Start up a cluster

#!/bin/sh

# This script tests the Loren cluster after a shutdown

# To run the script type 'sh cluster_test.sh'.

VASP=vasp_std

MPIRUN=mpiexec.hydra

#create a directory and input files

mkdir ~/test

cd ~/test

cat > INCAR <<!

SYSTEM = O atom in a box

ISMEAR = 0

!

cat > POSCAR <<!

O atom in a box

1.0 

8.0 0.0 0.0 

0.0 8.0 0.0 

0.0 0.0 8.0 

1 

cart 

0 0 0

!

cat > KPOINTS <<!

Gamma-point only

1 

rec 

0 0 0 1 

!

cp /share/apps/vasp/POTENTIALS/GGA-PBE/O/POTCAR .

#set up the test for the different queues

mpi=16

nodes=32

i=0

# test each queue

for j in 1 2 5 11 13 14 15 16 17 18 19 21 22 23 24 25 27 28 29 31

 do

  mkdir ~/test/$i-$j

 cp INCAR KPOINTS POSCAR POTCAR $i-$j

 cat > $i-$j/qvasp <<!

#!/bin/bash

#$ -N test_$i-$j

#$ -cwd

#$ -pe mpi $mpi

#$ -S /bin/bash

#$ -q all.q@compute-$i-$j.local

#$ -e vasp.err

#$ -o vasp.out

module purge

module load compilers/intel_16.0.3 apps/vasp_5.4.1

$MPIRUN $VASP > job.log

!

 cd $i-$j

 qsub qvasp

 cd ../

done

# Have user check if jobs are finished

user_input=0

until [ $user_input -eq "1" ]

 do

     qstat -f

                read -r -p "Have all test jobs finished? [Y/N] " response

                if [[ "$response" =~ ^([yY][eE][sS]|[yY])+$ ]]

                then

                        user_input=1

                fi

        done

# Once all jobs have finished print out the error files

echo "Print out VASP error files:"

i=0

# test each queue

for j in 1 2 5 11 13 14 15 16 17 18 19 21 22 23 24 25 27 28 29 31

 do

                echo "compute-$i-$j.local"

                echo "$(<$i-$j/vasp.err)" | tail -2

        done

printf "If the only error is 'cannot remove tmp directory' the simulation was successful. 

\nIf the error file reads 'cannot find vasp.err' it is likely the node is not functioning and you will need to do a hard reboot. 

\nIf it cannot find the intel compliers or vasp_std binary you need to copy the modulefiles and compilers to the node (see the UF-FLAMES 'admin' site)."

#!/bin/sh

# This script tests the Hermes cluster after a shutdown

# To run the script type 'sh cluster_test.sh'.

#create a directory and input files

mkdir ~/test

cd ~/test

cat > INCAR <<!

SYSTEM = O atom in a box

ISMEAR = 0

!

cat > POSCAR <<!

O atom in a box

1.0 

8.0 0.0 0.0 

0.0 8.0 0.0 

0.0 0.0 8.0 

1 

cart 

0 0 0

!

cat > KPOINTS <<!

Gamma-point only

1 

rec 

0 0 0 1 

!

cp /opt/VASP-resources/Potentials/GGA/O/POTCAR .

#set up the test for the different queues

mpi=8

for i in {0..3} ;

do

  if [ $i -eq 0 ]

 then 

  nodes=8

  name=all2

 elif [ $i -eq 1 ]

 then 

  nodes=24 

  name=all

 elif [ $i -eq 3 ]

 then 

  nodes=20

  name=eight

 else

  continue 

 fi

# test each queue

 for ((j=1;j<=nodes;j++));

 do

  mkdir ~/test/$i-$j

  cp INCAR KPOINTS POSCAR POTCAR $i-$j

  if  [ $i -eq 1 ] && [ $j -eq 11 ]

         then

   mpi=4

  elif [ $i -eq 1 ] && [ $j -gt 22 ]

  then

   name=single

   mpi=8

  elif [ $i -eq 0 ]

  then

   mpi=24

  else

   mpi=8

  fi

  cat > $i-$j/qvasp <<!

#!/bin/bash

#$ -N test_$i-$j

#$ -cwd

#$ -pe mpi $mpi

#$ -S /bin/bash 

#$ -q $name.q@compute-$i-$j.local

#$ -e vasp.err

#$ -o vasp.out

export LD_LIBRARY_PATH=/opt/intel/composer_xe_2011_sp1.8.273/mkl/lib/intel64

/opt/intel/openmpi-1.4.4/bin/mpirun /home/michele/bin/vasp5.3.5_openmpi_1.4.4 > job.log

!

  cd $i-$j

  qsub qvasp

  cd ../

 done

done

# Have user check if jobs are finished

user_input=0

until [ $user_input -eq "1" ]

        do

                qstat -f

                read -r -p "Have all test jobs finished? [Y/N] " response

                if [[ "$response" =~ ^([yY][eE][sS]|[yY])+$ ]]

                then

                        user_input=1

                fi

        done

# Once all jobs have finished print out the error files

echo "Print out VASP error files:"

for i in {0..3} ;

do

        if [ $i -eq 0 ]

        then

                nodes=8

                name=all2

        elif [ $i -eq 1 ]

        then

                nodes=24

                name=all

        elif [ $i -eq 3 ]

        then

                nodes=20

                name=eight

        else

                continue

        fi

        for ((j=1;j<=nodes;j++));

        do

                echo "$name.q@compute-$i-$j.local"

                echo "$(<$i-$j/vasp.err)"

        done

done

printf "If the error file reads 'cannot remove tmp directory' the simulation was successful. 

\nIf the error file reads 'cannot find vasp.err' the node is not functioning and you will need to do a hard reboot. 

\nIf it cannot find the intel compliers you need to fix a missing opt/intel directory (see the UF FLAMES 'admin' guide)."