[gmx-users] Test-set
Justin A. Lemkul
jalemkul at vt.edu
Fri May 8 18:31:31 CEST 2009
Zhanglin Ni wrote:
> The configurations are
> Linux version 2.6.27.21-170.2.56.fc10.i686.PAE (gcc version 4.3.2
> 20081105 (Red Hat 4.3.2-7) (GCC) ) #1 SMP Mon Mar 23 23:24:26 EDT 2009
> CPU1: Intel(R) Core(TM)2 Duo CPU E7400 @ 2.80GHz stepping 0a
> lspci
> 00:00.0 Host bridge: Intel Corporation 82G33/G31/P35/P31 Express DRAM
> Controller (rev 10)
> 00:02.0 VGA compatible controller: Intel Corporation 82G33/G31 Express
> Integrated Graphics Controller (rev 10)
> 00:1b.0 Audio device: Intel Corporation 82801G (ICH7 Family) High
> Definition Audio Controller (rev 01)
> 00:1d.0 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
> Controller #1 (rev 01)
> 00:1d.1 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
> Controller #2 (rev 01)
> 00:1d.2 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
> Controller #3 (rev 01)
> 00:1d.3 USB Controller: Intel Corporation 82801G (ICH7 Family) USB UHCI
> Controller #4 (rev 01)
> 00:1d.7 USB Controller: Intel Corporation 82801G (ICH7 Family) USB2 EHCI
> Controller (rev 01)
> 00:1e.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev e1)
> 00:1f.0 ISA bridge: Intel Corporation 82801GB/GR (ICH7 Family) LPC
> Interface Bridge (rev 01)
> 00:1f.2 IDE interface: Intel Corporation 82801GB/GR/GH (ICH7 Family)
> SATA IDE Controller (rev 01)
> 00:1f.3 SMBus: Intel Corporation 82801G (ICH7 Family) SMBus Controller
> (rev 01)
> 01:08.0 Ethernet controller: Intel Corporation 82801G (ICH7 Family) LAN
> Controller (rev 01)
>
> FAILED. Check files in field
> FAILED. Check files in tip4p
> FAILED. Check files in tip4pflex
> FAILED. Check files in water
>
> The water test seems was the worse one. it showed like
> ....
>>> 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
>
When I run the test set on my system (dual-core Intel MacBook), I get this in
the tail end of the checkvir.out for water:
Pressure (bar) step 50: 46893.3, step 50: 45119.8
Vir-XX step 50: -6211.69, step 50: -6436.94
Vir-XY step 50: -2423.21, step 50: -1896.98
Vir-XZ step 50: 667.327, step 50: 316.873
Vir-YX step 50: -2422.22, step 50: -1896.65
Vir-YY step 50: -3194.86, step 50: -2648.67
Vir-YZ step 50: -2208.7, step 50: -2641.28
Vir-ZX step 50: 667.878, step 50: 318.282
Vir-ZY step 50: -2207.77, step 50: -2640.33
Vir-ZZ step 50: -1482.41, step 50: -817.011
It seems that your system is not producing the Vir-XX component, which may be
what's causing the failure. The magnitude of difference between the other
energy terms is not substantially different from what I see (and my test passes).
I now also recall you reported the following originally in your checkpot.out:
There are 30 terms in the energy files
In my checkpot.out, the line reads:
There are 31 terms in the energy files
I suspect that is where the problem lies, but that is also where my usefulness
ends. Perhaps one of the developers can comment at this point as to the reason
for the missing energy term.
-Justin
> Thanks
> Johnny
>
>
>> Message: 1
>> Date: Thu, 07 May 2009 21:50:45 -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: <4A038FF5.3030902 at vt.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>>
>> 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
>>>
>
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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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