On Mon, Jan 14, 2019 at 6:05 PM Akash Banerjee <[email protected]> wrote: > > 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 build.sh is obsolete, please use the new build system 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. Well, you have to recompile gromacs with -fPIC, meaning as a shared library.
Alternatively, you can build you gromacs inside VOTCA using -DBUILD_OWN_GROMACS=ON. Christoph > > 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. -- 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.
