Hi Viktor,
It appears then that there's no fix currently available for the
anaconda version, is that correct? Is the only way to move forward to
recompile amber from source?
Thank you for your guidance,
Nate
On Fri, 2019-08-30 at 20:36 +0300, viktor drobot wrote:
> Hello! This problem was described some time ago (
>
https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.ambermd.org_201905_0050.html&d=DwIGaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=dOftBA5pGo8EYoQfiW-8eM4L1Wyjds69JkhEzUV6kWE&m=Nu7eiKQEQx22BWqt4JWSfQ_20elU1lrXM6yrLUB6sdE&s=gnM85BqN96Be4yRfO2q_pbwrtOPc3nnuRqZ2ji3-Tc4&e=
> )
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
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Received on Fri Aug 30 2019 - 11:00:03 PDT
