[gmx-users] gmxtest rb1

Juliana Angeiras juangeiras at yahoo.com.br
Wed Oct 15 14:13:42 CEST 2008


Hi,
 
I will to upgrade to 4.0
Thanks,
 
Juliana.

--- Em qua, 15/10/08, David van der Spoel <spoel at xray.bmc.uu.se> escreveu:

De: David van der Spoel <spoel at xray.bmc.uu.se>
Assunto: Re: [gmx-users] gmxtest rb1
Para: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Data: Quarta-feira, 15 de Outubro de 2008, 6:10

Juliana Angeiras wrote:
> 
> Hi all,
>  
> I'm still having problems with the simple test in the directory rb1. I

> have used gromacs 3.3.3 and gmxtest 3.3.3. The simple test in the 
> directory simple/rb1/ crashed. The complex test dec+water too, but the 
> problem seems not too serious as the related in the wiki. The 
> configuration and the output are below.
>  

Hi Juliana,

I have reproduced this bug. It has been fixed in the most recent CVS but 
not in the 3.3.3 tree. A fix will be in release 4.0.1. I willhave a 
quick look to see whether it is easy to port the fixes to 3.3 (although 
we would like everyone to upgrade to 4.0).


> Thanks,
>  
> Juliana.
> 
>  > I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some
>  > problems when i had ran the gmxtest. The output is posted below:
>  > ./gmxtest.pl all
>  > *** glibc detected *** mdrun: realloc(): invalid next size: 
> 0x09e070d0 ***
>  > ======= Backtrace: =========
>  > /lib/libc.so.6[0xb0d440]
>  > /lib/libc.so.6(realloc+0x1a7)[0xb0e377]
>  > mdrun[0x8136675]
>  > ======= Memory map: ========
>  > 00101000-00200000 r-xp 00000000 fd:00 250620    
/usr/lib/libX11.so.6.2.0
>  > 00200000-00204000 rwxp 000ff000 fd:00 250620    
/usr/lib/libX11.so.6.2.0
>  > 00204000-00205000 rwxp 00204000 00:00 0
>  > 002bf000-002c0000 rwxp 002bf000 00:00 0
>  > 004c7000-004c8000 rwxp 004c7000 00:00 0
>  > 00835000-00848000 r-xp 00000000 fd:00 197077     /lib/libnsl-2.5.so
>  > 00848000-00849000 r-xp 00012000 fd:00 197077     /lib/libnsl-2.5.so
>  > 00849000-0084a000 rwxp 00013000 fd:00 197077     /lib/libnsl-2.5.so
>  > 0084a000-0084c000 rwxp 0084a000 00:00 0
>  > 008bb000-008bc000 r-xp 008bb000 00:00 0          [vdso]
>  > 008bf000-008c0000 rwxp 008bf000 00:00 0
>  > 009e8000-009f0000 r-xp 00000000 fd:00 250635    
/usr/lib/libSM.so.6.0.0
>  > 009f0000-009f1000 rwxp 00007000 fd:00 250635    
/usr/lib/libSM.so.6.0.0
>  > 009fa000-00a11000 r-xp 00000000 fd:00 250634    
/usr/lib/libICE.so.6.3.0
>  > 00a11000-00a12000 rwxp 00016000 fd:00 250634    
/usr/lib/libICE.so.6.3.0
>  > 00a12000-00a14000 rwxp 00a12000 00:00 0
>  > 00a7f000-00a99000 r-xp 00000000 fd:00 197064     /lib/ld-2.5.so
>  > 00a99000-00a9a000 r-xp 00019000 fd:00 197064     /lib/ld-2.5.so
>  > 00a9a000-00a9b000 rwxp 0001a000 fd:00 197064     /lib/ld-2.5.so
>  > 00a9d000-00a9f000 r-xp 00000000 fd:00 250618    
/usr/lib/libXau.so.6.0.0
>  > 00a9f000-00aa0000 rwxp 00001000 fd:00 250618    
/usr/lib/libXau.so.6.0.0
>  > 00aa2000-00bdf000 r-xp 00000000 fd:00 197065     /lib/libc-2.5.so
>  > 00bdf000-00be1000 r-xp 0013c000 fd:00 197065     /lib/libc-2.5.so
>  > 00be1000-00be2000 rwxp 0013e000 fd:00 197065     /lib/libc-2.5.so
>  > 00be2000-00be5000 rwxp 00be2000 00:00 0
>  > 00be7000-00c0c000 r-xp 00000000 fd:00 197072     /lib/libm-2.5.so
>  > 00c0c000-00c0d000 r-xp 00024000 fd:00 197072     /lib/libm-2.5.so
>  > 00c0d000-00c0e000 rwxp 00025000 fd:00 197072     /lib/libm-2.5.so
>  > 00c10000-00c12000 r-xp 00000000 fd:00 197066     /lib/libdl-2.5.so
>  > 00c12000-00c13000 r-xp 00001000 fd:00 197066     /lib/libdl-2.5.so
>  > 00c13000-00c14000 rwxp 00002000 fd:00 197066     /lib/libdl-2.5.so
>  > 00d30000-00d35000 r-xp 00000000 fd:00 250619   
> /usr/lib/libXdmcp.so.6.0.0
>  > 00d35000-00d36000 rwxp 00004000 fd:00 250619   
> /usr/lib/libXdmcp.so.6.0.0
>  > 049e1000-049ec000 r-xp 00000000 fd:00 197087    
>  > /lib/libgcc_s-4.1.2-20080102.so.1
>  > 049ec000-049ed000 rwxp 0000a000 fd:00 197087    
>  > /lib/libgcc_s-4.1.2-20080102.so.1
>  > 08048000-082f8000 r-xp 00000000 fd:00 1104196   
>  > /usr/local/gromacs/bin/mdrun
>  > 082f8000-082ff000 rwxp 002b0000 fd:00 1104196   
>  > /usr/local/gromacs/bin/mdrun
>  > 082ff000-08304000 rwxp 082ff000 00:00 0
>  > 09df4000-09e15000 rwxp 09df4000 00:00 0
>  > b7e00000-b7e21000 rwxp b7e00000 00:00 0
>  > b7e21000-b7f00000 --xp b7e21000 00:00 0
>  > bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0          [stack]
>  > sh: line 1: 17103 Abortado                mdrun > mdrun.out
2>&1
>  > FAILED. Check files in rb1
>  > 1 out of 16 simple tests FAILED
>  > FAILED. Check files in dec+water
>  > 1 out of 14 complex tests FAILED
>  > All 63 kernel tests PASSED
>  > All 45 pdb2gmx tests PASSED
>  > I have tried install the gromacs in another machine with Fedora Core
3
>  > and the gcc 3.4.4 and i have got similar result
>  > ./gmxtest.pl all
>  > *** glibc detected *** realloc(): invalid next size: 0x08a48f88 ***
>  > sh: line 1: 12569 Aborted                 mdrun >mdrun.out
2>&1
>  > FAILED. Check files in rb1
>  > 1 out of 16 simple tests FAILED
>  > FAILED. Check files in dec+water
>  > 1 out of 14 complex tests FAILED
>  > All 63 kernel tests PASSED
>  > All 45 pdb2gmx tests PASSED
>  >
>  > So I think that the problem is not because i have used in the firts
>  > machine the gcc 4.1.2 compiler. I have seen similar problems in the
>  > mailing list, but i didn't find any solutions. Can anybody help
me?
>  > 
>  > Thanks,
>  > 
>  > Juliana.
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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