Hey Christoph To summarize , you are saying that if I link to Gromacs by adding -DGMX_DOUBLE to CPPFLAGS (keeping current gromacs) or upgrading gromacs then reinstalling VOTCA , probably newer release, will sort this issue. Right?
In any of these options, I am guessing, I will have to reinstall VOTCA! thanks sikandar On Tue, Sep 28, 2010 at 9:48 AM, Christoph Junghans < [email protected]> wrote: > Hi Sikandar, > > this is a combination of two things: > > 1. to link against double precision gromacs you will have to add > -DGMX_DOUBLE to your CPPFLAGS. this is a known bug in gromacs-4.0.7, which I > fixed a while ago in gromacs 4.5 and gromacs 4.0.8 (not released yet), when > using pkg-config. My advice is to update your gromacs version. > > Details for gromacs 4.0 here > < > http://repo.or.cz/w/gromacs.git/commit/3b4d46a1abcc4c3b999febf8aa83a1260053a674> > > and for gromacs 4.5 here: > < > http://repo.or.cz/w/gromacs.git/commit/053e0c52d9937eac9873ed2fa890e2b273488c8f > > > > 2.) There was a problem with the gmx 4.5 reader in votca-rc5 due to some > changes in gromacs, which have been solved in the developer version of > votca, so download it using Mercurial, see: > <http://code.google.com/p/votca/> > or wait until we have released votca-rc6 (expected for the end of the week) > > Cheers, > > Christoph > > Am 27.09.2010 22:04, schrieb Sikandar Mashayak: > >> csg_map gives this error ... >> >> Reading file topol.tpr, VERSION 4.0.5 (double precision) >> Segmentation fault >> >> votca version .. >> >> csg_fmatch, version 1.0_rc5 hgid: cce356ff52dd (compiled May 20 2010, >> 00:37:52) >> votca_tools, version 1.0_rc5 hgid: ed6908116baf (compiled May 20 2010, >> 00:37:19) >> gromacs, VERSION 4.0.7 >> >> when I run csg_map with gdb , "bt" command after segmentation fault gives >> following msg. >> >> #0 GMXTopologyReader::ReadTopology (this=0x80551f0, file=..., top=...) >> at gmxtopologyreader.cc:67 >> #1 0xb7facd89 in CGEngine::Run (this=0xbfffeffc) at cgengine.cc:187 >> #2 0x0804c399 in main (argc=7, argv=0xbffff1b4) at csg_map.cc:109 >> >> >> >> >> thanks >> sikandar >> >> On Tue, Sep 21, 2010 at 10:18 AM, Victor Ruehle<[email protected]> wrote: >> >> Hey, >>> >>> some checks: >>> >>> - did you source the same gromacs version against which you compiled >>> votca >>> - did you specify to write out forces in grompp file. it should be >>> nstxout = nstfout and you'll have to use the trr file, not trx >>> - does csg_map work? >>> - i see you are using double precision gromacs. There were some issues >>> with malfunction gromacs defines in combination with double precision, >>> could be an issue here... Which votca version are you using? >>> csg_fmatch --help should tell the version string including an hgid... >>> - if the above didn't help,can you please send debug information: >>> gdb csg_fmatch (without any further parameters) >>> and then type >>> run<here the parameters you run fmatch with> >>> If it stops with segmentation fault, please type bt (for backtrace) >>> and post the output. >>> >>> Cheers, >>> Victor >>> >>> >>> 2010/9/21 Sikandar Mashayak<[email protected]>: >>> >>>> hey Victor, I am trying out the command csg_fmatch with the options you >>>> specified. I am using my own 4ns GROMACS MD data for topol.tpr and >>>> >>> traj.trr >>> >>>> options, which I suppose should be fine. But I am getting this error... >>>> Reading file topol.tpr, VERSION 4.0.5 (double precision) >>>> Segmentation fault >>>> I get similar error when I try to run tutorial scripts for Propane.. >>>> Is there something wrong with my VOTCA installation or input files >>>> itself >>>> have errors! >>>> thanks >>>> sikandar >>>> On Tue, Sep 21, 2010 at 4:06 AM, Victor Ruehle<[email protected]> >>>> wrote: >>>> >>>>> >>>>> Hey, >>>>> oh, yea. that's only the atomistic run. fmatching run is misshing, but >>>>> just do after the atomistic run: >>>>> >>>>> csg_fmatch --top topol.tpr --trj traj.trr --cg water.xml.xml --options >>>>> fmatch.xml --begin 2000 --nframes<some-number> >>>>> >>>>> where<some-number> depends on how long you want to wait/accuracy you >>>>> want to get. For the first try someting around 30 should be ok, then >>>>> increase later. >>>>> >>>>> to get potetnials call csg_call table integrate (see recent posts) >>>>> >>>>> Cheers, >>>>> Victor >>>>> >>>>> 2010/9/20 Sikandar Mashayak<[email protected]>: >>>>> >>>>>> sorry forgot to provide the link of script file... which I am using to >>>>>> run >>>>>> FM algorithm ... >>>>>> >>>>>> >>>>>> >>> http://hg.votca.org/hgwebdir.cgi/tutorials/file/d9b7ba3b777b/spce/atomistic/run.sh >>> >>>> >>>>>> >>>>>> On Mon, Sep 20, 2010 at 4:12 PM, Sikandar Mashayak >>>>>> <[email protected]> >>>>>> wrote: >>>>>> >>>>>>> >>>>>>> Hi >>>>>>> I am wondering whether the Force Matching tutorial script for SPC/E >>>>>>> water >>>>>>> is complete? or is there any part of it is missing? >>>>>>> thanks >>>>>>> sikandar >>>>>>> >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups >>>>>> "votca" group. >>>>>> To post to this group, send email to [email protected]. >>>>>> To unsubscribe from this group, send email to >>>>>> [email protected]<votca%[email protected]> >>>>>> <votca%[email protected]<votca%[email protected]> >>>>>> > >>>>>> >>>>> . >>> >>>> For more options, visit this group at >>>>>> http://groups.google.com/group/votca?hl=en. >>>>>> >>>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> >>>> Groups >>> >>>> "votca" group. >>>>> To post to this group, send email to [email protected]. >>>>> To unsubscribe from this group, send email to >>>>> [email protected]<votca%[email protected]> >>>>> <votca%[email protected]<votca%[email protected]> >>>>> > >>>>> >>>> . >>> >>>> For more options, visit this group at >>>>> http://groups.google.com/group/votca?hl=en. >>>>> >>>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups >>>> "votca" group. >>>> To post to this group, send email to [email protected]. >>>> To unsubscribe from this group, send email to >>>> [email protected]<votca%[email protected]> >>>> <votca%[email protected]<votca%[email protected]> >>>> > >>>> >>> . >>> >>>> For more options, visit this group at >>>> http://groups.google.com/group/votca?hl=en. >>>> >>>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "votca" group. >>> To post to this group, send email to [email protected]. >>> To unsubscribe from this group, send email to >>> [email protected]<votca%[email protected]> >>> <votca%[email protected]<votca%[email protected]> >>> >. >>> >>> For more options, visit this group at >>> http://groups.google.com/group/votca?hl=en. >>> >>> >>> >> > -- > Dipl.-Phys. Christoph Junghans > Max Planck Institute for Polymer Research > Theory Group > POBox 3148 > D 55021 Mainz, Germany > > Phone: +49 6131 379 335 > Web: > http://www.mpip-mainz.mpg.de/~junghans<http://www.mpip-mainz.mpg.de/%7Ejunghans> > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected] <votca%[email protected]>. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
