Difference between revisions of "So you want to set up a lab"

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Here is how I would set up a computational lab, one that could join the [[Worldwide ZINC]] network.
 
Here is how I would set up a computational lab, one that could join the [[Worldwide ZINC]] network.
  
= Time Expectations =
 
When you have all the software and hardware, you can get a docking lab up and running at a basic level in less than a day. If you do not have all the software and hardware, it will take longer. If you've never run a molecular docking lab, allow a week to learn the basics.  Once you have a basic installation running, plan for a few days to [[get a queuing system working]] the way you like it.  We may be able to help. Ask us, but please read this wiki first.
 
 
{{TOCright}}
 
{{TOCright}}
  
= Tier 0 - Requirements and assumptions =
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= Requirements and assumptions =
This page describes setting up a full computational pharmacology research lab. We describe the minimum setup, plus options for expansion. The entry level assumes you can spend: $20K on servers and $2K on a workstation. You'll need an acoustically insulated air conditioned room. It would help to have someone with system administration experience for 100 hours (3 weeks) for the initial set up, and then 1 day/month for maintenance.
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This page describes setting up a full computational pharmacology research lab. We describe the minimum setup, plus options for expansion. The entry level assumes you can spend $20K on servers and $2K on a workstation, or you already own equivalent or better hardware. You'll need an acoustically insulated air conditioned room. Expect to spend a month to specify, order and deploy hardware, a week to install operating system level, a week to install middleware, and a week to install our software. Times will be longer if it is your first time.  Once running, expect 1 day/month/cluster plus 1 day/month/rack of sysadmin time to maintain your system.
  
= Tier 1 - Physical level =
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= Narrative =  
We describe an entry level system that can be easily expanded.
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Before starting, let's talk about what you need for a successful computational pharmacology cluster. [[Cluster Narrative]].
* O/S: We recommend [[Centos]].
 
* Hardware: We recommend Intel or AMD.  [[Supported platforms for DOCK 3.7]].
 
  
 +
= Physical level =
 +
We discuss options for acquiring various sizes of hardware in [[Cluster Theory]].  More thoughts: [[Acquire and deploy hardware]]. Allow a month to obtain and deploy hardware.
  
= Tier 2 - Operating System level =
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= Operating System level =
* [[Centos]] 6.3.   
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Here we use Operating system to describe all software components that are not particular to our field. Thus for the purposes of this discussion, python and a queuing system are considered part of the operating system level.  [[Install operating system]]. Allow one week for this step.
* [[Foreman]]
 
* DNS
 
* Authentication
 
* Perimeter security.
 
* [[SGE]]
 
  
== Set up a database server ==
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= Middleware level =
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We use middleware to mean 3rd party software required by our software that is specific to our field and that you would not normally expect to find installed on a new computer.
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Set up middleware for a [[Compbio middleware | computational drug discovery lab]]. Allow one week for this step.
  
== Add a new node to the cluster ==
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= Our Software =
[[How to spin up a new virtual machine]]
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Each product is licensed and distributed separately.  Allow at least a day for each product, more if the previous steps above are incomplete.
  
== Add new disk to the cluster ==
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* [[Install DOCK 3.7]]
[[Configure new disk]]
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* [[Install SEA]]
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* [[Install DOCK 6]]
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* [[Install ZINC]]
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* [[Install DOCK Blaster]]
  
== Deploy a workstation ==
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= Operations =  
[[Workstation Install]]
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Once the system is set up and running, it will need to be maintained. Please see the [[:Category:Sysadmin | system administrator's guide]]  
 
 
= Tier 3 - "Middleware" level =
 
Set up middleware for a [[Compbio middleware | computational drug discovery lab]].
 
 
 
= Set up psql/rdkit from scratch =
 
 
 
 
 
= Tier 4 - Server Application Software =
 
 
 
[[Install DOCK 3.7]]
 
 
 
[[Install SEA]]
 
 
 
[[Install DOCK 6]]
 
 
 
[[Install ZINC]]
 
 
 
[[Install DOCK Blaster]]
 
 
 
== [[ZINC]] ==
 
Here is how to set up ZINC from scratch on a new cluster.
 
 
 
* create database
 
* install software and web interface
 
* test
 
 
 
 
 
== Using git and github ==
 
 
 
= Tier 5 - Client Application Software =
 
 
 
[[PyMol]]
 
 
 
[[Chimera]]
 
 
 
[[Knime]]
 
 
 
[[Marvin]]
 
 
 
[[InstantJChem]]
 
 
 
= Tier 6 - Operations =
 
Monthly maintenance tasks.  
 
 
 
[[Backups]]
 
 
 
[[Security Review]]
 
 
 
[[Software upgrades]]
 
 
 
=== CCP4 ===
 
 
 
=== Chimera ===
 
 
 
== H. acquire and install docking.org software ==
 
 
 
=== dockenv ===
 
 
 
== I. configure docking.org software ==
 
  
 
[[Category:Sysadmin]]
 
[[Category:Sysadmin]]
 
[[Category:Tutorials]]
 
[[Category:Tutorials]]
 +
[[Category:Setup]]

Latest revision as of 19:38, 10 January 2019

Here is how I would set up a computational lab, one that could join the Worldwide ZINC network.

Requirements and assumptions

This page describes setting up a full computational pharmacology research lab. We describe the minimum setup, plus options for expansion. The entry level assumes you can spend $20K on servers and $2K on a workstation, or you already own equivalent or better hardware. You'll need an acoustically insulated air conditioned room. Expect to spend a month to specify, order and deploy hardware, a week to install operating system level, a week to install middleware, and a week to install our software. Times will be longer if it is your first time. Once running, expect 1 day/month/cluster plus 1 day/month/rack of sysadmin time to maintain your system.

Narrative

Before starting, let's talk about what you need for a successful computational pharmacology cluster. Cluster Narrative.

Physical level

We discuss options for acquiring various sizes of hardware in Cluster Theory. More thoughts: Acquire and deploy hardware. Allow a month to obtain and deploy hardware.

Operating System level

Here we use Operating system to describe all software components that are not particular to our field. Thus for the purposes of this discussion, python and a queuing system are considered part of the operating system level. Install operating system. Allow one week for this step.

Middleware level

We use middleware to mean 3rd party software required by our software that is specific to our field and that you would not normally expect to find installed on a new computer. Set up middleware for a computational drug discovery lab. Allow one week for this step.

Our Software

Each product is licensed and distributed separately. Allow at least a day for each product, more if the previous steps above are incomplete.

Operations

Once the system is set up and running, it will need to be maintained. Please see the system administrator's guide