wiki:PromotFAQ

ProMoT Frequently Asked Questions

How can I run ProMoT using Windows XP/Vista/7?

The preferred file to start ProMoT is promot.bat. It starts both the Kernel and the GUI. You could also start both parts separately (using promot-server.bat and promot-gui.bat respectively).
The file promot.exe is only used to start the lisp image promot.dxl and will be implicitly called by promot.bat.

How can I install ProMoT from source?

First for compiling the Lisp sources you will need Allegro Common Lisp 8.2.
The free express version is not sufficient as it does not include the required CORBA middleware Orblink.
For the Java sources JDK 1.6.0 will be required.
The configuration is based on automake. You will need to run

  1. configure
  2. make
  3. make install

I get an error message “Promot Session not found, please start server” when starting promot.bat (on Windows) or the promot script (on Linux). What can I do?

In the majority of cases the problem is that the GUI of ProMoT tries to connect the server which is not completely launched. Have a look into the console where the server is started, wait until the Lisp interpreter prompt occurs:

; Publishing this server as Promot000
.....
[changing package from "COMMON-LISP-USER" to "PROMOT-KERNEL"] 
PK(1): 

Now click to “retry” in the error dialog. The GUI should start.
For later starts there are several possibilities: Either you start the server and the GUI from separate scripts (promot-server.bat and promot-ui.bat on Windows / promot-server and promot-ui on Linux) or you edit promot(.bat) and increase the time to wait between server and GUI start in the following line:

(sleep 3;${dir}/promot-ui "$@") &

If this all does not work, try the following options:

  • make sure that you use java version 6.0,
  • and the hostname on linux does not start with a number (Then you should change the hostname in /etc/hosts).
  • the directory for the binding handle of the server is the same like the one for the GUI:
    ...
    Published server in directory: /home/.../.corba-binding/org/mpg/dcts/promot/.../ 
    ...
    Looking for Server Filebinder uses /home/.../.corba-binding
    ...
    

The software is not responding anymore, is it possible to save my changes anyhow?

You can try to kill just the java GUI (via an xkill, or killing the process in the console; in emacs you can kill the buffer *compilation*). Go to the server (on the console or the *promot-server* buffer in emacs). If the server looks OK (Press Enter, the prompt PK(..): appears) start a new GUI on the running server, then your model will not be lost. It is still present in the server..

ProMoT version 0.8.3: If it's not possible to start a GUI on the running server, go to the server prompt (either on the console or in the *promot-server* buffer in emacs), press Enter, PK(..): should appear. Now type: (save-all "~/current_model.mdl"). This will save all loaded classes into the file current_model.mdl in your home.

On a 64-bit system I have installed ProMoT with 32-bit shared library and the 64-bit version of Diana. Will my simulation work?

Yes, ProMoT generates c++ files for your model, which are then compiled using dianac (Diana compiler based on g++/gcc) and simulated with Diana (python).
ProMoT and Diana are independent programs.

I can not run the Perl scripts for synthetic biology under Windows

Make sure you have installed Perl (e.g. http://strawberryperl.com/) and the PATH variable contains a path to Perl. Furthermore, the file association of .pl files have to be set.

CORBA Failure (COMM_FAILURE) during read of model, e.g. during start of Visual Editor or Visual Explorer

The error message will look like:

WARNING: "IOP00410215: (COMM_FAILURE) Read of full message failed :
bytes requested = 5,033,716 bytes read = 540,372 max wait time = 3,000
total time spent waiting = 3,190"

The maximal waiting time is set, to the default value of "3000", in promot-ui (for linux) or promot-ui.bat (windows). This parameter is passed in the statement -Dcom.sun.CORBA.transport.ORBTCPReadTimeouts=100:3000:300:10. A workaround is to adjust the "ORBTCPReadTimeouts" to a value like "1:15000:300:1". These values will configure the socket to check the it every 1ms and gives the client 15000ms time to respond.

-Dcom.sun.CORBA.transport.ORBTCPReadTimeouts=1:15000:300:1

Now everything should work fine.

This issue was experienced with Java Versions 1.5-1.6. It does not appeared in previous JDK versions. It seems to be happened only on Windows operating systems (WindowsXP, Windows7-32bit, Windows7-64bit).

I have found a bug, where do I report it?

You can create a new ticket in the ProMoT ticket system.

Last modified 7 years ago Last modified on Apr 11, 2012, 4:34:21 PM