Re: [gmx-users] glibc error with g_density (only for some cases)
Arun kumar wrote: Dear David, My gcc compiler version is 4.0.1. Is there any problem with this version?? On 5/18/07, David van der Spoel [EMAIL PROTECTED] wrote: Arun kumar wrote: Hai Mark.. Thanks for your suggestions. I will think about my problem clearly and will post a message with much care so that every one can easily read. Also I can get a response. About g_density I will check once again the log file and post the reply here. But I think there is nothing went wrong in my simulations in between 500 and 1500 time steps. I am able to evaluate all properties for those frames also. Anyway I will check once again. Thanks and regards Arun Kumar On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I use g_density -b 500 I get the following error *** glibc detected *** free(): invalid next size (normal): 0x00713260 *** Aborted This is either a compilation problem or a bug, but most likely the first. Did you use gcc 4.1.x by any chance? That compiler is broken. gcc 4.0.1 should be fine as far as I know. You are welcome to submit a bugzilla with input that reproduces the problem. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] glibc error with g_density (only for some cases)
Dear David, I will check the reproducibility of the result once again. And then I will submit the bugzilla with all inputs I used for these simulations. Regards, Arun On 5/19/07, David van der Spoel [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear David, My gcc compiler version is 4.0.1. Is there any problem with this version?? On 5/18/07, David van der Spoel [EMAIL PROTECTED] wrote: Arun kumar wrote: Hai Mark.. Thanks for your suggestions. I will think about my problem clearly and will post a message with much care so that every one can easily read. Also I can get a response. About g_density I will check once again the log file and post the reply here. But I think there is nothing went wrong in my simulations in between 500 and 1500 time steps. I am able to evaluate all properties for those frames also. Anyway I will check once again. Thanks and regards Arun Kumar On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I use g_density -b 500 I get the following error *** glibc detected *** free(): invalid next size (normal): 0x00713260 *** Aborted This is either a compilation problem or a bug, but most likely the first. Did you use gcc 4.1.x by any chance? That compiler is broken. gcc 4.0.1 should be fine as far as I know. You are welcome to submit a bugzilla with input that reproduces the problem. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arun kumar.V M.E Chemical ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] glibc error with g_density (only for some cases)
Arun kumar wrote: Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I use g_density -b 500 I get the following error *** glibc detected *** free(): invalid next size (normal): 0x00713260 *** Aborted It is giving a empty density.xvg file I get same error if I use g_density -b 1000 I checked the reproducibility of the error.. I am getting it always(I mean I am using g_density once again again, Not simulating the system once again again) But when I use g_density -b 1500 or more I am getting densities normally. Actually i am doing simulations at 4 different temperatures. But I am getting the error only for three temperatures For one temperature Every thing is fine.. Gromacs version I am using is : 3.3.1 I checked the archives and in google I found a similar error in archives for make_ndx After checking in google I came to know that its a common bug with glibc package of different versions. Now i want to know is there anything wrong in my simulations(possibilities) and also how I can rid of these errors. You stand a much better chance of getting a response if you make your requests easy to read. That means using conventional English punctuation, ie. not ending most sentences with an ellipsis. Your use of ellipses in the above text makes it read like it is a stream of consciousness that you haven't thought through clearly. That makes people not want to do your work - thinking clearly about your problem and describing it well - and thus never getting around to giving you any insight. I have never used g_density, but I had look at the man page for 30 seconds and I can think of two reasons why doing an analysis starting at point c would work when it doesn't work starting at a or b, when abc. Since it only happens for one of your 4 near-identical simulations, this suggests one of my reasons isn't right... and so I think there is a problem with your output between b and c for the one that breaks. Go and look at the log file and see what went wrong. I didn't apply much knowledge here, I just thought about the problem clearly. Perhaps this would have occurred to you if you'd thought about things this way before posting :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] glibc error with g_density (only for some cases)
Arun kumar wrote: Hai Mark.. Thanks for your suggestions. I will think about my problem clearly and will post a message with much care so that every one can easily read. Also I can get a response. About g_density I will check once again the log file and post the reply here. But I think there is nothing went wrong in my simulations in between 500 and 1500 time steps. I am able to evaluate all properties for those frames also. Anyway I will check once again. Thanks and regards Arun Kumar On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I use g_density -b 500 I get the following error *** glibc detected *** free(): invalid next size (normal): 0x00713260 *** Aborted This is either a compilation problem or a bug, but most likely the first. Did you use gcc 4.1.x by any chance? That compiler is broken. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] glibc error with g_density (only for some cases)
Dear David, My gcc compiler version is 4.0.1. Is there any problem with this version?? On 5/18/07, David van der Spoel [EMAIL PROTECTED] wrote: Arun kumar wrote: Hai Mark.. Thanks for your suggestions. I will think about my problem clearly and will post a message with much care so that every one can easily read. Also I can get a response. About g_density I will check once again the log file and post the reply here. But I think there is nothing went wrong in my simulations in between 500 and 1500 time steps. I am able to evaluate all properties for those frames also. Anyway I will check once again. Thanks and regards Arun Kumar On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I use g_density -b 500 I get the following error *** glibc detected *** free(): invalid next size (normal): 0x00713260 *** Aborted This is either a compilation problem or a bug, but most likely the first. Did you use gcc 4.1.x by any chance? That compiler is broken. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arun kumar.V M.E Chemical ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
