Tasks

Manual for eScience at CU

• Responsible persons: Jittrathep Sukultanasorn

To do

• Create an example of C++ code to run on eScience machine. The code template should contains few parameters which will be changed later from script.
• Create an example of shell script to replace a parameters, compile and run on eScience machine
  • Try to use sed on shell script
• Write a manual
• You need at least three file
  • submit_script.pbs (template)
  • testC.cpp (template)
  • submit.(c)sh

Idea

• Run submit.(c)sh [par1] [par2] [par3]
• It will create new folder, and copy template of submit_script.pbs, testC.cpp to the new folder
• compile testC.cpp in the new folder
• submit a job on that folder

Example of submit_script.pbs

#### PBS Part ####
#PBS -N Test_Job
#PBS -S /bin/bash 
#PBS -l nodes=1:ppn=1
#PBS -q short
#### End Part ####

cd $HOME/batch/test-2
echo -e "Run on $(hostname)"
echo -e "Start at $(date)\n"
./testC
echo -e "\nFinish at $(date)"

Need to

• Apply for eScience account

Multicore Mathematica run on eScience machine

• Responsible persons: Vichayanun Wachirapusitanand

Need to

• Apply for eScience account
• Add chula as group (tell Phat)
• Try to write mathematica code with non-interactive mode (i.e. no plot)
  • All outputs, including plots and histograms, should be kept on files
  • All input should be done with input file
  • You will need LaunchKernels[2] to run 12 cores (keep 4 cores for another jobs)
• Write a manual

To do

Example of submit_script.pbs

#### PBS Part ####
#PBS -N Test_Mathematica
#PBS -S /bin/bash 
#PBS -l nodes=1:ppn=12
#PBS -q mathshort
#PBS -W group_list=chula
#PBS -W x=gres:MathKernel+1  <=== not sure we need it (check!)
#### End Part ####
 
module load mathematica

cd $HOME/batch/test-4-16Cores
echo -e "Run on $(hostname)"
echo -e "Start at $(date)\n"
math -script testParallel2.m
echo -e "\nFinish at $(date)"

Example of mathematheca parallel code

(* ::Package:: *)

d=0.000005

y[t_]:=1/(ProductLog[(1/d-1)*Exp[1/d-1-t]]+1)	(*analytical solution*)
relerr[t_,s_]:=Abs[(y[t]-x[t]/.s)/y[t]]			(*relative error of solution s at time t*)
g[v_]:={v[[1]],v[[2]][[1]],relerr[1/d,v[[2]][[2]][[1]]]}	(*helper function*)

(*compute numerical solutions for 6 different step sizes*)
LaunchKernels[12]
tbl=ParallelTable[{step,Timing[NDSolve[{x'[t]==x[t]^2-x[t]^3,x[0]==d},x,{t,0,2/d},MaxStepSize->step,MaxSteps->10000000]]},{step,5,3,-0.01}]
CloseKernels[]

SetOptions[$Output,FormatType->OutputForm]    (*better output when called with-script*)
Print[Grid[Join[{{"Stepsize","Time","Error at 1/d"}},Map[g,tbl]]]]    (*print the result*)

Install node-6 to eScience with CMSSW

• Responsible persons:

To do

• Install new VM on node-6 using SLC6 or CC7
• Install CMSSW on that machine
• Try to submit CMSSW job on that machine

Update Mathematica to 10.X

• Responsible persons:

To do

• Update Mathematica to version 10.X

-- PhatSrimanobhas - 2016-07-04