[gmx-users] Run test in parallel

Thu Aug 7 06:35:02 CEST 2008

Dear Yang,

Thank you for your quick reply.

I checked the log files and then found that the mpirun command cannot
find the mdrun(executable) file..
I modified to use the absolute path in the gmxtest.pl and ran it.
However some tests still failed.

% ./gmxtest.pl -np 8 all
Will test on 8 processors
FAILED. Check files in angles125
1 out of 16 simple tests FAILED
FAILED. Check files in dec+water
No topol.tpr file in fe_test. grompp failed
FAILED. Check files in fe_test
2 out of 14 complex tests FAILED
All 63 kernel tests PASSED
Error not all 45 pdb2gmx tests have been done successfully
Only 0 energies in the log file

Can I ignore above error messages?

Thank you in advance.

Regards,
Teru

2008/8/7 Yang Ye <leafyoung at yahoo.com>:
> I would guess that you have got gromacs installed correctly from the
> two-process tests.
>
> The failure of eight-core test may depends how you start your MPI daemon
> or other factors that mdrun could be not running at all. Paste your log
> file from eight-core test or just wait for some one has experience with
> OpenMPI.
>
> Regards,
> Yang Ye
>
> ikedaike wrote:
>>
>> Hi
>>
>> I built GROMACS-3.3.3 with GCC-3.4.6 and OpenMPI-1.2.5 on CentOS
>> 4.5(Intel Core2 Duo).
>> I tested with gmxtest-3.3.3 and all tests passed in non-parallel.
>> However, when I tested in parallel, I encountered the following messages.
>>
>> [Use 2 Cores]
>> % ./gmxtest.pl -np 2 all
>> Will test on 2 processors
>> All 16 simple tests PASSED
>> FAILED. Check files in dec+water
>> 1 out of 14 complex tests FAILED
>> All 63 kernel tests PASSED
>> Error not all 45 pdb2gmx tests have been done successfully
>> Only 0 energies in the log file
>>
>> Can I ignore above messages about the pdb2gmx test?
>>
>> [Use 8 Cores]
>> % ./gmxtest.pl -np 8 all
>> Will test on 8 processors
>> FAILED. Check files in angles1
>> FAILED. Check files in angles125
>> FAILED. Check files in bham
>> FAILED. Check files in bonds1
>> FAILED. Check files in bonds125
>> FAILED. Check files in dih1
>> FAILED. Check files in dih125
>> FAILED. Check files in g96angles1
>> FAILED. Check files in g96angles125
>> FAILED. Check files in g96bonds1
>> FAILED. Check files in g96bonds125
>> FAILED. Check files in imp1
>> FAILED. Check files in imp36
>> FAILED. Check files in morse
>> FAILED. Check files in rb1
>> FAILED. Check files in rb125
>> 16 out of 16 simple tests FAILED
>> FAILED. Check files in acetonitrilRF
>> FAILED. Check files in aminoacids
>> FAILED. Check files in argon
>> FAILED. Check files in butane
>> FAILED. Check files in dec+water
>> FAILED. Check files in ethyleenglycol
>> No topol.tpr file in fe_test. grompp failed
>> FAILED. Check files in fe_test
>> FAILED. Check files in field
>> FAILED. Check files in nacl
>> FAILED. Check files in sw
>> FAILED. Check files in tip4p
>> FAILED. Check files in tip4pflex
>> FAILED. Check files in urea
>> FAILED. Check files in water
>> 14 out of 14 complex tests FAILED
>> FAILED. Check files in kernel010
>> FAILED. Check files in kernel020
>> FAILED. Check files in kernel030
>> FAILED. Check files in kernel100
>> FAILED. Check files in kernel101
>> FAILED. Check files in kernel102
>> FAILED. Check files in kernel103
>> FAILED. Check files in kernel104
>> FAILED. Check files in kernel110
>> FAILED. Check files in kernel111
>> FAILED. Check files in kernel112
>> FAILED. Check files in kernel113
>> FAILED. Check files in kernel114
>> FAILED. Check files in kernel120
>> FAILED. Check files in kernel121
>> FAILED. Check files in kernel122
>> FAILED. Check files in kernel123
>> FAILED. Check files in kernel124
>> FAILED. Check files in kernel130
>> FAILED. Check files in kernel131
>> FAILED. Check files in kernel132
>> FAILED. Check files in kernel133
>> FAILED. Check files in kernel134
>> FAILED. Check files in kernel200
>> FAILED. Check files in kernel201
>> FAILED. Check files in kernel202
>> FAILED. Check files in kernel203
>> FAILED. Check files in kernel204
>> FAILED. Check files in kernel210
>> FAILED. Check files in kernel211
>> FAILED. Check files in kernel212
>> FAILED. Check files in kernel213
>> FAILED. Check files in kernel214
>> FAILED. Check files in kernel220
>> FAILED. Check files in kernel221
>> FAILED. Check files in kernel222
>> FAILED. Check files in kernel223
>> FAILED. Check files in kernel224
>> FAILED. Check files in kernel230
>> FAILED. Check files in kernel231
>> FAILED. Check files in kernel232
>> FAILED. Check files in kernel233
>> FAILED. Check files in kernel234
>> FAILED. Check files in kernel300
>> FAILED. Check files in kernel301
>> FAILED. Check files in kernel302
>> FAILED. Check files in kernel303
>> FAILED. Check files in kernel304
>> FAILED. Check files in kernel310
>> FAILED. Check files in kernel311
>> FAILED. Check files in kernel312
>> FAILED. Check files in kernel313
>> FAILED. Check files in kernel314
>> FAILED. Check files in kernel320
>> FAILED. Check files in kernel321
>> FAILED. Check files in kernel322
>> FAILED. Check files in kernel323
>> FAILED. Check files in kernel324
>> FAILED. Check files in kernel330
>> FAILED. Check files in kernel331
>> FAILED. Check files in kernel332
>> FAILED. Check files in kernel333
>> FAILED. Check files in kernel334
>> 63 out of 63 kernel tests FAILED
>> Error not all 45 pdb2gmx tests have been done successfully
>> Only 0 energies in the log file
>>
>> I don't know why the all tests failed.
>> Could you please give the information about test in parallel ?
>>
>> Thank you in advance.
>>
>> Teru
>> _______________________________________________
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>
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