[gmx-users] Test-set

[Zhanglin Ni]

Thanks, Justin. Then does it mean I cannot use the program to do simulation 
at this point? any suggestion on it?
Johnny

> Date: Fri, 08 May 2009 12:31:31 -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: <4A045E63.1080706 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> 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