Research Computing Configuration

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This page describes the configuration of the two new research computing machines. This configuration runs on our Research Computing Hardware. Note that the configuration of the DIGITS DevBox is on its own page.

Both machines

Fan Control

Unless you want to go insane from the sound of fans cycling full on and off, you'll want to fix the IPMI fan settings. These are stored in the BIOS but not accessible through the BIOS screens. Instead, you should connect to the boxes by BMC over the network. The BMC IPv4 address is displayed during POST.

To read all about IPMI, see https://www.supermicro.com/products/nfo/IPMI.cfm I also found these helpful:

Note the that default BMC username and password is ADMIN and ADMIN. You can download the SMCIPMITool (2.21.0_build.181029) and do the following, though I couldn't work out how to send manual configuration instructions using it: 

.\SMCIPMITool.exe 192.168.2.80 ADMIN ADMIN ipmi fan
.\SMCIPMITool.exe 192.168.2.80 ADMIN ADMIN ipmi fan 0

The trick is to change the thresholds for the fans, especially the lower threshold. On a linux box: 

sudo apt-get install ipmitool
  1. Reset the BMC if you've screwed it up (or if your fans are full on all the time)
  2. Check that the current mode is optimal (2)
  3. Take a look at the sensor multiple times to see that the fan is hitting the constraint (run multiple times to coincide with different sound levels)
  4. Reset the lower thresholds on the fans
  5. Enjoy a perfectly reasonable fan speed that doesn't fluctuate unduly
ipmitool -I lan -U ADMIN -P ADMIN -H 192.168.2.80 raw 0x3c 0x40
ipmitool -I lan -U ADMIN -P ADMIN -H 192.168.2.80 raw 0x30 0x45 0x00
ipmitool -I lan -U ADMIN -P ADMIN -H 192.168.2.80 sensor
ipmitool -I lan -U ADMIN -P ADMIN -H 192.168.2.80 sensor thresh FAN3 lower 120 220 320

Note that the thresholds are derived from -20% off 400 (min as per Noctua spec), then same -100, then same -200.

For the ARCTIC F8 PWM, the min is something like 250 at 5v (see https://www.arctic.ac/us_en/arctic-f8-pwm.html). I therefore used 100, 150, 200, which seemed to stabilize the fans nicely at a 300rpm idle on one box and 400rpm on the other.

Note that the BMC IP for mother often turns up on 192.168.2.70. You can see the IP address of the localhost by running: 

ipmitool lan print

Bios Settings

Because we want the NVMe drives to be bootable, we need to use (U)EFI for both machines:

  • Change CPU1 Slot 1 and 2 to EFI (from Legacy)
  • Change Onboard Video OPROM to EFi (from Legacy)
  • LAN device to EFI
  • Boot to EFI
  • Priority to onboard: auto
  • Boot install order CD above drive above Shell

This ultimately seems to be a problem for unsigned Nvidia drivers in Linux, which make putting a GPU into the dbase server box a major issue. I tried disabling validation and adding a key to secure boot (not sure that it happened) but nothing I could do would fix the resulting driver issue. 

mokutil --disable-validation
sudo update-secureboot-policy --new-key
sudo update-secureboot-policy --enroll-key

RDP Server

The RDP server runs Windows 2019 Server. It installs directly off the media on to the NVMe drive. Don't worry about the RAID array during the installation, we do that later.

After installation:

  • Set computer name
  • Storage Pool
    • RAID 1 - Mirroring
  • Active Directory Controller
  • Remote Desktop Connection
    • RD Connection Broker
    • RD Licensing
    • RD Session Host
    • RD Vizualization Host

Change password complexity requirements: https://blog.tiga.tech/disable-the-password-complexity-for-active-directory-on-a-domain-controller/

Update

The GPU was removed from the RDP and the chipset drivers from Supermicro were installed (files are in E:/installs/drivers). This addressed all the device issues.

The following software was uninstalled:

  • CUDA Development 10.1
  • CUDA Documentation 10.1
  • CUDA Samples 10.1
  • CUDA Visual Studio Integration 10.1
  • NVIDIA GeForce Experience 3.18.0.94
  • NVIDIA Graphics Driver 419.67
  • NVIDIA HD Audio Diver 1.3.38.13
  • NVIDIA Nsight Compute v2019.1
  • NVIDIA Nsight Systems v2018.3.3
  • NVIDIA Nsight Visual Studio Edition
  • NVIDIA PhysX System Software 9.12.0218
  • NVIDIA Toos Extension SDK
  • NVIDIA USBC Driver 1.1.27.831

Dbase Server

The dbase server runs Ubuntu 18.04. You can mostly follow the instructions at https://www.pugetsystems.com/labs/hpc/The-Best-Way-To-Install-Ubuntu-18-04-with-NVIDIA-Drivers-and-any-Desktop-Flavor-1178/

It is important to use the alternative installation iso, not the default cloud based one. However, you can set up the partitions using the standard live CD, which is more user friendly for partitioning.

Partitioning

Partition as:

  • 400G NVMe as ext4 and / (create new using whole drive, automatically sets aside 512m for /boot/efi)
  • 1.2T as ext4 and /data (do it manually)
  • RAID 10 for HDDs, all active then format at ext4 and mount at /bulk (DO NOT PARTITION! Just set up the software RAID and format.)

Standard Packages

Install the following straight from the media:

  • LAMP Server
  • Mail Server
    • Postfix - Internet Site
    • MailName: mother.edegan.com
  • PostgreSQL
  • Samba
  • OpenSSH

Then: 

sudo apt-get install tasksel
tasksel
 -> Ubuntu Desktop

A useful apt cheatsheet is: https://www.acpsd.net/site/handlers/filedownload.ashx?moduleinstanceid=53976&dataid=56016&FileName=Ubuntu%20Cheat%20Sheet.pdf

Get the system up to date: 

apt-get update
apt-get upgrade

Samba

This guide is helpful: https://linuxconfig.org/how-to-configure-samba-server-share-on-ubuntu-18-04-bionic-beaver-linux

Check samba is running 

samba --version

Then fix the conf file: 

cp /etc/samba/smb.conf /etc/samba/smb.conf.bak
vi /etc/samba/smb.conf
	workgroup=mothergroup
 	usershare allow guests = no
	;comment [printers] and [print$]
    
	[bulk]
	comment = Bulk RAID Array
	path = /bulk
	browseable = yes
	create mask= 0775
	directory mask = 0775
	read only = no
	guest ok = no

Test the parameters, change the permissions and ownership: 

testparm /etc/samba/smb.conf
chmod 770 /bulk
groupadd smbusers
chown :smbusers /bulk

Now add the researcher account, and add it to the samba share 

groupadd -g 1001 researcher
useradd -g researcher -G smbusers -s /bin/bash -p 1234 -d /home/researcher -m 
researcher
passwd researcher
	hint: littleamount
smbpasswd -a researcher

Finally restart samba: 

systemctl restart smbd
systemctl restart nmbd

Check it works: 

smbclient -L localhost
(no root password)

And add users to the samba group: 

useradd ed smbusers

PostgreSQL

This guide is helpful: https://linuxconfig.org/install-postgresql-on-ubuntu-18-04-bionic-beaver

Test it! 

psql --help
ss -nlt
	postgres is listening on 543

Back up the config file and try a manual launch: 

cp /etc/postgresql/10/main/postgresql.conf /etc/postgresql/10/main/postgresql.conf.bak
mkdir /data/postgres
chown postgres:postgres postgres
su postgres
cd /usr/lib/postgresql/10/bin
./initdb -D /data/postgres

Now, tune the database server. See https://www.postgresql.org/docs/10/runtime-config-resource.html and https://wiki.postgresql.org/wiki/Tuning_Your_PostgreSQL_Server 

vi /etc/postgresql/10/main/postgresql.conf
 data_directory = '/data/postgres' #custom 1.2Tb NVME SSD
 listen_addresses = '*'
 max_connections = 10
 shared_buffers = 128GB 
 huge_pages = try                        # on, off, or try
 temp_buffers = 8GB                      # min 800kB
 work_mem = 4GB                          # min 64kB
 maintenance_work_mem = 64GB             # min 1MB
 max_stack_depth = 6MB
 max_wal_senders = 5   #MUST SET THIS TO BE LESS THAN max_connections
 effective_cache_size = 384GB

Now fix the hba.conf file for access rights: 

cp /etc/postgresql/10/main/pg_hba.conf /etc/postgresql/10/main/pg_hba.conf.bak
vi /etc/postgresql/10/main/pg_hba.conf

change
 local all all peer
to 
 local all all trust

Don't do this bit for now:
	 local   all             postgres                   peer 
	 local   all             postgres                   md5

And restart! 

service postgresql restart
ss -nlt

If postgres isn't listening then it didn't start despite the message at 

service postgresql status

Then we note that Postgres bins are in in: 

cd /usr/lib/postgresql/10/bin

Check: 

cat /etc/init.d/postgresql
cat /usr/share/postgresql-common/init.d-functions

To diagnose error do manual start as postgres from /usr/lib/postgresql/10/bin: 

pg_ctl -w -D /data/postgres -o '--config-file=/etc/postgresql/10/main/postgresql.conf.new' start

To check it is working: 

ss -nlt
psql postgres
SHOW data_directory;
SHOW work_mem;

When it is all ok, you can go back to using 

service postgresql restart
(it should take a few secs)

Make the researcher user! 

createuser --interactive researcher

Add Extensions

Finally, add some extentions 

apt-get install postgresql-plperl-10
apt-get install postgresql-plpython-10
apt-get install postgresql-10-plr
apt-get install postgresql-10-postgis-2.4 
apt-get install postgresql-10-postgis-scripts
apt-get install postgis
apt-get install postgis-gui

As postgres: 

psql template1
CREATE EXTENSION plr;
CREATE EXTENSION plperl;
CREATE EXTENSION plpythonu

Mediawiki

We had a back off of an old MySQL mediawiki dbase and the contents of the mediawiki directory, and we wanted to restore the old wiki. This is what we did.

Restore the old dbase: 

cd /bulk/mcnair/Web/mysqldump 
 dbase is mcnair
mysql -h localhost < web_mysqldump_backup_Fri_Aug_24_15_35_47_2018.sql

Connect to MySQL and check what we have: 

mysql
connect
show databases;
use mcnair;
show tables;

If you need to: systemctl stop mysql systemctl start mysql

Get the old install: 

cd home/home/mcnair/Downloads/
tar -xvzf mediawiki-1.26.2.tar.gz

Add php-xml 

apt-get install php-xml
apachectl restart

We then had to fix the passwords in the dbase: 

#Note: change passwords from hints before running
mysql
SELECT User, Host, Password FROM mysql.user;
UPDATE mysql.user SET Password = PASSWORD('tsn') WHERE User = 'root';
UPDATE mysql.user SET Password = PASSWORD('tsn') WHERE User = 'debian-sys-maint';
UPDATE mysql.user SET Password = PASSWORD('tsn') WHERE User = 'mcnair_wp';
FLUSH PRIVILEGES;

At this point, the basics are working, so go to http://192.168.2.92/mediawiki/mw-config/index.php and fill it out as per the old instructions (see Test Web Server Documentation and Web Server Documentation

Now overwrite LocalSettings.php with the old configuration: 

cd /home/ed/Downloads/
mv LocalSettings.php /var/www/html/mediawiki/

Fix the requirements for mediawiki 

apt-get install php-xml
apachectl restart

Allow short URLS, so enable mod-rewrite (if not already enabled) 

a2enmod rewrite
systemctl restart apache2

Now fix the apache conf file 

cp /etc/apache2/sites-available/000-default.conf /etc/apache2/sites-available/000-default.conf.bak
vi /etc/apache2/sites-available/000-default.conf 
       Alias /wiki /var/www/html/mediawiki/index.php
       #Enable the rewrite engine
       RewriteEngine On
       #Rewrite / to Main Page
       RewriteRule ^/*$ %{DOCUMENT_ROOT}/mediawiki/index.php [L]
service restart apache2

Now create phpinfo page for debugging 

cd /var/www/html
vi phpinfo.php
	<?php echo phpinfo(); ?>
	#Browse to 192.168.2.92/phpinfo.php
	Shows Phar is installed and running
	Shows log is /var/log/apache2

Check pcntl is enabled 

php --ri pcntl
#Note that some pcntl functions are listed as disabled in phpinfo.php
dpkg -s snmp
apt-get install snmp

The Big Try

The process is as follows:

  1. Move the contents of /var/lib/mediawiki to somewhere else
  2. Move the contents of /bulk/mcnair/Web/www/var/www/html/mediawiki in
  3. Drop databases
  4. Restore databases
  5. Pray

Or more specifically: 

mv /var/lib/mediawiki/ /var/lib/firstmediawikitry
mkdir /var/lib/mediawiki
cp -r /bulk/mcnair/Web/www/var/www/html/mediawiki /var/lib/
#Change password for dbase in LocalSettings.php
mysql -p
DROP DATABASE mcnair;
DROP DATABASE wordpress;
cd /bulk/mcnair/Web/mysqldump 
mysql -p -h localhost < web_mysqldump_backup_Fri_Aug_24_15_35_47_2018.sql
apachectl restart

When we did this, we got a blank page! Don't panic. 

cd /var/log/apache2
cat error.log
apt-get install php7.2-mbstring
apachectl restart

Fix LocalSettings.conf again 

change domain name, contact detail, etc.
Need to fix mail...
Also left GoogleAnalytics extension loaded for now...
Change enable_semantics IP address

Fix the Infoboxes: 

chmod a+x /var/libr/mediawiki/extensions/Scribuntu...
chcon -t httpd_sys_script_exec_t /var/lib/mediawiki/Scribuntu...
mv /etc/apache2/sites-available/000-default.conf /etc/apache2/sites-available/000-default.conf.new
mv /etc/apache2/sites-available/000-default.conf.bak /etc/apache2/sites-available/000-default.conf
apachectl restart
mv /etc/apache2/sites-available/000-default.conf.new /etc/apache2/sites-available/000-default.conf
apachectl restart

We were left with a problem were the page would never finish loading. This turned out to be a problem with the fonts in the Vector skin, which we had previously customized. We tried to fix the problem in the dbase as below but to no avail. 

SELECT * FROM externallinks WHERE el_id=2599;
UPDATE externallinks SET el_to = 'http://192.178.2.92/mediawiki/resources/assets/fonts/OpenSans-Regular.ttf' WHERE el_id = 2720;
UPDATE externallinks SET el_index = 'http://192.178.2.92/mediawiki/resources/assets/fonts/OpenSans-Regular.ttf' WHERE el_id = 2720;
UPDATE externallinks SET el_to = 'http://192.178.2.92/mediawiki/resources/assets/fonts/OpenSans-Italic.ttf' WHERE el_id = 2721;
UPDATE externallinks SET el_index = 'http://192.178.2.92/mediawiki/resources/assets/fonts/OpenSans-Italic.ttf WHERE el_id = 2721;
UPDATE externallinks SET el_to = 'http://192.178.2.92/mediawiki/resources/assets/fonts/OpenSans-Bold.ttf ' WHERE el_id = 2722;
UPDATE externallinks SET el_index = 'http://192.178.2.92/mediawiki/resources/assets/fonts/OpenSans-Bold.ttf ' WHERE el_id = 2722;
UPDATE externallinks SET el_to = 'http://192.178.2.92/mediawiki/resources/assets/fonts/OpenSans-BoldItalic.ttf WHERE el_id = 2723;
UPDATE externallinks SET el_index = '192.178.2.92/mediawiki/resources/assets/fonts/OpenSans-BoldItalic.ttf' WHERE el_id = 2723;
UPDATE externallinks SET el_to = 'http://192.178.2.92/mediawiki/resources/assets/fonts/BonvenoCF-Light.otf' WHERE el_id = 2724;
UPDATE externallinks SET el_index = 'http://192.178.2.92/mediawiki/resources/assets/fonts/BonvenoCF-Light.otf' WHERE el_id = 2724;
UPDATE externallinks SET el_to = 'http://192.178.2.92/mediawiki/resources/assets/fonts/franklin-gothic-book.ttf' WHERE el_id = 2739;
UPDATE externallinks SET el_index = 'http://192.178.2.92/mediawiki/resources/assets/fonts/franklin-gothic-book.ttf' WHERE el_id = 2739;
UPDATE externallinks SET el_to = 'http://192.178.2.92/wiki/Carried_Interest_Debate' WHERE el_id = 2599;
UPDATE externallinks SET el_index = 'http://192.178.2.92/wiki/Carried_Interest_Debate' WHERE el_id = 2599;

What did work was: 

cd /var/www/html/mediawiki/skins
diff -r Vector VectorBackup
cp -r Vector/ VectorFromMcNair
vi /skins/Vector/variables.less

replace all font-family statements with "Linux Libertine", Georgia, Times, sans-serif, serif;

When I rebooted the MySQL database was inaccessible for reasons unknown... I followed this page: https://www.howtoforge.com/setting-changing-resetting-mysql-root-passwords 

service mysql stop
mysqld_safe --skip-grant-tables &
mkdir -p /var/run/mysqld
chown mysql:mysql /var/run/mysqld
mysqld_safe --skip-grant-tables &

And then all was good!

Confirm Account

We had some issues with some of the extensions, particularly confirm account. To debug the wiki add this line to LocalSettings.php 

$wgShowExceptionDetails = true;

Fix the confirm account, see https://www.mediawiki.org/wiki/Extension:ConfirmAccount#Minimal_settings and add lines to LocalSettings.conf. 

apt-get install php7.2-dev 
apt-get install php-pear
pear
pear -version
pear config-get php_dir
	/usr/share/php
phpinfo returns:
	/etc/php/7.2/apache2/php.ini

Then make check_pear.php as per http://pear.php.net/manual/en/installation.checking.php. It should return bool true

Finally: 

php -c /etc/php/7.2/apache2/php.ini -r 'echo get_include_path()."\n";'

.:/usr/share/php 

uncomment 
; UNIX: "/path1:/path2"
include_path = ".:/usr/share/php"

See https://www.mediawiki.org/wiki/Manual:$wgSMTP

Wordpress

From Test Web Server Documentation it doesn't look like we had to install anything before we installed Wordpress. The restoration plan is therefore:

  1. Restore the dbase (done already when we restored the mediawiki dbase)
  2. Copy over all of the wordpress files
  3. Create a /blog alias in apache
  4. Check the permissions and pray

So we did: 

cd /bulk/mcnair/Web/www/var/www/html
cp -r ./blog/ /var/www/html/blog
cd /var/www/html/blog/

Check Apache2.conf 

vi /etc/apache2/apache2.conf
 looks fine

Temporarily force some settings 

vi wp-config.php
 define('WP_HOME','http://www.edegan.com/blog');
 define('WP_SITEURL','http://www.edegan.com/blog');
 define('DB_PASSWORD', 'tsn');

Make some changes to the dbase 

mysql
connect wordpress;
SELECT ID, user_login, user_pass FROM wp_users;
UPDATE wp_users SET user_pass=MD5('newstrongpassword') WHERE ID = 4;
select * from wp_options where option_name='siteurl';
select * from wp_options where option_name='home';
UPDATE wp_options SET option_value='http://www.edegan.com/blog' WHERE option_name='siteurl';
UPDATE wp_options SET option_value='http://www.edegan.com/blog' WHERE option_name='home';

Now you can comment out the WP_HOME and WP_SITEURL settings in wp-config.php and change them (if you want) from the wp-admin interface: http://www.edegan.com/blog/wp-admin.

The following plugin had to be disabled:

  • Social Share WordPress Plugin - AccessPress Social Share

Finally, fix the permalink issue by setting 

vi /etc/apache2/apache2.conf
 AllowOverride All

Then yay!

The whole thing needs updating, a new skin (or at least clean up), and some of the plugins don't work. But the basics are now up and running.

Updating

Go in to the wp-admin interface and hit update. It seemed to work fine!

Run the site-health.php tool: http://www.edegan.com/blog/wp-admin/site-health.php 

apt-get install php7.2-gd
apt-get install php7.2-bcmath 
Get and make imagemagick -- see https://www.tutorialspoint.com/articles/how-to-install-imagemagick-on-ubuntu 
 magick -help
apachectl restart

Also, update all of the plugins and remove the one inactive plugin that was causing problems earlier.

Other Web Server

For Google Analytics we linked the domain to dredegan@gmail.com on the Google Dashboard and added the key to LocalSettings.php. See http://edutechwiki.unige.ch/en/Mediawiki_installation#Google_Analytics

We also added write permissions to the images directory for www-data 

chown -R www-data images/

Nvidia

The original intention was to install a GPU into the Dbase server, as GPU compute tasks wouldn't interfere (much) with the main operation of the server. The problem seems to be a combination of an unsigned Nvidia driver, Ubuntu 18.04, UEFI, and Secureboot (or not). See https://medium.com/@nolanmudge/installing-an-nvidia-graphics-driver-with-a-ubuntu-14-04-and-up-efi-boot-52725dd6927c 

Regardless here are some useful commands:

See what drivers are being used 

apt-get install ubuntu-drivers-common
ubuntu-drivers devices
cat /proc/driver/nvidia/version

See the display hardware config 

sudo lshw -c display
 If shows *-display UNCLAIMED and no driver associated with it
 https://askubuntu.com/questions/762254/why-do-i-get-required-key-not-available-when-install-3rd-party-kernel-modules

Just try to work out what is going on: 

ubuntu-drivers devices
lsmod
lshw -c display
sudo lspci -vk
ls -l /sys/firmware/efi/

Try installing CUDA and its driver: https://www.pugetsystems.com/labs/hpc/How-To-Install-CUDA-10-together-with-9-2-on-Ubuntu-18-04-with-support-for-NVIDIA-20XX-Turing-GPUs-1236/ And then: https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html#post-installation-actions And may: https://xcat-docs.readthedocs.io/en/stable/advanced/gpu/nvidia/verify_cuda_install.html

Try installing the bundled cuda toolkit 

apt-get install nvidia-cuda-toolkit
apt-get install cuda-samples-7-0 -y
cd /usr/local/cuda-7.0/samples
make

Try installing the bundled nvidia driver 

sudo apt install nvidia-driver-415

Purge nvidia drivers and add the experimental repo 

apt-get purge nvidia*
sudo add-apt-repository ppa:graphics-drivers

Get the latest driver from Nvidia and make it 

wget http://us.download.nvidia.com/XFree86/Linux-x86_64/418.43/NVIDIA-Linux-x86_64-418.43.run
apt-get install gcc
apt-get install make
sh NVIDIA-Linux-x86_64-418.43.run
cat /var/log/nvidia-installer.log

View system logs: 

journalctl -xb

Remove nouveau if being used (https://help.ubuntu.com/community/BinaryDriverHowto/Nvidia) 

sudo ubuntu-drivers devices
sudo apt-get --purge remove xserver-xorg-video-nouveau
nvidia-xconfig

Add a secure boot key 

sudo update-secureboot-policy --new-key
sudo update-secureboot-policy --enroll-key

Disable/enable secureboot: 

mokutil --disable-validation
 create 8-12 char password (same as ed's)
 Reboot and disable secureboot
mokutil --enable-validation

Other

pdftk

I installed pdftk and configured it as follows: 

snap install pdftk
ln -s /snap/pdftk/current/usr/bin/pdftk /usr/bin/pdftk

Its man page (kinda) is here: https://www.pdflabs.com/docs/pdftk-man-page/

But generally you want to do use it combine files: 

pdftk *.pdf cat output newfile.pdf
pdftk a.pdf b.pdf cat output newfile.pdf

If you want to reduce a file that has large images in it, then the following sometimes works: 

pdf2ps 1.pdf 1.ps
ps2pdf -dPDFSETTINGS=/screen -dDownsampleColorImages=true -dColorImageResolution=144 -dColorImageDownsampleType=/Bicubic 1.ps 1.pdf

To do

Mobile Front End

It seems that the Extension:MobileFrontend isn't working properly.

Does php have mbstring support?

First check the apache version: 

apache2 -v
 Server version: Apache/2.4.29 (Ubuntu)
 Server built:   2018-10-10T18:59:25

And the php version: 

php -v
 PHP 7.2.17-0ubuntu0.18.04.1 (cli) (built: Apr 18 2019 14:12:38) ( NTS )
 Copyright (c) 1997-2018 The PHP Group
 Zend Engine v3.2.0, Copyright (c) 1998-2018 Zend Technologies
   with Zend OPcache v7.2.17-0ubuntu0.18.04.1, Copyright (c) 1999-2018, by Zend Technologies

Try just installing it: 

apt-get install php7.2-mbstring

This failed because of an issue with dpkg. I rebooted and then: 

dpkg --configure -a
apt --fix-broken install

Then it installed but threw a notice about a modified configuration file. The differences were too large to show. I kept the old file (/etc/php/7.2/apache2/php.ini) for comparison to the new one (/usr/lib/php/7.2/php.ini-production).

In the old file, uncomment the mbstring extension and exif (after it) too, then reload the config and check it worked: 

service apache2 reload
php -i | grep mbstring

So everything seems fine (the extension it is listed as loaded in Special:Version), but the interface still has obvious issues.

Check the skin

From Special:Version 

MediaWiki	1.26.2
PHP	7.2.24-0ubuntu0.18.04.2 (apache2handler)
MySQL	5.7.25-0ubuntu0.18.04.2
Lua	5.1.5

Vector is the only installed skin.

And it looks like my version of mediawiki is too old to support Minerva Neue

Upgrade mediawiki

Essentially, follow instructions in Manual:Upgrading:

Backup

I just moved everything to a different directory, backed off the dbase, and started again. 

cd /var/lib
mv mediawiki mediawikibackup26082020
mysqldump --user=root --password=password  > dbase.sql

New Install

Get a new version, put it in /var/lib/mediawiki (leaving the old shortcuts pointing there), then copy in the files. 

wget https://releases.wikimedia.org/mediawiki/1.34/mediawiki-1.34.2.tar.gz
tar -xvzf mediawiki-1.34.2.tar.gz 
mv mediawiki-1.34.2 mediawiki
rm mediawiki-1.34.2.tar.gz
cp mediawiki26082020/LocalSettings.php mediawiki/LocalSettings.php
cp -a mediawiki26082020/images/ mediawiki/
  Note: you don't need to change permissions because we used -a. This also copied the .htaccess file. Everything should be ok...
cp /var/lib/mediawiki26082020/resources/assets/EdEganDotCotWikiGreenTab.png /var/lib/mediawiki/resources/assets/
 Note: that's my wiki logo
cd /var/lib/mediawiki/maintenance/
php update.php

Retrieve and configure extensions

Get the bulk of them... 

mkdir installs
cd installs

wget https://extdist.wmflabs.org/dist/extensions/LabeledSectionTransclusion-REL1_34-4aa6bfa.tar.gz
tar -xzf LabeledSectionTransclusion-REL1_34-4aa6bfa.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/extensions/MobileFrontend-REL1_34-6a8ef84.tar.gz
tar -xzf MobileFrontend-REL1_34-6a8ef84.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/extensions/ImportUsers-REL1_34-2f1a670.tar.gz
tar -xzf ImportUsers-REL1_34-2f1a670.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/extensions/Scribunto-REL1_34-f7bc2e3.tar.gz
tar -xzf Scribunto-REL1_34-f7bc2e3.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/extensions/googleAnalytics-REL1_34-6441403.tar.gz
tar -xzf googleAnalytics-REL1_34-6441403.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/extensions/MultiUpload-REL1_34-e018c1d.tar.gz
tar -xzf MultiUpload-REL1_34-e018c1d.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/extensions/UserMerge-REL1_34-3517022.tar.gz
tar -xzf UserMerge-REL1_34-3517022.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/skins/MinervaNeue-REL1_34-ba11b7b.tar.gz
tar -xzf MinervaNeue-REL1_34-ba11b7b.tar.gz -C /var/lib/mediawiki/skins

wget https://extdist.wmflabs.org/dist/extensions/ConfirmAccount-REL1_34-3ffa446.tar.gz
tar -xzf ConfirmAccount-REL1_34-3ffa446.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/extensions/MassEditRegex-REL1_34-d3570f1.tar.gz
tar -xzf MassEditRegex-REL1_34-d3570f1.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/extensions/DataTransfer-REL1_34-1fc1c61.tar.gz
tar -xzf DataTransfer-REL1_34-1fc1c61.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/extensions/HTMLets-REL1_34-a8227c3.tar.gz
tar -xzf HTMLets-REL1_34-a8227c3.tar.gz -C /var/lib/mediawiki/extensions

wget https://extdist.wmflabs.org/dist/skins/MinervaNeue-REL1_34-ba11b7b.tar.gz
tar -xzf MinervaNeue-REL1_34-ba11b7b.tar.gz -C /var/lib/mediawiki/skins

wget https://extdist.wmflabs.org/dist/extensions/GeoData-REL1_34-8a52fa4.tar.gz
tar -xzf GeoData-REL1_34-8a52fa4.tar.gz -C /var/lib/mediawiki/extensions

Do the semantic mediawiki install and config. Last time, we installed Semantic Mediawiki using composer, which is the preferred method. See Web_Server_Documentation. 

cd installs
php -r "copy('https://getcomposer.org/installer', 'composer-setup.php');"
php -r "if (hash_file('sha384', 'composer-setup.php') === '8a6138e2a05a8c28539c9f0fb361159823655d7ad2deecb371b04a83966c61223adc522b0189079e3e9e277cd72b8897') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;"
php composer-setup.php --install-dir=/usr/local/bin --filename=composer
#php -r "unlink('composer-setup.php');"
vi composer.local.json
 {
     "require": {
         "mediawiki/semantic-media-wiki": "~3.1",
         "mediawiki/semantic-result-formats": "~3.1"
     }
 }
composer update --no-dev
Add line to LocalSettings.php
 enableSemantics('192.168.2.92');
php maintenance/update.php
cd ../extensions/
#https://www.mediawiki.org/wiki/Extension:Page_Forms
git clone https://gerrit.wikimedia.org/r/mediawiki/extensions/PageForms.git
 add to LocalSettings.php

ConfirmAccount Bug

Installing ConfirmAccount gave an error whenever there was an account request. 

Warning: file_exists(): Unable to find the wrapper "mwstore" - did you forget to enable it when you configured PHP? in /../w/extensions/ConfirmAccount/backend/ConfirmAccount.class.php on line 29

This seemed to be a registered bug - see https://phabricator.wikimedia.org/T219859. It appears to happen as a consequence of the file_exists call, and is just a warning. It doesn't affect functionality. So I put an @ in front of the file_exists call, which is poor practice but it worked just fine. 

Line 29:  if ( $path && @file_exists( $path ) ) {

Other Config

Check pre-reqs are good for Scribuntu. 

php -r 'echo "pcre: " . ( extension_loaded( "pcre" ) ? PCRE_VERSION : "no" ) . "\n";'
php -r 'echo "mbstring: " . ( extension_loaded( "mbstring" ) ? "yes" : "no" ) . "\n";'

Fix some permissions: 

chmod a+x extensions/Scribunto/includes/engines/LuaStandalone/binaries/lua5_1_5_linux_64_generic/lua
chmod a+x extensions/SyntaxHighlight_GeSHi/pygments/pygmentize

Tune up php and Apache2: 

vi /etc/php/7.2/apache2/php.ini
 change upload_max_filesize to 4M
 
vi /etc/apache2/apache2.conf
  <Directory /var/www/wiki/images>
         Options -Indexes
  </Directory>
 
service apache2 restart

Also, add Special:MultiUpload|Upload multiple files to http://www.edegan.com/wiki/MediaWiki:Sidebar

MathML

I tried various methods to get MathML to work and always failed. It looks like the community bet on Mathoid working out, but there's been no development on it for 5 months now, and it looks dead. The good news, if that MathJax works just fine right out of the box: 

git clone https://github.com/jmnote/SimpleMathJax.git
wfLoadExtension( 'SimpleMathJax' );
$wgSmjInlineMath = [ [ "$", "$" ], [ "\\(", "\\)" ] ];
 Note: the last line lets you demark math with LaTeX-like syntax.

PDFEmbed

PDFEmbed was the extension that I never knew that I always wanted! 

git clone https://gitlab.com/HydraWiki/extensions/PDFEmbed.git
wfLoadExtension( 'PDFEmbed' );

SemanticACL

IntraACL (http://wiki.4intra.net/IntraACL) doesn't work with Mediawiki 1.34, so it's out. I also wasn't wild about its patch-based approach.

This time around I went with SemanticACL for access control. It's in beta but its actively maintained and its approach is simple, sane, and harnesses the power of what's already there. No hooks, no patches, no blah... just an extension that does what you want out of the box.

The only other real contender was Extension:AccessControl, which is stable. However, its approach just isn't as clean, and the author's request for funds to translate his documentation from Czech to English didn't endear me.

Useful Links for SemanticACL: 

wget https://extdist.wmflabs.org/dist/extensions/SemanticACL-REL1_34-01ae8be.tar.gz
tar -xzf SemanticACL-REL1_34-01ae8be.tar.gz -C /var/lib/mediawiki/extensions

In LocalSettings.php (for m1.34): 

require_once "$IP/extensions/SemanticACL/SemanticACL.php";

To configure security on a page (https://www.mediawiki.org/wiki/Extension:Semantic_ACL#Example) 

whitelist
team
 
whitelist
User:whoever

or equivalently (but silently):


BibTeX

The BibTeX extension doesn't work anymore. Though it never really worked, so it's not much of a loss. I should probably build a replacement...

Old machines

For the configuration of the servers built for the McNair Center, see the old Center IT page or the pages below:

Some of this information is still useful!

In addition, at UC Berkeley, Ed designed and built three machines - two postgresql database servers and a wiki server. The documentation is here:

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