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. 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