[AMBER] Bug in ambpdb in anaconda distribution?

From: Nathan Guerin <nguerin.cs.duke.edu>
Date: Fri, 30 Aug 2019 13:27:17 -0400


I've installed ambertools using the anaconda method, and most of
binaries I've run have workd well. I did find what appears to be a bug
in the ambpdb program though. When I run ambpdb, I get the following

ambpdb: error while loading shared libraries:
bld/ambertools_1556345835936/work/lib/libcpptraj.so: cannot open shared
object file: No such file or directory

When I run ldd on the binary to show where it's resolving the dynamic
libraries to, what I find is:

(base) ➜ anaconda3 ldd `which ambpdb`
        linux-vdso.so.1 (0x00007ffd67b30000)
bld/ambertools_1556345835936/work/lib/libcpptraj.so => not found
        libstdc++.so.6 =>
/var/tmp/local/anaconda3/bin/../lib/libstdc++.so.6 (0x00007fc146eaa000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6
        libgcc_s.so.1 =>
/var/tmp/local/anaconda3/bin/../lib/libgcc_s.so.1 (0x00007fc146e34000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6
        /lib64/ld-linux-x86-64.so.2 (0x00007fc146df9000)

This is in contrast to how libcpptraj.so is linked on another machine
where I've built amber from the source code:

nsg.asteroids ~> ldd (which ambpdb)
        linux-vdso.so.1 (0x00007ffdb4b55000)
        /home/nsg/bin/amber18/lib/libcpptraj.so (0x00007f250e321000)
        libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f250e0ff000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f250dfb9000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f250df9f000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f250ddd9000)
        libgfortran.so.5 => /lib64/libgfortran.so.5
        libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f250db24000)
        libz.so.1 => /lib64/libz.so.1 (0x00007f250db0a000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f250eb46000)
        libquadmath.so.0 => /lib64/libquadmath.so.0

The library in question is present in the anaconda install:

(base) ➜ anaconda3 ls -l lib/*cpptr*
-rwxrwxr-x 2 nguerin nguerin 9128451 Apr 27 02:52 lib/libcpptraj.so

But ambpdb just isn't using it.

Thanks for any help or guidance you may be able to give!

Best regards,
Nate Guerin

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Received on Fri Aug 30 2019 - 10:30:02 PDT
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