[gmx-users] gromacs 4.0.3 tests validations

[Ran Friedman]

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I think the tests for pdb2gmx are outdated.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.
>
> [tru at 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:
>
> [tru at 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 $par > grompp.out 2>&1");
>
> [tru at sillage gmxtest]$ ./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
>
> [tru at 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
>