***************************************************************** * TESTS FOR SERIAL GENERALIZED ENSEMBLE SIMULATIONS IN ORAC * ***************************************************************** These tests run in serial and parallel. The main prerequisite is: * MPI (Message Passing Interface) libraries and implementation/environment: MPICH2 [http://www.mcs.anl.gov/research/projects/mpich2/] -or- OPENMPI [http://www.open-mpi.org/] Other prerequisites depend on the MPI environment used. For example, for MPICH2 one must provide: * mpd.hosts file listing hosts to run in parallel * .mpd.conf file in user dir with secret password * ssh access to hosts listed in mpd.hosts ------------------------------------------------------------------------ BEFORE RUNNING THE TESTS ------------------------------------------------------------------------ * Build hybrid parallel (OpenMP/MPI) and OpenMP versions: cd ./configure -INTEL -FFTW -OMP -MPI make ! create an hybrid OMP/MPI executable in INTEL-FFTW-OMP-MPI dir ./configure -INTEL -FFTW -OMP make ! create an hybrid OMP executable in INTEL-FFTW-OMP dir * Adjust the variable O_ROOT in the first section of the Makefile of the current directory to your environment: O_ROOT = * start your MPI environment, e.g. for MPICH2 mpdallexit mpdboot -n ------------------------------------------------------------------------ TO RUN THE TESTS ------------------------------------------------------------------------ Tests are run through `make'. * to run all tests: `make -s' * to run tests of the serial version (test*_s): `make -s serial_tests' * to run tests of the parallel version (test*_p): `make -s parallel_tests' * to run individual tests `make -s testx_x.out' * to clean all old tests: `make clean' * to clean an individual test (for example test1_p): `make clean_test1_p' The tests will create directories test*_* with output files from each instance of the program, and a collection of output files called test*_*.out. These output files along with those into directories test*_* are to be compared to the reference ones deposited in the directory REF_OUT/test*_*. NOTE: the evolution of the Serial Generalized Ensemble simulation depends critically, among other things, on the generation of random numbers, and so on the architecture of the computer. Results may differ significantly from the enclosed reference outputs. ------------------------------------------------------------------------ SHORT DESCRIPTION OF TESTS ------------------------------------------------------------------------ - Please read the manual ( ${ORAC_DIR}/doc/orac-manual.pdf ) for a detailed description of the program and its input - The input examples do the following operations: (NOTE: You can change the number of processes in the parallel tests by modifying the variable NP in the Makefile.) test1_s.out,test1_p.out --> Run a cold start of the di-alanine peptide in vacuum using the serial/parallel version of simulated solute tempering. test2_s.out,test2_p.out --> Run a warm start of the di-alanine peptide in vacuum using output from test1* test3_s.out,test3_p.out --> Run a cold start of the deca-alanine peptide in vacuum using the serial/parallel (test3_s.in/test3_p.in) version of simulated tempering along the end-to-end collective coordinate. test4_s.out,test4_p.out --> Run a warm start of the deca-alanine peptide in vacuum using output from test3* test4.2_p.out --> Like test4_p, but the initial average of free energy differences is reset. test5_p.out --> Run a cold start of the di-alanine peptide in vacuum using the parallel version of simulated solute tempering. The ensemble free energies are constant during the simulation (read from "fixed_df.set" file). test6_p.out --> Run a warm start of the di-alanine peptide in vacuum using data from test5*. test7_p.out --> Run a cold start of the di-alanine peptide in water solution (NPT ensemble) using the parallel version of simulated solute tempering. test8_p.out --> Run a warm start of the di-alanine peptide in water solution (NPT ensemble) using the parallel version of simulated solute tempering. Note that in addition to the above tests, other tests using the above input files can be performed. These tests are generically termed as test?.1_s.out and test?.1_p.out where "?" can be 1, 2, 3 or 4. These runs test the option that allows the on-the-fly changing of the number of (latest) estimates used to evaluate free energy differences (see user guide for details). For example, the test test3.1_p runs with the input test3_p.in and use a number of free energy estimates specified in the file SGE_DF_FLY.set generated in the parent directory of PAR* directories (or generated in the working directory in the case of serial tests) Orac is known to work with OPENMPI and MPICH2 (Release 1.0.7).