Sender: LSF System <lsfadmin@cn130.scarf.rl.ac.uk>
Subject: Job 558952: <#BSUB -q scarf-lexicon-2;#BSUB -n 16;#BSUB -W 24:00;#BSUB -o %J.log;#BSUB -e %J.err;  export OMP_NUM_THREADS=8;export MP_TASK_AFFINITY=core:$OMP_NUM_THREADS; module load intel/14.0;module load gcc/6.2.0;module load numpy/1.10.4;export PATH=/home/clfg/scarf176/SMILEI-reinstall/anaconda2/bin:/home/clfg/scarf176/SMILEI-reinstall/openmpi-1.10.2/bin:/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/bin:${PATH};export LD_LIBRARY_PATH=/home/clfg/scarf176/SMILEI-reinstall/openmpi-1.10.2/lib:/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/lib:${LD_LIBRARY_PATH};export HDF5_ROOT_DIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16; export HDF5_DOCDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/doc;export HDF5_INCDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/include;export HDF5_INCLUDEDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/include;export HDF5_LIBDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/lib; export PYTHONHOME=/home/clfg/scarf176/SMILEI-reinstall/Python-2.7.12; DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"; mpirun ~/SMILEI-reinstall/smilei-novafix/smilei $DIR/input.py> in cluster <sctsc> Done

Job <#BSUB -q scarf-lexicon-2;#BSUB -n 16;#BSUB -W 24:00;#BSUB -o %J.log;#BSUB -e %J.err;  export OMP_NUM_THREADS=8;export MP_TASK_AFFINITY=core:$OMP_NUM_THREADS; module load intel/14.0;module load gcc/6.2.0;module load numpy/1.10.4;export PATH=/home/clfg/scarf176/SMILEI-reinstall/anaconda2/bin:/home/clfg/scarf176/SMILEI-reinstall/openmpi-1.10.2/bin:/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/bin:${PATH};export LD_LIBRARY_PATH=/home/clfg/scarf176/SMILEI-reinstall/openmpi-1.10.2/lib:/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/lib:${LD_LIBRARY_PATH};export HDF5_ROOT_DIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16; export HDF5_DOCDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/doc;export HDF5_INCDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/include;export HDF5_INCLUDEDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/include;export HDF5_LIBDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/lib; export PYTHONHOME=/home/clfg/scarf176/SMILEI-reinstall/Python-2.7.12; DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"; mpirun ~/SMILEI-reinstall/smilei-novafix/smilei $DIR/input.py> was submitted from host <ui3.scarf.rl.ac.uk> by user <scarf176> in cluster <sctsc> at Fri Jul  7 16:20:20 2017.
Job was executed on host(s) <8*cn130.scarf.rl.ac.uk>, in queue <scarf-lexicon-2>, as user <scarf176> in cluster <sctsc> at Fri Jul  7 16:20:21 2017.
                            <8*cn107.scarf.rl.ac.uk>
</home/clfg/scarf176> was used as the home directory.
</home/clfg/scarf176/jholloway/SMILEI/newversionruns/novabug-AUTHORPATCH/1ns-cladcolion> was used as the working directory.
Started at Fri Jul  7 16:20:21 2017.
Terminated at Fri Jul  7 17:36:47 2017.
Results reported at Fri Jul  7 17:36:47 2017.

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
#BSUB -q scarf-lexicon-2
#BSUB -n 16
#BSUB -W 24:00
#BSUB -o %J.log
#BSUB -e %J.err
 
export OMP_NUM_THREADS=8
export MP_TASK_AFFINITY=core:$OMP_NUM_THREADS

module load intel/14.0
module load gcc/6.2.0
module load numpy/1.10.4
export PATH=/home/clfg/scarf176/SMILEI-reinstall/anaconda2/bin:/home/clfg/scarf176/SMILEI-reinstall/openmpi-1.10.2/bin:/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/bin:${PATH}
export LD_LIBRARY_PATH=/home/clfg/scarf176/SMILEI-reinstall/openmpi-1.10.2/lib:/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/lib:${LD_LIBRARY_PATH}
export HDF5_ROOT_DIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16

export HDF5_DOCDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/doc
export HDF5_INCDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/include
export HDF5_INCLUDEDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/include
export HDF5_LIBDIR=/home/clfg/scarf176/SMILEI-reinstall/hdf5-1.8.16/lib

export PYTHONHOME=/home/clfg/scarf176/SMILEI-reinstall/Python-2.7.12

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

mpirun ~/SMILEI-reinstall/smilei-novafix/smilei $DIR/input.py

------------------------------------------------------------

Successfully completed.

Resource usage summary:

    CPU time :                                   71701.00 sec.
    Max Memory :                                 627.12 MB
    Average Memory :                             582.15 MB
    Total Requested Memory :                     -
    Delta Memory :                               -
    Max Swap :                                   273145 MB
    Max Processes :                              21
    Max Threads :                                151
    Run time :                                   4592 sec.
    Turnaround time :                            4587 sec.

The output (if any) follows:

                    _            _
  ___           _  | |        _  \ \   Version : ??-??
 / __|  _ __   (_) | |  ___  (_)  | |   
 \__ \ | '  \   _  | | / -_)  _   | |
 |___/ |_|_|_| |_| |_| \___| |_|  | |  
                                 /_/    
 
 

 Reading the simulation parameters
 --------------------------------------------------------------------------------
 HDF5 version 1.8.16
	 Python version 2.7.11
	 Parsing pyinit.py
	 Parsing ??-??
	 Parsing pyprofiles.py
	 Parsing /home/clfg/scarf176/jholloway/SMILEI/newversionruns/novabug-AUTHORPATCH/1ns-cladcolion/input.py
	 Parsing pycontrol.py
	 Calling python _smilei_check
 

 Geometry: 2d3v
 --------------------------------------------------------------------------------
	 (nDim_particle, nDim_field) : (2, 2)
	 Interpolation_order : 2
	 (res_time, sim_time) : (7.443229, 26870.057685)
	 (n_time,   timestep) : (200000, 0.134350)
	            timestep  = 0.950000 * CFL
	 dimension 0 - (res_space, sim_length) : (5.000000, 32.000000)
	             - (n_space_global,  cell_length) : (160, 0.200000)
	 dimension 1 - (res_space, sim_length) : (5.000000, 32.000000)
	             - (n_space_global,  cell_length) : (160, 0.200000)
 

 Initializing MPI
 --------------------------------------------------------------------------------
	 Number of MPI process : 16
	 Number of patches : 
		 dimension 0 - number_of_patches : 16
		 dimension 1 - number_of_patches : 16
	 Patch size :
		 dimension 0 - n_space : 10 cells.
		 dimension 1 - n_space : 10 cells.
	 Dynamic load balancing frequency: every 0 iterations.
 

 OpenMP
 --------------------------------------------------------------------------------
	 Number of thread per MPI process : 8
 

 Initializing the restart environment
 --------------------------------------------------------------------------------
 

 Initializing moving window
 --------------------------------------------------------------------------------
 

 Initializing particles & fields
 --------------------------------------------------------------------------------
	 Creating Species :
	 Laser parameters :
	 Parameters for collisions #0 :
		 Collisions between species (0 3) and (2)
		 Coulomb logarithm: 0.000000
		 Debug every 2000 timesteps
		 Collisional ionization with atomic number 1
	 Adding particle walls:
		 Nothing to do
 

 Initializing Patches
 --------------------------------------------------------------------------------
	 First patch created
		 Approximately 10% of patches created
		 Approximately 20% of patches created
		 Approximately 30% of patches created
		 Approximately 40% of patches created
		 Approximately 50% of patches created
		 Approximately 60% of patches created
		 Approximately 70% of patches created
		 Approximately 80% of patches created
		 Approximately 90% of patches created
	 All patches created
		 Species 0 (elecCore) created with 344 particles
		 Species 1 (ionCore) created with 344 particles
		 Species 2 (hydrogen) created with 50856 particles
		 Species 3 (ionisede) created with 0 particles
 

 Initializing Diagnostics, antennas, and external fields
 --------------------------------------------------------------------------------
	 Diagnostic Fields #0  :
		 Ex Ey Rho_elecCore Rho_ionCore 
	 Done initializing diagnostics
 

 Solving Poisson at time t = 0
 --------------------------------------------------------------------------------
	 Poisson solver converged at iteration: 169, relative err is ctrl = 0.909072 x 1e-14
	 Poisson equation solved. Maximum err = 0.000000 at i= -1
 Time in Poisson : 0.070151
 

 Applying external fields at time t = 0
 --------------------------------------------------------------------------------
 

 Initializing diagnostics
 --------------------------------------------------------------------------------
 

 Running diags at time t = 0
 --------------------------------------------------------------------------------
 

 Cleaning up python runtime environement
 --------------------------------------------------------------------------------
	 Checking for cleanup() function:
	 python cleanup function does not exists
	 Calling python _keep_python_running() :
		 Closing Python
 

 Memory consumption
 --------------------------------------------------------------------------------
	 (Master) Species part = 0 MB
	 Global Species part = 0.002 GB
	 Max Species part = 0 MB
	 (Master) Fields part = 0 MB
	 Global Fields part = 0.006 GB
	 Max Fields part = 0 MB
 

 Time-Loop started: number of time-steps n_time = 200000
 --------------------------------------------------------------------------------
        timestep       sim time   cpu time [s]   (    diff [s] )
    20000/200000     2.6871e+03     1.9405e+02   (  1.9405e+02 )
    40000/200000     5.3741e+03     4.1223e+02   (  2.1818e+02 )
    60000/200000     8.0611e+03     6.2574e+02   (  2.1351e+02 )
    80000/200000     1.0748e+04     8.5955e+02   (  2.3381e+02 )
   100000/200000     1.3435e+04     1.1353e+03   (  2.7580e+02 )
   120000/200000     1.6122e+04     1.4465e+03   (  3.1117e+02 )
   140000/200000     1.8809e+04     1.8129e+03   (  3.6636e+02 )
   160000/200000     2.1496e+04     2.4304e+03   (  6.1752e+02 )
   180000/200000     2.4183e+04     3.4249e+03   (  9.9448e+02 )
   200000/200000     2.6870e+04     4.5804e+03   (  1.1555e+03 )
 

 End time loop, time dual = 26870.125
 --------------------------------------------------------------------------------
 

 Time profiling : (print time > 0.001%)
 --------------------------------------------------------------------------------
 Time in time loop :	4580.390	88.658% coverage
 	     Particles	102.894	2.246%
 	       Maxwell	16.218	<1%
 	   Diagnostics	148.646	3.245%
 	     Densities	2.854	<1%
 	    Collisions	183.900	4.015%
 	    Mov window	5.655	<1%
 	Sync Particles	921.600	20.121%
 	   Sync Fields	596.364	13.020%
 	Sync Densities	2062.287	45.024%
 
	 Printed times are averaged per MPI process
 		 See advanced metrics in profil.txt
 

 END
 --------------------------------------------------------------------------------


PS:

Read file <558952.err> for stderr output of this job.