502 on Create Merge Request

Summary

I have 500+ MB Repo that I just un-nested the entire project from a top level directory. When I try to create MR the server goes into over drive then throws a 502 after a bit(30-60 seconds). Adding memory and cPU din't help as only 1 cpu ever gets used.

Expected behavior

From what I read in gitlab-ce#13267 & gitlab-ce#13912 I would expect it to let me know it can't show the full diff but still allow me to create a MR.

Actual behavior

502 Whoops, GitLab is taking too much time to respond.

Results of GitLab application Check

Checking GitLab Shell ...

GitLab Shell version >= 3.6.6 ? ... OK (3.6.6)
Repo base directory exists?
default... yes
Repo storage directories are symlinks?
default... no
Repo paths owned by git:git?
default... yes
Repo paths access is drwxrws---?
default... yes
hooks directories in repos are links: ... 
13/4 ... ok
3/5 ... ok
3/7 ... ok
3/8 ... ok
13/9 ... ok
13/10 ... ok
13/11 ... ok
13/12 ... ok
13/13 ... ok
4/14 ... ok
25/15 ... ok
13/16 ... ok
30/18 ... ok
30/20 ... repository is empty
30/21 ... repository is empty
2/22 ... repository is empty
21/23 ... ok
3/24 ... ok
2/25 ... ok
Running /opt/gitlab/embedded/service/gitlab-shell/bin/check
Check GitLab API access: OK
Access to /var/opt/gitlab/.ssh/authorized_keys: OK
Send ping to redis server: OK
gitlab-shell self-check successful

Checking GitLab Shell ... Finished

Checking Sidekiq ...

Running? ... yes
Number of Sidekiq processes ... 1

Checking Sidekiq ... Finished

Checking Reply by email ...

Reply by email is disabled in config/gitlab.yml

Checking Reply by email ... Finished

Checking LDAP ...

LDAP is disabled in config/gitlab.yml

Checking LDAP ... Finished

Checking GitLab ...

Git configured with autocrlf=input? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config outdated? ... no
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory setup correctly? ... yes
Init script exists? ... skipped (omnibus-gitlab has no init script)
Init script up-to-date? ... skipped (omnibus-gitlab has no init script)
projects have namespace: ... 
13/4 ... yes
3/5 ... yes
3/7 ... yes
3/8 ... yes
13/9 ... yes
13/10 ... yes
13/11 ... yes
13/12 ... yes
13/13 ... yes
4/14 ... yes
25/15 ... yes
13/16 ... yes
30/18 ... yes
30/20 ... yes
30/21 ... yes
2/22 ... yes
21/23 ... yes
3/24 ... yes
2/25 ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.1.0 ? ... yes (2.3.1)
Your git bin path is "/opt/gitlab/embedded/bin/git"
Git version >= 2.7.3 ? ... yes (2.7.4)
Active users: 5

Checking GitLab ... Finished

Results of GitLab environment info

System information
System:		Ubuntu 16.04
Current User:	git
Using RVM:	no
Ruby Version:	2.3.1p112
Gem Version:	2.6.6
Bundler Version:1.13.6
Rake Version:	10.5.0
Sidekiq Version:4.2.1

GitLab information
Version:	8.13.5
Revision:	09cedb5
Directory:	/opt/gitlab/embedded/service/gitlab-rails
DB Adapter:	postgresql
URL:		https://gitlab.tangorguild.com
HTTP Clone URL:	https://gitlab.tangorguild.com/some-group/some-project.git
SSH Clone URL:	git@gitlab.tangorguild.com:some-group/some-project.git
Using LDAP:	no
Using Omniauth:	no

GitLab Shell
Version:	3.6.6
Repository storage paths:
- default: 	/var/opt/gitlab/git-data/repositories
Hooks:		/opt/gitlab/embedded/service/gitlab-shell/hooks/
Git:		/opt/gitlab/embedded/bin/git