[gmx-users] Run test in parallel

Yang Ye leafyoung at yahoo.com
Thu Aug 7 07:07:06 CEST 2008 

ikedaike wrote:
> 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?
>   
Most likely. I checked those errors before and they are indeed not 
errors. gmxtest suite is not just not very up-to-date with gromacs.
> 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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