Hello! This problem was described some time ago (
http://archive.ambermd.org/201905/0050.html)
The cause is erroneous linking of libcpptraj.so in Makefile. Watch out: in
both cases (anaconda build or your own) you have hardcoded full name of
library, not the base name.
пт, 30 авг. 2019 г., 20:27 Nathan Guerin <nguerin.cs.duke.edu>:
> Hello,
>
> 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
> error:
>
> ====================================
> ambpdb: error while loading shared libraries:
> /home/haichit/miniconda3/conda-
> 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)
> /home/haichit/miniconda3/conda-
> 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
> (0x00007fc146a5b000)
> 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
> (0x00007fc14666a000)
> /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
> (0x00007f250db3a000)
> 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
> (0x00007f250dac0000)
> ======================================
>
> 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 - 11:00:02 PDT
