[gmx-users] gromacs 4.0.3 tests validations

[Tru Huynh]

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
-- 
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru at pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France