PHP Fatal error: Allowed memory size of x bytes exhausted – How to fix this error

We have a client with Antagonist in Holland and it has had multiple brief downtimes over the last couple of weeks. We are already no longer using Slimstat as it seemed to be rather demanding memory wise. But the downtimes still continued. “PHP Fatal error: Allowed memory size of x bytes exhausted” was the key error we found out. Here is how we dealt with it.

Allowed Memory Size Exhausted

As stated we soon saw in the logs that there was an issue with the PHP memory limit set. We got too many well known general errors like:

PHP Fatal error:  Allowed memory size of x bytes exhausted

We found this specific error using WP Debug in the debug.log file:

[02-Dec-2016 03:38:22 UTC] PHP Fatal error:  Allowed memory size of 268435456 bytes exhausted (tried to allocate 20480 bytes) in /home/account/domains/ on line 1832

and another one an hour later:

[02-Dec-2016 04:08:50 UTC] PHP Fatal error:  Allowed memory size of 268435456 bytes exhausted (tried to allocate 20480 bytes) in /home/account/domains/ on line 1832


The file wp-db.php the error refers to is the file used to interact with the database. It is based on the ezSQL class by Justin Vincent. It contains the useful global $wpdb There is a Codex article on it as well. There on the line 1832 of wp-db.php you will find:

while ( $row = mysqli_fetch_object( $this->result ) ) {
 $this->last_result[$num_rows] = $row;

That does mean that during a database fetch query more memory than allowed was asked for. This is still rather vague though and does not help much. More on a better analysis option a little later.

When we checked the general error log we only found:

Fri Dec 02 00:11:18.364110 2016] [ssl:warn] [pid 689240] AH01909: server certificate does NOT include an ID which matches the server name
[Fri Dec 02 04:49:58.434566 2016] [include:error] [pid 683238] [client] unable to include "/403.shtml" in parsed file /opt/error_pages/403_antagonist.shtml, subrequest setup returned 403, referer:

This error is not related to the issue though. And as the Antagonist cycles the logs rather quickly we will have to wait for more useful logs to show up.

Raising PHP Memory

So clearly we needed to raise the memory. This at least to avoid downtime. First we had to find out the amount of RAM used in DirectAdmin*. When you convert the bytes to megabytes you will see it passes 256MB:

bytes to megabytes

Location to check the PHP RAM limit varies from hoster to hoster. So is the place where you can raise memory usage for PHP. Some hosters will allow you to raise PHP memory in .htaccess or a custom php.ini file, others give you full root access to change the core php.ini.

When we checked the PHP settings in DirectAdmin – where Antagonist allow you to change it – we found out the limit was set at a puny 128MB so we raised it to 512MB:

Antagonist DirectAdmin PHP settings

We do prefer max 256MB for most non e-commerce sites though so we will start monitoring things more to figure out why this is happening.

WordPress Memory Limit

If this did not help you probably have to add one or two lines of code to wp-config.php to tell WordPress to really use the extra RAM given  (Codex Article). In our case we may add the following if need be:

define( 'WP_MEMORY_LIMIT', '512M' );

With most of our WooCommerce setups this is needed. In the case of memory allocation issues like ours we probably can just stick to change in PHP config itself.

Analysing Higher RAM Demand

To figure out what plugin or queries are the most demanding I normally use two plugins:

P3 Profiler has unfortunately not been updated in over 2 years so is no 100% very reliable. But still a great plugin that shows what your plugins and theme is using as a percentage of the whole.

The Query Monitor is more detailed as it will really show what particular queries are very demanding. Is a better option if you are the theme or plugin developer and want to improve the overall performance of your baby. For end users it is however more difficult to put to good use.

NB We are focussing here on backend stuff as the issue is related to database queries.  For frontend stuff  and site performance you can use tools like GMetrix, Chrome Inspector.  Also See this article for more .

Causes of Higher RAM Demand

Normally a plugin like Wordfence doing security scans, a statistics plugin like Slimstat or a backup plugin like BackupBuddy are the culprit as they all demand more than the average plugin. Site scans and backups as well as dealing with site traffic statistics tend to demand a lot. Lot’s of queries being fired, lots of I/O. That does not mean that these aren’t great plugins though. Some hosters just limit you quite a bit on memory or I/O (Especially GoDaddy!). Especially shared hosters.

In our case it was Wordfence demanding a bit more of the site every now and then. That and some heavy brute force password attacks that come and go. We are limiting the failed login attempts more now and we are considering stopping the use of Wordfence though we really love it.


If you want to keep on working with these or other demanding plugins you often need to upgrade your hosting package. Dropping the use of certain plugins tends to go only so far as some you simply cannot live without. So upgrade when need be. Unless there is space for the hoster to give you more RAM and they are willing too. You should at least be able to get 256MB. Even 512MB for running WooCommerce.

If you are on shared hosting, well, that often means you will need to upgrade to a better package. That has been my and my clients’ experience. In the end a better package, especially on a VPS or managed WordPress hosting service, will be best for most of you.




Roots Trellis Errors

In this post I will be collecting Roots Trellis local and remote provisioning, deployment and general setup errors with solutions I came up with. The list is growing and growing so make sure you press control or command f to search for your specific error or use the search box.

Local Setup Errors

I have had quite a few errors setting up my local box and I will gather them here for future reference.

Composer not installed properly

Sometimes vagrant provisioning just hangs on the installation of dependencies and more specifically Composer for PHP dependency management. When I then try to load the local site after the Ansible playbook stopped there I get to see an NGINX 403 access denied error locally.

 TASK: [wordpress-install | Install Dependencies with Composer] **************** 
failed: [default] => (item={'key': '', 'value': {'site_install': True, 'permalink_structure': '/%postname%/', 'admin_user': 'admin', 'local_path': '../site', 'cache': {'duration': '30s', 'enabled': False}, 'ssl': {'enabled': False}, 'multisite': {'enabled': False, 'subdomains': False}, 'site_title': 'Example Site', 'admin_password': 'admin', 'env': {'db_name': 'domain_dev', 'db_user': 'imagewize_dbuser', 'wp_env': 'development', 'db_password': 'domain_dbpassword', 'disable_wp_cron': True, 'wp_home': '', 'wp_siteurl': ''}, 'site_hosts': [''], 'admin_email': ''}}) => {"changed": true, "cmd": ["composer", "install"], "delta": "0:00:00.062962", "end": "2015-12-29 10:11:13.064551", "item": {"key": "", "value": {"admin_email": "", "admin_password": "admin", "admin_user": "admin", "cache": {"duration": "30s", "enabled": false}, "env": {"db_name": "domain_dev", "db_password": "domain_dbpassword", "db_user": "domain_dbuser", "disable_wp_cron": true, "wp_env": "development", "wp_home": "", "wp_siteurl": ""}, "local_path": "../site", "multisite": {"enabled": false, "subdomains": false}, "permalink_structure": "/%postname%/", "site_hosts": [""], "site_install": true, "site_title": "Example Site", "ssl": {"enabled": false}}}, "rc": 1, "start": "2015-12-29 10:11:13.001589", "stdout_lines": [], "warnings": []}
stderr: You are running composer with xdebug enabled. This has a major impact on runtime performance. See
Composer could not find a composer.json file in /srv/www/
To initialize a project, please create a composer.json file as described in the "Getting Started" section

Best solution I found is

vagrant destroy


vagrant up

Just a

vagrant provision

did not do the trick

Package cannot be authenticated

Local setup errors setting up my Vagrant Box I seem to get often when I do not use my VPN are:

The following SSH command responded with a non-zero exit status.
Vagrant assumes that this means the command failed!
apt-get install -y bindfs
Stdout from the command:
Reading package lists...
Reading state information...
The following NEW packages will be installed:
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
Need to get 25.1 kB of archives.
After this operation, 89.1 kB of additional disk space will be used.
WARNING: The following packages cannot be authenticated!
Stderr from the command:
E: There are problems and -y was used without --force-yes

The package cannot be authenticated somehow. No idea why really, but seems to happen to me out here in Bahrain. Solution is using another network or a VPN and running

vagrant provision

to set all up well locally.

Unexpected Exception: TaskInclude

Installation goes well, but just before all is done you get

ERROR! Unexpected Exception: 'TaskInclude' object has no attribute 'has_triggered'
Ansible failed to complete successfully. Any error output should be
visible above. Please fix these errors and try again.

No solution yet either, besides destroying the box and starting from scratch. Googling did not dig up any dirt either. Well, one sort of related thread here, but has done me no good. Apparently the Ansible 2.1.0 version has a regression so 2.0.2 needed to be installed. See Roots Discourse thread here. Could not do that using Homebrew so had to remove Ansible, and then install it using Python’s Pip. There I had issues getting it to install at all due to OSX Mavericks and El Capitan issues. Found a solution for that here. Also needed a Python setuptools upgrade to avoid other errors  such as:

ERROR! Unexpected Exception: (setuptools 1.1.6 (/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python), Requirement.parse('setuptools>=11.3'))

SO thread here.

Dict Object has no Attribute

Setting up or provisioning the local server / Vagrant box I ran into this error as well:

TASK: [wordpress-setup | Create/assign database user to db and grant permissions] *** 
fatal: [default] => One or more undefined variables: 'dict object' has no attribute ''Provisioning Errors

Check if vault.yml has the correct site name.

Unable to find Inventory File

ERROR: Unable to find an inventory file, specify one with -i ?

This error showed up  when I want to provision a server I did provisioning on before using a different project and I forgot about. Better to start out with an empty instance. Command leading to this error is:

ansible-playbook server.yml -e env=staging

Solution was wiping out Trellis and start from scratch and then provision again

502 Bad Gateway

After provisioning a local vagrant box I ran into this error:

502 Bad Gateway

Suspending the Vagrant box and restarting did not help. Checking the logs you may see something like:

*8 connect() to unix:/var/run/php-fpm-wordpress.sock failed (2: No such file or directory) while connecting to upstream, client:, server:, request: "GET /favicon.ico HTTP/1.1", upstream: "fastcgi://unix:/var/run/php-fpm-wordpress.sock:", host: "", referrer: ""

Meaning there was an issue with Fast CGI. The path to the socket should be


So I opened


and adjusted it. Then restarted the server:

sudo service nginx restart

No joy. Still was loaded from another location it seems though I could not locate it inside php.ini. So I destroyed the box:

vagrant destroy


 vagrant up

and re-created it. And then all was well again. If I do bump into this issue again and manage to solve it manually I will let you guys know.

sSMTP Installation Error

Another provisioning error I seem to get when I work with multiple domain names connected to one elastic IP is an issue installing sSMTP

 failed: [] => {"failed": true}
 stderr: hostname: Name or service not known
 dpkg: error processing package ssmtp (--configure):
 subprocess installed post-installation script returned error exit status 1
 Errors were encountered while processing:
 E: Sub-process /usr/bin/dpkg returned an error code (1)
stdout: Reading package lists...
 Building dependency tree...
 Reading state information...
 The following NEW packages will be installed:
 0 upgraded, 1 newly installed, 0 to remove and 4 not upgraded.
 Need to get 46.2 kB of archives.
 After this operation, 8192 B of additional disk space will be used.
 Get:1 trusty/universe ssmtp amd64 2.64-7 [46.2 kB]
 Preconfiguring packages ...
 Fetched 46.2 kB in 0s (366 kB/s)
 Selecting previously unselected package ssmtp.
 (Reading database ... 70521 files and directories currently installed.)
 Preparing to unpack .../ssmtp_2.64-7_amd64.deb ...
 Unpacking ssmtp (2.64-7) ...
 Processing triggers for man-db ( ...
 Setting up ssmtp (2.64-7) ...
msg: '/usr/bin/apt-get -y -o "Dpkg::Options::=--force-confdef" -o "Dpkg::Options::=--force-confold" install 'ssmtp'' failed: hostname: Name or service not known
 dpkg: error processing package ssmtp (--configure):
 subprocess installed post-installation script returned error exit status 1
 Errors were encountered while processing:
 E: Sub-process /usr/bin/dpkg returned an error code (1)

I found an issue mentioning it here at Github suggesting to check /etc/hosts and /etc/hostname. Hostname had imagewize (copied from Dreamhost instance name given). Still working on this issue and adding possible FQDN . They also suggested using a domain name, but I guess I my case it was using one domain too many. In the end I moved one staging site to another server.


Publickey – Permission denied

Another issue I run into sometimes is an issue with the SSH public key:

GATHERING FACTS ***************************************************************
fatal: [] => SSH Error: Permission denied (publickey).
while connecting to
It is sometimes useful to re-run the command using -vvvv, which prints SSH debug output to help diagnose the issue.

Often this means one of these issues:

  • your SSH public key is not OK so you need to update your remote server at Digital Ocean or DreamCompute with the latest for example
  • you switched server and need to change IP inside hosts/<environment>
  • wrong username to access server – make sure the users.yml has the correct user – For DreamCompute it should not be admin but dhc-user.

Deployment Errors

Another error trying to deploy  I got was really odd or by the looks of it initially as it mentioned paths to Ansible files I could not locate right away and stuff leading to SSH key issues in the end:

./ staging
PLAY [Deploy WP site] *********************************************************
GATHERING FACTS ***************************************************************
ok: []

TASK: [deploy | Initialize] ***************************************************
failed: [] => {"failed": true, "parsed": false}
Traceback (most recent call last):
File "/home/web/.ansible/tmp/ansible-tmp-1451380440.18-256782094434614/deploy_helper", line 2026, in
File "/home/web/.ansible/tmp/ansible-tmp-1451380440.18-256782094434614/deploy_helper", line 382, in main
changes += deploy_helper.create_path(facts['project_path'])
File "/home/web/.ansible/tmp/ansible-tmp-1451380440.18-256782094434614/deploy_helper", line 276, in create_path
File "/usr/lib/python2.7/", line 150, in makedirs
makedirs(head, mode)
File "/usr/lib/python2.7/", line 157, in makedirs
mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/srv/www'
OpenSSH_6.9p1, LibreSSL 2.1.8
debug1: Reading configuration data /Users/jasper/.ssh/config
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 21: Applying options for *
debug1: auto-mux: Trying existing master
debug1: mux_client_request_session: master session id: 2
Shared connection to closed.

Error was related to previous provision issue and a clean slate with a clean remote server and new Trellis installation was all I could come up with to solve it all.

NGINX Error 404

I also bumped into a:

404 Not Found

error. This was simply due to the fact that I had provisioned, but hadn’t deployed. Yet. Once that was done all was well.

Wrong Subtree

TASK: [deploy | Fail if project_subtree_path is set incorrectly] ************** 
failed: [] => {"failed": true}
msg: subtree is set to 'site' but that path does not exist in the repo. Edit `subtree_path` for '' in `wordpress_sites.yml`.

Make sure you have added the correct repo to the wordpress_sites.yml and that the subtree is correctly set. Last time I switched from Github to Bitbucket (free private repos!) but I did not adjust the repository.

Repo Access Error

Had an issue a few times that I suddenly had an error that the remote repository could no longer be accessed while I could push and pull from the Github repository. This made it impossible to deploy. See the errors below:

TASK [deploy : Clone project files] ********************************************
System info:
 Ansible; Darwin
 Trellis at "Fix #639 - WP 4.6 compatibility: update WP-CLI to 0.24.1"
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

fatal: []: FAILED! => {"censored": "the output has been hidden due to the fact that 'no_log: true' was specified for this result"}

TASK [deploy : Failed connection to remote repo] *******************************
System info:
 Ansible; Darwin
 Trellis at "Fix #639 - WP 4.6 compatibility: update WP-CLI to 0.24.1"
Git repo cannot be accessed. Please
verify the repository exists and you have SSH forwarding set up correctly.
More info:

fatal: []: FAILED! => {"changed": false, "failed": true}

NO MORE HOSTS LEFT *************************************************************
 [WARNING]: Could not create retry file 'deploy.retry'. [Errno 2] No such
file or directory: ''

The issue in the end was probably related to my upgrade to OSX Sierra and some system and or keychain changes. I had to enter my passphrase earlier. And somehow the key had to be added to the keychain again as well. This as a simple:

ssh-add -K
Identity added: /Users/jasper/.ssh/id_rsa (/Users/jasper/.ssh/id_rsa)

After that I could access all again and deploy the latest changes to the site.