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Cardiac Physiome Society workshop: November 6-9, 2017 , Toronto

Using JSim Multiprocessing

This page is for the current JSim version 2.0. Click here for the earlier JSim 1.6 version.

This page talks about JSim multiprocessing (MP), the ability for a single JSim session to take advantage of multiple computer processors to increase calculation speed.

Contents:

Current JSim MP Support

Most (but not all) JSim models support MP. JSim models support MP unless they contain the following:

JSim MP support is currently limited to multirun analyses (loops, sensitivity analysis, optimization, Monte Carlo, functional imaging) on shared memory multi-processors. JSim multi-run analyses take advantage of MP by running up to N model runs in parallel, assuming N system processors are available. Benchmark tests indicate near 100% processor utilization up to 4 system processors, with progressively more modest gains for additional processors. The actual speed gain you realize will depend upon the specifics of your computer hardware and operating system. On a system of N processors, ideal speed gains would be as follows:

Activating JSim MP

JSim MP support may be activated via the -mp command line switch (in jsim, jsfim or jsbatch), or via Preferences menu in the JSim GUI.

JSim MP operates by creating parallel computational threads (when possible) which Java distributes evenly over available system processors (N in number). The maximum useful number of parallel threads is N. Using more is counter-productive because the threads will compete with each other for resources. Users configure JSim MP by specifying the maximum number of parallel computate threads to be used. JSim enforces that this number is between 1 and N (inclusive).

The following example activates JSim using a maximum of 4 compute threads. If the system running the command does not have that many processors, then the number of processors actually present is used. This means you can't hurt yourself by specifying too many processors:

      jsim -mp 4 [other arguments]

In the JSim GUI, MP is activated/deactivated via the "Multiprocessing configuration..." item in the Preferences menu of the Project tab. This configuration box is not available for single-processors systems or for sessions using a remote server (such as JSim applets). Note that this JSim Preference is not currently preserved between sessions, due to the experimental nature of JSim MP. Once MP is considered stable, this Preference will be preserved between sessions.

Regardless of activation method above, MP is actually used only on models that support it (no PDEs or non-reentrant F&P, see above). JSim recognizes MP-unsupported models automatically. Therefore, you do not normally need to worry about toggling MP on and off during a session depending on the model (however, see exceptions below). To determine whether a JSim model supports MP, select "View plan text" in the model's Debug tab or specify -oplan in jsbatch. A boolean attribute labeled "Allow MP Runs:" gives this information.

There are two reasons you might choose to deactivate MP once it has been activated:

  1. MP is still somewhat experimental. If you encounter unstable behavior under MP, you should report the bug to NSR and run deactivate MP until the problem is resolved.
  2. MP optimization requires more memory than single-processor optimization because storage must be allocated for parallel model runs. If you are running a large model, this may potentially exhaust system memory. Alternatives are to increase JSim's memory allocation or deactivate MP during the optimization.

Future JSim MP Support

Non-reentrant F&P

JSim allows embedded procedural code, however this code must be reentrant in order to work properly on multiple processors. This restriction is not expected to be lifted, except possibly in the case of future cluster support (see below). Model writers interested in writing reentrant F&P should consult this document .

Fpack (legacy XSIM) models

Fpack models rely on procedural code in Fortran common blocks, and are not-reentrant. See comments above regarding non-reentrant F&P.

Sensitivity analysis

Currently, the unperturbed run in a sensitivity analysis must complete before additional perturbed runs are done in parallel. In the future, this situation will be improved so that all runs (perturbed and unperturbed) are done in parallel.

Optimization algorithms

The Simplex and GGopt optimization algorithms do not support MP. However, JSim's other optimization algorithms do.

Single run MP

In future JSim versions, the calculations in a single model run may be parallelizable, allowing multiple processors to be utilized. Whether a single model can utilize MP for effective speedup depends upon the nature of the equations. Some possible candidates for parallelization are:

  1. Models that use parallel pathways, for example a blood tissue exchange model with multiple parallel arterioles in which each arteriole is calculated independently.
  2. Models that use parallel PDE solver algorithms. Currently, JSim does not provide any such algorithms, but they exist and may be incorporated into future versions of JSim.
  3. Large ODE models may be seperable into fast and slow interaction blocks (for example, two organs separated by a blood flow). It is possible such blocks could be recognized by the JSim compiler and made to calculate in parallel. This is a difficult problem, however, and so should be viewed as a future goal.

Distributed-memory computation (clusters)

A compute cluster is a set of networked computers running common software for a particular task. Cluster nodes do not share a common memory, so message passing protocols between nodes must be implemented to coordinate computations on common models and datasets. Such message passing induces overhead, meaning clusters are inherently less efficient at closely coupled parallel computation than shared memory systems. However, clusters can be very efficient and economical for loosely coupled parallel computation because an N-node cluster is usually cheaper than an N-processor shared memory system (for large N).

JSim cluster support is under consideration. The most likely scenario is that jsserver will updated to allow separate model runs to be farmed out to available cluster nodes automatically. Prospects for multi-run MP analyses (loops, sensitivity analysis, optimization) on clusters are very good, since such computations are loosely coupled. Single-run MP speedup via clusters is more problematic because the parallel threads are more closely coupled. While single-run cluster MP is possible, it must be considered a long term objective at this point.

It is possible that future JSim cluster support would allow MP support for models containing non-reentrant F&P, such as Fpack models. More information will be available on this topic once clustering becomes available.

Comments or Questions?

[This page was last modified 06Jul12, 3:21 pm.]

Model development and archiving support at physiome.org provided by the following grants: NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.