My guess is that you have a libnetcdf.so.* in your LD_LIBRARY_PATH.
On my machine I do not:
echo $LD_LIBRARY_PATH
/opt/gnu/gcc/4.6.1/lib64:/opt/gnu/gcc/4.6.1/lib:/opt/cuda/5.0.35/lib:/opt/c
uda/5.0.35/lib64:/opt/mpich2/gcc/eth/lib:/opt/gnu/gcc/4.8.1/lib64:/opt/gnu/
gcc/4.8.1/lib:/opt/gnu/gmp/lib:/opt/gnu/mpc/lib:/opt/gnu/mpfr/lib
none of which contain a libnetcdf.so.*
Now there is a $AMBERHOME/lib/libnetcdf.so.7
and if I add:
export LD_LIBRARY_PATH=$AMBERHOME/lib:$LD_LIBRARY_PATH
then things work fine.
But we've never required such a thing as part of our installation
procedure. Have things changed?
All the best
Ross
On 1/28/14, 10:20 PM, "T Luchko (Lists)" <tluchko.lists.gmail.com> wrote:
>
>On Jan 28, 2014, at 9:12 PM, 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
>>
>>
>
>I did a fresh pull and canšt reproduce this (Mac 10.9.1, gcc 4.7).
>
>BTW, from your log, this is a NAB issue and not RISM specific. No idea
>what the problem is though.
>
>Tyler
>
>
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Received on Tue Jan 28 2014 - 23:00:03 PST
