[gmx-developers] Re: gromacs-4.0.4

Bernhard Bandow bandow at rrzn.uni-hannover.de
Wed Mar 18 10:58:43 CET 2009


I am not quite shure if this part of the output of kernel020/md.log says
that fortran was used instead of the handcoded SSE routines:
...
  Table routines are used for coulomb: FALSE
  Table routines are used for vdw:     FALSE
  Cut-off's:   NS: 0.01   Coulomb: 0.01   BHAM: 0.9
  Determining largest Buckingham b parameter for table
  Buckingham b parameters, min: 0, max: 43.33
  System total charge: 0.000
  Generated table with 950 data points for 1-4 COUL.
  Tabscale = 500 points/nm
  Generated table with 950 data points for 1-4 LJ6.
  Tabscale = 500 points/nm
  Generated table with 950 data points for 1-4 LJ12.
  Tabscale = 500 points/nm

  Enabling SPC water optimization for 196 molecules.

  Configuring nonbonded kernels...
  Testing x86_64 SSE support... present.
...

So I compiled again omitting the '--enable-fortran' option. This caused
a number of tests in simple and complex to fail as well as the same
tests in kernel as described below.

David van der Spoel schrieb:
> Bernhard Bandow wrote:
>> Dear developers,
>>
>> During installing and testing gromacs4.0.4 together with its test suite
>> a number of tests failed. Unfortunately playing around with compiler
>> options, linking against different fft libraries as well as changing
>> paramters in grompp.mdp files did not solve the problem - some tests
>> still fail and I got stuck here.
>>
>> Since other postings regarding the same topic are part of another
>> mailing list I would like to put an abstract here.
>>
>> i)The tests were run on one node of a linux cluster employing 8 cores.
>>   Each node is a dual socket blade with two quad core cpus.
>>   /proc/cpuinfo says:
>>
>>   processor       : 0
>>   vendor_id       : GenuineIntel
>>   cpu family      : 6
>>   model           : 23
>>   model name      : Intel(R) Xeon(R) CPU           E5472  @ 3.00GHz
>>   stepping        : 6
>>   cpu MHz         : 2992.496
>>   cache size      : 6144 KB
>>   physical id     : 0
>>   siblings        : 4
>>   core id         : 0
>>   cpu cores       : 4
>>   fpu             : yes
>>   fpu_exception   : yes
>>   cpuid level     : 10
>>   wp              : yes
>>   flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
>>   mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall
>>   nx lm constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr dca
>>   lahf_lm
>>   bogomips        : 5990.08
>>   clflush size    : 64
>>   cache_alignment : 64
>>   address sizes   : 38 bits physical, 48 bits virtual
>>   power management:
>>
>>   ... until processor 7
>>
>>   The OS is SUSE Linux Enterprise Server 10 (x86_64), version 10,
>>   patchlevel 2.
>>
>> ii)Gromacs was compiled with Intel 11.0.069 compiler using mvapich2
>>    Further options in configure were:
>>    --enable-fortran
> 
> Can you please check whether fortran was actually used (in the md.log
> file), if so please turn it off and try again. Fortran is a lot slower
> than the handcoded SSE routines, which may also imply it has not been
> tested to the same degree.
> 
>>    --enable-mpi
>>    --with-fft=mkl
>>    --enable-shared
>>    The system gromacs is intended to run on uses mpiexec to initiate
>>    message passing. So gmxtest.pl was modified at line 31 to:
>>
>>    $mdprefix = "mpiexec -np $parallel"
>>
>>    In order to exclude details of compilation and linking the
>>    optimisation level was then reduced until -O0, and the intel-mkl was
>>    replaced by fftw3.1.2.
>>
>> iii)As an example for failing tests in 'kernel' kernel020 fails with
>>   /kernel020/checkvir.out  containing:
>>
>>   LJ-14            step   0:      -63.1209,  step   0:      6.50742
>>   Potential        step   0:      -321.601,  step   0:     -251.972
>>   Kinetic En.      step   0:       15.0135,  step   0:      29.0739
>>   Total Energy     step   0:      -306.588,  step   0:     -222.898
>>   Temperature      step   0:       1.93226,  step   0:      3.74185
>>   Pressure (bar)   step   0:      -3095.37,  step   0:     -2497.79
>>   Vir-XX           step   0:       1127.45,  step   0:      1075.85
>>   Vir-XY           step   0:        63.524,  step   0:      21.7773
>>   Vir-XZ           step   0:      -264.813,  step   0:     -260.354
>>   Vir-YX           step   0:       63.5241,  step   0:      21.7775
>>   Vir-YY           step   0:       803.252,  step   0:      581.702
>>   Vir-ZX           step   0:      -264.813,  step   0:     -260.355
>>   Vir-ZZ           step   0:       321.207,  step   0:      176.574
>>
>> The deviations are obvious.
>>
>> I hope this helps to locate the reason for the tests to fail in order to
>>  come to a set of tests that help to test installations of gromacs.
>>
>> Best regards
>>
>> Bernhard Bandow
>>
>> David van der Spoel schrieb:
>>> Bernhard Bandow wrote:
>>>> Dear Prof. van der Spoel,
>>>>
>>>> as I have reported some days before we observe a number of tests in
>>>> gromacs-4.0.4 failing. Those of the complex category can all be
>>>> fixed if
>>>> the hints to change parameters for electrostatics or thermostats.
>>>> Reducing the Compiler optimisation to -O0 does additionally fix
>>>> problems
>>>> with two of the pbd2gmx tests. For the kernel tests we observe the same
>>>> pattern of failing tests that were also reported elsewhere:
>>>>
>>>> Testing kernel020 . . . FAILED. Check files in kernel020
>>>> Testing kernel120 . . . FAILED. Check files in kernel120
>>>> Testing kernel121 . . . FAILED. Check files in kernel121
>>>> Testing kernel122 . . . FAILED. Check files in kernel122
>>>> Testing kernel123 . . . FAILED. Check files in kernel123
>>>> Testing kernel124 . . . FAILED. Check files in kernel124
>>>> Testing kernel220 . . . FAILED. Check files in kernel220
>>>> Testing kernel221 . . . FAILED. Check files in kernel221
>>>> Testing kernel222 . . . FAILED. Check files in kernel222
>>>> Testing kernel223 . . . FAILED. Check files in kernel223
>>>> Testing kernel224 . . . FAILED. Check files in kernel224
>>>> Testing kernel320 . . . FAILED. Check files in kernel320
>>>> Testing kernel321 . . . FAILED. Check files in kernel321
>>>> Testing kernel322 . . . FAILED. Check files in kernel322
>>>> Testing kernel323 . . . FAILED. Check files in kernel323
>>>> Testing kernel324 . . . FAILED. Check files in kernel324
>>>>
>>>> Changing parameters in these cases is not successful. The situation
>>>> remains even if the program is linked against fftw3.1.2 libraries
>>>> instead of the intel mkl.
>>>> As a scientist it think it is very imnportant to have a tool which
>>>> functionality can be tested well in order to obtain results which
>>>> can be
>>>> trusted. For my own problems this of course also depends on my
>>>> abilities
>>>> in writing proper input.
>>>> My concern at the HLRN is to provide knowledge for the users of our
>>>> computing center how to install and run the installed software.
>>>> Please tell me if or how I can contribute to a solution e.g. by testing
>>>> or writing to people of the gromacs team without addressing only one
>>>> person.
>>>>
>>> The best place is the gmx-developers list. You are also welcome to
>>> submit a bugzilla.
>>>
>>> There were some rumors that the kernels fail in parallel, but not
>>> sequentially but I haven't tested.
>>>
>>>
>>>> Best regards
>>>>
>>>> Bernhard Bandow
>>
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> 
> 




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