I can reproduce this.
There are 3 possible solutions:
(1) Someplace (I don't know where yet - I haven't found it in nab.c) there
is a -lnetcdf
but that link line should have a -static so that it links to the .a instead
of the .so
or
(2) export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib
before you run the executable
or
(3) Find the -lnetcdf flag and replace it with the full path
$AMBERHOME/lib/libnetcdf.so (or .a)
[giese.buzet nab]$ ../../bin/nab -o duplex duplex.nab
I see duplex depends on libnetcdf, but that's not in my ld path
[giese.buzet nab]$ ldd duplex
linux-vdso.so.1 => (0x00007fffe13ff000)
libfftw3.so.3 => /usr/lib64/libfftw3.so.3 (0x0000003003400000)
libnetcdf.so.7 => not found <--------------
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003f14400000)
libgfortran.so.3 => /usr/lib64/libgfortran.so.3 (0x00007fd2cae8e000)
libm.so.6 => /lib64/libm.so.6 (0x0000003f28400000)
libc.so.6 => /lib64/libc.so.6 (0x0000003f13c00000)
/lib64/ld-linux-x86-64.so.2 (0x0000003f13800000)
libquadmath.so.0 => /usr/lib64/libquadmath.so.0 (0x0000003902c00000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003902800000)
Of course, it doesn't run
[giese.buzet nab]$ ./duplex
./duplex: error while loading shared libraries: libnetcdf.so.7: cannot open
shared object file: No such file or directory
Let me add that directory to my ld path
[giese.buzet nab]$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib
[giese.buzet nab]$ ./duplex
(ok - it runs)
When you link to a dynamic library without specifying the full path, it
only marks the name of the library to be searched for within the executable.
When you run the executable, it searches the directories in your ld search
paths...
LD_LIBRARY_PATH
/etc/ld.so.conf
/etc/ld.so.conf.d/*
...for the library at run time.
If you link to a shared library with the full path, then it (at least in my
experience on the machines I've run on) it stores the full path of the
shared library within the executable so that the library does not need to
be within your ld path at runtime.
Of course, linking to the static archive avoids these issues altogether.
-Tim
On Wed, Jan 29, 2014 at 12:12 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi All,
>
> Has anybody else seen issues with netcdf shared libraries?
>
> Latest git tree as of 9pm PST today.
>
> ./configure gnu
> make -j8 install
> make test
>
> cd leap/glycam && ./Run_tests.bash clean
> cd nab && make -k test testrism
> make[3]: Entering directory
> `/cbio/jclab/home/rcw/amber/AmberTools/test/nab'
> Running test to make dna duplex:
>
> ./duplex: error while loading shared libraries: libnetcdf.so.7: cannot
> open shared object file: No such file or directory
> ./Run.duplex: Program error
> make[3]: *** [duplex_test] Error 1
> Running test to computed 3DNA deformation energies:
>
> ./deform: error while loading shared libraries: libnetcdf.so.7: cannot
> open shared object file: No such file or directory
> ./Run.deform: Program error
> make[3]: *** [deform_test] Error 1
> Running Reflexive test:
>
> ./refl: error while loading shared libraries: libnetcdf.so.7: cannot open
> shared object file: No such file or directory
> ./Run.reflexive: Program error
> make[3]: *** [reflexive_test] Error 1
> Running test of sub() and gsub()
>
>
> ... etc ...
>
> does this for ALL the rism tests and then everything looks good
>
> ./Run.rism_xmin: Program error
> make[3]: *** [rism_xmin] Error 1
> make[3]: Target `testrism' not remade because of errors.
> make[3]: Leaving directory `/cbio/jclab/home/rcw/amber/AmberTools/test/nab'
> make[2]: *** [test.nab] Error 2
> cd cpptraj && make -k test
> make[3]: Entering directory
> `/cbio/jclab/home/rcw/amber/AmberTools/test/cpptraj'
> make test.main
> make[4]: Entering directory
> `/cbio/jclab/home/rcw/amber/AmberTools/test/cpptraj'
> **************************************************************
> TEST: /cbio/jclab/home/rcw/amber/AmberTools/test/cpptraj/Test_General
>
> CPPTRAJ: General tests
> diffing distance.dat.save with distance.dat
> PASSED
> ==============================================================
> diffing rmsd.dat.save with rmsd.dat
>
> ... etc ...
>
>
> Seems like rism is relying on system netcdf for some reason? - Or
> something else is wrong.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Associate Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Associate Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
>
>
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Received on Tue Jan 28 2014 - 23:00:03 PST
