[votca] special tpr for RDF calculations
Hello, I encountered a very strange (looks like legacy) issue with v1.4.1. In my earlier IBI iterations (with v1.3) I normally used special topol-rdf.tpr which was different from normal CG simulation topol.tpr by not including the intra-molecular pairs in the RDF stats (done by csg_stat). I wanted to make sure my previous results are reproduced by v1.4.1, so copied all the initialisation files into a new directory and tried to run once again. After the very first iteration I checked the obtained RDFs and they were all wrong - corresponding to normal topol.tpr (including intra-pairs) and not topol-rdf.tpr (excluding intra-pairs)! I guess there might have been changes made to locations or names of tags in settings.xml between the VOTCA versions, but I could not identify those changes by referring to the most recent manual (both v1.4.1 and development versions). Below is the relevant extract from my settings.xml file. Any clue, hint, advice are most welcome! Thanks in advance. Andrey --- gmx grompp mpirun -n 4 mdrun_mpi -multidir sim_0 sim_1 sim_2 sim_3 -tablep table.xvg -tableb table_b?.xvg table_a?.xvg table_d?.xvg 0 0.001 1 2.5 maindir Length of the block for the error analysis 100 Special mapping file for rdf calculations needed for bonded interactions dopc_cg-map11.xml Gromacs binary topol (tpr) file to be used for csg_stat topol-rdf.tpr yescalculate error on the rdf: yes/no --- -- 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Missing, not found Eigen3 during VOTCA installation
On Sat, Jul 21, 2018 at 7:42 PM, Christoph Junghans wrote: > > > On Fri, Jul 20, 2018 at 18:59 'Andrey Brukhno' via votca < > votca@googlegroups.com> wrote: > >> By now I have installed SQLITE3, compiled latest version of Gromacs and >> currently installing VOTCA. >> > I think i found that issue and fixed it in: > https://github.com/votca/csg/pull/255 > and > https://github.com/votca/votca/pull/76 > > Good to know! +if(DEFINED WITH_SQLITE3 AND NOT WITH_SQLITE3) sounds weird - perhaps it's just the computer logic :) just kidding... > > BTW, the Gromacs flag -DWITH_GMX=ON did not work for me either. >> > Can you be a bit more specific what the problem was? > > I wanted VOTCA to install Gromacs along with itself as it did before (build script for v1.3 did), but the flag -DWITHGMX=ON provided to cmake did not do that (seemed like it ignored the flag), so I had to install Gromacs newest version by myself. > >> Not sure what was the issue with the flag -DWITH_SQLITE3=OFF, but my >> cmake version was below 3, so I had to reinstall it too. >> > Yeah, due to using C++11 we need CMake-3.1 now, but that should give an > error immediately. > > Yes, I was installing on my laptop and did not check the cmake version first. Then, after checking it, I was surprised it did not complain as it did on my work desktop. Andrey > Christoph > >> >> Thanks >> Andrey >> >> >> >> On Sat, Jul 21, 2018 at 1:48 AM, Christoph Junghans >> wrote: >> >>> >>> >>> On Fri, Jul 20, 2018, 16:49 'Andrey Brukhno' via votca < >>> votca@googlegroups.com> wrote: >>> Well, I tried to follow your instructions in this thread for "stable" branch. >>> Just checked, worked for me. Can you open an github issue with all the >>> details (commands, output etc.) >>> >>> Thanks, >>> >>> Christoph >>> Andrey On Fri, 20 Jul 2018 22:41 Christoph Junghans, wrote: > On Fri, Jul 20, 2018 at 3:11 PM, 'Andrey Brukhno' via votca > wrote: > > The problem is, I remembered this option for the old build script > and tried > > to use it with cmake but still got the error "sqlite3 not found". > Which version of VOTCA are you using now? > > > > > Andrey > > > > On Fri, 20 Jul 2018 21:56 Christoph Junghans, > wrote: > >> > >> On Fri, Jul 20, 2018 at 11:08 AM, 'Andrey Brukhno' via votca > >> wrote: > >> > Christoph, > >> > > >> > What is the flag for cmake not to search for SQLITE3? > >> WITH_SQLITE3=OFF, btw you can just look up the options in ccmake. > >> > >> Christoph > >> > > >> > Thanks > >> > Andrey > >> > > >> > > >> > On Thu, Jul 19, 2018 at 8:18 PM, Christoph Junghans < > jungh...@votca.org> > >> > wrote: > >> >> > >> >> On Thu, Jul 19, 2018 at 10:57 AM, 'Andrey Brukhno' via votca > >> >> wrote: > >> >> > > >> >> > > >> >> > On Thursday, July 19, 2018 at 4:48:14 PM UTC+1, Christoph > Junghans > >> >> > wrote: > >> >> >> > >> >> >> >> > >> >> >> >> > We recently fixed an issue in the Eigen3 detection: > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > https://github.com/votca/votca/commit/ > 8fdcedae9b46e1739fa2ef8589cd5a8f6881d420 > >> >> >> >> > which includes: > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > https://github.com/votca/tools/commit/ > 3ee8b88e6022772b843f21a04f66a5bd8bfddd09 > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > https://github.com/votca/csg/commit/ > c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf > >> >> >> >> > Did you use that version? > >> >> >> > > >> >> >> > > >> >> >> > No, I have not tried any newer version yet. My aim was to > get the > >> >> >> > latest > >> >> >> > release installed, which spack did succeed to do (v1.4.1). > >> >> >> But then I don't understand your original error because > votca-csg > >> >> >> 1.4.1 doesn't depend on Eigen3. > >> >> > > >> >> > > >> >> > I guess I meant (implicitly) that I tried to follow the > instructions > >> >> > for > >> >> > installation using cmake found on one of the VOTCA's webpages, > and > >> >> > that's > >> >> > when I encountered the error message about eigen3 (not sure > now what > >> >> > version > >> >> > it was, but I think 1.5.1). But then I went the spack way and > was > >> >> > satisfied. > >> >> > Since then I have not tried cmake for any other version. But I > may > >> >> > try > >> >> > on my > >> >> > home PC soon. > >> >> I see, it is a bit confusing in the README of the new > buildsystem, > >> >> hopefully that makes it more clear: > >> >> > >> >> > >> >> https://github.com/votca/votca/commit/ > 40cbeb2daf4b4647292cf423e9755125cb7c3380 > >> >> >
Re: [votca] Missing, not found Eigen3 during VOTCA installation
Ok, good to know! - Not that I could follow the workflow by the link though. Andrey On Sat, Jul 21, 2018 at 7:33 PM, Christoph Junghans wrote: > > > On Thu, Jul 19, 2018 at 09:47 Christoph Junghans > wrote: > >> On Thu, Jul 19, 2018 at 9:33 AM, 'Andrey Brukhno' via votca >> wrote: >> > >> > >> > On Thursday, July 19, 2018 at 3:27:52 PM UTC+1, Christoph Junghans >> wrote: >> >> >> >> On Wed, Jul 18, 2018 at 12:20 PM, Christoph Junghans < >> jung...@votca.org> >> >> wrote: >> >> > On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca >> >> > wrote: >> >> >> Hello, >> >> >> >> >> >> The last time I was installing the CSG package in my Ubuntu >> (up-to-date >> >> >> 2014 >> >> >> LTS) I got this error from cmake: eigen3 not found, with a >> suggestion >> >> >> to >> >> >> provide the path to it. I then downloaded the library from their >> >> >> website, >> >> >> installed it and added its include directory to both my $PATH and to >> >> >> the >> >> >> environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake >> >> >> still >> >> >> complained and stopped with the same error, even when I fed it the >> >> >> flag: >> >> >> -DEIGEN3_INCLUDE_DIR=. >> >> > Just a reminder that 2014 was already 4 years ago ;-) >> > >> > >> > Thanks, up to now it did not hurt to stay with that version, but >> eventually >> > yes an upgrade is pending. :) >> > >> >> >> >> > We recently fixed an issue in the Eigen3 detection: >> >> > >> >> > https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a >> 8f6881d420 >> >> > which includes: >> >> > >> >> > https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5 >> bd8bfddd09 >> >> > >> >> > https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6 >> b108750ecf >> >> > Did you use that version? >> > >> > >> > No, I have not tried any newer version yet. My aim was to get the latest >> > release installed, which spack did succeed to do (v1.4.1). >> But then I don't understand your original error because votca-csg >> 1.4.1 doesn't depend on Eigen3. >> >> > >> > BTW, when I tried to install with apt-get nothing happened: no votca >> package >> > found. Perhaps it would only work for 2016(+) Ubuntu? >> Yes, only 2016.4 and later: >> https://packages.ubuntu.com/search?keywords=votca-csg; >> searchon=names=all=all >> and v1.4.1 only in Ubuntu 18.04! >> >> > >> >> >> >> > >> >> >> >> >> >> Not sure what went wrong, but I had to use alternative way of >> >> >> installation >> >> >> via spack, and it worked eventually, although it lloked like spack >> >> >> installed >> >> >> ALL the dependencies along with VOTCA in a separate directory, >> which is >> >> >> of >> >> >> course an overkill. >> >> > That is Spack's design, so don't complain to me! And yes we need to >> >> > update the dependencies of the VOTCA package in Spack. >> >> https://github.com/spack/spack/pull/8757 >> > >> > >> > I see... Otherwise I also noticed that spack installs csg and tools >> > separately in two directories beside each other. But then VOTCARC.bash >> etc >> > occur in the tools/bin and VOTCASHARE points at votca_tools/share >> instead of >> > votca_csg/share, so the scripts/inverse are not found. I had to reset >> > VOTCASHARE correctly in my .bashrc. >> Good point I will have to think, how to fix that. I think the VOTCARC >> file should get installed to start with as csg_inverse will >> auto-detect the location (using csg_call in your PATH) if VOTCASHARE >> isn't set. > > I dropped the install of the confusing VOTCARC in: > >> https://github.com/spack/spack/pull/8771 > > Christoph > >> >> >> Christoph >> >> > >> > I mentioned this for other users to be aware. >> > >> > Andrey >> >> >> >> >> >> >> >> >> >> I suppose this post is just to notify the current developers that >> there >> >> >> might be some issue with finding an exiasting Eigen3 dir. >> >> > Thanks for letting us know, can you try if above versions fix the >> issue >> >> > for you? >> >> > >> >> > Christoph >> >> >> >> >> >> Thanks >> >> >> Andrey >> >> >> >> >> >> -- >> >> >> 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 votca+un...@googlegroups.com. >> >> >> To post to this group, send email to vo...@googlegroups.com. >> >> >> 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 >> >> >> >> >> >> >> >> -- >> >> 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 votca+unsubscr...@googlegroups.com. >> > To post to this group, send email to
Re: [votca] Missing, not found Eigen3 during VOTCA installation
On Fri, Jul 20, 2018 at 18:59 'Andrey Brukhno' via votca < votca@googlegroups.com> wrote: > By now I have installed SQLITE3, compiled latest version of Gromacs and > currently installing VOTCA. > I think i found that issue and fixed it in: https://github.com/votca/csg/pull/255 and https://github.com/votca/votca/pull/76 BTW, the Gromacs flag -DWITH_GMX=ON did not work for me either. > Can you be a bit more specific what the problem was? > Not sure what was the issue with the flag -DWITH_SQLITE3=OFF, but my cmake > version was below 3, so I had to reinstall it too. > Yeah, due to using C++11 we need CMake-3.1 now, but that should give an error immediately. Christoph > > Thanks > Andrey > > > > On Sat, Jul 21, 2018 at 1:48 AM, Christoph Junghans > wrote: > >> >> >> On Fri, Jul 20, 2018, 16:49 'Andrey Brukhno' via votca < >> votca@googlegroups.com> wrote: >> >>> Well, I tried to follow your instructions in this thread for "stable" >>> branch. >>> >> Just checked, worked for me. Can you open an github issue with all the >> details (commands, output etc.) >> >> Thanks, >> >> Christoph >> >>> >>> Andrey >>> >>> On Fri, 20 Jul 2018 22:41 Christoph Junghans, >>> wrote: >>> On Fri, Jul 20, 2018 at 3:11 PM, 'Andrey Brukhno' via votca wrote: > The problem is, I remembered this option for the old build script and tried > to use it with cmake but still got the error "sqlite3 not found". Which version of VOTCA are you using now? > > Andrey > > On Fri, 20 Jul 2018 21:56 Christoph Junghans, wrote: >> >> On Fri, Jul 20, 2018 at 11:08 AM, 'Andrey Brukhno' via votca >> wrote: >> > Christoph, >> > >> > What is the flag for cmake not to search for SQLITE3? >> WITH_SQLITE3=OFF, btw you can just look up the options in ccmake. >> >> Christoph >> > >> > Thanks >> > Andrey >> > >> > >> > On Thu, Jul 19, 2018 at 8:18 PM, Christoph Junghans < jungh...@votca.org> >> > wrote: >> >> >> >> On Thu, Jul 19, 2018 at 10:57 AM, 'Andrey Brukhno' via votca >> >> wrote: >> >> > >> >> > >> >> > On Thursday, July 19, 2018 at 4:48:14 PM UTC+1, Christoph Junghans >> >> > wrote: >> >> >> >> >> >> >> >> >> >> >> > We recently fixed an issue in the Eigen3 detection: >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420 >> >> >> >> > which includes: >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09 >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf >> >> >> >> > Did you use that version? >> >> >> > >> >> >> > >> >> >> > No, I have not tried any newer version yet. My aim was to get the >> >> >> > latest >> >> >> > release installed, which spack did succeed to do (v1.4.1). >> >> >> But then I don't understand your original error because votca-csg >> >> >> 1.4.1 doesn't depend on Eigen3. >> >> > >> >> > >> >> > I guess I meant (implicitly) that I tried to follow the instructions >> >> > for >> >> > installation using cmake found on one of the VOTCA's webpages, and >> >> > that's >> >> > when I encountered the error message about eigen3 (not sure now what >> >> > version >> >> > it was, but I think 1.5.1). But then I went the spack way and was >> >> > satisfied. >> >> > Since then I have not tried cmake for any other version. But I may >> >> > try >> >> > on my >> >> > home PC soon. >> >> I see, it is a bit confusing in the README of the new buildsystem, >> >> hopefully that makes it more clear: >> >> >> >> >> >> https://github.com/votca/votca/commit/40cbeb2daf4b4647292cf423e9755125cb7c3380 >> >> >> >> Christoph >> >> > >> >> >> >> >> >> >> >> >> > >> >> >> > BTW, when I tried to install with apt-get nothing happened: no >> >> >> > votca >> >> >> > package >> >> >> > found. Perhaps it would only work for 2016(+) Ubuntu? >> >> >> Yes, only 2016.4 and later: >> >> >> >> >> >> >> >> >> >> >> >> https://packages.ubuntu.com/search?keywords=votca-csg=names=all=all >> >> >> and v1.4.1 only in Ubuntu 18.04! >> >> >> >> >> >> > >> >> >> >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> Not sure what went wrong, but I had to use alternative way of >> >> >> >> >> installation >> >> >> >> >> via spack, and it worked eventually, although it lloked like >> >> >> >> >>
Re: [votca] Missing, not found Eigen3 during VOTCA installation
On Thu, Jul 19, 2018 at 09:47 Christoph Junghans wrote: > On Thu, Jul 19, 2018 at 9:33 AM, 'Andrey Brukhno' via votca > wrote: > > > > > > On Thursday, July 19, 2018 at 3:27:52 PM UTC+1, Christoph Junghans wrote: > >> > >> On Wed, Jul 18, 2018 at 12:20 PM, Christoph Junghans > > >> wrote: > >> > On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca > >> > wrote: > >> >> Hello, > >> >> > >> >> The last time I was installing the CSG package in my Ubuntu > (up-to-date > >> >> 2014 > >> >> LTS) I got this error from cmake: eigen3 not found, with a suggestion > >> >> to > >> >> provide the path to it. I then downloaded the library from their > >> >> website, > >> >> installed it and added its include directory to both my $PATH and to > >> >> the > >> >> environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake > >> >> still > >> >> complained and stopped with the same error, even when I fed it the > >> >> flag: > >> >> -DEIGEN3_INCLUDE_DIR=. > >> > Just a reminder that 2014 was already 4 years ago ;-) > > > > > > Thanks, up to now it did not hurt to stay with that version, but > eventually > > yes an upgrade is pending. :) > > > >> > >> > We recently fixed an issue in the Eigen3 detection: > >> > > >> > > https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420 > >> > which includes: > >> > > >> > > https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09 > >> > > >> > > https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf > >> > Did you use that version? > > > > > > No, I have not tried any newer version yet. My aim was to get the latest > > release installed, which spack did succeed to do (v1.4.1). > But then I don't understand your original error because votca-csg > 1.4.1 doesn't depend on Eigen3. > > > > > BTW, when I tried to install with apt-get nothing happened: no votca > package > > found. Perhaps it would only work for 2016(+) Ubuntu? > Yes, only 2016.4 and later: > > https://packages.ubuntu.com/search?keywords=votca-csg=names=all=all > and v1.4.1 only in Ubuntu 18.04! > > > > >> > >> > > >> >> > >> >> Not sure what went wrong, but I had to use alternative way of > >> >> installation > >> >> via spack, and it worked eventually, although it lloked like spack > >> >> installed > >> >> ALL the dependencies along with VOTCA in a separate directory, which > is > >> >> of > >> >> course an overkill. > >> > That is Spack's design, so don't complain to me! And yes we need to > >> > update the dependencies of the VOTCA package in Spack. > >> https://github.com/spack/spack/pull/8757 > > > > > > I see... Otherwise I also noticed that spack installs csg and tools > > separately in two directories beside each other. But then VOTCARC.bash > etc > > occur in the tools/bin and VOTCASHARE points at votca_tools/share > instead of > > votca_csg/share, so the scripts/inverse are not found. I had to reset > > VOTCASHARE correctly in my .bashrc. > Good point I will have to think, how to fix that. I think the VOTCARC > file should get installed to start with as csg_inverse will > auto-detect the location (using csg_call in your PATH) if VOTCASHARE > isn't set. I dropped the install of the confusing VOTCARC in: > https://github.com/spack/spack/pull/8771 Christoph > > > Christoph > > > > > I mentioned this for other users to be aware. > > > > Andrey > >> > >> > >> >> > >> >> I suppose this post is just to notify the current developers that > there > >> >> might be some issue with finding an exiasting Eigen3 dir. > >> > Thanks for letting us know, can you try if above versions fix the > issue > >> > for you? > >> > > >> > Christoph > >> >> > >> >> Thanks > >> >> Andrey > >> >> > >> >> -- > >> >> 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 votca+un...@googlegroups.com. > >> >> To post to this group, send email to vo...@googlegroups.com. > >> >> 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 > >> > >> > >> > >> -- > >> 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 votca+unsubscr...@googlegroups.com. > > To post to this group, send email to votca@googlegroups.com. > > 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 > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To
