[gmx-users] can not pass gmxtest
Yang Ye
leafyoung at yahoo.com
Wed Nov 7 09:45:42 CET 2007
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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>>>
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>
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