Hi, I think the tests for pdb2gmx are outdated. Most fail due to warning(s) while running grompp, which were allowed with older versions. I'm not sure who maintains this tests - maybe a new version is due. Ran.
Tru Huynh wrote: > Hi, > > I am compiling gromacs on CentOS-3 x86_64 both serial and LAM-MPI version > (7.1.4) and I would like to validate the builds. > > [...@sillage gmxtest]$ rpm -q gcc fftw3 perl > gcc-3.2.3-59.x86_64 > fftw3-3.0.1-2_centos3.x86_64 > perl-5.8.0-98.EL3.x86_64 > > ./configure --prefix=... --with-x --enable-shared > make && make install > > test validation as stated at http://wiki.gromacs.org/index.php/Test-set > wget -O - ftp://ftp.gromacs.org/pub/tests/gmxtest-3.3.2.tgz| tar xzvf - > make tests > ... > All 16 simple tests PASSED > All 14 complex tests PASSED > All 63 kernel tests PASSED > Error not all 45 pdb2gmx tests have been done successfully > Only 0 energies in the log file > > -> The PASSED lines are fine to me, but what about the last 2 lines? > > I also compiled the double precision version with: > ./configure --prefix=... --with-x --enable-shared --disable-float > and the tests yields: > > [...@sillage gmxtest]$ ./gmxtest.pl -double all > All 16 simple tests PASSED > All 14 complex tests PASSED > All 63 kernel tests PASSED > readline() on closed filehandle PIPE at ./gmxtest.pl line 343. > readline() on closed filehandle PIPE at ./gmxtest.pl line 348. > ... > readline() on closed filehandle PIPE at ./gmxtest.pl line 348. > readline() on closed filehandle PIPE at ./gmxtest.pl line 343. > readline() on closed filehandle PIPE at ./gmxtest.pl line 348. > Error not all 45 pdb2gmx tests have been done successfully > Only 0 energies in the log file > > Should I be worried? > > About the parallel test (grompp -np N for gromacs 3.x) as previoulsy stated > on the > mailing list, one should use: > grompp -c system.gro -p topology.top -f something.mdp > mpirun -np N mdrun > > so > gmxtest.pl should read: > system("$grompp -maxwarn 10 $ndx >> /dev/null 2>&1"); > system("mpirun -$par mdrun -maxwarn 10 $ndx >> grompp.out 2>&1"); > > instead of: > system("$grompp -maxwarn 10 $ndx $par > grompp.out 2>&1"); > > [...@sillage gmxtest]$ ./gmxtest.pl -np 1 all > Will test on 1 processors > All 16 simple tests PASSED > All 14 complex tests PASSED > All 63 kernel tests PASSED > Error not all 45 pdb2gmx tests have been done successfully > Only 0 energies in the log file > > [...@sillage gmxtest]$ ./gmxtest.pl -np 2 all > Will test on 2 processors > FAILED. Check files in bham > 1 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 sw > FAILED. Check files in tip4p > FAILED. Check files in urea > FAILED. Check files in water > 7 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 > > Thanks. > > Tru > _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php