[AMBER] AmberTools hardcodes library names into binaries

From: viktor drobot <linux776.gmail.com>
Date: Sat, 4 May 2019 13:57:57 +0300

Hi all!

For the sake of convenience I'm creating package with AmberTools
software so it can be easily built everywhere. The problem is that some
software inside AmberTools package hardcodes libraries inside final
executables. For example, yesterday I noticed that ambpdb utility can't
be run because of missing library (even after loading AmberTools
modulefile which sets up proper LD_LIBRARY_PATH). ldd gives the
following for this binary:

[viktor.desolve-lab /opt/ambertools/bin]$ ldd ambpdb
     linux-vdso.so.1 (0x00007ffc33795000)
/opt/buildcache/makepkg/ambertools/src/amber18/lib/libcpptraj.so => not
found
     libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x000014b691895000)
     libm.so.6 => /usr/lib/libm.so.6 (0x000014b69174f000)
     libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x000014b691735000)
     libc.so.6 => /usr/lib/libc.so.6 (0x000014b691570000)
     /lib64/ld-linux-x86-64.so.2 => /usr/lib64/ld-linux-x86-64.so.2
(0x000014b691a87000)

need to say: package manager used (makepkg on Arch Linux) performs all
compiling operations inside its' own temporary directory and then moves
files in place. So, as you can see, ambpdb is linked against
full-specified path of libcpptraj.so instead of just libcpptraj.so
without full path. So when I trying to start ambpdb then I get the
following error:

[viktor.desolve-lab /tmp]$ ambpdb
ambpdb: error while loading shared libraries:
/opt/buildcache/makepkg/ambertools/src/amber18/lib/libcpptraj.so: cannot
open shared object file: No such file or directory

However, LD_LIBRARY_PATH is set up correctly:

[viktor.desolve-lab /tmp]$ echo $LD_LIBRARY_PATH
/opt/ambertools/lib

I digged a bit with source code and found that the problem is related to
the Makefile of ambpdb. Seems like libcpptraj.so is fed directly to the
linker with full path like simple object. If I change linking line and
then manually rebuild ambdpdb submodule then library dependencies are
working fine:

--- AmberTools/src/ambpdb/Makefile    2019-04-25 15:49:55.000000000 +0300
+++ AmberTools/src/ambpdb/Makefile 2019-05-03 18:13:21.416508507 +0300
.@ -26,7 +26,7 @@

  ambpdb: $(AMBPDB_OBJECTS) $(LIBCPPTRAJ)
      .echo "[AMBPDB]  CXX $@"
-    $(VB)$(CXX) -o ambpdb$(SFX) $(AMBPDB_OBJECTS) $(LIBCPPTRAJ) $(LDFLAGS)
+    $(VB)$(CXX) -o ambpdb$(SFX) $(AMBPDB_OBJECTS) $(LDFLAGS)
-L"/home/viktor/build/src/amber18/lib" -lcpptraj


  # Build rules

Now ldd deps looks fine:

[viktor.desolve-lab /tmp]$ ldd ambpdb
     linux-vdso.so.1 (0x00007fff7c5c0000)
     libcpptraj.so => not found
     libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x000014ff46390000)
     libm.so.6 => /usr/lib/libm.so.6 (0x000014ff4624a000)
     libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x000014ff46230000)
     libc.so.6 => /usr/lib/libc.so.6 (0x000014ff4606b000)
     /lib64/ld-linux-x86-64.so.2 => /usr/lib64/ld-linux-x86-64.so.2
(0x000014ff46582000)

And when I load AmberTools modulefile I get proper library dependencies
list:

[viktor.desolve-lab /tmp]$ module load ambertools/19
[viktor.desolve-lab /tmp]$ ldd ambpdb
     linux-vdso.so.1 (0x00007ffff413f000)
     libcpptraj.so => /opt/ambertools/lib/libcpptraj.so (0x0000151f9602f000)
     libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0000151f95e4a000)
     libm.so.6 => /usr/lib/libm.so.6 (0x0000151f95d04000)
     libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x0000151f95cea000)
     libc.so.6 => /usr/lib/libc.so.6 (0x0000151f95b25000)
     libgfortran.so.5 => /usr/lib/libgfortran.so.5 (0x0000151f958a9000)
     libnetcdf.so.15 => /usr/lib/libnetcdf.so.15 (0x0000151f95757000)
     libbz2.so.1.0 => /usr/lib/libbz2.so.1.0 (0x0000151f95744000)
     libz.so.1 => /usr/lib/libz.so.1 (0x0000151f9552d000)
     /lib64/ld-linux-x86-64.so.2 => /usr/lib64/ld-linux-x86-64.so.2
(0x0000151f96799000)
     libquadmath.so.0 => /usr/lib/../lib/libquadmath.so.0
(0x0000151f954ea000)
     libhdf5_hl.so.100 => /usr/lib/libhdf5_hl.so.100 (0x0000151f954c5000)
     libhdf5.so.103 => /usr/lib/libhdf5.so.103 (0x0000151f95142000)
     libcurl.so.4 => /usr/lib/libcurl.so.4 (0x0000151f950b3000)
     libsz.so.2 => /usr/lib/libsz.so.2 (0x0000151f94eb0000)
     libdl.so.2 => /usr/lib/libdl.so.2 (0x0000151f94eab000)
     libnghttp2.so.14 => /usr/lib/libnghttp2.so.14 (0x0000151f94e83000)
     libidn2.so.0 => /usr/lib/libidn2.so.0 (0x0000151f94e64000)
     libssh2.so.1 => /usr/lib/libssh2.so.1 (0x0000151f94e31000)
     libpsl.so.5 => /usr/lib/libpsl.so.5 (0x0000151f94e1e000)
     libssl.so.1.1 => /usr/lib/libssl.so.1.1 (0x0000151f94d8e000)
     libcrypto.so.1.1 => /usr/lib/libcrypto.so.1.1 (0x0000151f94aba000)
     libgssapi_krb5.so.2 => /usr/lib/libgssapi_krb5.so.2
(0x0000151f9486c000)
     libkrb5.so.3 => /usr/lib/libkrb5.so.3 (0x0000151f94583000)
     libk5crypto.so.3 => /usr/lib/libk5crypto.so.3 (0x0000151f9434e000)
     libcom_err.so.2 => /usr/lib/libcom_err.so.2 (0x0000151f94348000)
     libpthread.so.0 => /usr/lib/libpthread.so.0 (0x0000151f94327000)
     libaec.so.0 => /usr/lib/libaec.so.0 (0x0000151f9411e000)
     libunistring.so.2 => /usr/lib/libunistring.so.2 (0x0000151f93d9e000)
     libkrb5support.so.0 => /usr/lib/libkrb5support.so.0
(0x0000151f93b8f000)
     libkeyutils.so.1 => /usr/lib/libkeyutils.so.1 (0x0000151f93b88000)
     libresolv.so.2 => /usr/lib/libresolv.so.2 (0x0000151f93b6f000)
[viktor.desolve-lab /tmp]$ echo $LD_LIBRARY_PATH
/opt/ambertools/lib

Of course, there exists more robust way to link with necessary libraries
without specifying paths explicitly as I did above in Makefile for
ambpdb but it was only done for quick-testing purposes.

Also I can say that there are some other programs which hardcodes
library names inside their binaries - makepkg checks if final package
files include absolute paths to buildroot environment (in my case
/opt/buildcache/makepkg) and throws a warning. I can list all cases if
you need it.

What can we do to workaround that bug? May be we just should wait for an
official patch? Thank you!


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Received on Sat May 04 2019 - 04:00:02 PDT
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