[gmx-developers] Re: gromacs-4.0.4
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 19 18:45:56 CET 2009
Bernhard Bandow wrote:
> 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.
I can report the same results (with nearly identical output in
kernel020/checkvir.out) on a dual-core Intel MacBook with gcc-4.0.1. FFTW
version is 3.0.1. Gromacs was built with:
./configure --with-gsl CPPFLAGS="-I/usr/local/fftw/include -I/sw/include"
LDFLAGS="-L/usr/local/fftw/lib -L/sw/lib"
make
make install
-Justin
> 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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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