I don't know if it is relevant, but the netcdf build has been failing
for Amber_serial_intel-13.0.1 for a while. The last bit of the error
log is:
"
cruisecontrol_amber/projects/Amber_serial_intel-13.0.1/include -o
NetcdfFile.o NetcdfFile.cpp
NetcdfFile.cpp(71): error: expected an identifier
{
^
"
compilation aborted for NetcdfFile.cpp (code 2)
On 29/01/2014, T Luchko (Lists) <tluchko.lists.gmail.com> wrote:
> Since I'm on a mac (and don't have access to a Linux machine at the moment)
> things are a little different. However, my rism3d.snglpnt (a NAB
> executable) is correctly linked
>
> $ otool -L bin/rism3d.snglpnt
> bin/rism3d.snglpnt:
> /Users/tluchko/projects/amber/master/lib/libfftw3.3.dylib (compatibility
> version 7.0.0, current version 7.0.0)
> /Users/tluchko/projects/amber/master/lib/libnetcdf.7.dylib (compatibility
> version 10.0.0, current version 10.0.0)
> /opt/local/lib/libgcc/libgfortran.3.dylib (compatibility version 4.0.0,
> current version 4.0.0)
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
> (compatibility version 1.0.0, current version 4.0.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1197.1.1)
> /opt/local/lib/libgcc/libgcc_s.1.dylib (compatibility version 1.0.0,
> current version 1.0.0)
>
> and there is nothing of significance on my DYLD_LIBRARY_PATH (equivalent of
> LD_LIBRARY_PATH)
>
> $ echo $DYLD_LIBRARY_PATH
> /usr/local/cuda/lib:
>
> (the directory doesn't exist)
>
> FWIW, I ran configure with
>
> ./configure -noX11 -nomtkpp -macAccelerate gnu
>
> I'm not sure why this is coming up now. Checking the git logs, I don't see
> anything obvious. sff/ and nab/ directories haven't been touched since
> November. configure2 hasn't had a NetCDF change since November and the
> NetCDF libraries are basically hasn't been touched since November.
>
> Tyler
>
> On Jan 28, 2014, at 10:47 PM, Timothy Giese <timothyjgiese.gmail.com>
> wrote:
>
>> I can reproduce this.
>>
>> There are 3 possible solutions:
>>
>> (1) Someplace (I don't know where yet - I haven't found it in nab.c)
>> there
>> is a -lnetcdf
>> but that link line should have a -static so that it links to the .a
>> instead
>> of the .so
>>
>> or
>>
>> (2) export LD_LIBRARY_PATH=$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.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>>
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Received on Wed Jan 29 2014 - 01:00:02 PST
