Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund wrote: leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group As I said: "There's a call to clearPshift in do_merge which causes a segfault". Theres only one call to clearPshift in do_merge as far as I can remember. There is, and there are no code modifications necessary if the OP simply upgrades to version 4.5.3, which contains the proper code already. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund skrev 2010-12-18 21.15: leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? Sorry, forgot to answer this one. I could have a look, but so could you. I would *think* that 4.5.3 is ok in this respect. If you checkout the release-4-5-patches from git.gromacs.org you're definitely safe. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group As I said: "There's a call to clearPshift in do_merge which causes a segfault". Theres only one call to clearPshift in do_merge as far as I can remember. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group As I said: "There's a call to clearPshift in do_merge which causes a segfault". Theres only one call to clearPshift in do_merge as far as I can remember. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault in g_hbond
Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund skrev 2010-12-18 16.36:
Erik Marklund skrev 2010-12-18 16.23:
leila karami skrev 2010-12-18 16.18:
Dear Erik
excuse me, I sent .xtc and .tpr file your e-mail.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
I can reproduce the segfault. It doesn't happen without -hbn. I'll
have a crack at fixing it. I won't promise to have it done before
christmas, but I'll try.
Fixed it. There's a call to clearPshift in do_merge which causes a
segfault if g_hbond is run without -geminate. Here's what you do:
In gmx_hbond.c, enclose the call in an if-statement:
if (hb->per->pHist)
{
clearPshift(&(hb->per->pHist[a1][a2]));
}
I'll push this to the master and release branches some time today.
Thanks for reporting this.
Regards,
Erik
As it turns out, I (or possibly someone else) had already fixed this
issue in the master and release branches. Hence the solution is again to
update your gromacs installation.
Erik
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
--
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Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund skrev 2010-12-18 16.23:
leila karami skrev 2010-12-18 16.18:
Dear Erik
excuse me, I sent .xtc and .tpr file your e-mail.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
I can reproduce the segfault. It doesn't happen without -hbn. I'll
have a crack at fixing it. I won't promise to have it done before
christmas, but I'll try.
Fixed it. There's a call to clearPshift in do_merge which causes a
segfault if g_hbond is run without -geminate. Here's what you do:
In gmx_hbond.c, enclose the call in an if-statement:
if (hb->per->pHist)
{
clearPshift(&(hb->per->pHist[a1][a2]));
}
I'll push this to the master and release branches some time today.
Thanks for reporting this.
Regards,
Erik
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Segmentation fault in g_hbond
leila karami skrev 2010-12-18 16.18: Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group I can reproduce the segfault. It doesn't happen without -hbn. I'll have a crack at fixing it. I won't promise to have it done before christmas, but I'll try. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault in g_hbond
Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund skrev 2010-12-18 15.40: leila karami skrev 2010-12-18 15.38: Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only hbnum.xvg without segmentation fault. I'd like to see the actual output too, although it may not be ncessary if I can reproduce the error myself. how to file a bugzilla and attach a tpr and xtc/trr? I don't know. size of xtc file is large, how to attach this file to list? you could upload it somewhere and post a link to it. ..and here's the bugzilla tracker. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
leila karami skrev 2010-12-18 15.38: Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only hbnum.xvg without segmentation fault. I'd like to see the actual output too, although it may not be ncessary if I can reproduce the error myself. how to file a bugzilla and attach a tpr and xtc/trr? I don't know. size of xtc file is large, how to attach this file to list? you could upload it somewhere and post a link to it. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault in g_hbond
Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only hbnum.xvg without segmentation fault. how to file a bugzilla and attach a tpr and xtc/trr? I don't know. size of xtc file is large, how to attach this file to list? -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
Erik Marklund skrev 2010-12-18 15.02: leila karami skrev 2010-12-18 14.50: Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group Interesting. Could you file a bugzilla and attach a tpr and xtc/trr ? And could you provide the output from g_hbond, version 4.5.1? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
leila karami skrev 2010-12-18 14.50: Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group Interesting. Could you file a bugzilla and attach a tpr and xtc/trr ? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault in g_hbond
Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Segmentation fault in g_hbond
Hi, Upgrade to 4.5.x and see if the problem persists. I've hacked g_hbond quite a bit since 4.0.5. Erik leila karami skrev 2010-12-18 14.02: Dear gromacs users I'm using gromacs 4.0.5. with following command: g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn. my system contains protein, dna and water. when I use above command for protein and dna, there is no problem. segmentation fault is only for protein and water. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault in g_hbond
Dear gromacs users I'm using gromacs 4.0.5. with following command: g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn. my system contains protein, dna and water. when I use above command for protein and dna, there is no problem. segmentation fault is only for protein and water. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation fault in g_hbond
Dear gromacs users I used g_hbond tool for hydrogen bond analysis between protein and solvent (water molecules). I have encountered with : Select a group: 3 Selected 3: 'Protein' Select a group: 15 Selected 15: 'SOL' Checking for overlap in atoms between Protein and SOL Calculating hydrogen bonds between Protein (825 atoms) and SOL (22218 atoms) Found 7441 donors and 7654 acceptors Making hbmap structure...done. Reading frame 0 time0.000 Will do grid-seach on 14x14x14 grid, rcut=0.35 Back Off! I just backed up donor.xvg to ./#donor.xvg.2# Reading frame 400 time 1600.000 Found 27249 different hydrogen bonds in trajectory Found 33939 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 1/7441*Segmentation fault* How to fix it? any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
