Error while running spce/atomistic simulation

[Satyen Dhamankar]

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? 

[Christoph Junghans]

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
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Christoph Junghans
Web: http://www.compphys.de

[Satyen Dhamankar]

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. 

[Christoph Junghans]

On Wed, Mar 31, 2021 at 9:14 AM Satyen Dhamankar <saty...@gmail.com> 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

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