Thank you for the reply! On Sat, Jul 28, 2018 at 8:38 AM, Christoph Junghans <[email protected]> wrote:
> On Sat, Jul 28, 2018 at 6:33 AM, Aditi Khot <[email protected]> wrote: > > Hi, > > > > Thank you for the reply. Can I uninstall VOTCA without sudo? As you said > the > > installation is broken. > That depends on where you installed it? In your home directory you can > sure install it without sudo. > > Christoph > > > > 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]> 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]. > >> > 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. > >> > >> > >> > >> -- > >> 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. > > > > -- > 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. > -- Aditi Khot, Dual Degree Final Year, Chemical Engineering, Indian Institute of Technology, Madras. -- 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.
