[gmx-users] Run test in parallel

Thu Aug 7 07:35:59 CEST 2008

Dear Yang,

Thank you for your corporation.

Regards,
Teru

2008/8/7 Yang Ye <leafyoung at yahoo.com>:
> 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
>>>> _______________________________________________
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>