Re: [gmx-users] debugging
Hi Miro, This can be of great help and a wonderful learning experience; at the same time also an enormous time-sink. First, you did already do a bunch of very helpful work in trying to find the latest version, where things still work, have the error be reproducible on a test system. If you were to file an issue on gitlab here: https://gitlab.com/gromacs/gromacs/-/issues - note that we moved from redmine - with the test sytem attached, this would help tremendously in fixing the bug. If you are up for the joy of debugging yourself and possibly provide your solution to gromacs, here are the steps that I would take: 0. check that this issue has not been already reported and solved (try the latest patch release (you did that), check in gitlab issues) 1. identify the smallest system where the issue occurs (or at least reasonably small, so that you can test quickly) 2. have a debug built of gromacs, using -DCMAKE_BUILD_TYPE=Debug 3. Set up a good build and debug environment. This in itself can take some time to find something that works well for the system that you're on. For a quick start gdb might work as well, more visual aids via IDEs like vscode and clion, ... are very useful. 4. Find the line where the error occurs (segfaults are kind of nice because they are very clear errors, often in a specific line and often a result of overlooked memory management (we're working our way through removing this via modernisation to modern C++ standards, but not there yet)) 5. Look at the call hierarchy, try to understand the larger context that you're in. 6. Try to identify the smallest surrounding context in which the bug occurs, try to figure which function/class allocates the memory for the object that causes the segfault If there are tests and the context is not too large: 7. See if there are some tests written for this context. (usually there are corresponding .cpp files in the test folder where bugs occur), add a test that reproduces the buggy behaviour. 8. Compile the tests, change code, then recompile tests until your test passes. 9. Check that your intial case works, otherwise add more tests that catch the failing behaviour, fix, repeat Otherwise: Follow memory allocations, resizes, etc of the offending object, see if you can trigger the segfault earlier by trying to access memory that you know should be accessible. Finally open a new merge-request on gitlab (see under https://gitlab.com/gromacs/gromacs/-/merge_requests), or create a merge request from the issue you had opened. Wait for comments and code-review. Hope that gives you a feeling for the task on hand - I would personally definitely recommend at least looking *at* the source code and giving it a shot, also for the sake of getting a feel for the internal gears of GROMACS and just taking it as far as you can and have time. Happy coding, Christian On 2020-04-28 12:16, Miro Astore wrote: Hi all, I am interested in how Gromacs works at the back end but I don't have much C experience so this might be silly. I have noticed that one of my systems that includes virtual sites parses fine through grompp in gromacs 2019.1 and 3 but fails in 2020.1 with a segmentation fault. 21169 Segmentation fault (core dumped) I'd like to try and debug this further. Should I try and go after this myself? -- 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.
[gmx-users] debugging
Hi all, I am interested in how Gromacs works at the back end but I don't have much C experience so this might be silly. I have noticed that one of my systems that includes virtual sites parses fine through grompp in gromacs 2019.1 and 3 but fails in 2020.1 with a segmentation fault. 21169 Segmentation fault (core dumped) I'd like to try and debug this further. Should I try and go after this myself? -- Miro A. Astore (he/him) PhD Candidate | Computational Biophysics Office 434 A28 School of Physics University of Sydney -- 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] Debugging 'inconsistent shifts'
On 15 January 2015 at 19:44, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 11:25 AM, Kalev Takkis wrote: On 15 January 2015 at 00:09, Justin Lemkul jalem...@vt.edu wrote: On 1/14/15 4:44 PM, Kalev Takkis wrote: Hi, list! GROMACS complains about inconsistent shifts and suggests me to check my topology. I have so done, but the problem is not immediately obvious. How can I make it tell me exactly which atoms/bonds it finds faulty? What were you doing when the error came up? What was your exact command? What is your system? Temperature equilibration, commands given were gmx grompp -f nvt.mdp -c simcell_minim.gro -p simcell.top -o simcell_temp.tpr gmx mdrun -v -deffnm simcell_temp GROMACS version 5.0.4, ff OPLS-AA Equilibration finishes without other problems, I can continue with the next step without the system blowing up. The error is not encountered during minimisation, it finishes fine, energies are reasonable and no trace of inconsistent shifts is found in the log. System is chromatography column, silica slab with attached hydrocarbon chains. The crystal surface is infinite in xz plane, so the mdp file specifies pbc = xyz periodic_molecules = yes Have you verified that all the bonded terms that span a periodic boundary are specified correctly? The model is hacked together from silica unit cell and chains using pdb2gmx, so it's entirely possible that there is indeed something wrong with my system. I'd like to know where. When GROMACS encounters this error The topology is the first and most likely source of error. can I make it reveal more details? Which atoms/bonds are involved? Some diagnostics tool or verbosity switch to mdrun maybe? How soon does the system blow up? General troubleshooting advice is at http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_ Unstable_System It doesn't. Noticed the message in the terminal window when I was trying to improve the visual with trjconv after the production run. Then went back through the logs and found that it was first reported in NVE equilibration. All GROMACS tools have a -debug flag that can be set, but you'll dump out a massive file with a ton of information you don't need. If you're not used to reading through it, it can be more of an obstacle than a useful tool :) No kidding. 1 step run - 25MB log file. Fortunately grep was able to extract the list of wonky atoms in a nice concise manner. Thank you for the advice. All the best, Kalev -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] Debugging 'inconsistent shifts'
On 1/15/15 11:25 AM, Kalev Takkis wrote: On 15 January 2015 at 00:09, Justin Lemkul jalem...@vt.edu wrote: On 1/14/15 4:44 PM, Kalev Takkis wrote: Hi, list! GROMACS complains about inconsistent shifts and suggests me to check my topology. I have so done, but the problem is not immediately obvious. How can I make it tell me exactly which atoms/bonds it finds faulty? What were you doing when the error came up? What was your exact command? What is your system? Temperature equilibration, commands given were gmx grompp -f nvt.mdp -c simcell_minim.gro -p simcell.top -o simcell_temp.tpr gmx mdrun -v -deffnm simcell_temp GROMACS version 5.0.4, ff OPLS-AA Equilibration finishes without other problems, I can continue with the next step without the system blowing up. The error is not encountered during minimisation, it finishes fine, energies are reasonable and no trace of inconsistent shifts is found in the log. System is chromatography column, silica slab with attached hydrocarbon chains. The crystal surface is infinite in xz plane, so the mdp file specifies pbc = xyz periodic_molecules = yes Have you verified that all the bonded terms that span a periodic boundary are specified correctly? The model is hacked together from silica unit cell and chains using pdb2gmx, so it's entirely possible that there is indeed something wrong with my system. I'd like to know where. When GROMACS encounters this error The topology is the first and most likely source of error. can I make it reveal more details? Which atoms/bonds are involved? Some diagnostics tool or verbosity switch to mdrun maybe? How soon does the system blow up? General troubleshooting advice is at http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System All GROMACS tools have a -debug flag that can be set, but you'll dump out a massive file with a ton of information you don't need. If you're not used to reading through it, it can be more of an obstacle than a useful tool :) -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.
Re: [gmx-users] Debugging 'inconsistent shifts'
On 15 January 2015 at 00:09, Justin Lemkul jalem...@vt.edu wrote: On 1/14/15 4:44 PM, Kalev Takkis wrote: Hi, list! GROMACS complains about inconsistent shifts and suggests me to check my topology. I have so done, but the problem is not immediately obvious. How can I make it tell me exactly which atoms/bonds it finds faulty? What were you doing when the error came up? What was your exact command? What is your system? Temperature equilibration, commands given were gmx grompp -f nvt.mdp -c simcell_minim.gro -p simcell.top -o simcell_temp.tpr gmx mdrun -v -deffnm simcell_temp GROMACS version 5.0.4, ff OPLS-AA Equilibration finishes without other problems, I can continue with the next step without the system blowing up. The error is not encountered during minimisation, it finishes fine, energies are reasonable and no trace of inconsistent shifts is found in the log. System is chromatography column, silica slab with attached hydrocarbon chains. The crystal surface is infinite in xz plane, so the mdp file specifies pbc = xyz periodic_molecules = yes The model is hacked together from silica unit cell and chains using pdb2gmx, so it's entirely possible that there is indeed something wrong with my system. I'd like to know where. When GROMACS encounters this error can I make it reveal more details? Which atoms/bonds are involved? Some diagnostics tool or verbosity switch to mdrun maybe? All the best, Kalev -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] Debugging 'inconsistent shifts'
On 1/14/15 4:44 PM, Kalev Takkis wrote: Hi, list! GROMACS complains about inconsistent shifts and suggests me to check my topology. I have so done, but the problem is not immediately obvious. How can I make it tell me exactly which atoms/bonds it finds faulty? What were you doing when the error came up? What was your exact command? What is your system? -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.
[gmx-users] Debugging 'inconsistent shifts'
Hi, list! GROMACS complains about inconsistent shifts and suggests me to check my topology. I have so done, but the problem is not immediately obvious. How can I make it tell me exactly which atoms/bonds it finds faulty? All the best, Kalev Takkis Institute of Chemistry Faculty of Science and Technology University of Tartu Ravila 14a Tartu 50411 ESTONIA -- 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.
