Log in to Jed

1. Sinteract -c 16 -m 60G -t 3:0:0 Eunok : can be neglected
2. 
   2. 
   module load gcc
   module load openmpi
   module load python
   module list
   
   3. git clone https://github.com/Nek5000/Nek5000.git
   
   4. cd Nek5000
   
   5. Edit bin/makenek to have something below that matches your setup:
   #-------------------------------------------------------------------------------
   # Nek5000 config
   #-------------------------------------------------------------------------------
   
   # source path 
   NEK_SOURCE_ROOT="$HOME/Nek5000" 
   
   # Fortran/C compiler
   FC="mpif77"
   CC="mpicc"
   
   # Linker
   LD="$FC"
   
   # config options (set to "?" to get a list)
   #PPLIST="PARRSB DPROCMAP HYPRE"  !!! Eunok: this part should be remain commented.
   
   6. cd short_tests/eddy
   
   7. cp -iv SIZE.legacy SIZE
   
   8. ../../bin/makenek eddy_uv

Then, prepare batch file. Example the name of batchfile "nek2.run"

#!/bin/bash

#SBATCH --mail-user=eunok.yim@epfl.ch

#SBATCH --mail-type=ALL

#SBATCH --job-name="test"

#SBATCH --mem 4000

#SBATCH --chdir /home/yim/

#SBATCH --ntasks-per-node 4

#SBATCH --cpus-per-task 1

#SBATCH --time 1:0:0

#SBATCH -A head  ## This part can be removed if you are attached to only one unit. 

module purge

module load gcc

module load openmpi

module load python

echo $1 > SESSION.NAME

echo `pwd`'/' >> SESSION.NAME

echo "SESSION.NAME --------------------------"

cat SESSION.NAME

echo "---------------------------------------"

srun ./nek5000 $1 > output.txt

Important!! Nek5000 in Jed: choose lpmin correctly in the SIZE file. (~7700 elements per processor) 

Example: For a problem with total no. elements 300000, you need to put lpmin = ceil(300000/7700) = 40

The name of your run file should be there…

sbatch nek2.run nameofrun