Tuesday, November 12, 2013

Plumed utility usage: sum_hills and HILLS file

parallel.f90  serial.f90  sum_hills.f90 files are avaialble.
I use module to link library. In the following part, s denotes step. It seems that gcc is better.
s1: module load  gcc_4.4.7-ompi_1.6.5 (module list, module load, module avail, module unload)
s2:  mpif90 -O3 sum_hills.f90 parallel.f90 -o sum_hills_mpi.x
You should have sum_hills_mpi.x generated.s3. ldd sum_hills_mpi.x
Output:
        linux-vdso.so.1 =>  (0x00007fff205fd000)
        libmpi_f90.so.1 => /sw/openmpi-1.6.5_gcc-4.4.7/lib/libmpi_f90.so.1 (0x00002b18668f0000)
        libmpi_f77.so.1 => /sw/openmpi-1.6.5_gcc-4.4.7/lib/libmpi_f77.so.1 (0x00002b1866af5000)
        libmpi.so.1 => /sw/openmpi-1.6.5_gcc-4.4.7/lib/libmpi.so.1 (0x00002b1866d28000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00002b18670d9000)
        libgfortran.so.3 => /usr/lib64/libgfortran.so.3 (0x00002b18672de000)
        libm.so.6 => /lib64/libm.so.6 (0x00002b18675d0000)
        libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x00002b1867853000)
        librt.so.1 => /lib64/librt.so.1 (0x00002b1867a59000)
        libnsl.so.1 => /lib64/libnsl.so.1 (0x00002b1867c62000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00002b1867e7a000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b186807e000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b186828c000)
        libc.so.6 => /lib64/libc.so.6 (0x00002b18684a8000)
        /lib64/ld-linux-x86-64.so.2 (0x00002b18666d2000)
s4: gfortran -O3 sum_hills.f90 serial.f90 -o sum_hills.x   !OK. now serial version.
s5:  copy two *.x files to your bin directory.
s6. sum_hills.x -file HILLS -out fes.dat -ndim 3 -ndw 1 2 -kt 0.6 -ngrid 100 100 100
       -ndim: the dimensionality number.
       -ndw: the list of CVs in the desired order to plot the FES.
       -kt: KT specified by -kt (kT must be given in the energy units that were used
by in the code)

HILLS file
  first column      second     third               fourth
   time step          CV            SIGMA      Bias potential

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