User contributions
- 10:21, 21 January 2022 (diff | hist) . . (+513) . . Singularity with grid engine (current)
- 09:56, 28 July 2020 (diff | hist) . . (+263) . . Conda (current)
- 19:21, 22 July 2020 (diff | hist) . . (+717) . . N Firewall and iptables (Created page with "firstly the iptables was accidentally wiped when trying to mount marvin to kennedy. SGE failed and so did ldap authentication from the nodes on new users. solution for ldap...") (current)
- 19:14, 22 July 2020 (diff | hist) . . (+28) . . Main Page (→Cluster Administration) (current)
- 10:32, 22 July 2020 (diff | hist) . . (+288) . . Users and Groups (→Usage: How to add a new user) (current)
- 12:15, 19 June 2020 (diff | hist) . . (+3,534) . . N Disk management after shelf disk failure (Created page with " The software for your RAID controller was LSI (now Broadcom) MegaCli, I've not been able to find any evidence that there's a Redhat package but I have found a download. The...") (current)
- 12:12, 19 June 2020 (diff | hist) . . (+47) . . Main Page (→Cluster Administration)
- 13:03, 18 June 2020 (diff | hist) . . (+115) . . Users and Groups
- 09:40, 15 June 2020 (diff | hist) . . (-16) . . Main Page (→Cluster Administration)
- 09:40, 15 June 2020 (diff | hist) . . (+16) . . Main Page (→Cluster Administration)
- 20:28, 20 May 2020 (diff | hist) . . (+29) . . Frontend Restart (→sungrid engine not running on the centos 7 nodes) (current)
- 20:07, 20 May 2020 (diff | hist) . . (+67) . . Frontend Restart (→sungrid engine not running on the centos 7 nodes)
- 19:36, 19 May 2020 (diff | hist) . . (+142) . . Frontend Restart (→sungrid engine not running on the centos 7 nodes)
- 19:05, 19 May 2020 (diff | hist) . . (+102) . . Frontend Restart (→sungrid engine not running on the centos 7 nodes)
- 18:39, 19 May 2020 (diff | hist) . . (+398) . . Frontend Restart
- 12:48, 7 May 2020 (diff | hist) . . (+24) . . Kennedy manual (current)
- 12:47, 7 May 2020 (diff | hist) . . (+107) . . Kennedy manual
- 13:35, 6 May 2020 (diff | hist) . . (+323) . . Kennedy manual
- 13:32, 6 May 2020 (diff | hist) . . (+12) . . Kennedy manual
- 13:31, 6 May 2020 (diff | hist) . . (+105) . . Kennedy manual
- 13:30, 6 May 2020 (diff | hist) . . (+980) . . N Samba like connection (Created page with " == Windows net work connect in a samba like manner == http://stab.st-andrews.ac.uk/wiki/index.php/Windows_network_connect You probably don't know what samba is. This does...") (current)
- 13:28, 6 May 2020 (diff | hist) . . (+28) . . Kennedy manual
- 13:27, 6 May 2020 (diff | hist) . . (+338) . . N Submit a job and monitor queues (Created page with " == submit a job == to submit a shell which contains are the needed flags in the file. sbatch spades.sh ==Show information on the queues:== smap squeue (show the queue...") (current)
- 13:26, 6 May 2020 (diff | hist) . . (+38) . . Kennedy manual
- 13:25, 6 May 2020 (diff | hist) . . (+99) . . Slurm commands (current)
- 13:22, 6 May 2020 (diff | hist) . . (0) . . File:---C--Users-pjt6-Desktop-Picture1.png (PeterThorpe uploaded a new version of File:---C--Users-pjt6-Desktop-Picture1.png) (current)
- 13:21, 6 May 2020 (diff | hist) . . (0) . . N File:---C--Users-pjt6-Desktop-Picture1.png
- 13:20, 6 May 2020 (diff | hist) . . (+52) . . N Filezilla data transfer (Created page with "Media:file:///C:/Users/pjt6/Desktop/Picture1.png") (current)
- 13:18, 6 May 2020 (diff | hist) . . (+31) . . Kennedy manual
- 13:17, 6 May 2020 (diff | hist) . . (+539) . . N Pull and push to to and from MARVIN (Created page with " == Copy data from marvin – or push to marvin for backup == users will want to copy data from the backed up area Marvin to the temp work/ scratch space on Kennedy, and visa...") (current)
- 13:14, 6 May 2020 (diff | hist) . . (+41) . . Kennedy manual
- 13:13, 6 May 2020 (diff | hist) . . (+4) . . Mobaxterm for Windows (current)
- 13:13, 6 May 2020 (diff | hist) . . (+479) . . N Mobaxterm for Windows (Created page with "If you use previously use MOBA and want to continue to use it. This is how. You can use any ssh client you wish NOTE: for myself, this was done before we changed the way peop...")
- 13:12, 6 May 2020 (diff | hist) . . (+1) . . Loggin on to Kennedy (current)
- 13:12, 6 May 2020 (diff | hist) . . (+27) . . Loggin on to Kennedy
- 13:11, 6 May 2020 (diff | hist) . . (+609) . . N Loggin on to Kennedy (Created page with " == Log onto Kennedy using a terminal e.g. putty for Windows or terminal for Linux/ MAC == When you have received a password from the sys admins. You should be able to log...")
- 13:10, 6 May 2020 (diff | hist) . . (+26) . . Kennedy manual
- 13:08, 6 May 2020 (diff | hist) . . (+655) . . N Windows users (Created page with " == Windows: Create a public and private key using putty-gen == Type putty gen in the window search bar (download and install if needed) Click on generate and wiggle the mo...") (current)
- 13:05, 6 May 2020 (diff | hist) . . (+388) . . N Apple MAC people + Linux (Created page with " == create an ssh key using MAC or Linux platforms == open a terminal and enter the command "ssh-keygen". Accept all default filenames. Choose a passphrase when asked f...") (current)
- 13:05, 6 May 2020 (diff | hist) . . (-307) . . Creating ssh keys and logging on (current)
- 13:03, 6 May 2020 (diff | hist) . . (+402) . . N Creating ssh keys and logging on (Created page with " == the security we use requires ssh keys == '''Apple MAC people''' open a terminal and enter the command "ssh-keygen". Accept all default filenames. Choose a passphras...")
- 13:02, 6 May 2020 (diff | hist) . . (+39) . . Kennedy manual
- 13:00, 6 May 2020 (diff | hist) . . (+736) . . Quick start (current)
- 12:58, 6 May 2020 (diff | hist) . . (+119) . . Slurm commands (→slurm commands)
- 12:56, 6 May 2020 (diff | hist) . . (+1,328) . . N Slurm commands (Created page with " == slurm commands == note the BIOINF community are supposed to use the -p bigmem queue. The following are command line commands, or tags you can put in your shell scrip...")
- 12:55, 6 May 2020 (diff | hist) . . (+168) . . N Quick start (Created page with " Temporary quick start info can be found here. This is a work in progress until something official is made up. https://github.com/peterthorpe5/How_to_use_Kennedy_HPC")
- 12:54, 6 May 2020 (diff | hist) . . (-1,364) . . Kennedy manual (Replaced content with " *quick start *slurm commands")
- 12:52, 6 May 2020 (diff | hist) . . (+64) . . Main Page
- 12:48, 6 May 2020 (diff | hist) . . (+40) . . Kennedy manual
- 09:07, 6 May 2020 (diff | hist) . . (+1,196) . . Kennedy manual
- 09:00, 6 May 2020 (diff | hist) . . (+5) . . Kennedy manual
- 08:59, 6 May 2020 (diff | hist) . . (+162) . . N Kennedy manual (Created page with " Temp quick start info can be found here. This is a work in progress until something official is made up. https://github.com/peterthorpe5/How_to_use_Kennedy_HPC")
- 09:53, 3 March 2020 (diff | hist) . . (+1) . . StABDMIN (→StABDMIN Site) (current)
- 12:59, 11 February 2020 (diff | hist) . . (+75) . . Windows network connect (→Windows net work connect in a samba like manner) (current)
- 12:48, 11 February 2020 (diff | hist) . . (+800) . . N Windows network connect (Created page with "=Windows net work connect in a samba like manner= You probably don't know what samba is. This doesn't matter. ALl you need to know is - THIS IS COOL. install these on your...")
- 12:44, 11 February 2020 (diff | hist) . . (+30) . . Main Page (→Usage of Cluster)
- 16:01, 10 February 2020 (diff | hist) . . (+21) . . Main Page
- 10:37, 10 February 2020 (diff | hist) . . (+261) . . N Sending emails from command line examples (Created page with "this is info for future work: # examples https://blog.edmdesigner.com/send-email-from-linux-command-line/ # this works on marvin and keenedy cat contents_of_file.tx | s...") (current)
- 10:00, 10 February 2020 (diff | hist) . . (+48) . . Main Page (→Cluster Administration)
- 15:30, 14 November 2019 (diff | hist) . . (+816) . . N Reset a password (Created page with "so basically you cant. Be I have managed to recreate the account using the the new user script. But manually entering the command, U=test06 smbldap-groupadd -a $NU smbldap...") (current)
- 15:28, 14 November 2019 (diff | hist) . . (+23) . . Main Page (→Cluster Administration)
- 09:49, 14 November 2019 (diff | hist) . . (+67) . . Emailing (→Introduction) (current)
- 13:03, 11 November 2019 (diff | hist) . . (+96) . . Allow user access to other peoples data (current)
- 12:34, 11 November 2019 (diff | hist) . . (-7) . . StABDMIN (→Restarting the server)
- 12:33, 11 November 2019 (diff | hist) . . (+2) . . StABDMIN (→Restarting the server)
- 11:09, 8 November 2019 (diff | hist) . . (+210) . . N Ldap is not ldap (Created page with "try this command: ldapsearch -x Miguel decided to go for a certain flavour of it, called smbldap-tools, may be because Redhat recommended it. This seems to be a wrapper for...") (current)
- 11:01, 8 November 2019 (diff | hist) . . (+23) . . Main Page (→Cluster Administration)
- 11:00, 8 November 2019 (diff | hist) . . (+562) . . Users and Groups (→Users)
- 18:10, 1 November 2019 (diff | hist) . . (+39) . . Frontend Restart (→The main critical issue)
- 18:09, 1 November 2019 (diff | hist) . . (+272) . . Frontend Restart (→The main critical issue)
- 16:06, 16 October 2019 (diff | hist) . . (+1,120) . . N RAM and RAM slots (Created page with "ssh into a node By the looks of this they can support LOTS of RAM: [root@node4 ~]# dmidecode -t 16 [root@node3 ~]# dmidecode -t memory | grep -i size Size: No Mod...") (current)
- 16:06, 16 October 2019 (diff | hist) . . (+24) . . Main Page (→Cluster Administration)
- 10:39, 9 October 2019 (diff | hist) . . (+48) . . StABDMIN
- 10:12, 9 October 2019 (diff | hist) . . (+562) . . Backups (current)
- 16:12, 8 October 2019 (diff | hist) . . (+52) . . N Allow user access to other peoples data (Created page with "setfacl -m u:USERNAME:rwx /storage/home/users/folder")
- 16:11, 8 October 2019 (diff | hist) . . (+46) . . Main Page (→Cluster Administration)
- 12:10, 8 October 2019 (diff | hist) . . (+101) . . N Webstie and word press (Created page with "log into it here and use the "one " password system: http://medhandbook.st-andrews.ac.uk/wp-login.php") (current)
- 12:09, 8 October 2019 (diff | hist) . . (+29) . . Main Page (→Cluster Administration)
- 09:32, 7 October 2019 (diff | hist) . . (+1,024) . . N Mounting drives (Created page with "= when rebooting head nodes, shelf and storage sometimes are lost = Make sure they are uncommented in the /etc/fstab file. http://stab.st-andrews.ac.uk/wiki/index.php/Fronte...") (current)
- 09:30, 7 October 2019 (diff | hist) . . (+22) . . Main Page (→Cluster Administration)
- 09:29, 26 September 2019 (diff | hist) . . (+91) . . RedHat (→Work around) (current)
- 15:15, 25 September 2019 (diff | hist) . . (+362) . . RedHat (→Work around)
- 10:58, 19 September 2019 (diff | hist) . . (+658) . . RedHat (→Work around)
- 10:34, 19 September 2019 (diff | hist) . . (+34) . . RedHat (→Work around)
- 10:31, 19 September 2019 (diff | hist) . . (+92) . . RedHat (→Work around)
- 10:29, 19 September 2019 (diff | hist) . . (+633) . . RedHat (→Work around)
- 08:57, 17 September 2019 (diff | hist) . . (+186) . . RedHat (→Work around)
- 08:53, 17 September 2019 (diff | hist) . . (+164) . . RedHat (→Work around)
- 08:51, 17 September 2019 (diff | hist) . . (+32) . . RedHat (→Work around)
- 08:51, 17 September 2019 (diff | hist) . . (+661) . . RedHat (→Work around)
- 11:17, 11 September 2019 (diff | hist) . . (+310) . . RedHat (→Work around)
- 10:23, 5 August 2019 (diff | hist) . . (+762) . . N Restart a node (Created page with "Restarting a node 1) Best way, most likely wont work. Sudo su. Ssh into node to be restarting Type reboot. 2) Log into Marvin (use LINUX machine) ssh marvin…. -X...") (current)
- 11:01, 19 June 2019 (diff | hist) . . (+35) . . Users and Groups (→Usage: How to add a new user)
- 11:01, 19 June 2019 (diff | hist) . . (+23) . . Users and Groups (→Usage)
- 15:04, 11 June 2019 (diff | hist) . . (+601) . . N Ansible (Created page with " Export ANSIBLE_INVENTORY=/storage/home/users/ansible/hosts Or Export ANSIBLE_INVENTORY=/storage/home/users/ansible/hosts ansible-playbook nodes.yml -e @vault/marvinNodes...") (current)
- 14:49, 11 June 2019 (diff | hist) . . (+14) . . Main Page (→Cluster Administration)
- 14:26, 28 May 2019 (diff | hist) . . (+1) . . Singularity with grid engine
- 14:26, 28 May 2019 (diff | hist) . . (+89) . . Singularity with grid engine
- 12:08, 24 May 2019 (diff | hist) . . (+1) . . Singularity with grid engine
- 12:08, 24 May 2019 (diff | hist) . . (+46) . . Singularity with grid engine
- 12:07, 24 May 2019 (diff | hist) . . (+46) . . Singularity with grid engine
- 12:04, 24 May 2019 (diff | hist) . . (+68) . . Singularity with grid engine
- 12:01, 24 May 2019 (diff | hist) . . (-2) . . Singularity with grid engine
- 12:00, 24 May 2019 (diff | hist) . . (+649) . . Singularity with grid engine
- 11:57, 24 May 2019 (diff | hist) . . (+115) . . Singularity with grid engine
- 11:40, 24 May 2019 (diff | hist) . . (-1,912) . . Singularity with grid engine
- 11:13, 24 May 2019 (diff | hist) . . (+1) . . Singularity with grid engine
- 11:13, 24 May 2019 (diff | hist) . . (+324) . . Singularity with grid engine
- 09:01, 24 May 2019 (diff | hist) . . (+2,342) . . Singularity with grid engine
- 15:18, 8 May 2019 (diff | hist) . . (+546) . . N Queue Manager : shell script command (Created page with "Put these at the top of your shell script if you want this functionality, remove or add as desired: #!/bin/bash #$ -V ## pass all environment variables to the job, VERY...") (current)
- 15:16, 8 May 2019 (diff | hist) . . (+43) . . Main Page (→Queue Manager Tips)
- 15:14, 8 May 2019 (diff | hist) . . (+1,197) . . N Queue Manager emailing when jobs run (Created page with "You have four options to make it email you: 1) Add the commands to your shell script at the top: #$ -m e #$ -M youmail@st-andrews.ac.uk 2) Add to your .bash_profile (...") (current)
- 15:13, 8 May 2019 (diff | hist) . . (+43) . . Main Page (→Queue Manager Tips)
- 15:35, 13 March 2019 (diff | hist) . . (+76) . . Conda (→conda)
- 13:53, 13 March 2019 (diff | hist) . . (+202) . . Conda (→conda)
- 09:37, 20 February 2019 (diff | hist) . . (+69) . . Conda (→conda)
- 13:08, 18 February 2019 (diff | hist) . . (+3) . . Conda (→conda)
- 10:51, 18 February 2019 (diff | hist) . . (+230) . . Conda (→conda)
- 10:49, 18 February 2019 (diff | hist) . . (+457) . . Conda (→conda)
- 10:42, 14 February 2019 (diff | hist) . . (-1) . . Conda (→conda installs: This is the future)
- 10:40, 14 February 2019 (diff | hist) . . (+7) . . Conda (→conda installs: This is the future)
- 10:39, 14 February 2019 (diff | hist) . . (+966) . . Conda (→conda installs: This is the future)
- 10:34, 14 February 2019 (diff | hist) . . (+2) . . Conda (→conda and perl)
- 10:32, 14 February 2019 (diff | hist) . . (+711) . . Conda (→conda installs: This is the future)
- 10:26, 14 February 2019 (diff | hist) . . (+923) . . Conda
- 10:43, 7 February 2019 (diff | hist) . . (+45) . . Restart a node) (→2) Log into Marvin (use LINUX machine)) (current)
- 14:32, 6 February 2019 (diff | hist) . . (+30) . . Restart a node) (→2) Log into Marvin (use LINUX machine))
- 10:38, 1 February 2019 (diff | hist) . . (-1) . . Main Page (→Cluster Administration)
- 10:38, 1 February 2019 (diff | hist) . . (+882) . . N Restart a node) (Created page with "= 1) Best way, most likely wont work. = sudo su ssh into node to be restarting Type reboot This should bring the node back if there are no other problems. Node10 is known...")
- 10:33, 1 February 2019 (diff | hist) . . (+22) . . Main Page (→Cluster Administration)
- 14:39, 22 January 2019 (diff | hist) . . (+84) . . Diamond (→key points made) (current)
- 12:29, 22 January 2019 (diff | hist) . . (+245) . . Diamond (→key points made)
- 11:53, 22 January 2019 (diff | hist) . . (+163) . . N How to use the cluster training course (Created page with "please go to the following and follow the PowerPoint presentations of how to use the cluster: https://github.com/peterthorpe5/Sys_admin/tree/master/cluster_course") (current)
- 11:52, 22 January 2019 (diff | hist) . . (+45) . . Main Page (→Usage of Cluster)
- 11:24, 22 January 2019 (diff | hist) . . (+63) . . Users and Groups (→Users)
- 11:21, 22 January 2019 (diff | hist) . . (+28) . . Users and Groups (→Groups)
- 11:19, 22 January 2019 (diff | hist) . . (+47) . . Users and Groups (→Users)
- 09:36, 18 January 2019 (diff | hist) . . (+7) . . Frontend Restart (→Bring all nodes down before restart)
- 09:35, 18 January 2019 (diff | hist) . . (+99) . . Frontend Restart (→Bring all nodes down before restart)
- 09:29, 18 January 2019 (diff | hist) . . (+47) . . Frontend Restart (→Bring all nodes down before restart)
- 09:25, 18 January 2019 (diff | hist) . . (+3) . . Frontend Restart (→Bring all nodes down before restart)
- 12:29, 3 January 2019 (diff | hist) . . (+49) . . N Message of the day (Created page with "to update the message of the day: nano /etc/motd") (current)
- 12:28, 3 January 2019 (diff | hist) . . (+25) . . Main Page (→Cluster Administration)
- 11:43, 21 November 2018 (diff | hist) . . (+207) . . N PIs storage sacrifice (Created page with "final list of PIs willing to sacrifice their storage (additional 4.5TB): Silvia Paracchini Nathan Bailey Gordon Cramb Michael Ritchie John Jones Janet Cox Singh Matthew Holde...") (current)
- 11:42, 21 November 2018 (diff | hist) . . (+28) . . Main Page (→Cluster Administration)
- 15:41, 23 October 2018 (diff | hist) . . (-496) . . Conda
- 15:40, 23 October 2018 (diff | hist) . . (+13) . . Main Page (→Documented Programs)
- 15:38, 23 October 2018 (diff | hist) . . (+259) . . Available Software (→module load approach) (current)
- 15:37, 23 October 2018 (diff | hist) . . (-260) . . Available Software (→Conda. THIS IS THE FUTURE. We highly recommend this)
- 15:37, 23 October 2018 (diff | hist) . . (+8) . . Available Software (→Conda. THIS IS THE FUTURE. We highly recommend this)
- 15:36, 23 October 2018 (diff | hist) . . (+1,233) . . Available Software (→Introduction)
- 15:32, 23 October 2018 (diff | hist) . . (+3,842) . . N Conda bioconda (conda stuff) (current)
- 15:26, 23 October 2018 (diff | hist) . . (+21) . . Main Page (→Cluster Administration)
- 15:25, 23 October 2018 (diff | hist) . . (+2,065) . . N Updating BLAST databases (Created page with "= crontab runs every sunda: updates all balstable dbs = > more PT_download_BLAST_db.sh #!/bin/bash #$ -cwd set -euo pipefail # script to convert donwload NR cd /she...") (current)
- 15:12, 23 October 2018 (diff | hist) . . (+8,773) . . N Users disk usage (Created page with "= The following script is set to run every night via crontab = This get the usage of each user's home directory, puts it in a file. Then calls the python script to compare t...") (current)
- 15:08, 23 October 2018 (diff | hist) . . (+54) . . Main Page (→Cluster Administration)
- 15:05, 23 October 2018 (diff | hist) . . (+394) . . Diamond
- 14:57, 23 October 2018 (diff | hist) . . (+982) . . Blast (added blast databases with tax db.) (current)