I had the same problem very recently. The problem was that the environment directory used for cuda libraries in the bashrc file was probably coinciding with a cpptraj variable, so the program was looking for the correct libraries under the wrong folder.
You can test this rather easily, try removing the "export LD_LIBRARY_PATH" line from the bash_profile or bashrc file and just run "cpptraj" without feeding any scripts. If it works, then that's the problem. I just added a "source $AMBERHOME/amber.sh" to my .bashrc file and it works now. Hope it helps.
Best,
Alican
Sent from my iPhone
> On Apr 20, 2017, at 10:13 PM, Khatcharin Siriwong <khatcharin.s.gmail.com> wrote:
>
> Dear All,
>
> I have installed AmberTools17 on Ubuntu with bash shell.
> - $AMBERHOME was set, and "source amber.sh" was done after "./configure gnu"
> - Everything was fine for make install and make test (there was no any
> error and failed, for both serial and parallel installation)
> - there are libsander.so and libnetcdf.so in $AMBERHOME/lib
> - I also set AMBERHOME and PATH in file ".bash_profile" as same as other
> softwares (no .bashrc file)
>
> But when I run cpptraj or cpptraj.MPI, I got message
>
> "cpptraj: error while loading shared libraries: libsander.so: cannot open
> shared object file: No such file or directory"
>
> also
>
> "cpptraj.MPI: error while loading shared libraries: libnetcdf.so.7: cannot
> open shared object file: No such file or directory"
>
> I also installed on CentOS, but only cpptraj.MPI works properly.
>
> Please give me any suggestion. Thank you very much in advance for your
> kindness.
>
> Best Regards,
> Khatcharin
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Received on Thu Apr 20 2017 - 20:00:02 PDT
