I recently got APBS to finally work on my rMBP (Mavericks installed). It took a lot to fiddle with, but here is a description of what I did to get it working. I’m no computer expert by any means, but google helped me through this process. All in all it took about 3 hours to get fully installed. I apologize if I left something out or if people feel this is incorrect. But it worked for me. The instructions and files are listed below.
First switch to macpolhybrid if you haven’t alreadymake sure you have Xcode installed and that command line tools are installedrun this in terminal to update command line tools
a GUI will open up and click install
you may also have to make sure you have the Developer package of Xcode installed. Run it regardless to be sure.
xcode-select —switch /your/path/to/Xcode.app/Contents/Developer
Make sure you point to the correct location of your Xcode.app
Now install fink (this takes quite a while)<pymolapbsplugin-code-28-trunk.zip>put fink in a location that you want to stay /your/path/to/Programs for example.open terminal where the tar ball is.run these commandstar -xvf fink-0.36.0.tarcd fink-0.36.0./bootstrap/sw/bin/pathsetup.shquit terminal and reopen terminal to update fink (your environment for fink should now be set up)fink selfupdate-rsyncfink index -fnow you have finkopen terminal and runfink install apbs(you may run into python27 issues. if this happens , open terminal run: fink install python27 Another thing that may be an issue is changing fink to the ‘unstable’ version, it didn’t happen to me but if it does there is a website that can be used to change to the unstable release)this will put the proper binaries and other things for apbs into /sw directorynext install this plugin for apbs into pymolthe apbsplugin.py file is in the /src folderthe plugin gui should automatically scan to find the binaries for the plugin.you can also run pdq2pqr locally on the mac too (instead of using the server) and use it with the apbs plugin prior to ‘set the grid’open terminal and runfink install pdb2pqrthis takes a long time alsoGood luck!ryanuniversity of cincinnatiOn Nov 13, 2013, at 10:38 AM, Baker, Nathan <Nathan.Baker@pnnl.gov> wrote:------------------------------------------------------------------------------Hi Sarah –I’m adding Keith Fligg to this email to see if he can work with Andrew to help fix the problem.Thank you,--Nathan BakerLaboratory FellowPacific Northwest National Laboratory+1-509-375-3997From: Sarah Witzke [mailto:firstname.lastname@example.org]
Sent: Tuesday, November 12, 2013 12:03 PM
Cc: Baker, Nathan; Aaron Oakley; email@example.com; Stevens, Andrew J (PNNL)
Subject: Re: [apbs-users] running apbs on OS X 10.8
I am having the same problems as Aaron when I try to install APBS on OS 10.8.5.Instead i downloaded the code from the git tree as suggested by Andrew.I followed the steps in the file "buildWith FETK.sh", but for the lines "cp -r build/x86_64-unknown-linux-gnu/include/ ." and "cp -r build/x86_64-unknown-linux-gnu/lib/ ." I replaced "unknown-linux-gnu" with "apple-darwin12.5.0".Then "cd ../build" and cmake -DENABLE_FETK=YES -DBUILD_SHARED_LIBS=YES ..This produced an error about not being able to extract contrib/tabibp - which makes sense, since tabibp is not included in the "contrib" folder.I downloaded the tabipb code myself and put tabipb.exe in contrib/tabibpThen I ran the cmake command again, which this time ran smoothly (except not installing the openmpi, which I do not need) - the last couple of lines of output is:*****------ -L/Users/witzke/apbs_test/apbs-code/lib -lapbs_geoflow;-lm;-L/Users/witzke/apbs_test/apbs-code/lib -L/opt/local/lib/gcc47 -lgfortran -ltabipb;-lmaloc;-lstdc++;-L/Users/witzke/apbs_test/apbs-code/fetk/lib;-lamd;-lpunc;-lmc;-lgamer;-lsuperlu;-lumfpack;-lblas;-lvf2c;-ltetgen;-ltriangle;-lg2c;-lreadline apbs_generic;apbs_pmgc;apbs_mg;apbs_geoflow;apbs_fem---- -std=c99-- Supplemental tools enabled-- Building mesh-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem-- Building manip-- libraries: apbs_generic;apbs_mg;apbs_pmgc;apbs_fem-- Configuring done-- Generating done-- Build files have been written to: /Users/witzke/apbs_test/apbs-code/build*****
Unfortunately however, when I type "make" I get this:*****[ 6%] Performing configure step for 'tabipb'CMake Error: The source directory "/Users/witzke/apbs_test/apbs-code/build/tabipb-prefix/src/tabipb" does not appear to contain CMakeLists.txt.Specify --help for usage, or press the help button on the CMake GUI.make: *** [tabipb-prefix/src/tabipb-stamp/tabipb-configure] Error 1make: *** [CMakeFiles/tabipb.dir/all] Error 2make: *** [all] Error 2****
I am not very good with compiling/installation/etc and I apologize if I have made stupid mistakes or should have known better, but I have spent very long time and am completely stuck now.Any help is greatly appreciated.
Kind regards,Sarah Witzke
Den lørdag den 17. august 2013 01.54.22 UTC+2 skrev Stevens, Andrew J (PNNL):Hi Aaron,What build system are you using (Xcode or gcc version)?You can also try compiling the git repository version instead of the release version:git clone http://git.code.sf.net/p/apbs/code apbs-codeBut it will take some time to download.Thanks,AndrewHi Aaron,I'm sorry about the problems you've experienced. Andrew, can you please help?Thanks,Nathan
On Aug 15, 2013, at 18:26, "Aaron Oakley" <aar...@uow.edu.au> wrote:Hi all,I just installed the latest distribution of APBS for OS X (APBS-1.4-osx).On the first attempt to execute I got:dyld: Library not loaded: libmaloc.dylibReferenced from: /usr/local/APBS-1.4-osx/bin/apbsReason: image not foundTrace/BPT trap: 5...so I updated the DYLD_LIBRARY_PATH environmental variable to include /usr/local/APBS-1.4-osx/libNow I get:dyld: Library not loaded: /usr/lib/libmpi_cxx.0.dylibReferenced from: /usr/local/APBS-1.4-osx/bin/apbsReason: image not foundTrace/BPT trap: 5Any help appreciated.a++------------------------------------------------------------------------------
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