Good time of day, dear lammps users!
Thank you for your useful answers.
System administrator tells me that I am running the program using only one processor although in PBS script
I wrote:
#PBS -l walltime=10:00:00,nodes=8:ppn=4, pvmem=550mb
#PBS -M
#PBS -m abe
#PBS -N job_name
#!/bin/sh
mpirun ./lmp_linux< in.Ne > log
But according to his notes:
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
58713.master tmog workq App0061 22125 8 1 – 10000 R 00:00
node129+node129+node129+node129+node131+node131+node131+node131+node130
+node130+node130+node130+node128+node128+node128+node128+node127+node127
+node127+node127+node126+node126+node126+node126+node125+node125+node125
$ cexec :123-131 uptime
************************* oscar_cluster *************************
--------- node123---------
23:56:08 up 44 days, 11:39, 0 users, load average: 0.00, 0.00, 0.00
--------- node124---------
23:56:08 up 12 days, 7:26, 0 users, load average: 0.00, 0.00, 0.00
--------- node125---------
23:56:08 up 52 days, 12:06, 0 users, load average: 0.00, 0.00, 0.00
--------- node126---------
23:56:08 up 52 days, 12:05, 0 users, load average: 0.00, 0.00, 0.00
--------- node127---------
23:56:08 up 52 days, 12:05, 0 users, load average: 0.00, 0.00, 0.00
--------- node128---------
23:56:08 up 52 days, 12:05, 0 users, load average: 0.00, 0.00, 0.00
--------- node129---------
23:56:08 up 52 days, 11:55, 0 users, load average: 1.00, 1.00, 1.00
--------- node130---------
23:56:08 up 52 days, 11:58, 0 users, load average: 0.00, 0.00, 0.00
--------- node131---------
23:56:08 up 52 days, 12:01, 0 users, load average: 0.00, 0.00, 0.00
Here is the modified makefile.linux I used to compile the program:
linux = RedHat Linux box, Intel icc, Intel ifort, MPICH2, FFTW
SHELL = /bin/sh
---------------------------------------------------------------------
compiler/linker settings
specify flags and libraries needed for your compiler
CC = mpicxx
CCFLAGS = -O
DEPFLAGS = -M
LINK = mpicxx
LINKFLAGS = -O
LIB = -lstdc++
ARCHIVE = ar
ARFLAGS = -rc
SIZE = size
---------------------------------------------------------------------
LAMMPS-specific settings
specify settings for LAMMPS features you will use
LAMMPS ifdef options, see doc/Section_start.html
LMP_INC =
MPI library, can be src/STUBS dummy lib
INC = path for mpi.h, MPI compiler settings
PATH = path for MPI library
LIB = name of MPI library
MPI_INC = -DMPICH_MPICXX
MPI_PATH =
MPI_LIB = -lmpich -lpthread
FFT library, can be -DFFT_NONE if not using PPPM from KSPACE package
INC = -DFFT_FFTW, -DFFT_INTEL, -DFFT_NONE, etc, FFT compiler settings
PATH = path for FFT library
LIB = name of FFT library
FFT_INC = -DFFT_FFTW -I/home/tmog/fftw2/include
FFT_PATH = -L/home/tmog/fftw2/lib
FFT_LIB = -lfftw
#-lfftw
additional system libraries needed by LAMMPS package libraries
these settings are IGNORED if the corresponding LAMMPS package
(e.g. gpu, meam) is NOT included in the LAMMPS build
SYSLIB = names of libraries
SYSPATH = paths of libraries
gpu_SYSLIB = -lcudart
meam_SYSLIB = -lifcore -lsvml -lompstub -limf
reax_SYSLIB = -lifcore -lsvml -lompstub -limf
user-atc_SYSLIB = -lblas -llapack
gpu_SYSPATH = -L/usr/local/cuda/lib64
meam_SYSPATH = -L/opt/intel/fce/10.1.015/lib
reax_SYSPATH = -L/opt/intel/fce/10.1.015/lib
user-atc_SYSPATH =
---------------------------------------------------------------------
build rules and dependencies
no need to edit this section
include Makefile.package
EXTRA_INC = (LMP_INC) (PKG_INC) (MPI_INC) (FFT_INC)
EXTRA_PATH = (PKG_PATH) (MPI_PATH) (FFT_PATH) (PKG_SYSPATH)
EXTRA_LIB = (PKG_LIB) (MPI_LIB) (FFT_LIB) (PKG_SYSLIB)
Link target
(EXE): (OBJ)
(LINK) (LINKFLAGS) (EXTRA_PATH) (OBJ) (EXTRA_LIB) (LIB) -o (EXE)
(SIZE) $(EXE)
Library target
lib: (OBJ) (ARCHIVE) (ARFLAGS) (EXE) $(OBJ)
Compilation rules
.o:.cpp
(CC) (CCFLAGS) (EXTRA_INC) -c <
.d:.cpp
(CC) (CCFLAGS) (EXTRA_INC) (DEPFLAGS) < > @
Individual dependencies
DEPENDS = (OBJ:.o=.d) include (DEPENDS)
Thank you for your attention!