On 2012-04-10 12:38, Steven Neumann wrote:
On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel
<[email protected] <mailto:[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:
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
<[email protected] <mailto:[email protected]>
<mailto:[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
>
> --
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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>.
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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