Gitlab-CE reconfigure time out on step "migrate gitlab-rails database" - gitlab

I try to update gitlab from version 9.5.10 to latest 10. I do 3 steps:
touch /etc/gitlab/skip-auto-migrations ( I don't need backup )
yum -y install gitlab-ce-10.8.7-ce.0.el7.x86_64
gitlab-ctl reconfigure
Gitlab crashes with an error after one hour:
...
Error executing action `run` on resource 'bash[migrate gitlab-rails database]'
================================================================================
Mixlib::ShellOut::CommandTimeout
--------------------------------
Command timed out after 3600s:
Command exceeded allowed execution time, process terminated
---- Begin output of "bash" "/tmp/chef-script20180907-58298-lhgdju" ----
STDOUT: == 20141126120926 AddMergeRequestRebaseEnabledToProjects: migrating ===========
-- transaction_open?()
-> 0.0000s
...
63: end
64: not_if "(test -f #{db_migrate_status_file}) && (cat #{db_migrate_status_file} | grep -Fx 0)"
65: only_if { node['gitlab']['gitlab-rails']['auto_migrate'] }
66: end
Compiled Resource:
------------------
# Declared in /opt/gitlab/embedded/cookbooks/cache/cookbooks/gitlab/recipes/database_migrations.rb:49:in `from_file'
bash("migrate gitlab-rails database") do
action [:run]
default_guard_interpreter :default
command nil
backup 5
returns 0
user nil
interpreter "bash"
declared_type :bash
cookbook_name "gitlab"
recipe_name "database_migrations"
code " set -e\n log_file=\"/var/log/gitlab/gitlab-rails/gitlab-rails-db-migrate-$(date +%Y-%m-%d-%H-%M-%S).log\"\n umask 077\n /opt/gitlab/bin/gitlab-rake gitlab:db:configure 2>& 1 | tee ${log_file}\n STATUS=${PIPESTATUS[0]}\n echo $STATUS > /var/opt/gitlab/gitlab-rails/upgrade-status/db-migrate-141d998df14e11465b19f94d3c4ccfa1-eb600b0\n exit $STATUS\n"
domain nil
not_if "(test -f /var/opt/gitlab/gitlab-rails/upgrade-status/db-migrate-141d998df14e11465b19f94d3c4ccfa1-eb600b0) && (cat /var/opt/gitlab/gitlab-rails/upgrade-status/db-migrate-141d998df14e11465b19f94d3c4ccfa1-eb600b0 | grep -Fx 0)"
only_if { #code block }
end
System Info:
------------
chef_version=13.6.4
platform=centos
platform_version=7.4.1708
ruby=ruby 2.3.7p456 (2018-03-28 revision 63024) [x86_64-linux]
program_name=/opt/gitlab/embedded/bin/chef-client
executable=/opt/gitlab/embedded/bin/chef-client
Recipe: gitlab::unicorn
* service[unicorn] action restart
ESC[32m- restart service service[unicorn]
Recipe: gitlab::sidekiq
* service[sidekiq] action restart
ESC[32m- restart service service[sidekiq]
Recipe: gitlab::gitlab-rails
* execute[clear the gitlab-rails cache] action run
ESC[32m- execute /opt/gitlab/bin/gitlab-rake cache:clear
Running handlers:
Running handlers complete
Chef Client failed. 25 resources updated in 01 hours 01 minutes 28 seconds
I found workaround but I don't want to risk changing the update procedure. GitLab is used in the production and use of more than 1000 people (An update check is performed on the copy of the database).
Does anyone know how to increase the timeout?

Ok, turning this into an answer so other people might be able to use this:
Unless someone knows of a way to override the default timeout for Mixlib::ShellOut in this case, it is possible to override that default of 3600 in opt/gitlab/embedded/lib/ruby/gems/2.4.0/gems/chef-13.6.4/lib/chef/provider/execute.rb line 44-48, which currently read:
def timeout
# original implementation did not specify a timeout, but ShellOut
# *always* times out. So, set a very long default timeout
new_resource.timeout || 3600
end
Increasing the 3600 there should help.

Related

gitlab-ctl reconfigure error by /var/opt/gitlab/postgresql/data -E UTF8

I tried these but it didn't work。
export LC_CTYPE=en_US.UTF-8
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
Error log
================================================================================
Error executing action `run` on resource 'execute[/opt/gitlab/embedded/bin/initdb -D /var/opt/gitlab/postgresql/data -E UTF8]'
================================================================================
There was an error running gitlab-ctl reconfigure:
execute[/opt/gitlab/embedded/bin/initdb -D /var/opt/gitlab/postgresql/data -E UTF8] (postgresql::enable line 54) had an error: Errno::EACCES: Permission denied - /opt/gitlab/embedded/bin/initdb
Full log
Recipe: postgresql::user
* account[Postgresql user and group] action create
* group[Postgresql user and group] action create (up to date)
* linux_user[Postgresql user and group] action create (up to date)
(up to date)
* directory[/var/opt/gitlab/postgresql] action create (up to date)
* file[/var/opt/gitlab/postgresql/.profile] action create (up to date)
Recipe: postgresql::sysctl
* gitlab_sysctl[kernel.shmmax] action create
* directory[create /etc/sysctl.d for kernel.shmmax] action create (up to date)
* file[create /opt/gitlab/embedded/etc/90-omnibus-gitlab-kernel.shmmax.conf kernel.shmmax] action create (up to date)
* link[/etc/sysctl.d/90-omnibus-gitlab-kernel.shmmax.conf] action create (up to date)
* execute[load sysctl conf kernel.shmmax] action nothing (skipped due to action :nothing)
(up to date)
* gitlab_sysctl[kernel.shmall] action create
* directory[create /etc/sysctl.d for kernel.shmall] action create (up to date)
* file[create /opt/gitlab/embedded/etc/90-omnibus-gitlab-kernel.shmall.conf kernel.shmall] action create (up to date)
* link[/etc/sysctl.d/90-omnibus-gitlab-kernel.shmall.conf] action create (up to date)
* execute[load sysctl conf kernel.shmall] action nothing (skipped due to action :nothing)
(up to date)
* gitlab_sysctl[kernel.sem] action create
* directory[create /etc/sysctl.d for kernel.sem] action create (up to date)
* file[create /opt/gitlab/embedded/etc/90-omnibus-gitlab-kernel.sem.conf kernel.sem] action create (up to date)
* link[/etc/sysctl.d/90-omnibus-gitlab-kernel.sem.conf] action create (up to date)
* execute[load sysctl conf kernel.sem] action nothing (skipped due to action :nothing)
(up to date)
Recipe: postgresql::enable
* directory[/var/opt/gitlab/postgresql] action create (up to date)
* directory[/var/opt/gitlab/postgresql/data] action create (up to date)
* directory[/var/log/gitlab/postgresql] action create (up to date)
* directory[/var/opt/gitlab/postgresql/data] action create (up to date)
* link[/var/opt/gitlab/postgresql/data] action create (skipped due to not_if)
* execute[/opt/gitlab/embedded/bin/initdb -D /var/opt/gitlab/postgresql/data -E UTF8] action run
================================================================================
Error executing action `run` on resource 'execute[/opt/gitlab/embedded/bin/initdb -D /var/opt/gitlab/postgresql/data -E UTF8]'
================================================================================
Errno::EACCES
-------------
Permission denied - /opt/gitlab/embedded/bin/initdb
Resource Declaration:
---------------------
# In /opt/gitlab/embedded/cookbooks/cache/cookbooks/postgresql/recipes/enable.rb
54: execute "/opt/gitlab/embedded/bin/initdb -D #{node['postgresql']['data_dir']} -E UTF8" do
55: user postgresql_username
56: not_if { pg_helper.bootstrapped? || pg_helper.delegated? }
57: end
58:
Compiled Resource:
------------------
# Declared in /opt/gitlab/embedded/cookbooks/cache/cookbooks/postgresql/recipes/enable.rb:54:in `from_file'
execute("/opt/gitlab/embedded/bin/initdb -D /var/opt/gitlab/postgresql/data -E UTF8") do
action [:run]
default_guard_interpreter :execute
command "/opt/gitlab/embedded/bin/initdb -D /var/opt/gitlab/postgresql/data -E UTF8"
backup 5
declared_type :execute
cookbook_name "postgresql"
recipe_name "enable"
domain nil
user "gitlab-psql"
not_if { #code block }
end
System Info:
------------
chef_version=15.14.0
platform=ubuntu
platform_version=22.04
ruby=ruby 2.7.2p137 (2020-10-01 revision 5445e04352) [x86_64-linux]
program_name=/opt/gitlab/embedded/bin/chef-client
executable=/opt/gitlab/embedded/bin/chef-client
Running handlers:
There was an error running gitlab-ctl reconfigure:
execute[/opt/gitlab/embedded/bin/initdb -D /var/opt/gitlab/postgresql/data -E UTF8] (postgresql::enable line 54) had an error: Errno::EACCES: Permission denied - /opt/gitlab/embedded/bin/initdb
Notes:
It seems you haven't specified an initial root password while configuring the GitLab instance.
On your first visit to your GitLab instance, you will be presented with a screen to set a
password for the default admin account with username `root`.
Running handlers complete
Chef Infra Client failed. 47 resources updated in 10 minutes 41 seconds
Notes:
It seems you haven't specified an initial root password while configuring the GitLab instance.
On your first visit to your GitLab instance, you will be presented with a screen to set a
password for the default admin account with username `root`.

Error after installing Gitlab on ubuntu 18.04

i want to install gitlab on ubuntu 18.04 but :-( !.
sudo apt-get install -y curl openssh-server ca-certificates
curl https://packages.gitlab.com/install/repositories/gitlab/gitlab-ee/script.deb.sh | sudo bash
sudo EXTERNAL_URL="http://gitlab.example.com" apt-get install gitlab-ee
any solution ?
if someone already solve the same problem or something similar, thanks in advance ;-)
result :
Recipe: postgresql::enable
* directory[/var/opt/gitlab/postgresql] action create
- create new directory /var/opt/gitlab/postgresql
- change mode from '' to '0755'
- change owner from '' to 'gitlab-psql'
* directory[/var/opt/gitlab/postgresql] action create (up to date)
* directory[/var/opt/gitlab/postgresql/data] action create
- create new directory /var/opt/gitlab/postgresql/data
- change mode from '' to '0700'
- change owner from '' to 'gitlab-psql'
* directory[/var/log/gitlab/postgresql] action create
- create new directory /var/log/gitlab/postgresql
- change mode from '' to '0700'
- change owner from '' to 'gitlab-psql'
* link[/var/opt/gitlab/postgresql/data] action create (skipped due to not_if)
* file[/var/opt/gitlab/postgresql/.profile] action create
- create new file /var/opt/gitlab/postgresql/.profile
- update content in file /var/opt/gitlab/postgresql/.profile from none to 3b0387
--- /var/opt/gitlab/postgresql/.profile 2019-12-13 02:51:57.452326848 +0100
+++ /var/opt/gitlab/postgresql/.chef-.profile20191213-11373-1qqmckf.profile 2019-12-13 02:51:57.448326813 +0100
## -1 +1,2 ##
+PATH=/opt/gitlab/embedded/bin:/opt/gitlab/bin:$PATH
- change mode from '' to '0600'
- change owner from '' to 'gitlab-psql'
* gitlab_sysctl[kernel.shmmax] action create
* directory[create /etc/sysctl.d for kernel.shmmax] action create (up to date)
* file[create /opt/gitlab/embedded/etc/90-omnibus-gitlab-kernel.shmmax.conf kernel.shmmax] action create
- create new file /opt/gitlab/embedded/etc/90-omnibus-gitlab-kernel.shmmax.conf
- update content in file /opt/gitlab/embedded/etc/90-omnibus-gitlab-kernel.shmmax.conf from none to 75a195
--- /opt/gitlab/embedded/etc/90-omnibus-gitlab-kernel.shmmax.conf 2019-12-13 02:51:57.464326950 +0100
+++ /opt/gitlab/embedded/etc/.chef-90-omnibus-gitlab-kernel20191213-11373-zkx5md.shmmax.conf 2019-12-13 02:51:57.464326950 +0100
## -1 +1,2 ##
+kernel.shmmax = 17179869184
* execute[load sysctl conf kernel.shmmax] action run
[execute] * Applying /etc/sysctl.d/10-console-messages.conf ...
kernel.printk = 4 4 1 7
* Applying /etc/sysctl.d/10-ipv6-privacy.conf ...
net.ipv6.conf.all.use_tempaddr = 2
net.ipv6.conf.default.use_tempaddr = 2
* Applying /etc/sysctl.d/10-kernel-hardening.conf ...
kernel.kptr_restrict = 1
* Applying /etc/sysctl.d/10-link-restrictions.conf ...
fs.protected_hardlinks = 1
fs.protected_symlinks = 1
* Applying /etc/sysctl.d/10-magic-sysrq.conf ...
kernel.sysrq = 176
* Applying /etc/sysctl.d/10-network-security.conf ...
net.ipv4.conf.default.rp_filter = 1
net.ipv4.conf.all.rp_filter = 1
net.ipv4.tcp_syncookies = 1
* Applying /etc/sysctl.d/10-ptrace.conf ...
kernel.yama.ptrace_scope = 1
* Applying /etc/sysctl.d/10-zeropage.conf ...
vm.mmap_min_addr = 65536
* Applying /usr/lib/sysctl.d/50-default.conf ...
net.ipv4.conf.all.promote_secondaries = 1
net.core.default_qdisc = fq_codel
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.sem.conf ...
sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-kernel.sem.conf": No such file or directory
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.shmall.conf ...
sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-kernel.shmall.conf": No such file or directory
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.shmmax.conf ...
kernel.shmmax = 17179869184
* Applying /etc/sysctl.d/90-omnibus-gitlab-net.core.somaxconn.conf ...
sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-net.core.somaxconn.conf": No such file or directory
* Applying /etc/sysctl.d/99-sysctl.conf ...
* Applying /etc/sysctl.conf ...
================================================================================
Error executing action `run` on resource 'execute[load sysctl conf kernel.shmmax]'
================================================================================
Mixlib::ShellOut::ShellCommandFailed
------------------------------------
Expected process to exit with [0], but received '255'
---- Begin output of sysctl -e --system ----
STDOUT: * Applying /etc/sysctl.d/10-console-messages.conf ...
kernel.printk = 4 4 1 7
* Applying /etc/sysctl.d/10-ipv6-privacy.conf ...
net.ipv6.conf.all.use_tempaddr = 2
net.ipv6.conf.default.use_tempaddr = 2
* Applying /etc/sysctl.d/10-kernel-hardening.conf ...
kernel.kptr_restrict = 1
* Applying /etc/sysctl.d/10-link-restrictions.conf ...
fs.protected_hardlinks = 1
fs.protected_symlinks = 1
* Applying /etc/sysctl.d/10-magic-sysrq.conf ...
kernel.sysrq = 176
* Applying /etc/sysctl.d/10-network-security.conf ...
net.ipv4.conf.default.rp_filter = 1
net.ipv4.conf.all.rp_filter = 1
net.ipv4.tcp_syncookies = 1
* Applying /etc/sysctl.d/10-ptrace.conf ...
kernel.yama.ptrace_scope = 1
* Applying /etc/sysctl.d/10-zeropage.conf ...
vm.mmap_min_addr = 65536
* Applying /usr/lib/sysctl.d/50-default.conf ...
net.ipv4.conf.all.promote_secondaries = 1
net.core.default_qdisc = fq_codel
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.sem.conf ...
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.shmall.conf ...
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.shmmax.conf ...
kernel.shmmax = 17179869184
* Applying /etc/sysctl.d/90-omnibus-gitlab-net.core.somaxconn.conf ...
* Applying /etc/sysctl.d/99-sysctl.conf ...
* Applying /etc/sysctl.conf ...
STDERR: sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-kernel.sem.conf": No such file or directory
sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-kernel.shmall.conf": No such file or directory
sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-net.core.somaxconn.conf": No such file or directory
---- End output of sysctl -e --system ----
Ran sysctl -e --system returned 255
Resource Declaration:
---------------------
# In /opt/gitlab/embedded/cookbooks/cache/cookbooks/package/resources/gitlab_sysctl.rb
46: execute "load sysctl conf #{new_resource.name}" do
47: command "sysctl -e --system"
48: action :nothing
49: end
50: end
Compiled Resource:
------------------
# Declared in /opt/gitlab/embedded/cookbooks/cache/cookbooks/package/resources/gitlab_sysctl.rb:46:in `block in class_from_file'
execute("load sysctl conf kernel.shmmax") do
action [:nothing]
default_guard_interpreter :execute
command "sysctl -e --system"
backup 5
declared_type :execute
cookbook_name "postgresql"
domain nil
user nil
end
System Info:
------------
chef_version=14.13.11
platform=ubuntu
platform_version=18.04
ruby=ruby 2.6.3p62 (2019-04-16 revision 67580) [x86_64-linux]
program_name=/opt/gitlab/embedded/bin/chef-client
executable=/opt/gitlab/embedded/bin/chef-client
================================================================================
Error executing action `create` on resource 'gitlab_sysctl[kernel.shmmax]'
================================================================================
Mixlib::ShellOut::ShellCommandFailed
------------------------------------
execute[load sysctl conf kernel.shmmax] (/opt/gitlab/embedded/cookbooks/cache/cookbooks/package/resources/gitlab_sysctl.rb line 46) had an error: Mixlib::ShellOut::ShellCommandFailed: Expected process to exit with [0], but received '255'
---- Begin output of sysctl -e --system ----
STDOUT: * Applying /etc/sysctl.d/10-console-messages.conf ...
kernel.printk = 4 4 1 7
* Applying /etc/sysctl.d/10-ipv6-privacy.conf ...
net.ipv6.conf.all.use_tempaddr = 2
net.ipv6.conf.default.use_tempaddr = 2
* Applying /etc/sysctl.d/10-kernel-hardening.conf ...
kernel.kptr_restrict = 1
* Applying /etc/sysctl.d/10-link-restrictions.conf ...
fs.protected_hardlinks = 1
fs.protected_symlinks = 1
* Applying /etc/sysctl.d/10-magic-sysrq.conf ...
kernel.sysrq = 176
* Applying /etc/sysctl.d/10-network-security.conf ...
net.ipv4.conf.default.rp_filter = 1
net.ipv4.conf.all.rp_filter = 1
net.ipv4.tcp_syncookies = 1
* Applying /etc/sysctl.d/10-ptrace.conf ...
kernel.yama.ptrace_scope = 1
* Applying /etc/sysctl.d/10-zeropage.conf ...
vm.mmap_min_addr = 65536
* Applying /usr/lib/sysctl.d/50-default.conf ...
net.ipv4.conf.all.promote_secondaries = 1
net.core.default_qdisc = fq_codel
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.sem.conf ...
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.shmall.conf ...
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.shmmax.conf ...
kernel.shmmax = 17179869184
* Applying /etc/sysctl.d/90-omnibus-gitlab-net.core.somaxconn.conf ...
* Applying /etc/sysctl.d/99-sysctl.conf ...
* Applying /etc/sysctl.conf ...
STDERR: sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-kernel.sem.conf": No such file or directory
sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-kernel.shmall.conf": No such file or directory
sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-net.core.somaxconn.conf": No such file or directory
---- End output of sysctl -e --system ----
Ran sysctl -e --system returned 255
Resource Declaration:
---------------------
# In /opt/gitlab/embedded/cookbooks/cache/cookbooks/postgresql/recipes/enable.rb
67: gitlab_sysctl "kernel.shmmax" do
68: value node['postgresql']['shmmax']
69: end
70:
Compiled Resource:
------------------
# Declared in /opt/gitlab/embedded/cookbooks/cache/cookbooks/postgresql/recipes/enable.rb:67:in `from_file'
gitlab_sysctl("kernel.shmmax") do
action [:create]
updated true
updated_by_last_action true
default_guard_interpreter :default
declared_type :gitlab_sysctl
cookbook_name "postgresql"
recipe_name "enable"
value 17179869184
end
System Info:
------------
chef_version=14.13.11
platform=ubuntu
platform_version=18.04
ruby=ruby 2.6.3p62 (2019-04-16 revision 67580) [x86_64-linux]
program_name=/opt/gitlab/embedded/bin/chef-client
executable=/opt/gitlab/embedded/bin/chef-client
Recipe: gitlab::gitlab-rails
* execute[clear the gitlab-rails cache] action run
- execute /opt/gitlab/bin/gitlab-rake cache:clear
Recipe:
* service[gitaly] action restart
- restart service service[gitaly]
Recipe: gitaly::enable
* runit_service[gitaly] action hup
- send hup to runit_service[gitaly]
Running handlers:
There was an error running gitlab-ctl reconfigure:
gitlab_sysctl[kernel.shmmax] (postgresql::enable line 67) had an error: Mixlib::ShellOut::ShellCommandFailed: execute[load sysctl conf kernel.shmmax] (/opt/gitlab/embedded/cookbooks/cache/cookbooks/package/resources/gitlab_sysctl.rb line 46) had an error: Mixlib::ShellOut::ShellCommandFailed: Expected process to exit with [0], but received '255'
---- Begin output of sysctl -e --system ----
STDOUT: * Applying /etc/sysctl.d/10-console-messages.conf ...
kernel.printk = 4 4 1 7
* Applying /etc/sysctl.d/10-ipv6-privacy.conf ...
net.ipv6.conf.all.use_tempaddr = 2
net.ipv6.conf.default.use_tempaddr = 2
* Applying /etc/sysctl.d/10-kernel-hardening.conf ...
kernel.kptr_restrict = 1
* Applying /etc/sysctl.d/10-link-restrictions.conf ...
fs.protected_hardlinks = 1
fs.protected_symlinks = 1
* Applying /etc/sysctl.d/10-magic-sysrq.conf ...
kernel.sysrq = 176
* Applying /etc/sysctl.d/10-network-security.conf ...
net.ipv4.conf.default.rp_filter = 1
net.ipv4.conf.all.rp_filter = 1
net.ipv4.tcp_syncookies = 1
* Applying /etc/sysctl.d/10-ptrace.conf ...
kernel.yama.ptrace_scope = 1
* Applying /etc/sysctl.d/10-zeropage.conf ...
vm.mmap_min_addr = 65536
* Applying /usr/lib/sysctl.d/50-default.conf ...
net.ipv4.conf.all.promote_secondaries = 1
net.core.default_qdisc = fq_codel
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.sem.conf ...
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.shmall.conf ...
* Applying /etc/sysctl.d/90-omnibus-gitlab-kernel.shmmax.conf ...
kernel.shmmax = 17179869184
* Applying /etc/sysctl.d/90-omnibus-gitlab-net.core.somaxconn.conf ...
* Applying /etc/sysctl.d/99-sysctl.conf ...
* Applying /etc/sysctl.conf ...
STDERR: sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-kernel.sem.conf": No such file or directory
sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-kernel.shmall.conf": No such file or directory
sysctl: cannot open "/etc/sysctl.d/90-omnibus-gitlab-net.core.somaxconn.conf": No such file or directory
---- End output of sysctl -e --system ----
Ran sysctl -e --system returned 255
Running handlers complete
Chef Client failed. 167 resources updated in 53 seconds
dpkg: error processing package gitlab-ee (--configure):
installed gitlab-ee package post-installation script subprocess returned error exit status 1
Errors were encountered while processing:
gitlab-ee
E: Sub-process /usr/bin/dpkg returned an error code (1)
The "Error executing actioncreateon resource 'gitlab_sysctl[kernel.shmmax" mostly points out to /sys being read-only.
See for instance omnibus-gitlab issue 1308
Set these values in /etc/sysctl.conf on the host, and run cat /etc/sysctl.conf /etc/sysctl.d/*.conf | sysctl -e -p - on the host.
Then run reconfigure in your lxc container again, it should detect that the kernel is already running with the necessary settings, and not make any changes.
Note: the values can be found here:
root#gitlab:~# cat /opt/gitlab/embedded/etc/90-omnibus-gitlab-*
kernel.sem = 250 32000 32 262
kernel.shmall = 4194304
kernel.shmmax = 17179869184
net.core.somaxconn = 1024
I recently tried out setting up the dev environment in a vagrant/lxc container (debian/jessie64 box) and I had to remount proc filesystem in rw mode (using mount -o remount rw /proc/sys) for setting the values.
I have found a temporary solution. (way it's work ??? xD )
I edit the file
sudo nano /opt/gitlab/embedded/cookbooks/package/resources/gitlab_sysctl.rb
section
Load the settings
to:
# Load the settings right away
#execute "load sysctl conf #{new_resource.name}" do
# command "sysctl -e --system"
# action :nothing
#end
execute "sysctl" do
command "/sbin/sysctl -e -p /etc/sysctl.conf"
action :nothing
end
enter code here
end
sudo gitlab-ctl reconfigure

Cannot update Yocto Bitbake Recipe for Bzip2 from 1.0.6 to 1.0.7 for CVE-2019-12900 for Nvidia Jetson Nano

On Ubuntu 18.04 I am trying to build a Yocto SD Card Image for the Nvidia Jetson Nano using the "meta-tegra" layer. I ran into the recent bzip2 issue that requires the latest bzip2 ( 1.0.7 ) to fix as detailed in these forum posts:
https://devtalk.nvidia.com/default/topic/1056301/b/t/post/5355418/
https://devtalk.nvidia.com/default/topic/1056381/jetson-agx-xavier/jetpack-4-2-xavier-install-failed/1
I found the latest bzip2 source here:
https://www.sourceware.org/bzip2/downloads.html
I tried playing with ${WORKDIR}, ${S}, do_compile_append, and do_install_append, however I keep getting errors related to the wrong source directory. I basically took the OE Bzip2 1.0.6 recipe and change the version source and checksums.
Please help me fix this build issue with yocto - thanks!
Bitbake Failure:
Initialising tasks: 100% |##########################################################################| Time: 0:00:00
Sstate summary: Wanted 382 Found 0 Missed 382 Current 45 (0% match, 10% complete)
NOTE: Executing SetScene Tasks
NOTE: Executing RunQueue Tasks
ERROR: bzip2-native-1.0.7-r5 do_compile: oe_runmake failed
ERROR: bzip2-native-1.0.7-r5 do_compile: Function failed: do_compile (log file is located at /home/ubuntu/Desktop/mts-jetson-yocto/build/tmp/work/x86_64-linux/bzip2-native/1.0.7-r5/temp/log.do_compile.115964)
ERROR: Logfile of failure stored in: /home/ubuntu/Desktop/mts-jetson-yocto/build/tmp/work/x86_64-linux/bzip2-native/1.0.7-r5/temp/log.do_compile.115964
Log data follows:
| DEBUG: Executing shell function do_compile
| NOTE: make -j 128
| make: *** No targets specified and no makefile found. Stop.
| ERROR: oe_runmake failed
| WARNING: exit code 1 from a shell command.
| ERROR: Function failed: do_compile (log file is located at /home/ubuntu/Desktop/mts-jetson-yocto/build/tmp/work/x86_64-linux/bzip2-native/1.0.7-r5/temp/log.do_compile.115964)
ERROR: Task (virtual:native:/home/ubuntu/Desktop/mts-jetson-yocto/layers/meta-mts/recipes-extended/bzip2/bzip2_1.0.7.bb:do_compile) failed with exit code '1'
Second Keyboard Interrupt, stopping...
Summary: 1 task failed:
virtual:native:/home/ubuntu/Desktop/mts-jetson-yocto/layers/meta-mts/recipes-extended/bzip2/bzip2_1.0.7.bb:do_compile
Summary: There were 2 ERROR messages shown, returning a non-zero exit code.
Current Broken Bitbake recipe:
SECTION = "console/utils"
LICENSE = "bzip2"
LIC_FILES_CHKSUM = "file://LICENSE;beginline=4;endline=37;md5=39406315f540c69bd05b1531daedd2ae"
PR = "r5"
SRC_URI = "https://www.sourceware.org/pub/bzip2/bzip2-1.0.7.tar.gz \
"
#WORKDIR = "${WORKDIR}/bzip-1.0.7"
#WORKDIR = "${BASE_WORKDIR}/${MULTIMACH_TARGET_SYS}/${PN}/${EXTENDPE}${PV}-${PR}/bzip2-1.0.7"
#S = "${WORKDIR}/bzip2-1.0.7"
#do_compile_prepend() {
# cd ../
#}
#do_install_prepend() {
# cd ../
#}
SRC_URI[md5sum] = "1a6a61cc867be4f3d6549037a09bf13e"
SRC_URI[sha256sum] = "e768a87c5b1a79511499beb41500bcc4caf203726fff46a6f5f9ad27fe08ab2b"
UPSTREAM_CHECK_URI = "https://www.sourceware.org/bzip2/"
UPSTREAM_VERSION_UNKNOWN = "1"
PACKAGES =+ "libbz2"
CFLAGS_append = " -fPIC -fpic -Winline -fno-strength-reduce -D_FILE_OFFSET_BITS=64"
inherit autotools update-alternatives ptest relative_symlinks
ALTERNATIVE_PRIORITY = "100"
ALTERNATIVE_${PN} = "bunzip2 bzcat bzip2"
#install binaries to bzip2-native under sysroot for replacement-native
EXTRA_OECONF_append_class-native = " --bindir=${STAGING_BINDIR_NATIVE}/${PN}"
do_install_ptest () {
sed -i -e "s|^Makefile:|_Makefile:|" ${D}${PTEST_PATH}/Makefile
}
FILES_libbz2 = "${libdir}/lib*${SOLIBS}"
PROVIDES_append_class-native = " bzip2-replacement-native"
BBCLASSEXTEND = "native nativesdk"
#addtask fix_path before do_compile
Two ideas:
Just apply the patch for the security issue, much easier. This patch is already on the oe-core list.
Take the upgrade patch that is also on the list

Slurm job expansion using the C API

I sent this question a few months ago to the slurm-dev list, but it is still unsolved.
The problem is: after trying to change the job size as describes the FAQ, I wanted to do it programatically using the API.
Everything seems to work fine before the step of updating the environment variables.
When I launch the application this is what I get:
$ salloc -N1 mpiexec -n 1 ./jobExpansion
salloc: Granted job allocation 559
srun: error: Only allocated 1 nodes asked for 4
In the squeue I can see that the allocation has changed, but srun cannot see the changes.
I continued debugging and if I executed:
$ salloc -N1
$ export SLURM_NODELIST=n04,n06,n00,n01
$ export SLURM_NNODES=4
$ mpiexec -n 1 ./jobExpansion
It worked.
So, I don't want to overwhelm with the complete code but, just in case you could help me I paste here the parts of the resizing:
slurm_init_job_desc_msg(&job);
job.user_id = getuid();
job.min_nodes = hostsToExpand;
job.dependency = (char *) malloc(sizeof (char)*20);
sprintf(job.dependency, (char *) "expand:%s", pID);
//$ salloc -N4 --dependency=expand:$SLURM_JOBID
slurm_alloc_msg_ptr = slurm_allocate_resources_blocking(&job, 0, NULL);
//$ scontrol update jobid=$SLURM_JOBID NumNodes=0
slurm_init_job_desc_msg(&job_update);
job_update.job_id = slurm_alloc_msg_ptr->job_id;
job_update.min_nodes = 0;
slurm_update_job(&job_update);
//exit
slurm_kill_job(slurm_alloc_msg_ptr->job_id, 9, 0);
//$ scontrol update jobid=$SLURM_JOBID NumNodes=ALL
slurm_init_job_desc_msg(&job_update);
job_update.job_id = procID;
job_update.min_nodes = INFINITE;
slurm_update_job(&job_update);
Everything points out the environment variables but I am not sure how to properly update them.
Thank you.
EDITED
If somebody would like test what I've said, here is the repository:
git clone https://siserte#bitbucket.org/siserte/slurm-job-expansion-test.git

systemtap global variable allocation failed

I want to use systemtap for extracting details of my linux production server. my systemtap script is
global bt;
global quit = 0
probe begin {
printf("start profiling...\n")
}
probe timer.profile {
if (pid() == target()) {
if (!quit)
{
bt[backtrace(), ubacktrace()] <<< 1
}
else
{
foreach ([sys, usr] in bt- limit 1000)
{
print_stack(sys)
print_ustack(usr)
printf("\t%d\n", #count(bt[sys, usr]))
}
exit()
}
}
}
probe timer.s(20) {
quit = 1
}
When I start run this script with command
sudo stap --ldd -d $program_name --all-modules \
-D MAXMAPENTRIES=10240 -D MAXACTION=20000 -D MAXTRACE=40 \
-D MAXSTRINGLEN=4096 -D MAXBACKTRACE=40 -x $program_pid \
profile.stp --vp 00001 > profile.out
It fails, and prints following error:
ERROR: error allocating hash
ERROR: global variable 'bt' allocation failed
WARNING: /usr/bin/staprun exited with status: 1
my production server memory info is
total used free shared buffers cached
Mem: 16008 15639 368 0 80 3090
-/+ buffers/cache: 12468 3539
I think it is enough, because in my test server, there is only 2G memory, and the systemtap script runs well for another server
Unfortunately, this is intended behavior, see my discussion here: https://sourceware.org/ml/systemtap/2015-q1/msg00033.html
The problem is that SystemTap allocates associative arrays at once (to prevent allocation failures in future) and on per-cpu basis (to prevent locking), which means that bt will require (2 * MAXSTRINGLEN + sizeof(statistic)) * MAXMAPENTRIES * NR_CPU =~ 2 Gb if NR_CPU == 128.
Reduce MAXSTRINGLEN (which is set to 4k in your case) or size of bt array:
global bt[128];

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