[gmx-users] Error: 4095 characters, fgets2 has size 4095

Steven Neumann s.neumann08 at gmail.com
Tue Apr 10 12:38:41 CEST 2012 

On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel
<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:

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 <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.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>
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