[gmx-developers] npme broken in latest cvs?

[hessb at mpip-mainz.mpg.de]

Hi,

I fixed this bug in CVS.
This was introduced a week ago on June 10.

Berk.

> Hi,
>
> It is a bug I put in recently.
>
> A fast fix is:
> diff -r1.119 pme.c
> 608c608,609
> <       rvec_inc(f[i],atc->f[local_pos]);
> ---
>  >       //rvec_inc(f[i],atc->f[local_pos]);
>  >         copy_rvec(atc->f[local_pos],f[i]);
> 612c613,614
> <       rvec_inc(f[i],pme->bufv[buf_index[node]]);
> ---
>  >       //rvec_inc(f[i],pme->bufv[buf_index[node]]);
>  >         copy_rvec(pme->bufv[buf_index[node]],f[i]);
>
> I have to think a bit to understand if this is a proper solution (also
> working
> single processor) or not.
>
> Berk.
>
>
> Atte Sillanpää wrote:
>> Hi,
>>
>> I've tried compiling the latest cvs-versions (mdrun version 55) on two
>> separate Opteron clusters using gnu and pgi-compilers but I get
>> crashing code. The cluster that I refer to below has two dual core
>> cpu:s on each node. I've managed to reproduce this with any input
>> files I've tried. See below, for a gmxcheck between a two step dd and
>> dd:npme run.
>>
>> 1) If I request only domain decomposition, the job runs ok.
>> 2) If I specifically ask for npme with the mdrun flag the jobs either
>> stall or crashe (see below).
>> 3) If I let mdrun to decide division to dd/npme (no dd/npme flags),
>> the code does not stall, but crashes within some tens of steps as
>> waters can't be settled etc.
>>
>> With the same configure options (nothing fancy, fftw 3.1.2) I get
>> working code (the source was checked out on 11th April). Any ideas
>> what could be the problem?
>>
>> Cheers,
>> Atte
>>
>> gmxcheck output between two runs with "-dd 2 2 1" and "-dd 2 1 1 -npme
>> 2":
>> ...
>> comparing energy file e_pme.edr and e_dd.edr
>>
>> Opened e_pme.edr as single precision energy file
>> Opened e_dd.edr as single precision energy file
>> There are 162 terms in the energy files
>>
>> There are 162 terms to compare in the energy files
>>
>> Reading energy frame      1 time    0.000           Vir-ZY
>> step   0:       1058.05,  step   0:      1056.45
>> Pres-ZY (bar)    step   0:      -95.3608,  step   0:     -95.2099
>> Reading energy frame      3 time    0.004           Kinetic En.
>> step   2:       58262.7,  step   2:      57779.1
>> Total Energy     step   2:       -362651,  step   2:      -363088
>> Temperature      step   2:       322.793,  step   2:      320.114
>> Pressure (bar)   step   2:       489.052,  step   2:      148.929
>> pV               step   2:       10406.1,  step   2:      3168.91
>> Vir-XX           step   2:       14573.3,  step   2:      17932.7
>> Vir-XY           step   2:      -2524.57,  step   2:     -2370.18
>> Vir-XZ           step   2:       2051.88,  step   2:      1733.56
>> Vir-YX           step   2:      -2632.26,  step   2:     -2475.74
>> Vir-YY           step   2:       16702.3,  step   2:      19691.3
>> Vir-YZ           step   2:       1213.29,  step   2:      675.571
>> Vir-ZX           step   2:       1978.46,  step   2:      1733.89
>> Vir-ZY           step   2:       1226.37,  step   2:      612.046
>> Vir-ZZ           step   2:         11378,  step   2:      15401.7
>> Pres-XX (bar)    step   2:       497.122,  step   2:      167.411
>> Pres-XY (bar)    step   2:        246.06,  step   2:      232.524
>> Pres-XZ (bar)    step   2:      -179.978,  step   2:     -150.756
>> Pres-YX (bar)    step   2:       256.182,  step   2:      242.446
>> Pres-YY (bar)    step   2:       263.995,  step   2:     -31.6074
>> Pres-YZ (bar)    step   2:       -112.03,  step   2:     -61.5908
>> Pres-ZX (bar)    step   2:      -173.078,  step   2:     -150.787
>> Pres-ZY (bar)    step   2:      -113.259,  step   2:     -55.6198
>> Pres-ZZ (bar)    step   2:       706.039,  step   2:      310.982
>> #Surf*SurfTen    step   2:       2056.54,  step   2:      1535.89
>> Coul-SR:CHOL-CHOL  step   2:   -0.00815666,  step   2:  -0.00819171
>> Coul-SR:CHOL-SOL  step   2:      -361.949,  step   2:     -362.405
>> Coul-SR:CHOL-Na  step   2:       3.20663,  step   2:      3.20127
>> Coul-SR:CHOL-Cl  step   2:    -0.0473165,  step   2:   -0.0468598
>> T-DPPC_POPC_POPG_CHOL  step   2:       314.493,  step   2:      313.836
>> T-SOL_Na_Cl      step   2:        329.66,  step   2:      325.308
>> Last energy frame read 3 time    0.004          Files read succesfully
>>
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