[gmx-users] can not pass gmxtest
Li Qiang
liqiang at bii.a-star.edu.sg
Wed Nov 7 09:35:45 CET 2007
hi yang,
thanks for the reply. Do you mean that the installation from SMP is not
right?
The error with self-compiled gromacs is in position restrain step with
unusual distances and the mdrun stops at step0 with "Segmentation fault
(core dumped)". but the mdrun with constraint can run, though I do not
know if it is right.
The possible reason is that I install from SMP of ubuntu but forget to
remove the self-compiled one. Several days ago the gromacs version from
SMP is 3.3.1. I though it was simpler to install GROMACS automatically
from that.
Could tell me how to remove GROMACS entirely so that I can reinstall
from fresh? Hope we can do it.
thank you very much.
Li Qiang
On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote:
> 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
> >
> >
> > _______________________________________________
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>
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