The FlowJo Diagnostic

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FlowJo Diagnostics is a set of macros which ships with FlowJo installers for the Windows computers. It is designed to detect and report low level problems in areas such as internet connectivity, file corruption, invalid installation and poor performance (system tuning and benchmarking.) The Diagnostic is also a way to launch CommanJo.

When FlowJo 10.0.6 or later is installed on a windows computer it will create a shortcut in the same Start Menu program group as FlowJo Vx.

  • Starting the Diagnostic
  • Making use of the information
  • Running benchmarks
  • Running CommanJo


Starting the Diagnostic

There are two ways to start the diagnostic: with console and without console.

To start the diagnostic without console, click Start menu, and in All Programs, under FlowJo Vx, click on the “FlowJoDiagnostic” shortcut.

Alternatively repeat the step above but hold down the “ctrl” key on your keyboard to launch this tool with console.

The other executable you see there, “FlowJo_V10_CL_diag.exe” is a special verbose launcher for FlowJo which reports more spam to the Console than the regular launcher. This spam is what the Diagnostic parses to determine problems.

When launched, the Diagnostic will begin with a scan of your disk for possible FlowJo installations. On traditional (spinning) disks this may take several seconds to a couple of minutes. On Solid-State disks, the time will be much less. Blank console windows may pop up during this process. Eventually the UI loads up. As shown below, the diagnostic found several flowjo installations:

Making use of the information

The Diagnostic tool has the following conveniences:

  • clicking on any path in the “Path” column will open that installation in an Explorer window.
  • MD5 Hash column was changed to show either the atomic revision number from our source code repository, or, if that revision corresponds to a known shipped version (as opposed to a beta) we will show that string instead. The shipping versions are matched by MD5 of the flowjo.jar file to the one published at the time of release.
  • clicking on the folder icon under the “Run” column will start FlowJo from that installation in interactive mode.
  • Clicking “Err“, “Lax” links will open those files in a text editor. “err” is the shorthand for error log, where Java stores problems encountered during runtime. The lax file is flowjo’s main configuration file, which stores variables like classpath and VM memory size.
  • Clicking “Uninstall” will launch the uninstaller utility for the selected FlowJo instance.
  • Clicking the Benchmark button once run a benchmark. You can also drag a folder full of Preferences files on this button.
  • Double-click the Prefs File button to open your prefs in a text editor.
  • Drag the Prefs File button to your desktop to copy the prefs file there.
  • Drag any prefs files to the Prefs File button, to place it in FlowJo’s preference folder.

Running benchmarks

The Diagnostic tool makes FlowJo benchmarking pretty easy. Usually our approach to this is that the hardware configuration is fixed, but you can modulate preferences and measure the results. There are two modes in which you can benchmark FJ:

  • Clicking the Benchmark button once will decompress and run a benchmark where a bunch of data is added to a workspace, gated, and batched in a layout. An average computer does this in about 10 seconds. The result will be displayed in the Result column in the Diagnostic panel.
  • The Benchmark button also allows you to drag a folder full of Preferences files. One benchmark will be executed for each prefs file. This is a good way to titrate the Performance and Engine preference settings which can alter your batch times. In this mode of execution, the benchmark timings are shown in console, and include extra information, including time to execute, file cache efficiency, and the total memory used during the session.