[gmx-developers] Re: gromacs-4.0.4

Bernhard Bandow bandow at rrzn.uni-hannover.de
Thu Mar 19 18:08:17 CET 2009


Dear developers,

further attemps to get gromacs-4.0.4 tests running are disappointing either:
Configuration was done with:
./configure --enable-fortran --with-fft=fftpack --enable-shared
again intel.compiler/11.0.069 was used.
Additionally on another machine the same configuration using
gcc/gfortran 4.3.3 was used.
The pattern of kernel tests that failed remains the same in both cases.
If all users of gromacs run the test suite I would expect more reports
on failing tests.
Any comment or hint is appreciated.

Best regards

Bernhard Bandow

Bernhard Bandow schrieb:
> 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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