[gmx-users] Test-set

Justin A. Lemkul jalemkul at vt.edu
Fri May 8 03:50:45 CEST 2009 


Zhanglin Ni wrote:
> The checkvir.out files looked like (I just show last few lines here):
> Pressure (bar)   step  50:       46893.3,  step  50:        44603
> Vir-XY           step  50:      -2423.21,  step  50:      -1880.2
> Vir-XZ           step  50:       667.327,  step  50:      307.438
> Vir-YX           step  50:      -2422.22,  step  50:     -1880.23
> Vir-YY           step  50:      -3194.86,  step  50:     -2655.73
> Vir-YZ           step  50:       -2208.7,  step  50:      -2608.7
> Vir-ZX           step  50:       667.878,  step  50:      308.434
> Vir-ZY           step  50:      -2207.77,  step  50:     -2608.41
> Vir-ZZ           step  50:      -1482.41,  step  50:     -680.999
> Files read succesfully
> 

Which failed test does this correspond to?

At this point, it would also be appropriate to report your system configuration 
- your OS, version, which compilers were used (and version), hardware, and 
anything else necessary to diagnose the problem.

-Justin

> 
> -Johnny
> 
> 
>> Message: 1
>> Date: Thu, 07 May 2009 12:44:23 -0400
>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] Test-set
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4A030FE7.2030107 at vt.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>> Any clues from any of the other *.out files?
>>
>> -Justin
>>
>> Zhanglin Ni wrote:
>>> Thanks for your reply.
>>> I checked the checkpot.out file.
>>> It didnot show the any energy values but
>>> "
>>> comparing energy file reference_s.edr and ener.edr
>>> There are 30 terms in the energy files
>>> There are 3 terms to compare in the energy files
>>> Files read succesfully
>>> "
>>> what the problem could be. Thanks.
>>> Johnny
>>>
>>>
>>>>
>>>> Zhanglin Ni wrote:
>>>>> Dear all,
>>>>> I installed gromacs-4.0.4, I followed the installation instruction. 
>>>>> the
>>>>> installation seemed no problem at all.  afterwards, I run test-set
>>>>> gmxtest-4.0.4 immediately.
>>>>> The results are
>>>>> All 16 simple tests PASSED
>>>>> FAILED. Check files in field
>>>>> FAILED. Check files in tip4p
>>>>> FAILED. Check files in tip4pflex
>>>>> FAILED. Check files in water
>>>>> 4 out of 14 complex tests FAILED
>>>>
>>>> So check the output of these tests; small rounding errors are
>>>> insignificant and
>>>> can cause the test to fail (as described on the wiki).
>>>>
>>>> The kernel failures you cite below have been reported before:
>>>>
>>>> http://bugzilla.gromacs.org/show_bug.cgi?id=313
>>>>
>>>> -Justin
>>>>
>>>>> FAILED. Check files in kernel020
>>>>> FAILED. Check files in kernel120
>>>>> FAILED. Check files in kernel121
>>>>> FAILED. Check files in kernel122
>>>>> FAILED. Check files in kernel123
>>>>> FAILED. Check files in kernel124
>>>>> FAILED. Check files in kernel220
>>>>> FAILED. Check files in kernel221
>>>>> FAILED. Check files in kernel222
>>>>> FAILED. Check files in kernel223
>>>>> FAILED. Check files in kernel224
>>>>> FAILED. Check files in kernel320
>>>>> FAILED. Check files in kernel321
>>>>> FAILED. Check files in kernel322
>>>>> FAILED. Check files in kernel323
>>>>> FAILED. Check files in kernel324
>>>>> 16 out of 63 kernel tests FAILED
>>>>> pdb2gmx tests PASSED
>>>>>
>>>>> How I can do to solve the problem since it was just installed. Thanks
>>>>> Johnny
>>>>>
> 
>> Message: 1
>> Date: Thu, 07 May 2009 12:44:23 -0400
>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] Test-set
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4A030FE7.2030107 at vt.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>> Any clues from any of the other *.out files?
>>
>> -Justin
>>
>> Zhanglin Ni wrote:
>>> Thanks for your reply.
>>> I checked the checkpot.out file.
>>> It didnot show the any energy values but
>>> "
>>> comparing energy file reference_s.edr and ener.edr
>>> There are 30 terms in the energy files
>>> There are 3 terms to compare in the energy files
>>> Files read succesfully
>>> "
>>> what the problem could be. Thanks.
>>> Johnny
>>>
>>>
>>>>
>>>> Zhanglin Ni wrote:
>>>>> Dear all,
>>>>> I installed gromacs-4.0.4, I followed the installation instruction. 
>>>>> the
>>>>> installation seemed no problem at all.  afterwards, I run test-set
>>>>> gmxtest-4.0.4 immediately.
>>>>> The results are
>>>>> All 16 simple tests PASSED
>>>>> FAILED. Check files in field
>>>>> FAILED. Check files in tip4p
>>>>> FAILED. Check files in tip4pflex
>>>>> FAILED. Check files in water
>>>>> 4 out of 14 complex tests FAILED
>>>>
>>>> So check the output of these tests; small rounding errors are
>>>> insignificant and
>>>> can cause the test to fail (as described on the wiki).
>>>>
>>>> The kernel failures you cite below have been reported before:
>>>>
>>>> http://bugzilla.gromacs.org/show_bug.cgi?id=313
>>>>
>>>> -Justin
>>>>
>>>>> FAILED. Check files in kernel020
>>>>> FAILED. Check files in kernel120
>>>>> FAILED. Check files in kernel121
>>>>> FAILED. Check files in kernel122
>>>>> FAILED. Check files in kernel123
>>>>> FAILED. Check files in kernel124
>>>>> FAILED. Check files in kernel220
>>>>> FAILED. Check files in kernel221
>>>>> FAILED. Check files in kernel222
>>>>> FAILED. Check files in kernel223
>>>>> FAILED. Check files in kernel224
>>>>> FAILED. Check files in kernel320
>>>>> FAILED. Check files in kernel321
>>>>> FAILED. Check files in kernel322
>>>>> FAILED. Check files in kernel323
>>>>> FAILED. Check files in kernel324
>>>>> 16 out of 63 kernel tests FAILED
>>>>> pdb2gmx tests PASSED
>>>>>
>>>>> How I can do to solve the problem since it was just installed. Thanks
>>>>> Johnny
>>>>>
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

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