On Wed, Mar 31, 2021 at 9:14 AM Satyen Dhamankar <[email protected]> wrote: > > Thank you for your response, Christoph. > > Yes, I did check my conf_cg.gro file, and it seems like I do have it done > correctly, with the 3 atoms being combined into 1 bead. So then ignore the warning for now.
> > I am not sure what you mean when you say if I have an LD_LIBRARY_PATH set in > my environment. > This is what I see when I do > echo $PATH > /home/satyend/software/spack/bin:/opt/rh/devtoolset-7/root/usr/bin:/usr/local/cmake3/bin:/opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/usr/local/intel/bin:/usr/licensed/anaconda3/2020.7/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin:/home/satyend/.local/bin:/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/bin:/home/satyend/.local2019/bin > > this is what I see when I do > echo $LD_LIBRARY_PATH > > /opt/rh/devtoolset-7/root/usr/lib64:/opt/rh/devtoolset-7/root/usr/lib:/opt/rh/devtoolset-7/root/usr/lib64/dyninst:/opt/rh/devtoolset-7/root/usr/lib/dyninst:/opt/intel/compilers_and_libraries_2019.5.281/linux/tbb/lib/intel64/gcc4.7:/opt/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64:/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64:/usr/local/intel/lib64 Maybe there is another libhdf5 somewhere in there...... Christoph > > Is this any help? I apologize for my lack of knowledge about these issues. > > On Wednesday, March 31, 2021 at 10:56:44 AM UTC-4 Christoph Junghans wrote: >> >> On Tue, Mar 30, 2021 at 10:28 PM Satyen Dhamankar <[email protected]> wrote: >> > >> > Hello, >> > >> > I am trying to follow the csg tutorials given in votca. I tried executing >> > the run.sh script in the folder spce/atomistic and I got errors, which I >> > have attached to this post. >> > >> > The commands that led to the error were: >> > >> > echo Calculating distributions >> > >> > csg_stat --top topol.tpr --trj traj.trr --cg water.xml --options >> > settings.xml --nt $nt --begin $equi >> > >> > echo "Mapping confout.gro to get the starting configuration for >> > coarse-grained runs of ibi/imc/re" >> > >> > csg_map --top topol.tpr --trj confout.gro --cg water.xml --out conf_cg.gro >> > >> > I obtained all the dependencies to run votca using spack, and to be able >> > to use csg_stat, csg_map from the terminal, I added the following to the >> > path: >> > >> > PATH=$PATH:~/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymv >> > udsn3en3wk5xxnie4j73nq/bin >> > >> > The path in bold are directories I obtained when I obtained spack the >> > following way: >> > >> > git clone https://github.com/spack/spack.git spack >> > >> > source spack/share/spack/setup-env.sh >> > >> > spack install votca-csg >> > >> > My question is, what am I doing wrong to encounter this error, and be >> > unable to run the tutorials? >> It looks to me like an HDF5 warning, but the end results are still >> written correctly. Can you check conf_cg.gro? >> Do you have any LD_LIBRARY_PATH set in your environment? >> >> Christoph >> > >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/04696986-e2dd-4075-be39-375fb7b077b7n%40googlegroups.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/7cadb16c-06da-4812-a1b7-34d17ed7ec04n%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e6HKMnSO3_boAJgcBUOu6vjATLu3v5DWGiwyvCFcABf2w%40mail.gmail.com.
