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Research Computing Configuration (view source)
Revision as of 19:55, 29 August 2020
, 19:55, 29 August 2020Created page with "This page describes the configuration of the two new research computing machines. This configuration runs on our Research Computing Hardware. Note that the configuration o..."
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:
*https://blog.pcfe.net/hugo/posts/2018-08-14-epyc-ipmi-fans/
*https://calvin.me/quick-how-to-decrease-ipmi-fan-threshold/
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
#Reset the BMC if you've screwed it up (or if your fans are full on all the time)
#Check that the current mode is optimal (2)
#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)
#Reset the lower thresholds on the fans
#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:
#Move the contents of /var/lib/mediawiki to somewhere else
#Move the contents of /bulk/mcnair/Web/www/var/www/html/mediawiki in
#Drop databases
#Restore databases
#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:
#Restore the dbase (done already when we restored the mediawiki dbase)
#Copy over all of the wordpress files
#Create a /blog alias in apache
#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===
*VNC!
*ImageMagick and uploads -- test
*Math extension later...
*Set up and configure Postfix mail server (https://www.digitalocean.com/community/tutorials/how-to-install-and-configure-postfix-on-ubuntu-18-04)
*Fix [[<haloacl-inclusion-denied>|Terms of Service]] on sign up page...
==Mobile Front End==
It seems that the [https://www.mediawiki.org/wiki/Extension:MobileFrontend 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 [https://www.mediawiki.org/wiki/Skin:Minerva_Neue Minerva Neue]
==Upgrade mediawiki==
Essentially, follow instructions in [https://www.mediawiki.org/wiki/Manual:Upgrading 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' );
$wgSmjInlineMath = [ [ "$", "$" ], [ "\\(", "\\)" ] ];
Note: the last line lets you demark math with LaTeX-like syntax.
====PDFEmbed====
PDFEmbed was the extension that I never knew that I always wanted!
git clone https://gitlab.com/HydraWiki/extensions/PDFEmbed.git
wfLoadExtension( 'PDFEmbed' );
====SemanticACL====
IntraACL (http://wiki.4intra.net/IntraACL) doesn't work with Mediawiki 1.34, so it's out. I also wasn't wild about its patch-based approach.
This time around I went with SemanticACL for access control. It's in beta but its actively maintained and its approach is simple, sane, and harnesses the power of what's already there. No hooks, no patches, no blah... just an extension that does what you want out of the box.
The only other real contender was Extension:AccessControl, which is stable. However, its approach just isn't as clean, and the author's request for funds to translate his documentation from Czech to English didn't endear me.
Useful Links for SemanticACL:
*https://www.mediawiki.org/wiki/Manual:User_rights#List_of_groups
*https://www.mediawiki.org/wiki/Category:Page_specific_user_rights_extensions
*https://www.mediawiki.org/wiki/Extension:Semantic_ACL
*https://www.mediawiki.org/wiki/Security_issues_with_authorization_extensions
wget https://extdist.wmflabs.org/dist/extensions/SemanticACL-REL1_34-01ae8be.tar.gz
tar -xzf SemanticACL-REL1_34-01ae8be.tar.gz -C /var/lib/mediawiki/extensions
In LocalSettings.php (for m1.34):
require_once "$IP/extensions/SemanticACL/SemanticACL.php";
To configure security on a page (https://www.mediawiki.org/wiki/Extension:Semantic_ACL#Example)
[[Visible to::whitelist]]
[[Visible to group::team]]
[[Editable by::whitelist]]
[[Editable by user::User:whoever]]
or equivalently (but silently):
{{#set: Visible to=whitelist|Visible to group::team}}
====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:
*[[Database Server Documentation]]
*[[RDP Documentation]]
**[[Server Backup Policy]]
**[[Power Backup]]
*[[Test Web Server Documentation]]
*[[Web Server Documentation]]
**[[Wiki Configuration]]
**[[Security on the wiki]]
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:
*[[Haas PhD Server Configuration]]
*[[Posgres Server Configuration]] -- documents the build of postgres2
==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:
*https://blog.pcfe.net/hugo/posts/2018-08-14-epyc-ipmi-fans/
*https://calvin.me/quick-how-to-decrease-ipmi-fan-threshold/
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
#Reset the BMC if you've screwed it up (or if your fans are full on all the time)
#Check that the current mode is optimal (2)
#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)
#Reset the lower thresholds on the fans
#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:
#Move the contents of /var/lib/mediawiki to somewhere else
#Move the contents of /bulk/mcnair/Web/www/var/www/html/mediawiki in
#Drop databases
#Restore databases
#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:
#Restore the dbase (done already when we restored the mediawiki dbase)
#Copy over all of the wordpress files
#Create a /blog alias in apache
#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===
*VNC!
*ImageMagick and uploads -- test
*Math extension later...
*Set up and configure Postfix mail server (https://www.digitalocean.com/community/tutorials/how-to-install-and-configure-postfix-on-ubuntu-18-04)
*Fix [[<haloacl-inclusion-denied>|Terms of Service]] on sign up page...
==Mobile Front End==
It seems that the [https://www.mediawiki.org/wiki/Extension:MobileFrontend 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 [https://www.mediawiki.org/wiki/Skin:Minerva_Neue Minerva Neue]
==Upgrade mediawiki==
Essentially, follow instructions in [https://www.mediawiki.org/wiki/Manual:Upgrading 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' );
$wgSmjInlineMath = [ [ "$", "$" ], [ "\\(", "\\)" ] ];
Note: the last line lets you demark math with LaTeX-like syntax.
====PDFEmbed====
PDFEmbed was the extension that I never knew that I always wanted!
git clone https://gitlab.com/HydraWiki/extensions/PDFEmbed.git
wfLoadExtension( 'PDFEmbed' );
====SemanticACL====
IntraACL (http://wiki.4intra.net/IntraACL) doesn't work with Mediawiki 1.34, so it's out. I also wasn't wild about its patch-based approach.
This time around I went with SemanticACL for access control. It's in beta but its actively maintained and its approach is simple, sane, and harnesses the power of what's already there. No hooks, no patches, no blah... just an extension that does what you want out of the box.
The only other real contender was Extension:AccessControl, which is stable. However, its approach just isn't as clean, and the author's request for funds to translate his documentation from Czech to English didn't endear me.
Useful Links for SemanticACL:
*https://www.mediawiki.org/wiki/Manual:User_rights#List_of_groups
*https://www.mediawiki.org/wiki/Category:Page_specific_user_rights_extensions
*https://www.mediawiki.org/wiki/Extension:Semantic_ACL
*https://www.mediawiki.org/wiki/Security_issues_with_authorization_extensions
wget https://extdist.wmflabs.org/dist/extensions/SemanticACL-REL1_34-01ae8be.tar.gz
tar -xzf SemanticACL-REL1_34-01ae8be.tar.gz -C /var/lib/mediawiki/extensions
In LocalSettings.php (for m1.34):
require_once "$IP/extensions/SemanticACL/SemanticACL.php";
To configure security on a page (https://www.mediawiki.org/wiki/Extension:Semantic_ACL#Example)
[[Visible to::whitelist]]
[[Visible to group::team]]
[[Editable by::whitelist]]
[[Editable by user::User:whoever]]
or equivalently (but silently):
{{#set: Visible to=whitelist|Visible to group::team}}
====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:
*[[Database Server Documentation]]
*[[RDP Documentation]]
**[[Server Backup Policy]]
**[[Power Backup]]
*[[Test Web Server Documentation]]
*[[Web Server Documentation]]
**[[Wiki Configuration]]
**[[Security on the wiki]]
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:
*[[Haas PhD Server Configuration]]
*[[Posgres Server Configuration]] -- documents the build of postgres2
