On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel <[email protected]>wrote:
> On 2012-04-10 12:02, Steven Neumann wrote: > >> Thank you for the reply. I do not have such files in my directory or in >> my force field. >> > did you mean dos2unix? > > try: > wc grompp.mdp > to count the number of lines. There should be may. > In fact grompp probably tells you which input file is erroneous, doesn't > it? > It does not provide the information which file is this. I checked every file with wc -L and it does not exceed 100. However I read that creating gurgle.dat - empty file may solve it. When I did it and process grmpp: Ignoring obsolete mdp entry 'title' Generated 67161 of the 67161 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 49536 of the 67161 1-4 parameter combinations WARNING: File is empty *** glibc detected *** grompp: double free or corruption (!prev): 0x0000000001cf0480 *** ======= Backtrace: ========= /lib64/libc.so.6[0x30fc675296] /lib64/libc.so.6(fclose+0x14d)[0x30fc665a1d] grompp[0x5a5952] grompp[0x59ba29] grompp[0x5a67bd] grompp[0x5a661f] grompp[0x5cb798] grompp[0x5a7184] grompp[0x41fd8c] grompp[0x41fa38] grompp[0x408a8d] grompp[0x405422] /lib64/libc.so.6(__libc_start_main+0xfd)[0x30fc61ecdd] grompp[0x404eaa] ======= Memory map: ======== 00400000-00756000 r-xp 00000000 00:1f 107224920 /apps/gromacs/4.5.4/bin/grompp 00855000-00865000 rwxp 00355000 00:1f 107224920 /apps/gromacs/4.5.4/bin/grompp 00865000-00894000 rwxp 00000000 00:00 0 01cde000-020a3000 rwxp 00000000 00:00 0 [heap] 30fbe00000-30fbe20000 r-xp 00000000 08:01 558856 /lib64/ld-2.12.so 30fc01f000-30fc020000 r-xp 0001f000 08:01 558856 /lib64/ld-2.12.so 30fc020000-30fc021000 rwxp 00020000 08:01 558856 /lib64/ld-2.12.so 30fc021000-30fc022000 rwxp 00000000 00:00 0 30fc200000-30fc202000 r-xp 00000000 08:01 554053 /lib64/libdl-2.12.so 30fc202000-30fc402000 ---p 00002000 08:01 554053 /lib64/libdl-2.12.so 30fc402000-30fc403000 r-xp 00002000 08:01 554053 /lib64/libdl-2.12.so 30fc403000-30fc404000 rwxp 00003000 08:01 554053 /lib64/libdl-2.12.so 30fc600000-30fc786000 r-xp 00000000 08:01 558857 /lib64/libc-2.12.so 30fc786000-30fc986000 ---p 00186000 08:01 558857 /lib64/libc-2.12.so 30fc986000-30fc98a000 r-xp 00186000 08:01 558857 /lib64/libc-2.12.so 30fc98a000-30fc98b000 rwxp 0018a000 08:01 558857 /lib64/libc-2.12.so 30fc98b000-30fc990000 rwxp 00000000 00:00 0 30fca00000-30fca17000 r-xp 00000000 08:01 558858 /lib64/libpthread-2.12.so 30fca17000-30fcc16000 ---p 00017000 08:01 558858 /lib64/libpthread-2.12.so 30fcc16000-30fcc17000 r-xp 00016000 08:01 558858 /lib64/libpthread-2.12.so 30fcc17000-30fcc18000 rwxp 00017000 08:01 558858 /lib64/libpthread-2.12.so 30fcc18000-30fcc1c000 rwxp 00000000 00:00 0 30fce00000-30fce83000 r-xp 00000000 08:01 558867 /lib64/libm-2.12.so 30fce83000-30fd082000 ---p 00083000 08:01 558867 /lib64/libm-2.12.so 30fd082000-30fd083000 r-xp 00082000 08:01 558867 /lib64/libm-2.12.so 30fd083000-30fd084000 rwxp 00083000 08:01 558867 /lib64/libm-2.12.so 30fd200000-30fd215000 r-xp 00000000 08:01 558866 /lib64/libz.so.1.2.3 30fd215000-30fd414000 ---p 00015000 08:01 558866 /lib64/libz.so.1.2.3 30fd414000-30fd415000 r-xp 00014000 08:01 558866 /lib64/libz.so.1.2.3 30fd415000-30fd416000 rwxp 00015000 08:01 558866 /lib64/libz.so.1.2.3 30fd600000-30fd607000 r-xp 00000000 08:01 558859 /lib64/librt-2.12.so 30fd607000-30fd806000 ---p 00007000 08:01 558859 /lib64/librt-2.12.so 30fd806000-30fd807000 r-xp 00006000 08:01 558859 /lib64/librt-2.12.so 30fd807000-30fd808000 rwxp 00007000 08:01 558859 /lib64/librt-2.12.so 30fe600000-30fe616000 r-xp 00000000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1 30fe616000-30fe815000 ---p 00016000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1 30fe815000-30fe816000 rwxp 00015000 08:01 558868 /lib64/libgcc_s-4.4.6-20110824.so.1 3106200000-3106347000 r-xp 00000000 08:01 738508 /usr/lib64/libxml2.so.2.7.6 3106347000-3106546000 ---p 00147000 08:01 738508 /usr/lib64/libxml2.so.2.7.6 3106546000-3106550000 rwxp 00146000 08:01 738508 /usr/lib64/libxml2.so.2.7.6 3106550000-3106551000 rwxp 00000000 00:00 0 310d600000-310d616000 r-xp 00000000 08:01 558894 /lib64/libnsl-2.12.so 310d616000-310d815000 ---p 00016000 08:01 558894 /lib64/libnsl-2.12.so 310d815000-310d816000 r-xp 00015000 08:01 558894 /lib64/libnsl-2.12.so 310d816000-310d817000 rwxp 00016000 08:01 558894 /lib64/libnsl-2.12.so 310d817000-310d819000 rwxp 00000000 00:00 0 2b3cd1d8b000-2b3cd1d9e000 rwxp 00000000 00:00 0 2b3cd1dad000-2b3cd1dae000 rwxp 00000000 00:00 0 2b3cd1dae000-2b3cd2020000 r-xp 00000000 00:1f 91899538 /apps/intel/fc/9.1.045/lib/libimf.so 2b3cd2020000-2b3cd211f000 ---p 00272000 00:1f 91899538 /apps/intel/fc/9.1.045/lib/libimf.so 2b3cd211f000-2b3cd2124000 rwxp 00271000 00:1f 91899538 /apps/intel/fc/9.1.045/lib/libimf.so 2b3cd2124000-2b3cd2125000 rwxp 00000000 00:00 0 2b3cd2125000-2b3cd230a000 r-xp 00000000 00:1f 92286570 /apps/intel/ict/mpi/3.1.038/lib64/libmpi.so.3.2 2b3cd230a000-2b3cd240a000 ---p 001e5000 00:1f 92286570 /apps/intel/ict/mpi/3.1.038/lib64/libmpi.so.3.2 2b3cd240a000-2b3cd241e000 rwxp 001e5000 00:1f 92286570 /apps/intel/ict/mpi/3.1.038/lib64/libmpi.so.3.2 2b3cd241e000-2b3cd245d000 rwxp 00000000 00:00 0 2b3cd245d000-2b3cd248d000 r-xp 00000000 00:1f 92286590 /apps/intel/ict/mpi/3.1.038/lib64/libmpigf.so.3.2 2b3cd248d000-2b3cd258c000 ---p 00030000 00:1f 92286590 /apps/intel/ict/mpi/3.1.038/lib64/libmpigf.so.3.2 2b3cd258c000-2b3cd258e000 rwxp 0002f000 00:1f 92286590 /apps/intel/ict/mpi/3.1.038/lib64/libmpigf.so.3.2 2b3cd258e000-2b3cd419c000 rwxp 00000000 00:00 0 7ffff1d4e000-7ffff1d67000 rwxp 00000000 00:00 0 [stack] 7ffff1dff000-7ffff1e00000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted (core dumped) Any clue? Please, help! > >> On Tue, Apr 10, 2012 at 10:59 AM, Carsten Kutzner <[email protected] >> <mailto:[email protected]>> wrote: >> >> Hi Steven, >> >> you might have to remove files with weird names (such as ._name) in >> the directory where you run >> grompp or in your forcefield directory. >> >> Carsten >> >> >> On Apr 10, 2012, at 11:52 AM, Steven Neumann wrote: >> >> > Dear Gmx Users, >> > >> > It is 1st time I came across such problem. While preparing my NPT >> simulation before umbrella samping: >> > >> > grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx >> -o npt0.tpr >> > >> > An input file contains a line longer than 4095 characters, while >> the buffer passed to fgets2 has size 4095. The line starts with: '20s' >> > >> > Its not about the files in bad format as I have never had this >> problem - I am using Gromacs 4.5.4 installed on the cluster, I am >> using PuTTy shell. I always use dos2gmx ibefore processing. >> > >> > Can you advise? >> > >> > Steven >> > >> > -- >> > gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > Please search the archive at >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]>>. >> >> >> > Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at >> >> http://www.gromacs.org/**Support/Mailing_Lists/Search<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 [email protected] >> <mailto:gmx-users-request@**gromacs.org<[email protected]>>. >> >> >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> >> >> >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > [email protected] http://folding.bmc.uu.se > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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