Failure to mount local folder with -v

[dbcraig]

Docker image running just fine in my VM until I try to mount local galaxy_storage with -v

galaxy-stable (19.01)
Linux 4.14.83+ x86-64
Docker version 18.06.1-ce, build 0ffa825

douglasbcraig@dbc-vm-docker-galaxy-1 ~ $ docker run -i -t -p 8080:80 -p 8021:21 -p 8022:22 -v /home/douglasbcraig/galaxy_storage/:/export/ bgruening/galaxy-stable
Enable Galaxy reports authentification 
tmpfs on /proc/kcore type tmpfs (rw,nosuid,size=65536k,mode=755)
Checking /export...
Disable Galaxy Interactive Environments. Start with --privileged to enable IE's.
Starting postgres
postgresql: started
Checking if database is up and running
Traceback (most recent call last):
  File "/usr/local/bin/check_database.py", line 9, in <module>
    from galaxy.model import User
  File "/galaxy-central/lib/galaxy/model/__init__.py", line 7, in <module>
    import base64
  File "/tool_deps/_conda/lib/python2.7/base64.py", line 9, in <module>
    import struct
  File "/tool_deps/_conda/lib/python2.7/struct.py", line 1, in <module>
    from _struct import *
ImportError: /galaxy_venv/lib/python2.7/lib-dynload/_struct.so: failed to map segment from shared object: Operation not permitted
Waiting for database
Traceback (most recent call last):
  File "/usr/local/bin/check_database.py", line 9, in <module>
    from galaxy.model import User
  File "/galaxy-central/lib/galaxy/model/__init__.py", line 7, in <module>
    import base64
  File "/tool_deps/_conda/lib/python2.7/base64.py", line 9, in <module>
    import struct
  File "/tool_deps/_conda/lib/python2.7/struct.py", line 1, in <module>
    from _struct import *
ImportError: /galaxy_venv/lib/python2.7/lib-dynload/_struct.so: failed to map segment from shared object: Operation not permitted
Waiting for database

... repeating forever

The local galaxy_storage directory is created and populated:

douglasbcraig@dbc-vm-docker-galaxy-1 ~/galaxy_storage $ ls -la
total 36
drwxr-xr-x 9 root          root          4096 Mar 22 20:34 .
drwxr-xr-x 4 douglasbcraig douglasbcraig 4096 Mar 22 20:34 ..
drwxr-xr-x 3 root          root          4096 Feb 22 18:43 .distribution_config
drwxr-xr-x 2          1450          1450 4096 Mar 22 20:34 ftp
drwxr-xr-x 8          1450          1450 4096 Mar 22 20:34 galaxy-central
drwxr-xr-x 3          1550          1550 4096 Mar 22 20:34 postgresql
drwxr-xr-x 2          1450          1450 4096 Feb 22 19:05 shed_tools
drwxr-xr-x 3          1450          1450 4096 Feb 22 19:08 tool_deps
drwxr-xr-x 3 root          root          4096 Mar 22 20:34 var

I've seen something similar in an older Issue #68, but this seems pretty vanilla use of -v

Doug

[bgruening]

@dbcraig is the mount point on some special filesystem? NFS or so?
Is the folder empty or is something already in this mounted folder?

[dbcraig]

Nothing special that I know. Simply at ~, which is where I'm running Docker.
This is a Google Cloud container-optimized VM, specifically:

Container-Optimized OS 72-11316.171.0 stable
Kernel: ChromiumOS-4.14.83 Kubernetes: 1.12.4 Docker: 18.06.1 Family: cos-stable

There are a few limitations listed, but nothing that jumps out to me (details).

Like I said, the Galaxy deployment starts up and behaves just fine if I don't mount the local folder. Specifically, if I open up the firewall on 8080 I can get at the Galaxy instance no problem.

I've tried it both ways: letting Galaxy create the folder, and I've also removed everything then created it myself prior to running Docker. In both cases Galaxy populates it, but then I get this error.

[bgruening]

Hi @dbcraig

I found a few interesting pages, that either indicates a problem with your cloud mount point, so your HOME, or some ulimit restrictions :(

• The .so file cannot import: "failed to map segment from shared object" rbgirshick/py-faster-rcnn#162
• https://www.core-admin.com/portal/kb-02082016-001-failed-to-map-segment-from-shared-object-cannot-allocate-memory

Do you have any other filesystems around that you can try? /tmp maybe?

[dbcraig]

Using /tmp ran into the same problem, however, found this issue with Docker. Remounting with exec solves the problem:

sudo mount /tmp -o remount,exec

There may be other implications with this "solution", so I'll do some more verification, but everything appears to be working now.

Surprised others haven't run into this with -v option. Maybe make a note in the Usage docs?
Thanks, @bgruening !

[zph001]

"ImportError: /galaxy_venv/lib/python2.7/lib-dynload/_struct.so: failed to map segment from shared object: Operation not permitted"

More likely it's permission problem of your setup, and that's why others including me don't have problems you have.