[gmx-developers] Re: gromacs-4.0.4
David van der Spoel
spoel at xray.bmc.uu.se
Tue Mar 17 19:37:08 CET 2009
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
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
More information about the gromacs.org_gmx-developers
mailing list