[Dock-fans] Dock 6.2 tests and parallelization problems
divanych at rambler.ru
Sat Apr 12 03:56:54 PDT 2008
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
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.
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