[gmx-users] can not pass gmxtest

[Yang Ye]

Hi,

You shall always try to build gromacs yourself. What's the error with 
tutorial?

Regards,
Yang Ye

On 11/7/2007 10:14 AM, Li Qiang wrote:
> hi all,
>
> I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package
> Manager(SPM). However, it can not pass the gamxtest with log as below,
> but Tutorials seems OK. 
> Actually I try to compile myself at the beginning. It is weird that the
> self-compiled one can pass the test but failed to run Tutorials with
> Segmental fault at PR MD step.
>
> Does anyboby know how to solve it? and how to uninstall GROMACS clear?
> thanks a lot.
>
> output from gmxtest:
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8
> ***
> ======= Backtrace: =========
> /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c]
> /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66]
> /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439]
> /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4]
> mdrun[0x8059f50]
> mdrun[0x805a72a]
> /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050]
> mdrun[0x804a491]
> ======= Memory map: ========
> 08048000-08062000 r-xp 00000000 08:04 2490502    /usr/bin/mdrun
> 08062000-08063000 rw-p 00019000 08:04 2490502    /usr/bin/mdrun
> 08063000-08085000 rw-p 08063000 00:00 0          [heap]
> b7800000-b7821000 rw-p b7800000 00:00 0 
> b7821000-b7900000 ---p b7821000 00:00 0 
> b79cc000-b79cd000 rw-p b79cc000 00:00 0 
> b79cd000-b79cf000 r-xp 00000000 08:04
> 2747181    /lib/tls/i686/cmov/libdl-2.6.1.so
> b79cf000-b79d1000 rw-p 00001000 08:04
> 2747181    /lib/tls/i686/cmov/libdl-2.6.1.so
> b79d1000-b79d5000 r-xp 00000000 08:04
> 2486327    /usr/lib/libXdmcp.so.6.0.0
> b79d5000-b79d6000 rw-p 00003000 08:04
> 2486327    /usr/lib/libXdmcp.so.6.0.0
> b79d6000-b79d8000 r-xp 00000000 08:04
> 2485527    /usr/lib/libXau.so.6.0.0
> b79d8000-b79d9000 rw-p 00001000 08:04
> 2485527    /usr/lib/libXau.so.6.0.0
> b79d9000-b79da000 rw-p b79d9000 00:00 0 
> b79da000-b7b1e000 r-xp 00000000 08:04
> 2747161    /lib/tls/i686/cmov/libc-2.6.1.so
> b7b1e000-b7b1f000 r--p 00143000 08:04
> 2747161    /lib/tls/i686/cmov/libc-2.6.1.so
> b7b1f000-b7b21000 rw-p 00144000 08:04
> 2747161    /lib/tls/i686/cmov/libc-2.6.1.so
> b7b21000-b7b24000 rw-p b7b21000 00:00 0 
> b7b24000-b7c11000 r-xp 00000000 08:04
> 2486347    /usr/lib/libX11.so.6.2.0
> b7c11000-b7c15000 rw-p 000ed000 08:04
> 2486347    /usr/lib/libX11.so.6.2.0
> b7c15000-b7c2a000 r-xp 00000000 08:04
> 2488182    /usr/lib/libICE.so.6.3.0
> b7c2a000-b7c2c000 rw-p 00014000 08:04
> 2488182    /usr/lib/libICE.so.6.3.0
> b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 
> b7c2d000-b7c34000 r-xp 00000000 08:04 2487000    /usr/lib/libSM.so.6.0.0
> b7c34000-b7c35000 rw-p 00006000 08:04 2487000    /usr/lib/libSM.so.6.0.0
> b7c35000-b7c58000 r-xp 00000000 08:04
> 2747187    /lib/tls/i686/cmov/libm-2.6.1.so
> b7c58000-b7c5a000 rw-p 00023000 08:04
> 2747187    /lib/tls/i686/cmov/libm-2.6.1.so
> b7c5a000-b7c6e000 r-xp 00000000 08:04
> 2747206    /lib/tls/i686/cmov/libnsl-2.6.1.so
> b7c6e000-b7c70000 rw-p 00013000 08:04
> 2747206    /lib/tls/i686/cmov/libnsl-2.6.1.so
> b7c70000-b7c73000 rw-p b7c70000 00:00 0 
> b7c73000-b7e27000 r-xp 00000000 08:04
> 2491023    /usr/lib/libgmx.so.4.0.0
> b7e27000-b7e30000 rw-p 001b3000 08:04
> 2491023    /usr/lib/libgmx.so.4.0.0
> b7e30000-b7e35000 rw-p b7e30000 00:00 0 
> b7e35000-b7f4a000 r-xp 00000000 08:04 2491025    /usr/lib/libmd.so.4.0.0
> b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025    /usr/lib/libmd.so.4.0.0
> b7f4b000-b7f4c000 rw-p b7f4b000 00:00 0 
> b7f4e000-b7f58000 r-xp 00000000 08:04 2747267    /lib/libgcc_s.so.1
> b7f58000-b7f59000 rw-p 0000a000 08:04 2747267    /lib/libgcc_s.so.1
> b7f59000-b7f5c000 rw-p b7f59000 00:00 0 
> b7f5c000-b7f76000 r-xp 00000000 08:04 2747274    /lib/ld-2.6.1.so
> b7f76000-b7f78000 rw-p 00019000 08:04 2747274    /lib/ld-2.6.1.so
> bfa98000-bfaad000 rwxp bfa98000 00:00 0          [stack]
> bfaad000-bfaae000 rw-p bfaad000 00:00 0 
> ffffe000-fffff000 r-xp 00000000 00:00 0          [vdso]
> FAILED. Check files in rb1
> 1 out of 16 simple tests FAILED
> FAILED. Check files in acetonitrilRF
> FAILED. Check files in dec+water
> 2 out of 14 complex tests FAILED
> All 63 kernel tests PASSED
> All 45 pdb2gmx tests PASSED
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>