Installing and Running

Questions

• I placed a purchase order for ADF. What happens next?
• What files should I download?
• What platforms are supported?
• Where do I find documentation?
• What is the latest version of ADF, ADF-GUI or BAND?
• Where do I download the ADF-GUI?

• Do I need a compiler to install ADF?
• How do I install ADF and BAND?
• How do I install the ADF-GUI?
• How much disk space does ADF require?
• How much memory does ADF require?
• If we choose to install PVM or MPI later, can we change the installation type while maintaining the same license file?
• I have a recent Linux version. Will ADF work?
• Are there known issues with SuSE Linux 9.x on 64 bit AMD processors?
• ADF-GUI does not work on my computer. What to do?

• How do I get a license file for my machine?
• Why do I get a message: LICENSE INVALID?
• Why do I get a message: LICENSE CORRUPT?
• How do I contact SCM with license questions?

• How do I run an ADF or BAND job?
• Problem with first ADF job: "no key found. QSTORE"
• Very long delays while starting ADF, sometimes on some nodes only
• libpvm [pidXXXX] /tmp/pvmd.xxxx: No such file or directory
• WARNING: FILE ALREADY EXISTED
• I tried an ADF calculation but some files are gone
• How do I use the examples on Windows?

• How can I visualize the results from ADF?
• How do I use the ADF-GUI?

• Is there an ADF mailing list?
• How do I get support from SCM?

Answers

After you have placed an (informal) purchase order for ADF, either by filling out the Purchase Order form or by contacting SCM directly at sales@scm.com, we only need a signed License Agreement from you before we can give you access to the software on our website. The signed license agreement should be faxed to SCM. Then you will receive a download username and password that allows you to download files from the Download section of our website.

The main Downloads page contains an overview of the versions that are available for your platform. We strongly recommend that you download the most recent version, which is the only supported one. This page contains a link to the most recent version. Different types of files are available for download:

• AtomicData: this contains platform independent files that are always needed,
  such as basis sets and force fields. should always be downloaded.
• Examples: this file contains a variety of input and output files for
  ADF, BAND, and property and Utility programs. Strongly recommended to download always,
  although not strictly necessary for proper execution of the program.
• Source: the (major part of) the source code for ADF and BAND.
  Can only be downloaded if the source code is included in your license.
  This file is also platform independent. Is needed if you wish to compile the program yourself.
• Executables: Always recommended for download, even if you also have the source.
  The files contain the executables for a particular platform.
• Install: these are needed only in case you have the source code.
  In that case they are necessary for building your own executables.

Basically all currently popular computer platforms are supported:

• Linux
• Windows
• Mac OS X
• Many UNIX varieties

The installation manual, the various User's Guides, tutorials, documented examples and literature references can all be downloaded from the Documentation section of the website.

At this moment (May 2006), ADF2006.01 is the latest version. Any new version will be announced when ready.

The ADF-GUI executables are included in the exec.*.tar.gz file that contains also the ADF executables, so no additional action is needed. The executables for the ADF-GUI modules in version ADF2006.01 include $ADFHOME/bin/adfinput(.exe) and adfview(.exe).

No. The basic ADF license refers to a version with pre-compiled executables. This means that you only have to unpack the executables provided by SCM and that you do not have to compile them yourself.
However, if you have obtained a license that includes also the source code, you will in principle need (exactly) the same compiler as was used by SCM. Details on the used Fortran and C compilers and their version numbers are available on the Downloads page.

A summary of the Installation instructions is available on the Download page of the version you wish to use. Full installation instruction are available in the Installation Manual. We strongly recommend that you read this document before installing ADF. Incorrect installation of ADF may for example result in inefficient execution of the executables.

Simply unpacking the executables for ADF will also unpack the executables for ADF-GUI. These are immediately ready for use, provided that your license file includes an entry for the ADF-GUI for the machine where you wish to use it. The ADFview and ADFinput tutorials help you on your way with the ADF-GUI.

A few GB are enough for almost all types of ADF calculations. In case of a parallel calculation most files on a node become smaller. This may help to circumvent the 2 GB file limit that may occur for certain very large ADF calculations on a single CPU of a Linux cluster.
BAND uses more disk space than ADF. This can amount to more than 10 GB for large calculations. Because BAND can split its files, it does not suffer from file size limits. Both ADF and BAND have possibilities to limit the amount of I/O by keeping (part of the) files in memory.

ADF does not require more than 256 MB if you are treating medium-sized molecules, say up to 50 atoms. If your molecules are too large, the calculation simply will not fit in memory. If you have 512 MB or 1 GB memory available per CPU, very large ADF and BAND calculations are possible.

Yes, the license file only contains information on the machines on which you wish to use the software, not on how you configure your ADF installation.

In principle, the ADF package is only guaranteed to work if you are using the same operating system as was used when SCM built the executables. This remains true if you have the source code. However, the ADF2003.01 was produced in such a way that it will work on a variety of Linux platforms. In some cases problems were observed with Redhat 9.0, Suse 8.2 or similar versions. In all those cases, the problems could be solved by using our dynamically linked executables instead. In that case you will also need to download the dynamical libraries from the Portland group for portability.
Separately compiled versions for Redhat 7 and Redhat 9 are available for adf2006.01, which should run out of the box.

There are issues with 32-bit glibc 2.3.2 on the x86_64 platform. The origin is not yet known. On some bigger jobs, ADF crashes with SIGSEGV in the pthread_mutex_trylock() function called from malloc(). If you get this error, the work-around is to add "export MALLOC_CHECK_=0" to $ADFBIN/start and $ADFBIN/adfs. If you have a better solution for this, please contact support@scm.com.

Unfortunately, the choice of platforms on which we can support the GUI (as well as ADF itself) is limited. But the good news is: you can compile ADF-GUI yourself. This option involves some work but it gives the best result. I'll try to explain how to compile ADF-GUI on your platform.

1. Download and unpack ADF source distribution
2. Download and unpack ADF binary distribution for your platform on top of the source.
3. Configure and compile serial version of ADF as you would normally do.
4. If you have cmake version 2+ installed, skip to step 9.
5. Untar Install/cmake*.tgz in ADFHOME
6. cd to the cmake source directory created in the previous step.
7. Run ./configure (pay attention to the --prefix option if you're installing it in a non-default location)
8. Run "make" followed by "make install".
9. Untar Install/vtk.tgz in $ADFHOME
10. Copy Install//CMakeCache.txt to VTK/CMakeCache.txt
11. Edit VTK/CMakeCache.txt in the parts containing path names
12. Run "cmake ." followed by "make" and watch the show. Compilation may take a few hours depending on the computer speed.
13. Run "make install". You should have a new ADF-GUI working now.

In order to use ADF, BAND, and the ADF-GUI you will need a license file from SCM. This license file will contain an end date and machine information. The machine information that SCM needs is produced by ADF if you execute it on the machine where you want to use it. In order to obtain the license file, you need to send this ADF output to admin@scm.com. The Installation manual explains how to perform your first ADF calculation.

ADF checks the file with the name given by the environment variable $SCMLICENSE which is best defined in your login shell. With the command "cat $SCMLICENSE" you can inspect its contents and compare it to the output of ADF. A license can be invalid for the following reasons:

• The machine you are running on is not listed in the license file (or the IDs do not match any longer).
• The version number in the license file is lower than the version number of your ADF version.
• You have a valid license file for some parts of our software (e.g. ADF) but not for others (e.g. ADF-GUI or BAND).
• The date in the license file (in the format MM/DD/YYYY) has past.
• Wrong newline characters in the license file, see answer to the LICENSE CORRUPT message.

It may be that your mail program affects the license file (especially the newline characters), or that you have modified it incorrectly by hand. This may cause the LICENSE CORRUPT message. Please try the fixlic and fix_license utilities in $ADFHOME/bin as explained in the installation manual that is available on our website. If that does not help, please notify SCM (support@scm.com), so we can have a closer look (this can always be easily solved).

Use the E-mail address admin@scm.com for any questions related to license files.

Many example run files are available in $ADFHOME/examples/adf and band. If you have a serial or PVM version, typing ./run in, for example, $ADFHOME/examples/adf/e_GO_H2O will execute a geometry optimization for water. The ADFinput module of the ADF-GUI will help you in setting up a similar run file for your own favorite molecule and type of calculation. If the ADF-GUI is not included in your license, you can use the run files in the $ADFHOME/examples directory as a starting point for your own calculations. The available options are described in the ADF User's Guide and other documents available for the Documentation section of the website.
For submitting an ADF or BAND job to a queuing system of a parallel machine: contact your system administrator.

The run files in the example directories are UNIX scripts, not ADF input files. If you try to use these as input for ADF one can get the QSTORE error. To execute the examples, do something like:
$ADFHOME/examples/adf/e_GO_H2O/run > out
(and not adf < run).

The license code tries to establish in which domain the current machine is located. This is accomplished by querying an external nameserver. If your machine is a stand alone machine, but somehow it thinks it is connected to a nameserver, the license code will try but never gets an answer. Thus it waits for a timeout. The same situation occurs when the machine can not reach the nameserver. This might happen when it is behind a gateway or firewall, depending on the configuration. Thus please make sure that you have not set a nameserver to be used for this machine (in /etc/resolv.conf), or make sure that the nameserver you have set can be reached.

The error messages starting with libpvm could be normal: it tells that ADF does not succeed in trying to run in parallel. ADF will next continue to run as a serial program. Ignore the error messages you may get from PVM if you are running on one processor. (For serial execution, PVM does not have to be installed.)

The WARNING: FILE ALREADY EXISTED means that not all files from the previous ADF calculation were cleaned up. To avoid this, it is easiest to start an ADF calculation in an empty directory.

The run scripts in the examples directory of the ADF2003.01 release contain certain rm commands to clean up after an ADF calculation is finished. On certain recent Linux versions, the defaults for the interpretation of the rm command have changed, with a result that more files may be removed than intended. The solution to this issue is to make sure that the value for the LC_COLLATE="C" (you can inspect the current value with the command "locale").
In adf2004.01 and later versions these rm commands are not present anymore in the example files.

There are two files for each example: run and outpt. The file called 'run' is a shell script that can be executed using sh.exe provided with ADF and 'outpt' is an example output file for comparison. The intention is that one can execute the 'run' file to test if one's ADF installation works correctly or, more commonly, one can create one's own task by modifying one of the examples.
Windows users unfamiliar with the command line shells (in this case bash) might need two extra steps. Simply rename the 'run' file to a file with the .run extension and you get a file executable from the Windows Explorer. For example, rename the run file in the e_GO_H2O folder to GO_H2O.run and you should see its icon change indicating that it's now a runnable file.

But this is not enough because if you double click on the file the output will be printed on the screen and will be lost after the calculation ends and the window disappears. In order to save the output one needs to redirect it to a file. To do this, open the file in a text editor but not in Notepad becase Notepad does not understand Unix-style text files. WordPad works perfectly. Replace the first occurence of $ADFBIN/<program name> <<eor to something like $ADFBIN/<program name> <<eor > example.out and all subsequent occurences to $ADFBIN/<program name> <<eor >> example.out. In this way, all output will be collected in the example.out file. We plan to change the example files in a future release so this additional step will no longer be required.

The easiest and recommended way is to use the modules of the ADF-GUI. With the adf2004.01 and later versions, the ADFview module is available for visualizing orbitals, densities, potentials, and other data fields, ADFmovie is available for following the movements of the nuclei (e.g. during geometry optimization or for vibrational normal mode) and ADFspectra is available for visualization of certain types of spectra (e.g. infrared or optical).

There are two clear and easy-to-follow tutorials for ADFinput and ADFview that provide a hands-on introduction to running ADF jobs and visualizing results. The tutorials can be downloaded from the Documentation part of the website.

Yes. The ADF mailing list is a platform for communication between users about the practical use of ADF. SCM may also comment on posting to the ADF-list and post advice on ADF usage that is expected to be of broad interest among ADF users. SCM strongly advise all active ADF users to subscribe to the mailing list (see our web site: http://www.scm.com/Other/adflist.html). The mailing list is not used for sending error reports to SCM (for which you can mail to support@scm.com).

You can send an E-mail to support@scm.com for all types of support questions: technical or scientific - although there may be cases where we have no answer to the latter type of question.
If you believe you have encountered a bug in the software, or otherwise undesirable behavior, please use this E-mail address as well, and provide as many details as you can, including version of ADF used, reproducibility of the problem, number of CPUs used in the calculation, type of machine and operating system.