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.
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 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.
