[Dock-fans] Dock 6.2 tests and parallelization problems

Dmitry Osolodkin divanych at rambler.ru
Sat Apr 12 03:56:54 PDT 2008


Hello all,

Could help me to solve a few problems with the installation and 
parallelization of DOCK 6.2 and 6.1? The system is a cluster of AMD 
Opteron processors, RHEL3, gss 3.2.3.

1. When I compile the serial version of DOCK6.2 with gcc 3.2.3 and 
default configuration, it is compiled successfully. After running 'make 
test', there is a great many of failures in almost all tests, rather 
often concerning different number of conformations obtained or notable 
differences in the atomic coordinates.

2. When I compile the parallel version of DOCK6.2 with gcc 3.2.3 and 
default configuration, it is compiled successfully. When I try to run 
the parallel computation with 'mpirun -np _any_ -nolocal -machinefile 
machine', it runs at only one processor. The same behavior is observed 
without the 'nolocal' flag.
Moreover, the computation can't be run from the desired directory, but 
only from my home directory: it creates '~/dock.in' with default options 
and tries to read all other files from '~/' even if all paths are 
pointed explicitly.

3. Parallel version of DOCK 6.1 (all bugfixes applied) virtual screening 
crashes with the SIGSEGV after about 300 of 2000 compounds screened. The 
number of compounds depends on the input ligand database, but is 
reprodicible for the different runs with the same database.

Best regards,
Dmitry Osolodkin


More information about the Dock-fans mailing list