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The goal of the MDStack project is to develop a distributed molecular dynamics toolbox that allows end scientists to cary our different steps of the MD pipeline on distributed computing resources, mainly XSEDE. Currently the following project are potential users of the MDStack toolbox:
- Binding Affinity Calculation (UCL, P. Coveney, Ole)
- Replica Exchange (Rutgers University, Emilio, Melissa)
- Ensemble/ExTASY (Rice University, Cecilia Clementi, Vivek)
- Multi-Task/Multi-Stage (Tom Bishop, Mark)
The goals of MDStack are defined as follows:
- Provide a stable and tested set of MD task tools to extract low-level, application- and machine-specific complexity from aforementioned projects.
- Allow the execution of different MD tasks (defined below) locally and remotely, including input and output data transfer.
- Provide a simple, homogenous interface (command line tool, API, configuration files) for different MD tasks and application kernels.
The MDStack will be based on BigJobAsync as infrastructure abstraction layer (job management and file transfer). BigJobAsync currently uses BigJob and SAGA internally to provide this functionality. This might change in the future, but in a non-disruptive way.
Execution Engine: BigJobAsync.
MDTask Skeleton: The MDTask skeleton is an abstract base class that defines the common interface (API) for all MD tasks. It also defines the format for the machine-, application- and kernel specific configuration files (something like THIS). It also provides a simple command line tool for non-programatic use.
Application Packages The application packages provide specific configuration files, examples and test data for the individual MDSteps. Application packages are integrated with the MDTask Skeleton.
+-----------+ +-----------+ +-----------+
|Step 1 Tool| |Step 2 Tool| |Step 3 Tool|
+---+-------+ +-----+-----+ +------+----+
| | |
| | |
| +---------------------+ |
| | API | |
| +---------------------+ |
| | MDTask Skeleton | |
+-------+---------------------+------+
| |
| |
+--------->| |<--------+
| +---------------------+ |
| ^ |
| | |
| | |
+-----+-------+ +------+------+ +-------+-----+
|App Package 1| |App Package 2| |App Package 3|
|-------------| |-------------| |-------------|
| | | | | |
| | | | | |
+-------------+ +-------------+ +-------------+
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MDTask application skeleton development (Ole, DL: Feb. 7)
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MMPBSA application package development (Ole, DL: Feb. 7)
- Example Job(s)
- Example Data
- Configuration parameters
- Machine Specifica
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Gromacs application package development (Vivek, DL: Feb. 7)
- Example Job(s)
- Example Data
- Configuration parameters
- Machine Specifica
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Amber (?) application package development (Melissa, DL: Feb. 7)
- Example Job(s)
- Example Data
- Configuration parameters
- Machine Specifica
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MMPBSA-MDTask Integration (Ole, DL: Feb. 21)
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Gromacs-MDTask Integration (Vivek, DL: Feb 21)
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Amber(?)-MDTask Integration (Melissa, DL: Feb 21)
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Experiments and Integration Testing (Ole, Mark, DL: Feb 28)
- TROY Experiments
- Buildbot integration
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Milestone 1 Release (Ole, DL: Mar. 5)
Jan. 22 Feb. 07 Feb. 28 Mar. 5
+ + + +
| | | |
[1] |+----------------+| | |
(Ole) |+----------------+| | |
| | | |
[2] |+----------------+| | |
(Ole) |+----------------+| | |
| | | |
[3] |+----------------+| | |
(Vivek) |+----------------+| | |
| | | |
[4] |+----------------+| | |
(Melissa) |+----------------+| | |
| | | |
[5] | |+-----------------+| |
(Ole) | |+-----------------+| |
| | | |
[6] | |+-----------------+| |
(Vivek) | |+-----------------+| |
| | | |
[7] | |+-----------------+| |
(Melissa) | |+-----------------+| |
| | | |
[8] |+------------------------------------+| |
(Mark, Ole)|+------------------------------------+| |
| | | |
[9] | | | +-+
(Ole) | | | +-+
| | | |
v v v v
- Free Energy Calculation
The first release of MDStack needs to be ready the first week of May when Cecilia Clementi is visiting our group.