This page will look better in a graphical browser that supports web standards, but is accessible to any browser or internet device.

Served by Samwise.

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

Administering a JSim Server

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

Introduction

This document describes how to run a JSim server, which allows JSim clients (such and jsim and jsbatch) to run in remote mode, that is, to perform their model calculations on a remote host rather than on their local machine. The primary reasons for doing this are:

  1. The server may have more computational power, allowing faster calculation of models than is available on the local host;
  2. The WWW applet version of JSim must always use remote mode, since JSim's computational engine relies, in part, on legacy C and Fortran numeric solvers that may not be run in an applet.

JSim server is available for Linux and MacOS and Windows. This document assumes reasonable familiarity with Unix system and computer network administration. Windows administrators will need to translate the directions appropriately for their systems.

Contents:

How JSim Servers Work

JSim servers are based on Java's Remote Method Invocation (RMI) protocol. A JSim server creates an RMI registry on a specified port (1099 by default), and registers an object (named JSimServer by default) that responds to client connection requests. A client in this case is a either single instance of jsim or jsbatch run with the -server switch or an WWW page containing the JSim applet. If a client's connection request is honored, a new client-specific server object (e.g. JSimServer.charlie0) is registered to handle all further requests from the client (such as building and running models). When the client terminates, it sends a disconnect request to the server, which removes the client-specific server from the registry.

Each client-specific server runs as a separate process (not a thread) in a separate JVM. The reasons for this are:

  1. Many native methods in the JSim numerical method library are not thread safe, so multiple concurrent runs cannot be supported within a single JVM.
  2. It simplifies client memory management, preventing one renegade client from bringing down the entire server.
  3. It allows the administrator to manage processes individually using OS specific tools (e.g. ps on Linux/MacOS).

The jsserver Manual

JSim server administration is done with the jsserver program (jsserver.db for those of you using JSim source distributions). Start a server using the "-start" switch. Stop the server with the "-stop" switch. A running server may be monitored with the -status switch or by examining the logfile created in the server's work directory.

Synopsis:

      Usage: jsserver command [options]
      Commands:
        -start dir      start server in given work directory
        -stop           stop server
        -status         query server status
        -connect ID     create client connection (debug only)
        -disconnect ID  disconnect client
      Startup Options:
        -sandbox                run clients in safe sandbox  (default)
        -nosandbox              run clients without safe sandbox
        -purgeFreq number      specify uncommunicative client purge freq in secs (default 90)
        -maxConnectTime number  specify max client connection time is secs (default 12*3600)
        -clientMax number       specify max # concurrent clients (default 10)
        -clientMemory number    specify max client memory in MB (default 600)
        -maxBuildTime number    specify model build timeout in secs (default 120)
        -maxRunTime number      specify mode run timeout in secs (default 3600))
        -sharedJVM              clients share server's JVM (debug only)
        -userPort number        specify user ports (default 0=RMI default ports)
      General Options:
        -name string    specify non-default server name
        -port number    specify server port (default 1099)

Commands

-start directory

Start the server in the given work directory. The work directory must already exist. This option runs in the foreground, so you must use operating-system appropriate methods to push it into the background if that is what you desire.

-stop

Stop the server. This disconnects all current clients immediately, so be careful when you do it.

-status

Print status display of the server.

-connect ID

For developer debugging purposes only.

-disconnect ID

Disconnect a client. May cause abrupt termination at the client end.

Switches

-port

Server port, 1099 by default.

-name

Server name, JSimServer by default.

-sharedJVM

For developer debugging purposes only.

-sandbox

Runs client models in the JSim Sandbox . This is on by default.

-nosandbox

Runs client models without the JSim sandbox. Never do this unless you enable operating system level access control to the appropriate port, insuring that only trusted hosts may access it. Even then, this may be a bad idea.

-purgeFreq number

Specifies how long (in seconds) a client connection is maintained in the absence of stay-alive requests. The default is 90. Values less than 60 are not allowed for performance reasons.

-maxConnectTime number

Specifies the maximum duration (in seconds) allowed for a client connection. The default is 12 hours.

-clientMax number

Specify maximum # of concurrent clients allowed. The default is 10.

-clientMemory number

Specify maximum client JVM memory in MB. The default is 600. This switch has no effect if -sharedJVM is also specified.

-maxBuildTime number

Specify timeout for model builds in seconds. Model builds may sometimes take arbitrarily long times to complete if they are underspecified. The default is 120.

-maxRunTime number

Specify timeout of model runs in seconds. The default is 3600 (1 hour). This feature does not work properly yet, but remains an option for the future.

-userPort number

Specifies the minimum in a range of clientMax+1 dynamic ports to be used by the server. By default, arbitrary port numbers are used. This switch become useful when traversing a firewall (see below) .

Cautions/Limitations

  1. A JSim server may not share an RMI registry with other RMI applications, including other JSim servers. One JSim server per port. You do not need to (and should not) run Sun's "rmiregistry" program on this same port.
  2. A JSim server has no built-in access control. Connecting clients submit a username and password, but jsserver does not currently validate these in any way. The server does not allow disabling of connection from potentially hostile internet sites. Disabling such connections must be done using appropriate operating-system or firewall mechanisms.
  3. Make sure you understand the JSim sandbox . jsserver runs client models in the sandbox by default. This may have the unfortunate effect of disabling some valid models. However, running in without the sandbox can leave you open to attack. See comments regarding the -nosandbox switch above.
  4. "jsim -server localhost" is NOT the same as "jsim". The former requires jsserver to be running on your local host.
  5. Connections to JSim server from jsim and jsbatch occasionally generate NullPointerExceptions on the initial model compile. Work continues to reproduce and fix this bug. JSim GUI users can usually continue work by simply pressing the model compile button.

Step-by-step Basic Server Administration

Here's what to do:

  1. Read this document in its entirety. If you don't understand the issues involved, maybe administrating a JSim server is not for you. There is no shame in this (unless you're a full-time system administrator).
  2. Create a non-privileged account (e.g. jsserver) to run the jsserver program. This can help protect you against jsserver bugs, security holes (if any) and yourself. Note: Under Windows, "non-privileged account" is not really a functional concept, so this protection measure will be less effective than in more security-oriented operating systems. But then if you were worried about security, you wouldn't be using Windows in the first place.
  3. Obtain a recent JSim distribution, and customize it appropriately, taking special care to understand the JSim sandbox. Install this under the jsserver user account.
  4. Decide on a port number to run the JSim service from. The default (1099) usually best, since it simplifies user connections. Make sure there are no conflicts in your system or network (especially firewalls) for this port.
  5. Decide on a name for the JSim server in the RMI registry. The default (JSimServer) is almost always the right choice, since it simplifies user connections.
  6. Create a work directory for your server (e.g. ~jsserver/WORK).
  7. Launch the jsserver (make sure you're in your new jsserver account!). For initial testing you might want to run it in the foreground. Once you're comfortable with its operation, you'll probably want to run it in the background. Using the default settings and the example work directory above the command would be:
          jsserver -start ~/WORK
    
  8. Check on the status of the server periodically by examining the logfile (e.g. ~/WORK/logfile) or by using the command:
          jsserver -status
    
  9. Test a connection to your server (see below).
  10. When it is time to say good-bye:
          jsserver -stop
    
  11. Depending upon server usage, you may need to clean out the jsserver work directory every so often. If you're clever, you might even figure out how to do this automatically. Be sure the server is not running when you do this.
  12. Once you're happy with your server, you'll need to inform potential users of its location and availability. Since they may be unfamiliar with connecting to a remote server, you may need to help them out (see below).

Connecting to a JSim Server

You may connect to a JSim server using jsim, jsbatch, the JSim applet or any other customized JSim client developed using the JSim source distribution. jsim and jsbatch both recognize the switch:

      -server [username@][scheme]hostname[:port][/servername]

All the elements in brackets (that is, all except the hostname) are optional:

When servers are running using the default port and servername the syntax reduces to something like:

      jsim -server brainiac.mit.edu

For information on connecting to a server from the JSim applet, see Administering a JSim-enabled Web Site .

Traversing a Firewall

A network firewall, sitting between a JSim server and its clients, induces complications for proper operation. A connection between client and server uses 3 separate TCP ports, the main server port (specified via the -port switch) and two dynamically assigned ports. By default, the dynamic ports are randomly assigned via Java RMI mechanisms. This can be problematic because firewalls often limit open ports. In such situations, the -userPort switch (above) narrows the range of ports that must be open. Note that all ports in the -userPort range must be open for guaranteed connection success, since the client may not specify which of the available ports will be used.

As an example, we'll consider a server "secret", hidden behind a firewall "firewall.paranoid.com", being accessed by a trusted client "client.org". The server will allow a maximum of 2 simultaneous clients. We'll use port 2099 for the main server and start the dynamic pool at 3010:

      jsserver -port 2099 -userPort 3010 -maxClient 2 -start SERVERDIR

We'll use ssh to forward the needed ports across the firewall. The -userPort pool is of size maxClients+1=3, so the needed ports are 2099, 3010, 3011 and 3012. From client.org:

      ssh -L 2099:secret:2099 -L 3010:secret:3010 \
        -L 3011:secret:3011 -L 3012:secret:3012 firewall.paranoid.com

Once the client has established the above connection, jsim may then be lauched (in a separate window) via:

      jsim -server localhost:2099

In the absence of ssh forwarding being available on the firewall, alternative security mechanisms accomplishing the same end should be discussed with the firewall administrator. If you have circumstances that cannot be addressed by JSim's current mechanisms, please contact the JSim development team.

Comments or Questions?

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