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Electrostatics / apbs

Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
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Linking issue with using pre-compiled binaries #79

Open xiki-tempula opened 4 years ago

xiki-tempula commented 4 years ago

Describe the bug I want to use the pre-compiled binary on osx and ubuntu

To Reproduce I downloaded the APBS-3.0.0 release APBS-3.0.0_Linux.zip and APBS-3.0.0_OSX-Darwin.zip

However, in the ubuntu platform, I got 

(base) XXX@XXX:~/APBS-3.0.0.Linux/bin$ ./apbs 
./apbs: error while loading shared libraries: libTABIPBlib.so: cannot open shared object file: No such file or directory

In the OSX platform 10.15.6, I got

(base) XXXX:bin XXX$ ./apbs dyld: Library not loaded: @rpath/libTABIPBlib.dylib Referenced from: /Users/XXX/Desktop/APBS-3.0.0.Darwin/bin/./apbs Reason: image not found Abort trap: 6

Expected behavior The software runs.

sobolevnrm commented 4 years ago

@xiki-tempula -- can you please tell us which version of Ubuntu you're using?

@intendo -- can you please help with this?

Thanks!

xiki-tempula commented 4 years ago

Ubuntu 18.04.4 LTS (GNU/Linux 5.4.0-47-generic x86_64)

ashermancinelli commented 4 years ago

Is the library in the lib directories of the tarball, and have you set your ld path accordingly?

intendo commented 4 years ago

@ashermancinelli I don't know that using LD_LIBRARY_PATH or LD_RUN_PATHwill fix the problem because of the missing libraries like libgomp.so and others provide by the compilers.

@xiki-tempula you may be able to run ldd ./apbs and see all the unresolved libraries and see if they exist on your system. You may have to install the GCC 9.2 compiler and developer packages to get all the missing libraries. If you can find them all, then you can use LD_LIBRARY_PATH to resolve all of them.

We are working on restructuring the code base to resolve all the external dependencies and create a new release.