getcwd: cannot access parent directories: Permission denied

[cjfields]

Testing this on our local cluster (CentOS 7) on GPFS:

[cjfields@biologin-hpcbio lpmx]$ ./Linux-x86_64-lpmx docker create ubuntu:16.04
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied
root@biologin-hpcbio:/# whoami
root

I suspect internal demo will work, but possibly will be issues connecting with file system?

[cjfields]

Actually, the permissions issues with the parent file system prevent the Youtube demo from working properly. Let me know what other details you might need.

root@biologin-hpcbio:/# cat /etc/os-release
NAME="Ubuntu"
VERSION="16.04.6 LTS (Xenial Xerus)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 16.04.6 LTS"
VERSION_ID="16.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
 subprocess dpkg-deb --control returned error exit status 2
/bin/tar: .: Cannot mkdir: Permission denied
/bin/tar: ./control: Cannot open: File exists
/bin/tar: ./md5sums: Cannot open: File exists
/bin/tar: ./prerm: Cannot open: File exists
/bin/tar: Exiting with failure status due to previous errors
dpkg-deb: error: subprocess tar returned error exit status 2
dpkg: error processing archive /var/cache/apt/archives/libpython3.5-stdlib_3.5.2-2ubuntu0~16.04.10_amd64.deb (--unpack):
 subprocess dpkg-deb --control returned error exit status 2
/bin/tar: .: Cannot mkdir: Permission denied
/bin/tar: ./md5sums: Cannot open: File exists
/bin/tar: ./control: Cannot open: File exists
/bin/tar: ./preinst: Cannot open: File exists
/bin/tar: ./conffiles: Cannot open: File exists
/bin/tar: Exiting with failure status due to previous errors
dpkg-deb: error: subprocess tar returned error exit status 2
dpkg: error processing archive /var/cache/apt/archives/vim-common_2%3a7.4.1689-3ubuntu1.4_amd64.deb (--unpack):
 subprocess dpkg-deb --control returned error exit status 2
/bin/tar: .: Cannot mkdir: Permission denied
/bin/tar: ./symbols: Cannot open: File exists
/bin/tar: ./control: Cannot open: File exists
/bin/tar: ./md5sums: Cannot open: File exists
/bin/tar: ./shlibs: Cannot open: File exists
/bin/tar: ./triggers: Cannot open: File exists
/bin/tar: Exiting with failure status due to previous errors
dpkg-deb: error: subprocess tar returned error exit status 2
dpkg: error processing archive /var/cache/apt/archives/libpython3.5_3.5.2-2ubuntu0~16.04.10_amd64.deb (--unpack):
 subprocess dpkg-deb --control returned error exit status 2
/bin/tar: .: Cannot mkdir: Permission denied
/bin/tar: ./md5sums: Cannot open: File exists
/bin/tar: ./postrm: Cannot open: File exists
/bin/tar: ./control: Cannot open: File exists
/bin/tar: ./preinst: Cannot open: File exists
/bin/tar: ./postinst: Cannot open: File exists
/bin/tar: Exiting with failure status due to previous errors
dpkg-deb: error: subprocess tar returned error exit status 2
dpkg: error processing archive /var/cache/apt/archives/vim-runtime_2%3a7.4.1689-3ubuntu1.4_all.deb (--unpack):
 subprocess dpkg-deb --control returned error exit status 2
/bin/tar: .: Cannot mkdir: Permission denied
sh: 0: getcwd() failed: Permission denied
E: Sub-process /usr/bin/dpkg returned an error code (1)

[JasonYangShadow]

Testing this on our local cluster (CentOS 7) on GPFS:

[cjfields@biologin-hpcbio lpmx]$ ./Linux-x86_64-lpmx docker create ubuntu:16.04
shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied
root@biologin-hpcbio:/# whoami
root

I suspect internal demo will work, but possibly will be issues connecting with file system?

Could you try running LPMX on the local host system, where LPMX's parent folder is not on GPFS? I am so sorry that I have not tested LPMX on such kind of system so there must be some bugs. I will try reproducing this issue locally and patch LPMX.

[JasonYangShadow]

The root reason is related to file system symlinks, and it is fixed in the latest release of LPMX. I tried different infrastructures to reproduce this issue, and finally got one that generates the same issue. Thank you so much!