At this point we need more information. You should post your entire
cmake log (i.e. the complete output of cmake) along with the exact way
you invoked cmake.
-Dan
On Sat, Mar 29, 2025 at 4:13 AM Russell Bertrand <bertrussell23.yahoo.in> wrote:
>
> Hi Den,
>
> Thank you for the reply. I managed to install the dependencies that you have mentioned. And still no success. I still get the same error:
>
> m_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
>
> Any other way to look into this. I successfully installed Amber24 in one of my colleagues system without any issue last week which also runs Debian-12 which was also installed by me ^_^. Any other suggestion that I should try?
>
> Many thanks,
>
> Russell
>
>
> On Friday, March 28, 2025 at 06:55:02 PM GMT+5:30, Daniel Roe via AMBER <amber.ambermd.org> wrote:
>
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Mar 29 2025 - 08:30:02 PDT
