Amber masthead
Filler image AmberTools22 Amber22 Manuals Tutorials Force Fields Contacts History
Filler image

Useful links:

Amber Home
Download Amber
Installation
MacOS
Windows
CentOS
Debian
Fedora
OpenSuse
Ubuntu
Arch/Manjaro
Containers
FAQ
Amber Citations
GPU Support
Updates
Mailing Lists
For Educators
File Formats

Frequently Asked Installation Questions




General Questions


How should I use this FAQ?

While straight reading of this FAQ can be useful, after the installation process is started our intention is that installers will search the FAQ using a verbatim error message and follow the answer's advice.


Where are the directions for installing Amber?

Shortcuts for getting Amber installed on popular Operating Systems (OSs) are listed under the "Installation" section in the web site table of contents on the left. For more details, see Chapter 2 of the Amber 2022 Reference Manual.


What should I do if I do not have the authority to install packages?

Many installers of Amber can install its prerequsites using their OS's package management tool; see the links listed under the "Installation" section in the web site table of contents on the left for details. However, some users may not have the access, authority, or privilege necessary to use these OS package management tools. Examples of such users are those at computing centers or at university computing laboratories. Of course, the prerequisites can be installed from scratch by downloading, reading the instructions, etc. But there are two much simpler approaches to try first.

The software may already be installed. Many computing platforms use modules to manage software; enter this command to search the software space, e.g.:

module spider boost

Generally, particular compilers, MPIs, etc. form what's called a software stack. You should try to find a stack that has all the tools you need. This command can help by showing what is available given the currently loaded modules:

module available

When you find what you need then load the modules, e.g.:

module load boost

You may need to specify a particular version. Finally, verify you have what you want with this command:

module list


Second, the software may be easily installed using an OS independent package manager such as conda or pip. Generally, computing centers have a python distribution module based on anaconda or miniconda. Load such a module and use conda to install a missing prerequisite, e.g.:

module load anaconda
conda install -c conda-forge bzip2

Should I upgrade to the current release?

In general, yes. In particular, bug fixes and basic improvements will make the upgrade worthwhile even if the new functionalities are not desired.


What if I have a question that is not answered here or in the manual?

You can join the Amber Users' Mail Reflector to contact other people who are also interested in Amber. Please search the archives before asking your question.



CMake Questions


3rd party program boost is required to build Amber, but it is disabled

This error is usually caused by some other missing prerequisite since Boost can be built during the Amber installation. So look at the previous messages in the cmake output or log.


Unable to build internal Boost without zlib and libbz2

This is usually caused by a missing BZip2 library. Verify that by searching for this text in the cmake output or log: Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR) And if found then follow that link for remediation.


Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)

This is usually caused by a missing prerequisite. Use the links listed under the "Installation" section in the web site table of contents on the left to learn how to meet this requirement. For users that do Not have the privilege to install software packages, see What should I do if I do not have the authority to install packages? for suggestions.


"How's that for maxed out?"

Last modified: Apr 27, 2022