Dear Yang, Thank you for your corporation.
Regards, Teru 2008/8/7 Yang Ye <[EMAIL PROTECTED]>: > 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 <[EMAIL PROTECTED]>: >> >>> >>> 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@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 [EMAIL PROTECTED] >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>>> >>>> >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> > > _______________________________________________ > gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
