To run ATK you need a license. You can try out the fully functional software with a demo/trial license for a period, but ultimately you need to buy a license to continue using it. This article explains some important concepts regarding the ATK licenses.
The license price depends on several things.
Please contact us to discuss these options and get some guidance what your optimal license configuration could look like, and we'll be very happy to provide a quotation.
As a customer of QuantumWise, you have access to free support via email (and some other benefits, like participation in user meetings etc) provided that you hold an active maintenance contract. During the maintenance period you may also upgrade, free of charge, to new versions of ATK.
Our license model does not care about which users have access to the software. It also doesn't put any limit on which computers that can run it, or whether you prefer to use Windows or Linux.
The only thing that is counted is the number of processes that can run concurrently. With 2 master licenses, at most 2 calculation jobs can be run at any given time; with 1 VNL license, one person can use the GUI at the time, and so on.
This is all handled by the license server, using a floating license technique. The license file itself is bound to the license server, but any computer that can connect to the license server can check out a license, until all features are checked out.
We normally issue all purchased licenses as floating. That means that a central server will handle the license, and any computer which can connect over the network to the server can check out a license and run the software.
In some special cases one can request to obtain a nodelocked license, which is constrained to running on a particular computer only. This is however not possible for parallel licenses.
You don't need any special license to take advantage of OpenMP threading on multicore computers.
To run ATK in parallel over MPI, on a cluster or a single machine, you need so-called slave licenses, in addition to the basic "master" license. Each master license allows one calculation to be executed at the time, and each slave license can add one more parallel MPI node to a calculation.
For more information on running ATK in parallel, see the Parallel Guide.
Upgrading to newer versions of ATK is free for users holding a valid maintenance contract. Often you just need to download and install the newer version, your license file should support it already. (This is only true if your license is already of the LM-X type for ATK 10.8 or later, and may not always be true even then. In any case, just contact us to get an updated license file!)
If you maintenance period has expired, please contact us for upgrade options.
No. ATK-DFT and ATK-SE are two different products. Thus, you need to purchase separate licenses for DFT and SemiEmpirical (the extended Hückel method). There is a significant discount for the second license if you already have one of them.
If you receive an updated standalone license file, for instance a prolonged demo/trial license, you don't need to reinstall the software. All you need to do is run the license configuration tool provided with ATK, as described in detail in the Installation Guide.
Note that on Linux it is necessary to log out and in again after changing the license setup, to get the Desktop icon to work with the new license configuration.
If you are running a license server and receive a new license file, the location of the license file should be obvious from the way the server is started. In this case, just replace the license file and restart the license server.
When you purchase a license file for the first time, most likely you are currently using a demo/trial license. On other occassions, we may send you a temporary standalone license file for testing or other purposes, when you are currently using a license server. In both cases, you need to switch the license configuration between floating and standalone.
The easiest way to do this is to use the license configuration tool provided with ATK, as described in detail in the Installation Guide.
There are two basic license types:
If you have a license server, but wish to use ATK/VNL on a computer which will not be connected to the network for a while, it is possible to borrow a license from the server.
If you want to use this feature, please contact QuantumWise, as it requires a change in your license file.
Once you have received an updated license file, follow the instructions below to borrow the license.
There are several troubleshooting tips in this FAQ for specific error messages. If you have a very general license problem, here are some tips that might lead to actually generating one of those error messages, or solve the issue in a simple way. It will also be much easier for us to help you troubleshoot the license problem if you go through these steps first and let us know the result.
To see how the license environment is currently set up, you can run the following commands in a terminal on Linux, or on Windows in Cygwin or similar:
echo $QUANTUM_LICENSE_PATHecho $QUANTUM_AUTOMATIC_SERVER_DISCOVERY
or on Windows (in a regular Windows "cmd" terminal):
echo %QUANTUM_LICENSE_PATH% echo %QUANTUM_AUTOMATIC_SERVER_DISCOVERY%
Alternatively, if ATK is installed on this machine, you can run
atk_license_config
and have a look at the first page after the startup screen - this will display the same information (and some more). This tool can also be used to change the license configuration.
If you think that the license variables are set correctly, you can check what licenses are available on the system by using (on Windows or Linux):
lmxendutil -licstat
This will report where ATK looks for licenses and what it found, and is particularly useful for checking floating licenses (when you are using a license server).
If you have a standalone license file, check that this file is readable by the current user, by using the following command:
cat $QUANTUM_LICENSE_PATH (Linux/Cygwin)type %QUANTUM_LICENSE_PATH% (Windows cmd)
If this doesn't produce the expected output (which is, that it prints out the contents of the license file), try
ls -l $QUANTUM_LICENSE_PATH (Linux/Cygwin)dir %QUANTUM_LICENSE_PATH% (Windows cmd)
This will show if the license file actually exists in the specified location. If it does, but you can't see it's contents - check the permissions of the file, maybe only root/Administrator can read it?
A lot of useful information about the license setup can be found in the Installation Guide and the LM-X End-User Guide, both of which are included in the ATK installation as well as available online.
When troubleshooting license problems, a very convenient tool is to define the environment variable QUANTUM_EXTENDEDLOG=license.log, then start ATK/VNL, and afterwards inspect the file license.log which will contain a detailed account of all license-related system settings, and very importantly how LM-X/ATK tried to locate a license (file or server) and whether or not it was successful.
If the license server refuses to start on Linux, check the output of
ldd lmx-serv-quantum
If you see something like
./lmx-serv-quantum: /lib64/tls/libc.so.6: version `GLIBC_2.4' not found (required by ./lmx-serv-quantum) libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000003ca4700000) libm.so.6 => /lib64/tls/libm.so.6 (0x0000003ca3f00000) libc.so.6 => /lib64/tls/libc.so.6 (0x0000003ca3c00000) /lib64/ld-linux-x86-64.so.2 (0x0000003ca3800000)
it means that this machine can not be used to run the license server, since it requires GLIC 2.4 or newer, and this machine uses GLIBC 2.3 (or lower).
ATK itself can however be run on any GLIBC version.
Normally ATK will locate active license servers automatically, as long as you are on the same network segment and there are no firewalls between your computer and the server. If there are firewalls which can't be opened for whatever reason, or you wish to access the license server remotely, e.g. from home or while traveling, a very convenient possibility is to set up an SSH tunnel to the license server.
By using a configuration file, it is possible to restrict access to the license features to certain computers, users, etc. The access is controlled using ALLOW and DENY statements, a bit like in a .htaccess file. The rules work a bit differently, however, so below we will present some simple examples to make it clearer.
If the error message
ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory
appears when you try to launch VNL, fix it by running
sudo apt-get install libjpeg62
This error typically appears on Ubuntu version 12.04 and later, where this library is not installed by default, as it was in earlier versions.
When running ATK on Windows 2008 Server edition (possibly also Windows 2010 Server), some users have experiened problems with the "side-by-side configuration". The error message reads:
The application has failed to start because its side-by-side configuration is incorrect.
To resolve this, download and install the relevant package in the list below:
Read More
If you get a segmentation fault while trying to run atkpython or vnl after installation, a solution might be to add the line
export LD_PRELOAD="libGLU.so libstdc++.so.6"
to your .bashrc file (in your home directory). We have seen this helps on Debian, Redhat 6.2, and a few other platforms.
If you get the error message "Command not found" when trying to run "vnl" or "atkpython" from a terminal window after installing ATK, then first of all try to close the terminal window and open a new one; this is needed for changes to the PATH and license environment variables to take effect.
If the problem persists, there are primarily two possibilities:
In both cases you need to restart the terminal for the changes to take effect. Check that the relevant ATK directories are in your PATH by typing "echo $PATH".
This should only appear on Linux. The solution is to log out and back in.
During installation, the license configuration is written to the file .profile in your home directory. The Desktop only reads this file on login, however.
If you prefer not to log out, for the moment, you can still launch VNL by opening a (new) terminal window and type "vnl".
On some Linux distributions, like OpenSUSE, the default version of the libpng library is different from what ATK needs.
The error message
OSError: libGL.so: cannot open shared object file: No such file or directory
may appear on Linux systems when you try to launch VNL for the first time. To solve it, create (as administrator) a new link in /usr/lib:
sudo ln -s /usr/lib/libGL.so.1.2 /usr/lib/libGL.so
If you have a 64-bit Linux, use /usr/lib64 instead.
First check that you actually have "libGL.so.1.2" in /usr/lib or /usr/lib64; it might be called "libGL.so.1" or something else instead, or located in another directory, depending on the video drivers. You can use
locate libGL
to find the correct file to link to.
When launching ATK for the first time, you may experience the following kind of error message:
QT ('Not available', '/home/user/atk/atkpython/lib/python2.6/site-packages/qtext.so: cannot restore segment prot after reloc: Permission denied')
The cause of this error are the new kernel security extensions from the Security-Enhanced Linux (SELinux) project, which are enabled in some newer Linux distributions, to allow finer-grained control over system security and shared library loading.
The solution is to register the relevant libraries in the security module to allow them to be relocated in memory. For each library for which the error appears, do
chcon -t texrel_shlib_t lib.so
where lib.so is the offending file.
On Ubuntu 12.04 and later, you may experience that the "Send To" button in VNL 12.8.0 only works once - after that it stops responding to clicks. To fix this, follow these steps.
Symptom: VNL has problems on Ubuntu, like fails to start up, or freezes immediately after startup, or is unable to show the 3D graphics windows properly.
Solution:
You may need to apply both - or only one - of these fixes, depending on your setup.
Notes
There are many reported problems on the incompatibility between compiz and Qt apps, so this is not something we can fix in VNL. See for example:
ATK 11.2 and higher is expected to run almost any newer Linux distribution, whether they use GLIBC 2.3 or 2.4. For ATK 10.8, there are however separate versions for GLIBC 2.3 and 2.4, so make sure to pick the relevant version for your platform.
The LM-X license server by default communicates on TCP and UDP port 6200. These ports must be opened on any firewalls separating the client and the license server. In practice, this is typically only an issue on Security-Enhanced Linux systems or if you have very strict firewall settings.
If you enter ATK in interactive mode (i.e., if you just type "atkpython" on the command line), you may be greeted with a rather lengthy message, asking you to "upgrade":
ImportError Traceback (most recent call last)/opt/QuantumWise/atk-10.8/atkpython/lib/site-packages/IPython/ipmaker.pyc in force_import(modname, force_reload) 61 reload(sys.modules[modname]) 62 else:---> 63 __import__(modname) 64 65ImportError: No module named ipy_user_confWARNING: /home/username/ipy_user_conf.py does not exist, please run %upgrade!WARNING: Loading of ipy_user_conf failed.
As the message suggests, enter the command (while you are still in ATK)
%upgrade
to resolve the issue.
The reason is that an existing configuration from a previous version of IPython (either an older ATK or another Python) exists for the user account. Upgrading in this way will not interfere with those older versions.
The symptoms of this error - which only should appear on Linux for ATK 10.8 - is that VNL launches fine, and you can open the Editor and Analyzer, but any attempt to open an instrument with a 3D viewport (like, the Builder, Viewer, Database, etc) results in VNL shutting down immediately.
If you are running from the command line, you will probably see a "Segmentation fault" error message.
The problem is caused by the video driver, specifically the OpenGL drivers, which doesn't support proper 3D manipulations. Most likely you are using Mesa drivers, which can be verified by running "glxinfo | grep -i mesa".
The solution is to upgrade to a newer version of ATK (11.2 or later), or upgrade your drivers to the vendor-specific ones from NVIDIA, ATI, etc, as relevant for your graphics card. The latter is always a good idea even for newer ATK versions, since it will enhance the 3D graphics performance significantly.
In principle, there is no limit on the system size, since ATK uses dynamic memory allocation. In practice, the system size is naturally limited by the amount of RAM on your computer.
The memory required for a specific calculation depends very strongly on parameters like method (DFT vs. extended Hückel), the number and type of atoms, the size of the unit cell, the mesh cut-off, the basis set, the number of k-points, FFT method vs. multigrid, and a few other parameters.
It should be possible to include between 500-1000 atoms with DFT if you have 8 Gb of RAM and don't use too high accuracy settings, and the FFT method. On the other hand, we have run an example with over 4,400 carbon atoms, using the Hückel method with multigrid; it allocated just below 14 Gb.
An important thing to note is that each MPI node uses the same amount of RAM. So if one assigns more than one MPI processes to the same node, the memory requirement goes up quickly on that node.
As a general rule, Atomistix ToolKit and the graphical user interface Virtual NanoLab runs on any "standard" Windows or Linux computer. The calculations, especially of large systems, can however consume a large amount of computational resources, so there are some special considerations to take into account.
Yes! In fact, on two levels: OpenMP threading on multicore processors, and over MPI on cluster. For more details, see the Parallel Guide.
We have collected a list of reference papers that discuss the basic concepts used in ATK.
Studies or publications where ATK has been used should include a reference to the version of the software, as well as to the most important methodology papers (naturally, XX.X below should be replaced with the actual version of ATK used):
If you are using the semi-empirical extended Hückel model in ATK, you should also refer to:
In cases where particular comments about the SIESTA basis sets or the general transport method are made, you may also want to include references to:
Yes, you can import (and in most cases also export) XYZ, CAR, CIF and VASP geometry files directly in ATK. More formats will be supported in the future - let us know which ones you would prefer!
If you see this error message in the license server logfile, please contact QuantumWise support. The licenses we issue do not by default support operation on virtual machines or terminal servers, but can be enabled to do so by request.
This error is very rare and only occurs for certain combinations of graphics cards and Linux distributions. A possible solution appears to be to by-pass the non-working drivers and use software 3D rendering, by writing in terminal before starting VNL
export LIBGL_ALWAYS_INDIRECT=true
The real solution would however be to get a better graphics card and/or proper OpenGL drivers (which however is not always possible for all Linux distributions and all cards).
The licenses we issue do not by default support operation on virtual machines or terminal servers, but can be enabled to do so by request. Please contact QuantumWise support.
You need a new license file, since the one which has been issued doesn't match the machine you are running on. Perhaps you switched network cards, or computer entirely. Please send us the output of
lmxendutil -hostid
This error can also appear when using a floating license server, in which case it will be seen in the log file.
This means the environment variable QUANTUM_LICENSE_PATH does not point correctly to the license file. The easiest way to fix this is to run the license configuration tool, select the "Standalone" option, and point it to the correct file.
The more complete error message looks like
*** glibc detected *** /opt/QuantumWise/atk-10.8.2/atkpython/bin/atkpython_exec: corrupted double-linked list: 0x00007f7141840000 ***> ======= Backtrace: =========> /lib/libc.so.6[0x7f71670019a8]> /lib/libc.so.6[0x7f7167004a9b]> /lib/libc.so.6(__libc_malloc+0x98)[0x7f7167005ad8]> /opt/QuantumWise/atk-10.8.2/atkpython/bin/../lib/libmkl_core.so(mkl_serv_allocate+0x182)[0x7f71646a4d8a]
This error can appear in the middle of a two-probe calculation if, at the same time,
There is an incompatibility, it seems, between hyperthreading and MKL. The solution is to either
If you are using the Job Manager to run a script which "imports" other scripts, the script to import must reside in the "home directory" of VNL, or in another directory that is part of the Python path.
The paths included by default in the Python path are "atkpython/lib/site-packages" (on Windows) or "atkpython/lib/python2.6/site-packages" (on Linux), inside the ATK installation directory, and the "home directory" which is the directory from where you started VNL (click the button "Home" in VNL to go to this directory). In case you used a desktop icon, the home directory is the "Start in" fold specified for the shortcut.
Thus, either move the script to be imported to a relevant folder from where it can be imported, or include the directory where the script resides explicitly in the Python path by inserting something like this in your script:
import syssys.path.append("c:/my files/scripts")
A simple solution is otherwise to run the script from the command line instead; as long as the script to be imported resides in the same directory as you are running from, it will work fine.
As a side note:
This is an indication of a problem with the geometry of the system. Perhaps atoms are too close to each other. Check the configuration carefully!
The full error message is
This application has requested the Runtime to terminate it in an unusual way.Please contact the application's support team for more information.
and although it can, in principle, mean many different things, most likely the calculation has requested more memory than is available on the computer.
This error should only appear in ATK 10.8. The solution is to upgrade to 11.2, or you can try to use the GLIBC 2.3 version of 10.8, even if you platform has GLIBC 2.4.
When running in parallel, sometimes you may see an error like
rank 1 in job 34 n7_3767 caused collective abort of all ranks exit status of rank 1: killed by signal 9
In most situations this is a case of "out of memory". Be careful not to run many MPI processes on the same node!
If you see this message when running
the license server is running, but doesn't have a valid license file.
Further information should be available in the license server logfile. Based on that, you can find further advise in this FAQ.
May appear when starting VNL 2008.10 on machines running Linux distributions configured for e.g. Korean or Chinese locale (language settings). To resolve this, insert the line
export LC_ALL=C
in your .bashrc file in your home directory. Restart the shell for the change to take effect.
This error sometimes appears when running ATK 10.8 in interactive mode. To solve it, upgrade to ATK 11.2.
It is important that the time zone and clock time on your computer is set correctly for the license system to operate properly. Ideally you should use a time server to periodically synchronize your clock automatically. Both Windows and Linux has easily accessible functions for this.
If for some reason the computer clock changes unpredictably by a large amount (changes to daylight savings etc are predictable, and do not cause problems), the license system can stop functioning, and you may encounter the error message
License Error: (Internal: 262 Context: -19996 Feature: VNL)(Err: 18) System clock has been set back
The immediate solution is to ensure that your clock and time zone is correctly set; this usually solves the problem, if not immediately then after a short while.
If the problem persists, it is possible to obtain a small utility from QuantumWise, which resets the clock data stored by the license system. This is however a last resort - and moreover the tool can only be used 3 times on a computer. Since usually the problem lies with the clock itself, it is not recommended to use this tool, but it can be provided on request.
First of all, you should only be using a license server if you have a floating license, which most likely you do if you have a purchased license, but otherwise you probably do not. Second, the license server must naturally be configured and started, before you can connect to it.
If you don't actually have a license server, the solution to this problem is thus to change the license configuration to standalone. The easiest way to do this is to run the tool atk_license_config from a terminal window (Linux or Windows); on Windows you can also use the shortcut "ATK License Configuration Utility" in the Start Menu (under Programs>QuantumWise>Atomistix ToolKit X.X>Utilities). In the license configuration utility, follow the instructions to choose the "Standalone" option and specify the location of the license file. See the Installation Guide for more details on managing the client license configuration.
If you do have a floating license, and a license server has been properly configured, the problem could simply be that the license server has been stopped; this is not least most likely the case if it used to work before, and now doesn't. If so, restart the license server and try again.
You can check for active license server on the network using the command
which works on both Linux and Windows.
It is also possible that the network connection between your computer and the license server is blocked by firewall rules.
This error message is unfortunate (but not under our control), as it is kind of inverted. The problem is, that the license you have is a floating network license, but you trying to use it as standalone. You need to configure and start a license server, using this license file, as described in the Installation Guide and then change the license environment setup on the client machine to "Floating".
Current ATK version:
12.8.2
(27 February 2013)
Visit the Forum
sheldrakes-bath
