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
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
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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
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
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
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
