[gmx-users] can not pass gmxtest
Li Qiang
liqiang at bii.a-star.edu.sg
Wed Nov 7 11:17:29 CET 2007
hi,
I just try to remove and rebuild and install GROMACS.
This time the self-built one also can not pass the test. The same errors
are reported:
+++++++++++++++++++++++++++++++++++++++++
liqiang at liqiang-desktop:~/gromacs-3.3.2$ sudo make tests
(if test -d "gmxtest"; then cd "gmxtest"; ./gmxtest.pl all; cd ..; \
else echo "No gmxtest directory found. Please download and
unpack it here.";\
fi)
*** glibc detected *** mdrun: realloc(): invalid next size: 0x08296ec8
***
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0x401b1b0c]
/lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0x401b3a66]
mdrun[0x8137065]
======= Memory map: ========
08048000-08278000 r-xp 00000000 08:04
2567562 /usr/local/gromacs/bin/mdrun
08278000-0827f000 rwxp 00230000 08:04
2567562 /usr/local/gromacs/bin/mdrun
0827f000-082a5000 rwxp 0827f000 00:00 0 [heap]
40000000-4001a000 r-xp 00000000 08:04 2747274 /lib/ld-2.6.1.so
4001a000-4001c000 rwxp 00019000 08:04 2747274 /lib/ld-2.6.1.so
4001c000-4001f000 rwxp 4001c000 00:00 0
4001f000-40029000 r-xp 00000000 08:04 2747267 /lib/libgcc_s.so.1
40029000-4002a000 rwxp 0000a000 08:04 2747267 /lib/libgcc_s.so.1
4002c000-40040000 r-xp 00000000 08:04
2747206 /lib/tls/i686/cmov/libnsl-2.6.1.so
40040000-40042000 rwxp 00013000 08:04
2747206 /lib/tls/i686/cmov/libnsl-2.6.1.so
40042000-40044000 rwxp 40042000 00:00 0
40044000-4011b000 r-xp 00000000 08:04
2488482 /usr/lib/libfftw3f.so.3.1.2
4011b000-40121000 rwxp 000d7000 08:04
2488482 /usr/lib/libfftw3f.so.3.1.2
40121000-40144000 r-xp 00000000 08:04
2747187 /lib/tls/i686/cmov/libm-2.6.1.so
40144000-40146000 rwxp 00023000 08:04
2747187 /lib/tls/i686/cmov/libm-2.6.1.so
40146000-4028a000 r-xp 00000000 08:04
2747161 /lib/tls/i686/cmov/libc-2.6.1.so
4028a000-4028b000 r-xp 00143000 08:04
2747161 /lib/tls/i686/cmov/libc-2.6.1.so
4028b000-4028d000 rwxp 00144000 08:04
2747161 /lib/tls/i686/cmov/libc-2.6.1.so
4028d000-40291000 rwxp 4028d000 00:00 0
40291000-402a5000 r-xp 00000000 08:04
2747231 /lib/tls/i686/cmov/libpthread-2.6.1.so
402a5000-402a7000 rwxp 00013000 08:04
2747231 /lib/tls/i686/cmov/libpthread-2.6.1.so
402a7000-402aa000 rwxp 402a7000 00:00 0
40300000-40321000 rwxp 40300000 00:00 0
40321000-40400000 ---p 40321000 00:00 0
bf808000-bf820000 rwxp bf808000 00:00 0 [stack]
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
+++++++++++++++++++++++++++++++++++++++++++++++++
On Wed, 2007-11-07 at 16:45 +0800, Yang Ye wrote:
> To "uninstall" GROMACS, you can type "which mdrun" to get its path and
> try to figure out where it has been installed. For GROMACS, it may
> reside under
> /usr/local/gromacs
>
> remove the whole directory with rm -fr.
>
> To ensure that you are using the self-built GROMACS, look for a file
>
> GMXRC.bash in the locations which you can find in "make install".
>
> Run it with
> source /path/to/GMXRC.bash
>
> Then you can make sure that you are using your own version.
>
> Put that line "source ..." into ~/.bashrc shall make it default for
> every login session.
>
> Regards,
> Yang Ye
>
> On 11/7/2007 4:35 PM, Li Qiang wrote:
> > 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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