[gmx-users] Error: 4095 characters, fgets2 has size 4095
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 10 13:06:40 CEST 2012
On 2012-04-10 12:38, Steven Neumann wrote:
>
>
> On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> 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:
weird. On what kind of machine are you running?
Did you do
source PATHTOGROMACS/bin/GMXRC
?
> 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 <http://ld-2.12.so>
> 30fc01f000-30fc020000 r-xp 0001f000 08:01 558856
> /lib64/ld-2.12.so <http://ld-2.12.so>
> 30fc020000-30fc021000 rwxp 00020000 08:01 558856
> /lib64/ld-2.12.so <http://ld-2.12.so>
> 30fc021000-30fc022000 rwxp 00000000 00:00 0
> 30fc200000-30fc202000 r-xp 00000000 08:01 554053
> /lib64/libdl-2.12.so <http://libdl-2.12.so>
> 30fc202000-30fc402000 ---p 00002000 08:01 554053
> /lib64/libdl-2.12.so <http://libdl-2.12.so>
> 30fc402000-30fc403000 r-xp 00002000 08:01 554053
> /lib64/libdl-2.12.so <http://libdl-2.12.so>
> 30fc403000-30fc404000 rwxp 00003000 08:01 554053
> /lib64/libdl-2.12.so <http://libdl-2.12.so>
> 30fc600000-30fc786000 r-xp 00000000 08:01 558857
> /lib64/libc-2.12.so <http://libc-2.12.so>
> 30fc786000-30fc986000 ---p 00186000 08:01 558857
> /lib64/libc-2.12.so <http://libc-2.12.so>
> 30fc986000-30fc98a000 r-xp 00186000 08:01 558857
> /lib64/libc-2.12.so <http://libc-2.12.so>
> 30fc98a000-30fc98b000 rwxp 0018a000 08:01 558857
> /lib64/libc-2.12.so <http://libc-2.12.so>
> 30fc98b000-30fc990000 rwxp 00000000 00:00 0
> 30fca00000-30fca17000 r-xp 00000000 08:01 558858
> /lib64/libpthread-2.12.so <http://libpthread-2.12.so>
> 30fca17000-30fcc16000 ---p 00017000 08:01 558858
> /lib64/libpthread-2.12.so <http://libpthread-2.12.so>
> 30fcc16000-30fcc17000 r-xp 00016000 08:01 558858
> /lib64/libpthread-2.12.so <http://libpthread-2.12.so>
> 30fcc17000-30fcc18000 rwxp 00017000 08:01 558858
> /lib64/libpthread-2.12.so <http://libpthread-2.12.so>
> 30fcc18000-30fcc1c000 rwxp 00000000 00:00 0
> 30fce00000-30fce83000 r-xp 00000000 08:01 558867
> /lib64/libm-2.12.so <http://libm-2.12.so>
> 30fce83000-30fd082000 ---p 00083000 08:01 558867
> /lib64/libm-2.12.so <http://libm-2.12.so>
> 30fd082000-30fd083000 r-xp 00082000 08:01 558867
> /lib64/libm-2.12.so <http://libm-2.12.so>
> 30fd083000-30fd084000 rwxp 00083000 08:01 558867
> /lib64/libm-2.12.so <http://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 <http://librt-2.12.so>
> 30fd607000-30fd806000 ---p 00007000 08:01 558859
> /lib64/librt-2.12.so <http://librt-2.12.so>
> 30fd806000-30fd807000 r-xp 00006000 08:01 558859
> /lib64/librt-2.12.so <http://librt-2.12.so>
> 30fd807000-30fd808000 rwxp 00007000 08:01 558859
> /lib64/librt-2.12.so <http://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 <http://libnsl-2.12.so>
> 310d616000-310d815000 ---p 00016000 08:01 558894
> /lib64/libnsl-2.12.so <http://libnsl-2.12.so>
> 310d815000-310d816000 r-xp 00015000 08:01 558894
> /lib64/libnsl-2.12.so <http://libnsl-2.12.so>
> 310d816000-310d817000 rwxp 00016000 08:01 558894
> /lib64/libnsl-2.12.so <http://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
> <ckutzne at gwdg.de <mailto:ckutzne at gwdg.de>
> <mailto:ckutzne at gwdg.de <mailto:ckutzne at gwdg.de>>> 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
> >
> > --
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> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
> <tel:%2B46184714205>.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> http://folding.bmc.uu.se <http://folding.bmc.uu.se/>
>
> --
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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