= ProMoT Frequently Asked Questions = [[PageOutline]] == 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). [[BR]] 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 [http://www.franz.com/products/allegrocl/ Allegro Common Lisp 8.2]. [[BR]] The free express version is not sufficient as it does not include the required CORBA middleware '''Orblink'''. [[BR]] For the Java sources JDK 1.6.0 will be required.[[BR]] 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: [[BR]] {{{ ; 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. [[BR]] 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: [[BR]] {{{ (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). [[BR]] 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:[[BR]] {{{ 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 [http://promottrac.mpi-magdeburg.mpg.de/trac/newticket ProMoT ticket system].