Hi Christoph, On Tue, Jan 8, 2019 at 4:34 PM Akash Banerjee <[email protected]> wrote: > > Hi Christoph, > Thank you for your response. > > On Tue, Jan 8, 2019 at 2:30 PM Akash Banerjee <[email protected]> wrote: > > > > Hi Christoph and other Votca developers, > > > > I am getting the errror- > > > > Error in `csg_stat': double free or corruption > > > > after 13 iterations. I understand that this error may occur due to wrong naming. However, csg_stat managed to map my system for 13 iterations and then went on to fail. > > Which version of VOTCA is this? Can you try the latest development > version instead? > > I used the build.sh script on the website. The version is 1.5-dev gitid: 648021c. I had recently built it on my cluster. Should I built is again using the same build.sh command? > > build.sh is obsolete, please use the new build system > (https://github.com/votca /votca/blob/master/share/doc/INSTALL.md#general-source-installation-instructions ) > instead! We made some fixes in csg_stat recently, so you could try a > more recent version of csg if you want
I rebuilt votca as per the instructions given above in my cluster ( stampede2.tacc.utexas.edu). I am stuck at the make-j5 command. The error on screen is as follows- *collect2: error: ld returned 1 exit status* *make[2]: *** [tools/src/tools/votca_property] Error 1* *make[1]: *** [tools/src/tools/CMakeFiles/votca_property.dir/all] Error 2* *make[1]: *** Waiting for unfinished jobs....* *[ 28%] Linking CXX shared library libvotca_csg.so* */opt/apps/gcc/5.4.0/bin/ld: /opt/apps/intel17/impi17_0/gromacs/2016.4/lib64/libgromacs.a(baseversion.cpp.o): relocation R_X86_64_32 against `_gmx_ver_string' can not be used when making a shared object; recompile with -fPIC* */opt/apps/intel17/impi17_0/gromacs/2016.4/lib64/libgromacs.a: error adding symbols: Bad value* *collect2: error: ld returned 1 exit status* *make[2]: *** [csg/src/libcsg/libvotca_csg.so.5] Error 1* *make[1]: *** [csg/src/libcsg/CMakeFiles/votca_csg.dir/all] Error 2* I tried recompiling using the -fPIG tag in the cmake command. It made no difference. Please advice me on what I can do. Thank you so much for your help! Kind Regards, Akash On Wed, Jan 9, 2019 at 3:48 PM Akash Banerjee <[email protected]> wrote: > Sure, I will have a look at it and let you know. > > Thanks Christoph. > > On Wed, Jan 9, 2019 at 3:08 PM Christoph Junghans <[email protected]> > wrote: > >> On Wed, Jan 9, 2019 at 8:36 AM Akash Banerjee <[email protected]> >> wrote: >> > >> > Thank you so much for your responses. I will do as you suggested. >> Also if the problem stays reproducible, could you open an issue here: >> https://github.com/votca/csg/issues and attach the input files. >> >> Christoph >> >> > >> > Kind regards, >> > Akash >> > >> > On Tue, Jan 8, 2019 at 7:56 PM Christoph Junghans <[email protected]> >> wrote: >> >> >> >> On Tue, Jan 8, 2019 at 4:34 PM Akash Banerjee <[email protected]> >> wrote: >> >> > >> >> > Hi Christoph, >> >> > Thank you for your response. >> >> > >> >> > On Tue, Jan 8, 2019 at 2:30 PM Akash Banerjee <[email protected]> >> wrote: >> >> > > >> >> > > Hi Christoph and other Votca developers, >> >> > > >> >> > > I am getting the errror- >> >> > > >> >> > > Error in `csg_stat': double free or corruption >> >> > > >> >> > > after 13 iterations. I understand that this error may occur due to >> wrong naming. However, csg_stat managed to map my system for 13 iterations >> and then went on to fail. >> >> > >> >> > Which version of VOTCA is this? Can you try the latest development >> >> > version instead? >> >> > >> >> > I used the build.sh script on the website. The version is 1.5-dev >> gitid: 648021c. I had recently built it on my cluster. Should I built is >> again using the same build.sh command? >> >> > >> >> build.sh is obsolete, please use the new build system >> >> ( >> https://github.com/votca/votca/blob/master/share/doc/INSTALL.md#general-source-installation-instructions >> ) >> >> instead! We made some fixes in csg_stat recently, so you could try a >> >> more recent version of csg if you want. >> >> >> >> > >> >> > > Also, I have another questions, please have a look at your >> convenience. >> >> > > >> >> > > I have run another system for 73 iterations and the values in >> the bonded potential table (table_b1.xvg) is nearly the same as the 1st >> iteration. I suspect that I am doing something wrong. >> >> > > I have plotted the potential and attached it to this post with >> the name potential_73th_iteration. I increased my simulation time for each >> iteration from 100 ps to 1 ns. This change didnt make any >> >> > > difference to the potentials. >> >> > You need to zoom in around 0.5 to see any changes as the changes only >> >> > happen around the minimum >> >> > >> >> > I got it. Should I be expecting negative values as a sign of >> accuracy? (I am picturing a Lenard Jones Plot with a well depth) >> >> Well, VOTCA shifts the potential, so that the minimum is at zero. So >> >> you will have to determine the delta from a local maximum or so. >> >> >> >> Christoph >> >> > >> >> > Thank you again for your responses. >> >> > >> >> > On Tue, Jan 8, 2019 at 6:20 PM Christoph Junghans < >> [email protected]> wrote: >> >> >> >> >> >> On Tue, Jan 8, 2019 at 2:30 PM Akash Banerjee <[email protected]> >> wrote: >> >> >> > >> >> >> > Hi Christoph and other Votca developers, >> >> >> > >> >> >> > I am getting the errror- >> >> >> > >> >> >> > Error in `csg_stat': double free or corruption >> >> >> > >> >> >> > after 13 iterations. I understand that this error may occur due >> to wrong naming. However, csg_stat managed to map my system for 13 >> iterations and then went on to fail. >> >> >> >> >> >> Which version of VOTCA is this? Can you try the latest development >> >> >> version instead? >> >> >> > >> >> >> > Please help me on the above. >> >> >> > >> >> >> > Also, I have another questions, please have a look at your >> convenience. >> >> >> > >> >> >> > I have run another system for 73 iterations and the values in >> the bonded potential table (table_b1.xvg) is nearly the same as the 1st >> iteration. I suspect that I am doing something wrong. >> >> >> > I have plotted the potential and attached it to this post >> with the name potential_73th_iteration. I increased my simulation time for >> each iteration from 100 ps to 1 ns. This change didnt make any >> >> >> > difference to the potentials. >> >> >> You need to zoom in around 0.5 to see any changes as the changes >> only >> >> >> happen around the minimum. >> >> >> >> >> >> Christoph >> >> >> >> >> >> > >> >> >> > >> >> >> > Thank you for your help! >> >> >> > >> >> >> > Kind regards, >> >> >> > Akash >> >> >> > >> >> >> > >> >> >> > -- >> >> >> > 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. >> >> > >> >> > >> >> > >> >> > -- >> >> > akash >> >> > >> >> > -- >> >> > 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. >> > >> > >> > >> > -- >> > akash >> > >> > -- >> > 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. >> > > > -- > akash > -- akash -- 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.
