MonolixSuite2018R2 installation and administration guide

1.About the installer

Operating system specifics

Windows specifics

No prerequisite. However, it will install a version Microsoft Visual C++ 2015 redistribuable (it was installing a version 2012 for MonolixSuite2016R1)

Linux specifics

Make sure you have gcc/g++/make installed or install them.The gcc version should be at least a 4.8 version.
Notice that we can provide on request a silent installer for Linux operating system.

Mac OS X 10.6 or higher specifics

– install and launch at least once Xcode, in order to being able to compile any C++ code  on your computer.
– install XQuartz (or X11 for osX < 10.7), close and restart your session at least once after the installation, in order to make the  system  recognize the path of X11.
These  operations must be done after any update or upgrade of your system.  XQuartz can be founded on Apple’s website, Xcode can be installed  using  App Store.app.

Installation

  • copy the installer on your Desktop or in a temporary directory,
  • double click on the executable and follow the instructions. The instructions are very simple and will allow you to define the installation folder, the shortcut menu name, …

Notice that the software should be installed in a directory without any special character in the path.

Additional folder created by MonolixSuite

When launching an application of MonolixSuite, a folder lixoft will be created in the user folder, i.e.
– C:\Users\UserName\lixoft for windows OS
– \home\UserName\lixoft for Linux OS
Two elements need to be noticed. First, the user must have the full permission on the lixoft folder. Indeed, we use this folder to add temporary files and compile the models. Secondly, we recommend to have no special character in the UserName to ensure smooth operation.

License

At the end of the installation, during the initialization, the license activation process occurs. It will check if you already have a license.
If you have a valid license, you will be able to run the software as the license is independent of the software version.
If not, a window will pop up requesting an activation key, or a licence file. If you do not have it, just click on the cross to cancel it. Two things have to be noticed:

  • If you do not have a valid license key, the software will be installed and you will be able to re-activate it later.
  • If your license key is valid for several software and/or for the MonolixSuite, the license request will be done for the first software and will automatically be validated for the other one.

Troubleshooting

If you have any trouble during the installation, see here or send an email to support-at-lixoft.com if you still have issues.

2.Floating licence management using RLM

The use of a floating license requires to set up a license server. We provide here the way to do it by your local IT. Notice that we also provide this as a cloud-based service. Please contact info@lixoft.com to know more on this cloud based service.

System requirements

  • The license server should be installed on a real machine, not on a virtual machine.
  • The machine hosting the license server should be a 64 bits machine
  • Other applications can be installed on the machine hosting the license server

Downloading and running the service

windows64Click on the icon above to download the license server. Unzip it and launch rlm.exe.

icon_lin64Click on the icon above to download the license server and launch ./rlm

The rlm server is delivered with an embedded Web Server to perform normal administration tasks. At this step there is no license available yet; the IT manager should use the web interface to download the license by following the procedure below.

License key activation

Note

  • The activation process requires an internet connection. Else wise, the license has to be created by Lixoft. Send a mail to support@lixoft.com with the following informations (MAC ADDRESS and IP Address of the machine hosting the license server.
  • You do not need to be on the machine hosting the license manager to get the license, it could be done on any machine connected to this machine.
  • On the following steps, the license server should be started (rlm.exe in Windows or ./rlm in Linux).

0/ In the web browser, type IpAddress:wsp, where IpAddress is the IP address of the machine hosting the license server and wsp is the web server port (5054 by default) (e.g. 192.168.46.248:5054). Click on “Activate license” in the left bar.

and BEGIN License Activation:

1/ Select activation server: Enter the ISV activation website: activate.lixoft.net. And click on Next button.

2/ Specify license activation key. Fill the ISV input with the string “lixoft” (without the quotes) and the License activation key with the activation key provided by Lixoft (key format is xxxx-xxxx-xxxx-xxxx)

3/ specify machine for nodelocked license or license server and license count and click on the Next buttonNotice, the license count cannot exceed the number of bought licenses.

4/ Specify license file location and click on the Next button. By default, it is located next to the executable and the associated name is activated1.lic. If it already exists, it increments the number.

5/ verify parameters and request license. Click on REQUEST LICENSE.

6/ Requesting license from internet. The license is generated and you need to restart the License server.

Frequent Asked Questions

  • Activation key already used. Notice that if you request too many license, the following message will appear
    Error generating License: -1005
    Activation key already used
    
    Attempting to access license generator at: activate.lixoft.net
    

    you can not request more license that you have purchased.

  • Access issue. It means that you can not access to our server to get the license. Please check your internet connection and/or your firewalls.
    Error generating License: -132
    Cannot connect to specified URL (-132)
    Attempting to access license generator at: activate.lixoft.com
    You were unable to connect to the URL you specified (activate.lixoft.com). Please make sure that this system is able to access the internet site activate.lixoft.com and try again.
    

License server management

The documentation of the management of the RLM server provided by Reprise Software is available at http://www.reprisesoftware.com/RLM_Enduser.html

Hostname, ports and firewall configuration

If for any reason, the server port or the server hostname is not registered in a DNS, it is possible to change these informations directly on licence file. The line HOST can be changed by HOST .

The license server opens three ports. These ports are as follows:

  • rlm web server port (default 5054) web browsers connect here. It is needed for manage the server through the interface.
  • rlm client connection port  (default 5053) this is the port that clients first connect to.  rlm redirects them to the ISV server client connection port
  • ISV server client connection port – clients connect here to check out licenses

Thus, if there is a firewall, the ports 5053, 5054 and the ISV port should be opened. These ports are configurable as could be seen in the following.

  • rlm web server port. If the web server port (5054) is not available you can launch license server with a new port by using the program option -ws (e.g: rlm -ws 5055). This port will be called the wsp in the following.
  • rlm client connection port (default 5053) this is the port that clients first connect to.  rlm redirects them to the ISV server client connection port. If the server port (5053) is not available, a file config.conf has to be created in the rlm directory and has to contain the following information: HOST {IP} {MAC ADDRESS} {NEW PORT} e.g. HOST 192.168.46.245 a8c0f82e 5060
  • ISV server client connection port – clients connect here to check out licenses. The ISV port can be set directly in license file by changing the ISV line as follow:
    ...
    ISV lixoft port=
    ...
    

What to share that with the users?

Classical floating usage

For this usage, the IT should send the users the .lic file. In that case, the user can

  • Set it when opening an application when the application is requesting a license,
  • Put it in his {USER_NAME}/lixoft/license folder.

Cluster floating usage

See here.

3.How to see that the applications are well installed ?

Here is for each application a simple procedure to be sure that everything is well installed

Datxplore

  1. Open Datxplore
  2. Go to the menu Project/Load demo as on the following figure
  3. A window with all the demos for Datxplore pops up. Then, choose the file theophylline.datxplore in the folder continuous and click on open.
  4. Datxplore should load the project and display the data set like on the following figure.
  5. Click on the Dataviewer frame and the following figure should appear should load the project and display the data set like on the following figure.
  6. Click on the toggle next to information to see all the informations concerning the data set

Mlxplore

  1. Open Mlxplore
  2. Go to the menu Project/Load demo as on the following figure
  3. A window with all the demos for Mlxplore pops up. Then, choose the file TumorGrowthModel.mlxplore in the folder CaseStudies\TumorGrowthInhibitionModel\ and click on open.
  4. Mlxplore loads the project and display the model like on the following figure.
  5. Run the project bu clicking on the arrow (in the green circle). The computation will run and the following figure is displayed

Monolix

  1. Open Monolix
  2. Go to the menu Demos and choose theophylinne_project is section 1.1
  3. Monolix loads the project and the interface looks like the following figure 
  4. Clicking on the “Run” button launches the scenario as on the following figure
  5. Close the scenario using the close button and the graphics are displayed behind on the Individual fits plot

Simulx

Simulx is a little bit different from the other applications because it does not have yet a user interface. To validate it, one should use R (version greater than 3.0.2) to run simulations.

  1. Open R or Rstudio
  2. The R-packages needed to run Simulx are defined here. Make sure you have all the required packages.
  3. Execute the following commands
    # Define the mlxR library
    library("mlxR")
    # Define the model
    myModel = inlineModel("[LONGITUDINAL]
    input = {V, Cl}
    EQUATION:
    Cc = pkmodel(V, Cl)")
    # Define the administration
    adm = list(time=3, amount=40)
    # Define the output
    Cc = list(name='Cc',time=seq(from=0, to=20, by=0.1))
    # Run the simulation
    res = simulx(model=myModel, parameter=c(V=10, Cl=4), output=Cc, treatment=adm)
    # Plot the concentration w.r.t. time
    print(ggplot(data=res$Cc, aes(x=time, y=Cc)) + geom_line(size=1))
    
  4. The computation is launched and the following graphic appears Simulx2
  5. In some cases, you might be asked after loading the library to specify the path to the installation directory of the Lixoft suite (usually “C:/ProgramData/Lixoft/MonolixSuite2018R2” for Windows). You can do it with the command:
setMlxLibraryPath("/path/to/MonolixSuite2018R2/")

4.What about MonolixSuite running on a cluster ?

MonolixSuite can run on a cluster.

Monolix installation

To run MonolixSuite on a cluster, each cluster node must have access to the MonolixSuite directory and to the user home directory. Thus, there are two possibilities.

  1. MonolixSuite is installed on each node. In that case, each node has a MonolixSuite installation.
  2. MonolixSuite installation is shared. MonolixSuite is installed on a master server. Each cluster node accesses to MonolixSuite through a shared directory (via CIFS, Network drive, NFS, …).

License management

On a cluster, we are managing the usage of our applications with the license management system described here.
The license management server is on a physical machine and manage the application through its license file. The associated license file has to be put in the folder {MonolixSuite install path}/config/system/access (and also {MonolixSuite install path}/bin/Monolix_mcr/runtime/config/system/access for MonolixSuite2016R1). So either on all nodes in the installation case 1, or only on the master server in the configuration 2.

Running Monolix on a cluster

To run Monolix with the command line: in the lib folder (typically $HOME/Lixoft/MonolixSuite2018R1/lib/)

monolix -p mlxtran_project_path

where mlxtran_project_path is a Monolix project with a .mlxtran extension. Notice that a typical project from the demo can be found here $HOME/Lixoft/MonolixSuite2018R1/resources/demos/monolix/1.creating_and_using_models/1.1.libraries_of_models/theophylline_project.mlxtran

Generally, a task is submitted to the cluster using a specific command, e.g. qsub in the case of Torque, PBS or GridEngine (former SGE). This command runs a script, provided as parameter, on a cluster node chosen by the cluster scheduler.To run Monolix on a cluster: in the lib folder (typically $HOME/Lixoft/MonolixSuite2018R1/lib/)

qsub qSubOptions monolix -p mlxtran_project_path

where qSubOptions corresponds to your cluster options.
To run using mpi with the command line: in the lib folder (typically $HOME/Lixoft/MonolixSuite2018R1/lib/)

mpirun mpiOptions distMonolix -p mlxtran_project_path

where mpiOptions corresponds to your mpi options. Notice that the mpirun call another program that requires another license.
In addition, the package was done with openmpi 1.6. If you have a more recent version (1.8, 1.10 or 2.0) version, you just have to create a symbolic link from your installation

  • from your installation of libmpi.so (usually in /usr/lib64/openmi/lib/libmpi.so.XX) to libmpi.so.1 (in our lib folder).
     sudo  ln -s your_installation_of_openmi/lib/libmpi.so.XX  installation_of_MonolixSuite2018R1/lib/libmpi.so.1
  • from your installation of libmpi.so (usually in /usr/lib64/openmi/lib/libmpi_cxx.so.XX ) to libmpi_cxx.so.1
    (in our lib folder).

     sudo  ln -s your_installation_of_openmi/lib/libmpi_cxx.so.XX   installation_of_MonolixSuite2018R1/lib/libmpi_cxx.so.1
    

For further assistance, contact us.

5.Troubleshooting

Downloading MonolixSuite

Problem: My web browser claims that the Monolix download website has insufficient reputation and suggests to stop the download.
Solution: Some browsers like Google Chrome and Internet Explorer may ask whether to keep or remove the MonolixSuite archive just after download because of the insufficient reputation of the Lixoft website, simply because it is insufficiently referenced. Please ignore the warning and choose to keep the file. You can use a MD5 tool to verify that the downloaded file is not corrupted.

Problem: The MonolixSuite archive is removed just after being downloaded.
Solution: Some antivirus may consider the MonolixSuite archive as risky and put it in quarantine or remove it. This is due to the fact that MonolixSuite embeds a compiler for the Mlxtran language. Two solutions are available:

  1. Deactivate your antivirus auto-protection process during download and installation, or
  2. Restore the file from the quarantine.

To restore the file from quarantine, please refer to the documentation of your antivirus software. For the most common examples:

  • Norton Antivirus: In the Norton product main window, double-click Security, and then click History, then Quarantine as explained here.
  • Avast Antivirus: Open Avast, Choose Maintenance, then Virus Chest as explained here.
  • Mcafee Antivirus: Click Navigation (or click the cog at the top right), and click Quarantined and Trusted Items as explained here.

You should see the downloaded file among the quarantined files. Execute the Restore action; the archive will be restored into the directory used for downloading. Click on the archive (ignore a possible “malware” warning, again related to the fact that MonolixSuite embers a compiler.), and installation will start.

Installing MonolixSuite

Problem: When launching the installer, my antivirus tells me that the executable file stopped working.
Solution: If your antivirus apparently stopped the execution, it is  just scanning the installation program. Thus, just “Close the program” and the installer will reopen automatically.

Running an application of MonolixSuite

Problem: When launching the standalone version, my antivirus tells me that some executable file is risky.
Solution: If your antivirus apparently removed an executable file, check if it was actually put on Quarantine, or removed. If it is in Quarantine, please restore it by following the same instructions as provided above. If the file was removed you will need to reinstall MonolixSuite. You should be able to add this file to your antivirus Trusted Zone or Trusted files.
In addition, you can define it in the trusted zone and thus not scan this folder.

Suggest Edit
Jonathan CHAUVINMonolixSuite2018R2 installation and administration guide