[gmx-users] g_covar Segmentation fault problem
Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. Do I need to lower the number of atoms to analyze or higher the frame numbers or is it ok if I use 4.6.3? Thanks. -- 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.
Re: [gmx-users] g_covar Segmentation fault problem
On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated versions work and which don't. To be safe: 4.6.x series, use version = 4.6.6 5.0.x series, use version 5.0.5 Any other version in the development repo (master, release-5-0, etc) -Justin On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] g_covar Segmentation fault problem
Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom. On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated versions work and which don't. To be safe: 4.6.x series, use version = 4.6.6 5.0.x series, use version 5.0.5 Any other version in the development repo (master, release-5-0, etc) -Justin On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] g_covar Segmentation fault problem
On 7/16/15 1:09 PM, gozde ergin wrote: Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom. Then use 4.6.7. Maybe my = should have been instead. The best bet when you get failures like this is to always upgrade to the latest version in whatever series you're trying to use. 4.6.7 should work. If not, 5.0.5 definitely does. -Justin On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated versions work and which don't. To be safe: 4.6.x series, use version = 4.6.6 5.0.x series, use version 5.0.5 Any other version in the development repo (master, release-5-0, etc) -Justin On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] g_covar Segmentation fault problem
Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
Re: [gmx-users] g_covar Segmentation fault problem
On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
