Hi, I can check all the possible combinations you listed in http://redmine.gromacs.org/issues/1834. Since my programming capability is limited, please direct me how to proceed for solving this issue?
On Tue, Oct 6, 2015 at 9:00 PM, Teemu Murtola <[email protected]> wrote: > Thanks for the clarification. I updated the Redmine issue ( > http://redmine.gromacs.org/issues/1834) with a summary and next steps. I > unfortunately do not have access to various systems to test the issue, but > I put some guesses on the possible reasons in the issue. > > Best regards, > Teemu > > On Tue, Oct 6, 2015, 07:37 Venkat Reddy <[email protected]> wrote: > > > Hi, > > Sorry for the confusion. Now I have generated a small xtc file and a very > > big pdb file. I can able to access small xtc file but unable to read the > > large pdb file (~10GB) (terminating with the same error as reported > > earlier). Does it mean my installation has some problem? > > > > On Mon, Oct 5, 2015 at 7:41 PM, Teemu Murtola <[email protected]> > > wrote: > > > > > Hi, > > > > > > That unfortunately doesn't tell us anything, since 1.5GB can still be > > read > > > with 32-bit file operations. You didn't answer any of the questions: > can > > > you open very small xtc files, or very large (requiring 64-bit access) > > > gro/pdb files, or not? We are still thinking that you should be able to > > > open any files smaller than 2GB just fine, but you are making confusing > > > claims that seem to contradict this, so this needs to be sorted out > > before > > > we can really conclude anything. > > > > > > Best regards, > > > Teemu > > > > > > On Mon, Oct 5, 2015, 08:32 Venkat Reddy <[email protected]> wrote: > > > > > > > Hi, > > > > Sorry for the delay in reply. > > > > I am able to access pdb/gro files of size 1.5 GB with Gromacs-5.1 > > > version. > > > > My Desktop is 32-bit whereas my xtc files were generated on our super > > > > cluster, which runs on 64-bit O.S. > > > > > > > > On Fri, Oct 2, 2015 at 9:46 AM, Teemu Murtola < > [email protected] > > > > > > > wrote: > > > > > > > > > Hi, > > > > > > > > > > On Thu, Oct 1, 2015 at 6:30 PM Szilárd Páll < > [email protected]> > > > > > wrote: > > > > > > > > > > > On Thu, Oct 1, 2015 at 8:01 AM, Venkat Reddy < > [email protected]> > > > > > wrote: > > > > > > > Gromacs-5.1 version can not read xtc files. However, it can > > access > > > > > single > > > > > > > frame gro/pdb files. > > > > > > > > > > > > > > > > > > > That's a bold claim that IMO requires equally strong proof. > > > > > > > > > > > > > > > > I agree with Szilard. Are you saying that you cannot even read a > > > > > single-frame xtc file with just a few kB in size? How about other > > > binary > > > > > files (e.g., trr)? How about large (>2GB) gro files? > > > > > > > > > > In your other mail to the list you were talking about a 32-bit > Ubuntu > > > VM. > > > > > > Are you sure you're not running into in incompatibility issue > > between > > > > the > > > > > > 32-bit binaries vs 64-bit xtc file(s) you're trying to read? > > > > > > > > > > > > > > > > I would still suspect that the underlying reason is that for some > > > reason, > > > > > 5.1 gets compiled without large file support in your system, which > > > makes > > > > > even plain fopen() fail on large files. The build system should > give > > an > > > > > error if it cannot find 64-bit file support, but the check may be > > > > > imperfect. Someone who can reproduce the issue (i.e., has access > to a > > > > > similar OS and other environment) should try what is actually > > required > > > to > > > > > get 64-bit file support working there. Based on the information you > > > > posted > > > > > in Redmine, the build system already checks that off_t is 64-bit > > > without > > > > > any extra defines on your system. The checks in the build system > have > > > not > > > > > changed between 5.0 and 5.1, though. > > > > > > > > > > Teemu > > > > > -- > > > > > 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 [email protected]. > > > > > > > > > > > > > > > > > > > > > -- > > > > 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 [email protected]. > > > -- > > > 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 [email protected]. > > > > > > > > > > > -- > > 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 [email protected]. > -- > 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 [email protected]. > -- 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 [email protected].
