One way until there is a new build to fix this particular instance is
to use the patchelf command to remove the offending *.so and add the
one that's shipped with the library.
(base) ➜ anaconda3 patchelf --remove-needed
/home/haichit/miniconda3/conda-
bld/ambertools_1556345835936/work/lib/libcpptraj.so ambpdb
(base) ➜ anaconda3 ldd
ambpdb
linux-vdso.so.1 (0x00007ffd5e8ea000)
libstdc++.so.6 => /var/tmp/local/anaconda3/lib/libstdc++.so.6
(0x00007fadfb4cf000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6
(0x00007fadfb080000)
libgcc_s.so.1 => /var/tmp/local/anaconda3/lib/libgcc_s.so.1
(0x00007fadfb459000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6
(0x00007fadfac8f000)
/lib64/ld-linux-x86-64.so.2 (0x00007fadfb41e000)
(base) ➜ anaconda3 patchelf --add-needed $PWD/lib/libcpptraj.so ambpdb
(base) ➜ anaconda3 ldd ambpdb
linux-vdso.so.1 (0x00007ffe176be000)
/var/tmp/local/anaconda3/lib/libcpptraj.so (0x00007f8f0016a000)
libstdc++.so.6 => /var/tmp/local/anaconda3/lib/libstdc++.so.6
(0x00007f8f00c3e000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6
(0x00007f8effdcc000)
libgcc_s.so.1 => /var/tmp/local/anaconda3/lib/libgcc_s.so.1
(0x00007f8f00bc8000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6
(0x00007f8eff9db000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3
(0x00007f8eff6aa000)
libbz2.so.1 => /lib/x86_64-linux-gnu/libbz2.so.1
(0x00007f8eff49a000)
libz.so.1 => /var/tmp/local/anaconda3/lib/./libz.so.1
(0x00007f8eff47a000)
/lib64/ld-linux-x86-64.so.2 (0x00007f8f00b8d000)
libquadmath.so.0 =>
/var/tmp/local/anaconda3/lib/./libquadmath.so.0 (0x00007f8eff440000)
Hope this helps someone in the future,
Nate Guerin
On Fri, 2019-08-30 at 13:42 -0400, Nathan Guerin wrote:
> 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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> > >
> >
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> >
>
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Received on Fri Aug 30 2019 - 11:00:03 PDT
