[gmx-users] gmxtest

[David van der Spoel]

Juliana Angeiras wrote:
> 
> Hi,
>  
> 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.
Which gromacs version?
Exactly which test crashes, is it rb1?

-- 
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