The following information should help to decipher some of the additional workunits that we will soon distribute.

We need to perform several quality control calculations during this phase of “Discovering Dengue Drugs-Together”. These calculations are in addition to our free energy drug discovery calculations against proteases from dengue, West Nile, and hepatitis C viruses. Large numbers of control calculations are necessary to accurately benchmark the novel and unprecedented free energy calculations used in this project. Unfortunately, these quality control calculations are too time-consuming to execute using off-grid supercomputer resources, and thus must be run on World Community Grid.

For the control calculations, we will dock well-characterized proteins against small molecule libraries that contain a few dozen known binders and a few thousand non-binders. These proteins are part of the stringent benchmarking and validation database known as the Directory of Useful Decoys (www.dud.docking.org).

The naming conventions for our quality control systems are:
ts01 = HIV protease and its known binders/non-binders
ts02 = trypsin and its known binders/non-binders
ts03 = HIV reverse transcriptase and its known binders/non-binders
ts04 = influenza virus neuraminidase and its known binders/non-binders
ts05 = human estrogen receptor and its known binders/non-binders

Again, we thank you for helping us discover dengue drugs together.

All my best,
Stan

The following information should help to decipher some of the additional workunits that we will soon distribute.

We need to perform several quality control calculations during this phase of “Discovering Dengue Drugs-Together”. These calculations are in addition to our free energy drug discovery calculations against proteases from dengue, West Nile, and hepatitis C viruses. Large numbers of control calculations are necessary to accurately benchmark the novel and unprecedented free energy calculations used in this project. Unfortunately, these quality control calculations are too time-consuming to execute using off-grid supercomputer resources, and thus must be run on World Community Grid.

For the control calculations, we will dock well-characterized proteins against small molecule libraries that contain a few dozen known binders and a few thousand non-binders. These proteins are part of the stringent benchmarking and validation database known as the Directory of Useful Decoys (www.dud.docking.org).

The naming conventions for our quality control systems are:
ts01 = HIV protease and its known binders/non-binders
ts02 = trypsin and its known binders/non-binders
ts03 = HIV reverse transcriptase and its known binders/non-binders
ts04 = influenza virus neuraminidase and its known binders/non-binders
ts05 = human estrogen receptor and its known binders/non-binders

Again, we thank you for helping us discover dengue drugs together.

All my best,
Stan

Welcome to Discovering Dengue Drugs - Together Phase 2. The purpose of this forum post is to help member understand what type of work unit is running on their machines and why there may be periods of no work.

To get started, there are 4 major types of work units for this project. These types are: Prerun, A, B, and C. Below is a work flow image to help visualise the different types of work units and how they relate to each other.


Full Size Image


Type Prerun: ("pb" in chart): These work units are run on our alpha grid, an internal grid of machines we use primarily for testing (alpha testing is performed before beta testing). This decision was made due to the high upload to runtime ratio and the relatively short amount of time it would take the alpha grid to run the type A work units.
Runtime: ~0.5 hour
Quantity: About 36,000 work units
Download: ~100 KBytes
Upload: ~20 MBytes
Identifier: pb
Results: Each Prerun work unit creates one type A work unit
Checkpoints: None

Type A ("ps" in chart): These work units are the very long running work units.
Runtime: 30-100 hours
Quantity: About 36,000 work units
Download: ~20 MBytes
Upload: ~2 MBytes
Identifier: ps
Results: Each type A work unit creates two type B work units: (one "se" and one "pe")
Checkpoints: 50 times within a work unit. Evenly throughout the run, every 2%.

Type B ("se" or "pe" in chart): These work units are faster with very frequent checkpoints.
Runtime: 5-10 Hours
Quantity: About 72,000 work units
Download: ~2MBytes (se) or ~20MBytes (pe)
Upload: ~2MBytes (se and pe)
Identifier: se, pe
Results: Each type B work unit creates about 250 to 350 type C workunits
Checkpoints: As frequently as every 10 seconds, but per member's project preferences

Type C: This type of work unit represents the bulk of the overall work to be done.
Runtime: 1 to 5 Hours
Quantity: About 22,000,000 work units.
Download: ~2MBytes (sq, sd, sr) or ~20MBytes (pq, pd, pr, pc, pl)
Upload: < 1MBytes
Identifier: pq, pd, pr, pc, pl, sq, sd, sr
Results: These are the final step. Results are sent to researchers
Checkpoints: As frequently as about 1 per minute, but per member's project preferences

At least two copies of each work unit are sent out to two different member machines. This is used to validate results and eliminate any errant computations. The Prerun work units will periodically arrive from the researchers to World Community Grid in batches of 1000 work units. Usually processing for these batches will be overlapped, so there will usually be all types of work units running at the same time. However, there may be periods of time when work units are not available. This is because during the Prerun, Type A, and Type B phases of the work flow, there are not a large number of work units available and due to some of the long processing times for these, the type C work units will require some waiting before they are ready to run.

Tips on identifiers. To find out what type of work unit you have you will notice that in the work unit name, there are 6 characters at the end. The first two of those 6 is the identifier. For example for work unit name "ly01_a015_pe0000", the identifier is "pe". From the information above, the "pe" identifier represents a type B work unit.
Thanks,
-Uplinger

Giba, in my last paragraph there is an example on a work unit name. The target is the first 4 characters. We first started on erlc. ts01, ts02 would be in that place. These work units will still follow the type's. Meaning they'll have pe/se for type B of ts02. (example name ts02_a001_pe0000) or type C for ts02 (ex ts02_a001_sq9302).

_Uplinger

What's TS06?

I got ts06_ a014_ ps0000_ 1, which seems to run fast on i7HTON.
94.840% = 19hrs+