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

2012-04-10 Thread David van der Spoel 

On 2012-04-10 12:38, Steven Neumann wrote:



On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel
mailto:sp...@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):
0x01cf0480 ***
=== 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: 
0040-00756000 r-xp  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  00:00 0
01cde000-020a3000 rwxp  00:00 0
[heap]
30fbe0-30fbe2 r-xp  08:01 558856
/lib64/ld-2.12.so 
30fc01f000-30fc02 r-xp 0001f000 08:01 558856
/lib64/ld-2.12.so 
30fc02-30fc021000 rwxp 0002 08:01 558856
/lib64/ld-2.12.so 
30fc021000-30fc022000 rwxp  00:00 0
30fc20-30fc202000 r-xp  08:01 554053
/lib64/libdl-2.12.so 
30fc202000-30fc402000 ---p 2000 08:01 554053
/lib64/libdl-2.12.so 
30fc402000-30fc403000 r-xp 2000 08:01 554053
/lib64/libdl-2.12.so 
30fc403000-30fc404000 rwxp 3000 08:01 554053
/lib64/libdl-2.12.so 
30fc60-30fc786000 r-xp  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 
30fc98b000-30fc99 rwxp  00:00 0
30fca0-30fca17000 r-xp  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  00:00 0
30fce0-30fce83000 r-xp  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 
30fd20-30fd215000 r-xp  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
30fd60-30fd607000 r-xp  08:01 558859
/lib64/librt-2.12.so 
30fd607000-30fd806000 ---p 7000 08:01 558859
/lib64/librt-2.12.so 
30fd806000-30fd807000 r-xp 6000 08:01 558859
/lib64/librt-2.12.so 
30fd807000-30fd808000 rwxp 7000 08:01 558859
/lib64/librt-2.12.so 
30fe60-30fe616000 r-xp  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
310620-3106347000 r-xp  08:01 738508
/usr/lib64/libxml2.so.2.7.6
3106347000-3106546000 ---p 00147000 08:01 738508
/usr/lib64/libxml2.so.2.7.6
3106546000-310655 rwxp 00146000 08:01 738508
/usr/lib64/libxml2.so.2.7.6
310655-3106551000 rwxp  00:00 0
310d60-310d616000 r-xp  08:01 558894
/lib64/libnsl-2.12.so 
310d616000-310d815000 ---p 00016000 08:01 558894
/lib64/libnsl-2.12.so

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

2012-04-10 Thread Steven Neumann 
On Tue, Apr 10, 2012 at 11:28 AM, David van der Spoel
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):
0x01cf0480 ***
=== 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: 
0040-00756000 r-xp  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  00:00 0
01cde000-020a3000 rwxp  00:00 0
[heap]
30fbe0-30fbe2 r-xp  08:01 558856
/lib64/ld-2.12.so
30fc01f000-30fc02 r-xp 0001f000 08:01 558856
/lib64/ld-2.12.so
30fc02-30fc021000 rwxp 0002 08:01 558856
/lib64/ld-2.12.so
30fc021000-30fc022000 rwxp  00:00 0
30fc20-30fc202000 r-xp  08:01 554053
/lib64/libdl-2.12.so
30fc202000-30fc402000 ---p 2000 08:01 554053
/lib64/libdl-2.12.so
30fc402000-30fc403000 r-xp 2000 08:01 554053
/lib64/libdl-2.12.so
30fc403000-30fc404000 rwxp 3000 08:01 554053
/lib64/libdl-2.12.so
30fc60-30fc786000 r-xp  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
30fc98b000-30fc99 rwxp  00:00 0
30fca0-30fca17000 r-xp  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  00:00 0
30fce0-30fce83000 r-xp  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
30fd20-30fd215000 r-xp  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
30fd60-30fd607000 r-xp  08:01 558859
/lib64/librt-2.12.so
30fd607000-30fd806000 ---p 7000 08:01 558859
/lib64/librt-2.12.so
30fd806000-30fd807000 r-xp 6000 08:01 558859
/lib64/librt-2.12.so
30fd807000-30fd808000 rwxp 7000 08:01 558859
/lib64/librt-2.12.so
30fe60-30fe616000 r-xp  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
310620-3106347000 r-xp  08:01 738508
/usr/lib64/libxml2.so.2.7.6
3106347000-3106546000 ---p 00147000 08:01 738508
/usr/lib64/libxml2.so.2.7.6
3106546000-310655 rwxp 00146000 08:01 738508
/usr/lib64/libxml2.so.2.7.6
310655-3106551000 rwxp  00:00 0
310d60-310d616000 r-xp  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  00:00 0
2b3cd1d8b000-2b3cd1d9e000 rwxp  00:00 0
2b3cd1dad000-2b3cd1dae000 rwxp  00:00 0
2b3cd1dae000-2b3cd202 r-xp  00:1f 91899538
/apps/intel/fc/9.1.045/lib/libimf.so
2b3cd202-2b3cd211f000 ---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  00:00 0
2b3cd2125000-2b3cd230a000 r-xp  00:1f 92286570
/apps/intel/ict/mpi/3.1.038/lib64/libmpi.so.3.2
2b3cd230a000-2b3cd240a000 ---p 001e5000 00:1f 92286570
/

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

2012-04-10 Thread David van der Spoel 

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?


On Tue, Apr 10, 2012 at 10:59 AM, Carsten Kutzner mailto:ckut...@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
 >
>  --
>  gmx-users mailing list gmx-users@gromacs.org

>  http://lists.gromacs.org/mailman/listinfo/gmx-users
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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.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Error: 4095 characters, fgets2 has size 4095

2012-04-10 Thread Steven Neumann 
Thank you for the reply. I do not have such files in my directory or in my
force field.

On Tue, Apr 10, 2012 at 10:59 AM, Carsten Kutzner  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 listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> 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 gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Error: 4095 characters, fgets2 has size 4095

2012-04-10 Thread Carsten Kutzner 
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 listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> 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 gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

2012-04-10 Thread Steven Neumann 
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 listgmx-users@gromacs.org
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Please search the archive at 
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