" so that the root user actually becomes the nobody user.

I suggest checking the NFS mount and export options, and possibly trying an installation to local disks rather than NFS disks (if possible)

Cheers,

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Chris.

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Regards,

Imam Toufique

213-700-5485

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[toufique]

Hi Vanessa,

I finally had some time to look into this earlier today.  Per your suggestion, I tried creating a container as myself, no luck: 

[itoufiqu@compute-7-2 ~]$ singularity -v create --size 30000 /tmp/debian_jessie_tvb.img

Increasing verbosity level (2)

Singularity version: 2.3.1-dist

Exec'ing: /data/apps/singularity/2.3.1/libexec/singularity/cli/create.exec

VERBOSE: Set messagelevel to: 2

VERBOSE: Initialize configuration file: /data/apps/singularity/2.3.1/etc/singularity/singularity.conf

VERBOSE: Initializing Singularity Registry

ERROR  : Singularity is not running with appropriate privileges!

ERROR  : Check installation path is not mounted with 'nosuid', and/or consult manual.

ABORT  : Retval = 255

[itoufiqu@compute-7-2 ~]$ whoami

itoufiqu

singularity was installed as 'root' .  Below is the config file: 

allow setuid = yes

max loop devices = 256

config passwd = yes

config group = yes

config resolv_conf = yes

mount proc = yes

mount sys = yes

mount dev = yes

mount home = yes

mount tmp = yes

mount hostfs = no

bind path = /etc/localtime

bind path = /etc/hosts

bind path = /dfs1

bind path = /dfs2

bind path = /data

user bind control = yes

enable overlay = yes

mount slave = yes

sessiondir max size = 16

What do I need to do get this fixed, please?

thanks.

[toufique]

Hi Chris, 

I could not find any files called "sexec-suid' in my 2.3.1 install.  here are the files with *-suid: 

itoufiqu@compute-7-2 2.3.1]$ find -iname "*-suid" | xargs ls -ld     

-rwsr-xr-x 1 root root 459305 Jun 27 18:06 ./libexec/singularity/bin/action-suid

-rwsr-xr-x 1 root root 246671 Jun 27 18:06 ./libexec/singularity/bin/create-suid

-rwsr-xr-x 1 root root 247359 Jun 27 18:06 ./libexec/singularity/bin/expand-suid

-rwsr-xr-x 1 root root 430784 Jun 27 18:06 ./libexec/singularity/bin/export-suid

-rwsr-xr-x 1 root root 430664 Jun 27 18:06 ./libexec/singularity/bin/import-suid

-rwsr-xr-x 1 root root 423496 Jun 27 18:06 ./libexec/singularity/bin/mount-suid

any ideas?  I am sort of stuck here ;- ) with this problem. 

thanks!

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[vanessa s]

Could you please show the output with --debug and singularity --version?

singularity --debug create --size 30000 /tmp/debian_jessie_tvb.img
singularity --version

and also throw in information about the host, if easy to get :) 

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[toufique]

Hi Vanessa,

command: 

singularity --debug create --size 30000 /tmp/debian_jessie_tvb_1.img . (not that this time i tried creating the container in /tmp .  So, no involvment of NFS here for the container) 

Here is the debug output:

Enabling debugging

Ending argument loop

Singularity version: 2.3.1-dist

Exec'ing: /data/apps/singularity/2.3.1/libexec/singularity/cli/create.exec

VERBOSE [U=2527,P=48257]   message_init()                            Set messagelevel to: 5

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Initialize configuration file: /data/apps/singularity/2.3.1/etc/singularity/singularity.conf

^[[0mDEBUG   [U=2527,P=48257]   singularity_config_parse()                Starting parse of configuration file /data/apps/singularity/2.3.1/etc/singularity/singularity.conf

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key allow setuid = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key max loop devices = '256'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key allow pid ns = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key config passwd = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key config group = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key config resolv_conf = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key mount proc = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key mount sys = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key mount dev = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key mount home = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key mount tmp = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key mount hostfs = 'no'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key bind path = '/etc/localtime'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key bind path = '/etc/hosts'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key bind path = '/dfs1'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key bind path = '/dfs2'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key bind path = '/data'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key user bind control = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key enable overlay = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key mount slave = 'yes'

^[[0mVERBOSE [U=2527,P=48257]   singularity_config_parse()                Got config key sessiondir max size = '16'

^[[0mDEBUG   [U=2527,P=48257]   singularity_config_parse()                Finished parsing configuration file '/data/apps/singularity/2.3.1/etc/singularity/singularity.conf'

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_init()               Initializing Singularity Registry

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'WRITABLE' = '1'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(WRITABLE, 1) = 0

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'LIBEXECDIR' = '/data/apps/singularity/2.3.1/libexec'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(libexecdir, /data/apps/singularity/2.3.1/libexec) = 0

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'COMMAND' = 'create'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(COMMAND, create) = 0

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'IMAGESIZE' = '30000'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(IMAGESIZE, 30000) = 0

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'MESSAGELEVEL' = '5'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(MESSAGELEVEL, 5) = 0

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'VERSION' = '2.3.1-dist'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(version, 2.3.1-dist) = 0

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'LOCALSTATEDIR' = '/data/apps/singularity/2.3.1/var'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(localstatedir, /data/apps/singularity/2.3.1/var) = 0

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'SYSCONFDIR' = '/data/apps/singularity/2.3.1/etc'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(sysconfdir, /data/apps/singularity/2.3.1/etc) = 0

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'BINDIR' = '/data/apps/singularity/2.3.1/bin'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(bindir, /data/apps/singularity/2.3.1/bin) = 0

^[[0mVERBOSE [U=2527,P=48257]   singularity_registry_set()                Adding value to registry: 'IMAGE' = '/tmp/debian_jessie_tvb_1.img'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_set()                Returning singularity_registry_set(IMAGE, /tmp/debian_jessie_tvb_1.img) = 0

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_get()                Returning NULL on 'HOME'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_get()                Returning NULL on 'TARGET_UID'

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_get()                Returning NULL on 'TARGET_GID'

^[[0mDEBUG   [U=2527,P=48257]   singularity_priv_init()                   Initializing user info

^[[0mDEBUG   [U=2527,P=48257]   singularity_priv_init()                   Set the calling user's username to: itoufiqu

^[[0mDEBUG   [U=2527,P=48257]   singularity_priv_init()                   Marking uinfo structure as ready

^[[0mDEBUG   [U=2527,P=48257]   singularity_priv_init()                   Obtaining home directory

^[[0mVERBOSE [U=2527,P=48257]   singularity_priv_init()                   Set home (via getpwuid()) to: /data/users/itoufiqu

^[[0mVERBOSE [U=2527,P=48257]   singularity_suid_init()                   Running SUID program workflow

^[[0mVERBOSE [U=2527,P=48257]   singularity_suid_init()                   Checking program has appropriate permissions

^[[0mVERBOSE [U=2527,P=48257]   singularity_suid_init()                   Checking configuration file is properly owned by root

^[[0mVERBOSE [U=2527,P=48257]   singularity_suid_init()                   Checking if singularity.conf allows us to run as suid

^[[0mDEBUG   [U=2527,P=48257]   singularity_config_get_bool_char_impl()   Called singularity_config_get_bool(allow setuid, yes)

^[[0mDEBUG   [U=2527,P=48257]   singularity_config_get_value_impl()       Returning configuration value allow setuid='yes'

^[[0mDEBUG   [U=2527,P=48257]   singularity_config_get_bool_char_impl()   Return singularity_config_get_bool(allow setuid, yes) = 1

^[[0mDEBUG   [U=2527,P=48257]   singularity_registry_get()                Returning NULL on 'NOSUID'

^[[0m^[[91mERROR   [U=2527,P=48257]   singularity_suid_init()                   Singularity is not running with appropriate privileges!

^[[0m^[[91mERROR   [U=2527,P=48257]   singularity_suid_init()                   Check installation path is not mounted with 'nosuid', and/or consult manual.

^[[0m^[[31mABORT   [U=2527,P=48257]   singularity_suid_init()                   Retval = 255

Some info on the host, let me know if you need more info: 

[itoufiqu@compute-7-2 2.3.1]$ cat /etc/redhat-release                                                         

CentOS release 6.8 (Final)                                                                                    

[itoufiqu@compute-7-2 2.3.1]$ uname -a                                                                                   

Linux compute-7-2.local 3.10.104-1.el6.elrepo.x86_64 #1 SMP Fri Oct 21 10:27:14 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux  

Thanks again!

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[vanessa s]

I think the line where it's hitting a bug is here:

https://github.com/singularityware/singularity/blob/adf5259ac94d7b213c649f073dcda32459b0c8b7/src/util/suid.c#L80

Specifically somewhere after this command:

( singularity_registry_get("NOSUID") != NULL )

When I run a similar command, I see the following:

VERBOSE [U=0,P=29387]      singularity_suid_init()                   Running SUID program workflow
VERBOSE [U=0,P=29387]      singularity_suid_init()                   Checking program has appropriate permissions
VERBOSE [U=0,P=29387]      singularity_suid_init()                   Checking configuration file is properly owned by root
VERBOSE [U=0,P=29387]      singularity_suid_init()                   Checking if singularity.conf allows us to run as suid
DEBUG   [U=0,P=29387]      singularity_config_get_bool_char_impl()   Called singularity_config_get_bool(allow setuid, yes)
DEBUG   [U=0,P=29387]      singularity_config_get_value_impl()       Returning configuration value allow setuid='yes'
DEBUG   [U=0,P=29387]      singularity_config_get_bool_char_impl()   Return singularity_config_get_bool(allow setuid, yes) = 1
DEBUG   [U=0,P=29387]      singularity_registry_get()                Returning NULL on 'NOSUID'
VERBOSE [U=0,P=29387]      singularity_priv_userns()                 Invoking the user namespace

and I return NULL too, but it doesn't error out. So you don't get to the last line to invoke the user namespace... I'm not completely sure about the issue, but given centos 6, I bet you it has to do with the OS / version.  Do others have thoughts? Could you try a completely new install with no changes to the config, and do a simple shell for some docker:// uri so I can recreate your use case exactly?

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[toufique]

hi Vanessa, 

what did you mean by trying a new install with no changes in the config?  I can reinstall 2.3.1 ( in a different install location)  -- is that what you meant?  Do I need to install ( ./configure, make, make install) as myself or 'root'? Does it help installing this as myself?  are there any plans to fix this bug? If not, should I try an older version of singularity?  

thanks.

[vanessa s]

Yes, just remove what you have, clone the repo fresh, and then run 

cd singularity 

./autogen.sh
./configure --prefix=/usr/local
make
sudo make install

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[toufique]

I see the latest release is 2.3.1.  I have the tarball already.  I can recompile 2.3.1 again. But I did not make any changes in my current build except adding the following lines:

bind path = /dfs1

bind path = /dfs2

bind path = /data

I am not sure if there is any other URL to clone from:

(when I search for latest release, I end up on the following page)

https://github.com/singularityware/singularity/releases/ 

Also, I just tried compiling 2.2.1, i get a simillar error: 

itoufiqu@compute-7-2 ~]$ singularity -vvv create  --size 300 /tmp/debian_jessie_tvb_2-2-1.img

increasing verbosity level (4)

ending argument loop

Exec'ing: /data/apps/singularity/2.2.1/libexec/singularity/cli/create.exec --sizeERROR: Calling user must be root!

[itoufiqu@compute-7-2 ~]$ which singularity        

/data/apps/singularity/2.2.1/bin/singularity < -- note that I am using version 2.2.1 here

 

If this is an OS issue (possibly OS being older ? ) issue, would it be possible to provide a patch (back ported?) to help address this issue?  We are really counting on singularity to work in our environment in UC Irvine, we have plans to move to a much newer version of Debian distro, but we can't at this time.  We looked into docker, but it is something that we can't do cluster-wide.  Singularity seems to be the tool that we can run through the cluster, especially being on an older OS.  

Thanks again for all the help!

[vanessa s]

Hey Toufique,

I just tried this out in a Docker image:

docker run -it --privileged centos:6.8 bash

First I tried installing from the tarball for 2.3.1

yum install -y wget gcc
wget https://github.com/singularityware/singularity/releases/download/2.3.1/singularity-2.3.1.tar.gz
tar -xzvf singularity-2.3.1.tar.gz

cd singularity-2.3.1 

 ./configure --prefix=/usr/local
make
sudo make install   (on docker you are sudo so I didn't need the sudo bit :O)

 Did it go somewhere?

[root@595a27c176f2 singularity-2.3.1]# which singularity
/usr/local/bin/singularity

I ran your example command, but I got a different error:

singularity -vvv create  --size 300 /tmp/debian_jessie_tvb_2-2-1.img

VERBOSE: Running child program: /sbin/mkfs.ext3
Singularity: create-suid (U=0,P=11951)> Failed to exec program /sbin/mkfs.ext3: No such file or directory
ERROR  : Failed to exec program /sbin/mkfs.ext3: No such file or directory
Singularity: create-suid (U=0,P=11951)> Retval = 255
ABORT  : Retval = 255
INFO   : Image is done: /tmp/debian_jessie_tvb_2-2-1.img

guess I can't make filesystems? let's install a bunch of crap from Google searches and see if we can after that:

yum install -y e2fsprogs-1.41.12-23.el6.x86_64  < -- I found with "yum whatprovides */mkfs.ext3"

trying again...

singularity -vvv create  --size 300 /tmp/meatball.img
INFO   : Image is done: /tmp/meatball.img

success! Let's import..

# singularity import /tmp/meatball.img docker://ubuntu
Docker image path: index.docker.io/library/ubuntu:latest
Cache folder set to /root/.singularity/docker
Importing: base Singularity environment
Importing: /root/.singularity/docker/sha256:e0a742c2abfd5e2a6f8ed15b1c78e873cf9559b96a04204daf6de5df01e3124c.tar.gz
Importing: /root/.singularity/docker/sha256:486cb8339a27635fa93dc47aa0c689326a0a7cce388966d16daf8d265436cf7f.tar.gz
Importing: /root/.singularity/docker/sha256:dc6f0d824617ad8a5d1163a5b2084814665dd83156317ad06ccf14deb517a053.tar.gz
Importing: /root/.singularity/docker/sha256:4f7a5649a30e3f318ce5d7e4dbcbbeb6c0938c4cbae4d4a641fe910562ff4978.tar.gz
Importing: /root/.singularity/docker/sha256:672363445ad2c734e29221a6b47f4e614b5adc8a3cdca3364f62db2ed2bdff0c.tar.gz
Importing: /root/.singularity/metadata/sha256:fe44851d529f465f9aa107b32351c8a0a722fc0619a2a7c22b058084fac068a4.tar.gz
[root@595a27c176f2 sbin]# singularity shell /tmp/meatball.img 
Singularity: action-suid (U=0,P=12168)> USER=root, IMAGE='meatball.img', COMMAND='shell'
Singularity: Invoking an interactive shell within container...
Singularity meatball.img:/sbin> uname -a
Linux 595a27c176f2 4.4.0-87-generic #110-Ubuntu SMP Tue Jul 18 12:55:35 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Singularity meatball.img:/sbin> 

so I can't reproduce your error with 2.3.1, and it's one of those things I can only go as far as to reproduce your basic setup, but it's not actually the cluster setup you have. What I would suggest you do is what I've done, get a new instance (Docker or actual machine somewhere) and recreate the installation. Then you can compare your cluster version with your (hopefully working) instance version, and figuring out the bug will come down to identifying differences in the error output of the two (**importantly produced on the same host, same singularity install) and then tracing that.

Hope this was helpful! 

Best,

Vanessa

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[toufique]

Hi Vanessa, 

Sorry I could not reply to your message earlier.  Thanks for doing all the testing for us!  Very much appreciated! 

The issue that I ran into was the 'nosuid' NFS mount option in the NFS disk singularity was installed. Since changing that mount option (at this point) would not be practical, we decided to install it in DFS and we were able to use the tool as expected -- which is, create container/ bootstrap with 'sudo' and then use the container with regular username(s) for 'run' , 'exec' , etc. commands. 

Thanks again for all help, you guys are great! ;-) 

--imam 

[vanessa s]

Woohoo!! Glad to hear it worked. If this were on Github... [ Close Issue ]

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