Manage Lab Websites: Difference between revisions

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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This page is perpetually out-of-date.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 ==
== List of Websites ==
Last updated on 08/18/2025
{| class="wikitable"
{| class="wikitable"
|Website
!Website
|Server
!Machine:Port
|Run on
!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: https://www.bkslab.org/
|n-5-13:5002
|docker
|epyc
|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
|-
|-
|BKSLab, IrwinLab
|Dudez: http://dudez.docking.org/
|gimel : port 5002, 5004
|
|
|Files2 (169.230.75.3)
|Yes
|-
|Excipients: http://excipients.docking.org/
|gimel:8093
|Supervisord
|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/
|n-5-13:5004
|docker
|epyc
|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
|-
|-
|Excipients, TLDR (formerly Tools18)
|Smallworld Private: http://swp.docking.org/
|gimel2 : port 8093, 5000
|abacus:8080
|Supervisord
|screen
|epyc
|Yes
|-
|-
|Transportal
|Smallworld Super Private: http://swc.docking.org/
|omega : port 8123
|abacus:5099
|screen
|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/
|epyc-A40:5011
|systemd
|Files2 (169.230.26.43)
|Yes
|-
|Tool-Selector: http://tool-selector.ucsf.bkslab.org/
|
|
|Vav (169.230.26.43)
|Yes
|-
|-
|SEA
|Transportal: http://transportal.docking.org/
|gimel2 : port 6068
|n-9-23 : port 8123
|screen
|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
|-
|Chemistry Commons: https://commons.docking.org/
|epyc2:5010
|docker
|epyc
|Yes
|-
|-
|}
|}


== Restart Instructions ==
== Restart Instructions after UPS==
=== For websites running on Screen ===
=== For websites running on Docker ===
* Become khtang on gimel
Login to machine using sudoer account.
  $ screen -ls
  $ sudo docker ps //to list all apps, including non-running
$ sudo docker start <name>


21546.SEA (Detached)
To restart a container
23528.transportal (Detached)
  $ sudo docker restart <name>
22877.conference (Detached)
16132.upload (Detached)
24786.oeb_lib_building (Detached)
4796.ShopAppMol (Detached)
  19162.FASTROCS-server (Detached)


$ screen -r <screen_id>
=== For websites running on Screen ===


==== SEA ====
==== 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 SEAserver-stop-devel
  $ make all
  $ make all
  $ make SEAserver-start-devel
  $ make SEAserver-start-devel
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
==== Start Supervisord ====
$ supervisord
=== For websites running on Systemd ===
==== Restart applications ====
$ sudo systemctl restart <name>


==== Transportal ====
<b>TLDR</b> is running on epyc-A40 and managed by systemd
$ cd  /mnt/nfs/soft/www/apps/transportal/src/transportal
  $ sudo systemctl restart tldr
  $ python manage.py runserver 0.0.0.0:8123


=== For websites running on Supervisord ===
 
* Become root on server the website runs on
[[Category:Sysadmin]]
[[Category:Curator]]

Latest revision as of 00:44, 19 August 2025

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 08/18/2025

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: https://www.bkslab.org/ n-5-13:5002 docker epyc 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/ n-5-13:5004 docker epyc 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/ epyc-A40:5011 systemd 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
Chemistry Commons: https://commons.docking.org/ epyc2:5010 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

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

Start Supervisord

$ supervisord

For websites running on Systemd

Restart applications

$ sudo systemctl restart <name>

TLDR is running on epyc-A40 and managed by systemd 

$ sudo systemctl restart tldr
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