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 2024 Reference Manual.
What should I do if I do not have the authority to install packages?
Many installers of Amber can install its prerequisites 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.
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