Hi,
This error just means that the internal books library needs zlib and
bzlib2, and they don't appear to be on the system you're trying to
install Amber on. You can either install the necessary dev libraries
with 'apt-get install <library>' or you can try the attached script,
which will try to download and build some of the small common
libraries that Amber needs (I use this when I'm on a system where I
don't have root privileges); it will put them in a subdirectory from
wherever you execute it called AmberPrograms and print some info on
how to use it in cmake. Caveat emptor, it's been only minimally
tested, so if you have the ability to 'sudo' on your machine you might
just want to install the zlib/bzlib packages (I don't remember exactly
what they are on debian - maybe libz-dev and libbz2-dev?).
Good luck,
-Dan
On Fri, Mar 28, 2025 at 5:24 AM Russell Bertrand via AMBER
<amber.ambermd.org> wrote:
>
> Hi,
> I am trying to install Amber24 in my local machine running Debian-12. I am following the instruction from the manual. And I did no modification or added any argument to the run_cmake file. However, I am encountering the following error and I have no idea what it says. Could someone point me in right direction as to how to troubleshoot and solve this issue.
> Error trace:. . .-- Looking for boost::iostreams::bzip2_decompressor() and boost::iostreams::gzip_decompressor() in libboost_atomic.so.1.74.0 libboost_thread.so.1.74.0 libboost_system.so.1.74.0 libboost_program_options.so.1.74.0 libboost_iostreams.so.1.74.0 libboost_regex.so.1.74.0 libboost_chrono.so.1.74.0 libboost_timer.so.1.74.0 libboost_chrono.so.1.74.0 libboost_filesystem.so.1.74.0 libboost_regex.so.1.74.0 libboost_graph.so.1.74.0 - found
> -- Could NOT find MBX (missing: MBX_DIR)
> -- Could not find MBX. To locate it, add its install dir to the prefix path.
> -- Could NOT find tng_io (missing: tng_io_DIR)
> -- Could not find tng_io. To locate it, add its install dir to the prefix path.
> -- Could NOT find nlopt (missing: nlopt_LIBRARY nlopt_INCLUDE_DIR)
> -- Could not find nlopt. To locate it, add its install dir to the prefix path.
> -- Did not find external nlopt
> -- The following libraries were found on your system, but are not being used: boost
> -- This is because the Amber devs have frequently seen broken installs of these libraries causing trouble.
> -- To tell Amber to link to these libraries, you can select individual ones using -DFORCE_EXTERNAL_LIBS=<names>.
> -- Alternatively, you can request that Amber link to all libraries it finds using -DTRUST_SYSTEM_LIBS=TRUE.
> -- KMMD not added to 3RDPARTY_SUBDIRS :
> -- : ucpp-1.3;cpptraj/src/readline;fftw-3.3
> -- Cannot find PLUMED. You will still be able to load it at runtime. If you want to link it at build time, set PLUMED_ROOT to where you installed it.
> CMake Error at cmake/3rdPartyTools.cmake:1215 (message):
> Unable to build internal Boost without zlib and libbz2.
> Call Stack (most recent call first):
> CMakeLists.txt:218 (include)
>
>
> -- Configuring incomplete, errors occurred!
> See also "/home/russellb/extpacks/amber/amber24_src/build/CMakeFiles/CMakeOutput.log".
> See also "/home/russellb/extpacks/amber/amber24_src/build/CMakeFiles/CMakeError.log".
>
> If errors are reported, search for 'CMake Error' in the cmake.log file.
>
> If the cmake build report looks OK, you should now do the following:
>
> make install
> source /home/russellb/extpacks/amber/amber24/amber.sh
>
> Consider adding the last line to your login startup script, e.g. ~/.bashrc
> Could someone shed some light on this? Any help would be much appreciated.
> Thanks,
>
> Russell
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> AMBER.ambermd.org
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Received on Fri Mar 28 2025 - 06:30:02 PDT
