Hi, Thank you for the reply. Can I uninstall VOTCA without sudo? As you said the installation is broken.
Thanks, Aditi. On Friday, July 27, 2018 at 6:18:58 PM UTC-4, Christoph Junghans wrote: > > On Fri, Jul 27, 2018 at 8:28 AM, Aditi Khot <[email protected] > <javascript:>> wrote: > > Hi, > > > > I get this error "csg_property: error while loading shared libraries: > > libboost_program_options.so.1.67.0: cannot open shared object file: No > such > > file or directory" when I run "csg_property --help". > This hints towards your VOTCA installation being broken. > Have you sourced VOTCARC.bash? > Otherwise you need to add the path of > libboost_program_options.so.1.67.0 to your LD_LIBRARY_PATH. > > > > > The settings.xml file > > is as below. It is the file from the tutorial with the addition of the > > lammps command and the number of iterations is set to 1 instead of 300. > I just ran "csg_inverse --debug --options settings.xml" from > spce/ibi_lammps > and that generated a 45MB file starting with: > + msg 'For a more verbose log see: inverse.log' > > Can you reproduce the bug with the unmodified settings.xml? > And what bash version are using (bash --version)? > > Christoph > > > > <cg> > > <!-- example for a non-bonded interaction entry --> > > <non-bonded> > > <!-- name of the interaction --> > > <name>CG-CG</name> > > <!-- types involved in this interaction --> > > <type1>1</type1> > > <type2>1</type2> > > <!-- dimension + grid spacing of tables for calculations --> > > <min>0.0</min> > > <max>0.9</max> > > <step>0.01</step> > > <inverse> > > <!-- target distribution (rdf) --> > > <target>CG-CG.dist.tgt</target> > > <lammps> > > <!-- name of the table for lammps run --> > > <table>CG_CG.pot</table> > > <table_begin>0.20</table_begin> > > <table_bins>0.002</table_bins> > > </lammps> > > </inverse> > > </non-bonded> > > > > <!-- general options for inverse script --> > > <inverse> > > <!-- 300*0.00831451 lammps units --> > > <kBT>2.49435</kBT> > > <!-- use lammps as simulation program --> > > <program>lammps</program> > > <!-- lammps specific options --> > > <lammps> > > <!-- lammps script to run !--> > > <script>spce.in</script> > > <!-- topology to be used by csg_stat !--> > > <topol>topol.xml</topol> > > <!-- traj file created by lammps !--> > > <traj>traj.dump</traj> > > <!-- lammps command !--> > > <command>/depot/bsavoie/apps/lammps/exe/lmp_mpi_180501</command> > > </lammps> > > <initial_configuration>maindir</initial_configuration> > > <!-- these files are copied for each new run --> > > <filelist>spce.data spce.in topol.xml spce.dump</filelist> > > <!-- do so many iterations --> > > <iterations_max>1</iterations_max> > > <!-- ibi: inverse biltzmann imc: inverse monte carlo --> > > <method>ibi</method> > > </inverse> > > </cg> > > > > > > Thanks, > > Aditi. > > > > On Thursday, July 26, 2018 at 11:39:16 PM UTC-4, Christoph Junghans > wrote: > >> > >> > >> > >> On Thu, Jul 26, 2018, 18:41 Aditi Khot <[email protected]> wrote: > >>> > >>> Hi, > >>> > >>> Thanks for the reply. I am using the latest master version too. When I > >>> run the command "csg_inverse --debug --options settings.xml", it > terminates > >>> before running any simulations. The following text is printed in the > debug > >>> mode: > >>> enable_logging > >>> + local log > >>> + [[ -z '' ]] > >>> ++ csg_get_property cg.inverse.log_file > >>> Terminated > >>> > >>> I know it terminates at the 'enable_logging' command in the script > >>> inverse.sh. It terminates before the simulation even starts. Please > tell me > >>> what is going wrong! > >> > >> I don't know, because I cannot reproduce it! > >> Which git sha are you using? (Run "git log -1" in the csg folder) > >> > >> Can you try to run "csg_property --help"? > >> Can you post your seetings.xml? > >> > >> Christoph > >>> > >>> > >>> Thanks, > >>> Aditi, > >>> > >>> > >>> On Thursday, July 26, 2018 at 7:35:16 PM UTC-4, Aditi Khot wrote: > >>>> > >>>> Hi, > >>>> > >>>> I also have the same issue, I get the same thing at the end when I > >>>> switch on debug mode and it doesn't generate the inverse.log file. I > am > >>>> running the tutorial file of IBI on SPCE water model with LAMMPS. I > just > >>>> installed VOTCA. Could there be something wrong with the > installation? > >>>> > >>>> > >>>> Thanks, > >>>> Aditi. > >>>> > >>>> On Tuesday, July 21, 2015 at 12:07:19 PM UTC-4, Christoph Junghans > >>>> wrote: > >>>>> > >>>>> 2015-07-21 9:22 GMT-06:00 Jingyi Hu <[email protected]>: > >>>>> > > >>>>> > Hi Sikandar, > >>>>> > > >>>>> > thanks for the answer. The program just terminated immediately > >>>>> > without > >>>>> > generating the inverse.log file... > >>>>> It seems there was something wrong in the debug mode, this should > fix > >>>>> it: > >>>>> > >>>>> < > https://code.google.com/p/votca/source/detail?r=c7167b548826d76fd38bc5a6d2324d19ccfa378f&repo=csg> > > > >>>>> > >>>>> But as Sikandar pointed out already, usually looking the log file > >>>>> (default inverse.log) should sufficient. The debug mode is really > last > >>>>> resort as it produces gigabytes in log file. > >>>>> > >>>>> Christoph > >>>>> > >>>>> > > >>>>> > Regards > >>>>> > > >>>>> > Jin > >>>>> > > >>>>> > 在 2015年7月21日，下午4:10，Sikandar Mashayak <[email protected]> 写道： > >>>>> > > >>>>> > Hi Jin, > >>>>> > > >>>>> > Did you check the inverse.log file? It may contain more > information > >>>>> > about > >>>>> > the error, if any. > >>>>> > > >>>>> > -- > >>>>> > Sikandar > >>>>> > > >>>>> > On Tue, Jul 21, 2015 at 7:58 AM, jingyi.hu <[email protected]> > >>>>> > wrote: > >>>>> >> > >>>>> >> Hi, > >>>>> >> > >>>>> >> I followed the ibi tutorial successfully before. However, when I > >>>>> >> used my > >>>>> >> own files to build ibi model, the program terminated without > giving > >>>>> >> any > >>>>> >> error when I typed: > >>>>> >> > >>>>> >> csg_inverse --debug --options settings.xml > >>>>> >> > >>>>> >> The end of the debugging information shows as below: > >>>>> >> ... > >>>>> >> enable_logging > >>>>> >> + local log > >>>>> >> + [[ -z '' ]] > >>>>> >> ++ csg_get_property cg.inverse.log_file > >>>>> >> Terminated > >>>>> >> > >>>>> >> Can anybody help me with this problem? > >>>>> >> > >>>>> >> Regards > >>>>> >> > >>>>> >> Jin > >>>>> >> > >>>>> >> -- > >>>>> >> 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 post to this group, send email to [email protected]. > >>>>> >> Visit this group at http://groups.google.com/group/votca. > >>>>> >> For more options, visit https://groups.google.com/d/optout. > >>>>> > > >>>>> > > >>>>> > -- > >>>>> > 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 post to this group, send email to [email protected]. > >>>>> > Visit this group at http://groups.google.com/group/votca. > >>>>> > For more options, visit https://groups.google.com/d/optout. > >>>>> > > >>>>> > -- > >>>>> > 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 post to this group, send email to [email protected]. > >>>>> > Visit this group at http://groups.google.com/group/votca. > >>>>> > For more options, visit https://groups.google.com/d/optout. > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> Christoph Junghans > >>>>> Web: http://www.compphys.de > >>> > >>> -- > >>> 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 post to this group, send email to [email protected]. > >>> Visit this group at https://groups.google.com/group/votca. > >>> For more options, visit https://groups.google.com/d/optout. > > > > -- > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
