Manage Lab Websites
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We are trying to migrate all services to gitlab. This page is perpetually out-of-date. Look at gitlab first. If not there, look below.
List of Websites
Last updated on 05/17/2023
| Website | Machine:Port | Run on | Hosted in (httpd/conf.d) | Working |
|---|---|---|---|---|
| Amis: https://amis.docking.org/ | n-9-38:5066 | docker | epyc | Yes |
| Arthor: https://arthor.docking.org/ | nun, samekh, n-9-22; Port 8000 | Screen | epyc | Yes |
| BKSLab: http://www.bkslab.org/ | gimel:5002 | Supervisord | Vav (169.230.26.43) | Yes |
| Blaster: https://blaster.docking.org/ | Vav (169.230.26.43, can not be moved to files2) | Yes | ||
| Cartblanche22: https://cartblanche22.docking.org/ | n-9-22:5068 | docker | epyc | Yes |
| Covalent: http://covalent.docking.org/ | Vav (169.230.26.43, can not be moved to files2) | Yes | ||
| DSF: https://dsf.docking.org/ | Vav (169.230.26.43) | No (wrong website) | ||
| Duc: https://duc.docking.org/ | Vav (169.230.26.43) | No | ||
| Dud: https://dud.docking.org/ | Vav (169.230.26.43, can not be moved to files2) | Yes | ||
| Dude18: http://dude18.docking.org/ | Vav (169.230.26.43) | No | ||
| Dude: http://dude.docking.org/ | Vav (169.230.26.43, can not be moved to files2) | Yes | ||
| Dudez: http://dudez.docking.org/ | Files2 (169.230.75.3) | Yes | ||
| Excipients: http://excipients.docking.org/ | gimel:8093 | Supervisord | Vav (169.230.26.43) | Yes |
| Gitlab: https://gitlab.docking.org/ | Files2 (169.230.75.3) | No | ||
| HG: https://hg.docking.org/ | Files2 (169.230.75.3) | No | ||
| IrwinLab: http://irwinlab.compbio.ucsf.edu/ | gimel:5004 | Supervisord | Vav (169.230.26.43) | Yes |
| Khanh: http://khanh.docking.org/ | Vav (169.230.26.43) | Yes | ||
| Metabolite: http://metabolite.docking.org/ | Tau (169.230.26.43, can not be moved to files2) | showing wrong website | ||
| Deepchemworkshop: http://deepchemworkshop.docking.org/ | Vav (169.230.26.43) | Yes | ||
| Prices: http://prices.docking.org/ | gimel:5022 | Tau (169.230.26.43) | No | |
| Psicquic: http://psicquic.docking.org/ | Tau (169.230.26.43) | Yes (broken???) | ||
| Reactor: http://reactor.docking.org/ | Vav (169.230.26.43) | Yes | ||
| Transporters: http://transporters.ucsf.bkslab.org/ | Vav (169.230.26.43) | Yes | ||
| Sea16: http://sea16.docking.org/ | gimel:8086 | Files2 (169.230.75.3) | Yes | |
| SEC: http://sec.docking.org/ | Vav (169.230.26.43) | Yes | ||
| Smallworld Public: http://sw.docking.org/ | abacus:5020 | screen | epyc | Yes |
| Smallworld Private: http://swp.docking.org/ | abacus:8080 | screen | epyc | Yes |
| Smallworld Super Private: http://swc.docking.org/ | abacus:5099 | screen | epyc | Yes |
| Stats: http://stats.docking.org/ | Vav (169.230.26.43, can not be moved to files2) | No | ||
| Symp: http://symp.docking.org/ | Vav (169.230.26.43) | No | ||
| TLDR http://tldr.docking.org/ | gimel2:5000 | Supervisord | Files2 (169.230.26.43) | Yes |
| Tool-Selector: http://tool-selector.ucsf.bkslab.org/ | Vav (169.230.26.43) | Yes | ||
| Transportal: http://transportal.docking.org/ | n-9-23 : port 8123 | screen | Vav (169.230.26.43) | Yes |
| Upload: http://upload.docking.org/ | Tau (169.230.26.43) | Yes | ||
| Zinc12: http://zinc12.docking.org/ | Tau (169.230.26.43, can not be moved to files2) | Yes | ||
| Zinc15: http://zinc15.docking.org/ | epyc2:5064 | docker | epyc | Yes |
| Zinc20: http://zinc20.docking.org/ | epyc2:5065 | docker | epyc | Yes |
Restart Instructions after UPS
For websites running on Docker
Login to machine using sudoer account.
$ sudo docker ps //to list all apps, including non-running $ sudo docker start <name>
To restart a container
$ sudo docker restart <name>
For websites running on Screen
SEA
SEA is running on a screen on gimel
Become www on gimel
$ cd /nfs/soft/www/apps/seadev/ On bash shell $ source tools/anaconda2/bin/activate sea16 $ cd work/seaware/seaware-academic $ make SEAserver-stop-devel $ make all $ make SEAserver-start-devel Ctrl A+D to detach screen
Transportal
Login n-9-23 and become www
$ screen -ls $ screen -r transportal $ cd /mnt/nfs/soft/www/apps/transportal/ $ source envs/production-3.6/bin/activate.csh $ cd /nfs/soft/www/home/apps/transportal/src/transportal_2022/transportal $ python manage.py runserver 0.0.0.0:8123 Ctrl A+D to detach screen
For websites running on Supervisord
Restart applications
- Become root on server the website runs on gimel
$ supervisorctl status //to list all of current running apps $ supervisorctl restart <name> i.e $ supervisorctl restart bks-lab
TLDR is running on gimel2 and managed by supervisord
$ supervisorctl restart tldr
Start Supervisord
$ supervisord