Hi, 1) Yes, I can access the same xtc with older gromacs versions. 2) I can't access even smaller xtc files with 5.1 I will file a bug report for the same. Thank you
On Wed, Sep 30, 2015 at 9:28 PM, Teemu Murtola <teemu.murt...@gmail.com> wrote: > Hi, > > This sounds like the build system is not compiling Gromacs with 64-bit file > support like it should. Can you access the same file on the same system > with earlier Gromacs versions? Can you access smaller files with 5.1? > > Could you file a bug report at redmine.gromacs.org, and include at least > the following: > * information on your operating system > * contents of CMakeCache.txt, src/config.h, and src/gmxpre-config.h from > your build tree > * how you invoked cmake to configure the build. > > Teemu > > On Wed, Sep 30, 2015, 11:59 Venkat Reddy <venkat...@gmail.com> wrote: > > > Hi Teemu, > > Thanks for the prompt reply. Yes, the xtc file size is larger than 2GB > > (approx. 50GB) and both system.xtc and traj.xtc are same files. I am > > extremely sorry for the confusion :) > > > > On Wed, Sep 30, 2015 at 11:31 AM, Teemu Murtola <teemu.murt...@gmail.com > > > > wrote: > > > > > Thanks for testing it, I see that there is still room for improvement > in > > > getting more context information into the error messages. I'm a bit > > > confused by the difference between your original report of system.xtc > vs > > > traj.xtc in the new message, but that may not matter that much. Is your > > xtc > > > file larger that 2GB in size? > > > > > > On Wed, Sep 30, 2015, 07:53 Venkat Reddy <venkat...@gmail.com> wrote: > > > > > > > Hi Teemu, > > > > Thank you for providing the patch. But the patched version is giving > > > > following error message: > > > > > > > > Program: gmx rdf, VERSION 5.2-dev > > > > Source file: src/gromacs/utility/path.cpp (line 406) > > > > Function: static void gmx::File::throwOnError(const > > > > gmx::File::NotFoundInfo&) > > > > > > > > System I/O error: > > > > Failed to access file 'traj.xtc'. > > > > The file could not be opened. > > > > Reason: Value too large for defined data type > > > > (call to fopen() returned error code 75) > > > > > > > > I would like to inform you that I have installed this patched version > > to > > > a > > > > non-standard location. > > > > > > > > > > > > On Wed, Sep 30, 2015 at 8:39 AM, Teemu Murtola < > > teemu.murt...@gmail.com> > > > > wrote: > > > > > > > > > Hi, > > > > > > > > > > I now changed the check to provide more details (in 5140 > > > > > <https://gerrit.gromacs.org/5140>). If you haven't figured out > what > > > the > > > > > issue was, you could try building the source code from the above > > link, > > > > and > > > > > running it to get more details. > > > > > > > > > > There is not much we can do to help diagnose the issue further, > > unless > > > > you > > > > > can provide additional information on the file system contents. > Also > > > note > > > > > that if you provide an input file name that looks like a valid file > > > name > > > > > (with the correct extension), Gromacs 5.1 will use it as is, or > give > > an > > > > > error if it does not exist. Previous versions silently tried to > > append > > > > all > > > > > kinds of extensions if the file did not exist (or could not be > read) > > > even > > > > > in such a case, and could then use some other file as input. > > > > > > > > > > Best regards, > > > > > Teemu > > > > > > > > > > On Sat, Sep 26, 2015 at 11:56 AM Teemu Murtola < > > > teemu.murt...@gmail.com> > > > > > wrote: > > > > > > > > > > > This error has nothing to do with the contents of the file, but > > > rather > > > > > the > > > > > > operating system appears to be telling Gromacs that the file > cannot > > > be > > > > > > opened or that it is not a regular file. With the information > here, > > > > it's > > > > > > difficult to say anything more; if you want to debug this > further, > > > the > > > > > > relevant function is gmx::File::exists(). > > > > > > > > > > > > It would be useful to know what's the problem so that the check > (or > > > the > > > > > > error message) can be improved. > > > > > > > > > > > > Best regards, > > > > > > Teemu > > > > > > > > > > > > On Fri, Sep 25, 2015, 21:20 Venkat Reddy <venkat...@gmail.com> > > > wrote: > > > > > > > > > > > >> Hi Tsjerk, > > > > > >> Thank you for the quick reply. Yes I can access it with other > > > > versions, > > > > > >> like 4.5.5, 5.0.4. > > > > > >> > > > > > >> On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar < > > > tsje...@gmail.com > > > > > > > > > > >> wrote: > > > > > >> > > > > > >> > Hi Venkat, > > > > > >> > > > > > > >> > Does it exist? Is it accessible? The XTC format did not change > > > since > > > > > the > > > > > >> > early years of Gromacs. Can you access it with a different > > > version? > > > > > >> > > > > > > >> > Cheers, > > > > > >> > > > > > > >> > Tsjerk > > > > > >> > On Sep 25, 2015 19:52, "Venkat Reddy" <venkat...@gmail.com> > > > wrote: > > > > > >> > > > > > > >> > > Dear all, > > > > > >> > > I have a trajectory file generated by gromacs-4.5.5. > Recently > > I > > > > > tried > > > > > >> to > > > > > >> > > plot radial distribution function using 'gmx rdf' tool > > available > > > > in > > > > > >> > > gromacs-5.1. But I am getting the following error. > > > > > >> > > Error in user input: > > > > > >> > > Invalid command-line options > > > > > >> > > In command-line option -f > > > > > >> > > File 'system.xtc' does not exist or is not accessible. > > > > > >> > > > > > > > >> > > I knew that gromacs old trajectories can be analysed using > new > > > > > version > > > > > >> > > tools. But why I am facing this error? > > > > > >> > > > > > > > >> > > > > > > > >> > > With regards > > > > > >> > > Venkat Reddy Chirasani > > > > > >> > > PhD student > > > > > >> > > Laboratory of Computational Biophysics > > > > > >> > > Department of Biotechnology > > > > > >> > > IIT Madras > > > > > >> > > Chennai > > > > > >> > > INDIA-600036 > > > > > >> > > -- > > > > > >> > > Gromacs Users mailing list > > > > > >> > > > > > > > >> > > * Please search the archive at > > > > > >> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > > > before > > > > > >> > > posting! > > > > > >> > > > > > > > >> > > * Can't post? Read > > http://www.gromacs.org/Support/Mailing_Lists > > > > > >> > > > > > > > >> > > * For (un)subscribe requests visit > > > > > >> > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > > or > > > > > >> > > send a mail to gmx-users-requ...@gromacs.org. > > > > > >> > > > > > > > >> > -- > > > > > >> > Gromacs Users mailing list > > > > > >> > > > > > > >> > * Please search the archive at > > > > > >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > > before > > > > > >> > posting! > > > > > >> > > > > > > >> > * Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > > > >> > > > > > > >> > * For (un)subscribe requests visit > > > > > >> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > or > > > > > >> > send a mail to gmx-users-requ...@gromacs.org. > > > > > >> > > > > > > >> > > > > > >> > > > > > >> > > > > > >> -- > > > > > >> With Best Wishes > > > > > >> Venkat Reddy Chirasani > > > > > >> PhD student > > > > > >> Laboratory of Computational Biophysics > > > > > >> Department of Biotechnology > > > > > >> IIT Madras > > > > > >> Chennai > > > > > >> INDIA-600036 > > > > > >> -- > > > > > >> Gromacs Users mailing list > > > > > >> > > > > > >> * Please search the archive at > > > > > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > > before > > > > > >> posting! > > > > > >> > > > > > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > >> > > > > > >> * For (un)subscribe requests visit > > > > > >> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > or > > > > > >> send a mail to gmx-users-requ...@gromacs.org. > > > > > >> > > > > > > > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > > posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > > > > > > -- > > > > With Best Wishes > > > > Venkat Reddy Chirasani > > > > PhD student > > > > Laboratory of Computational Biophysics > > > > Department of Biotechnology > > > > IIT Madras > > > > Chennai > > > > INDIA-600036 > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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