root / examples / Vasp / Serial / run_Path_PBS @ 1
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| 1 | 1 | equemene | #PBS -S /bin/sh |
|---|---|---|---|
| 2 | 1 | equemene | #PBS -N PathSer0.02 |
| 3 | 1 | equemene | #PBS -l nodes=1:Other |
| 4 | 1 | equemene | #PBS -q OneL |
| 5 | 1 | equemene | #PBS -o PathSer0.02.batch-log |
| 6 | 1 | equemene | #PBS -j oe |
| 7 | 1 | equemene | #PBS -M Paul.Fleurat-Lessard@ens-lyon.fr |
| 8 | 1 | equemene | #PBS -m aeb |
| 9 | 1 | equemene | |
| 10 | 1 | equemene | |
| 11 | 1 | equemene | #!/bin/bash |
| 12 | 1 | equemene | |
| 13 | 1 | equemene | home_dir=$PBS_O_WORKDIR |
| 14 | 1 | equemene | work_dir=$PBS_O_WORKDIR |
| 15 | 1 | equemene | Job=Test_Vasp_Serial |
| 16 | 1 | equemene | numb=run1 |
| 17 | 1 | equemene | |
| 18 | 1 | equemene | ###################################### |
| 19 | 1 | equemene | # |
| 20 | 1 | equemene | # you might have to change the following variables |
| 21 | 1 | equemene | # |
| 22 | 1 | equemene | ###################################### |
| 23 | 1 | equemene | # |
| 24 | 1 | equemene | # Where is Path.exe ?? |
| 25 | 1 | equemene | # |
| 26 | 1 | equemene | PathExe=~/Programs/Carte/src/Path.exe |
| 27 | 1 | equemene | # |
| 28 | 1 | equemene | # Where is VASP ? |
| 29 | 1 | equemene | # |
| 30 | 1 | equemene | export VASP=/home/dloffred/VASP_SOURCES/Intel_P4/VASP46_CINEB |
| 31 | 1 | equemene | # |
| 32 | 1 | equemene | # Whre is mpirun ? |
| 33 | 1 | equemene | # |
| 34 | 1 | equemene | export MPIRUN=/usr/local/mpich-intel-090404/bin/mpirun |
| 35 | 1 | equemene | # |
| 36 | 1 | equemene | # Some libraries... |
| 37 | 1 | equemene | # |
| 38 | 1 | equemene | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/fc/9.1.037/lib/:/opt/intel/cc/9.1.045/lib:/usr/lib:/opt/intel/mkl/8.1/lib/32 |
| 39 | 1 | equemene | export PATH=/opt/intel/fc/9.1.037/bin/:/opt/intel/cc/9.1.045/bin/:$PATH:$HOME/bin:/usr/local/mpich-intel9/bin |
| 40 | 1 | equemene | export LD_RUN_PATH=$LD_RUN_PATH:/opt/intel/fc/9.1.037/lib/:/opt/intel/cc/9.1.045/lib |
| 41 | 1 | equemene | export MANPATH=$MANPATH:/opt/intel/fc/9.1.037/man/:/opt/intel/cc/9.1.045/man |
| 42 | 1 | equemene | export LANG=C |
| 43 | 1 | equemene | # |
| 44 | 1 | equemene | #Usually nothing has to be changed after this line |
| 45 | 1 | equemene | # |
| 46 | 1 | equemene | ################################################# |
| 47 | 1 | equemene | |
| 48 | 1 | equemene | |
| 49 | 1 | equemene | |
| 50 | 1 | equemene | |
| 51 | 1 | equemene | ################################# |
| 52 | 1 | equemene | # |
| 53 | 1 | equemene | # We create the machinefile |
| 54 | 1 | equemene | # |
| 55 | 1 | equemene | # even if it is not really needed for SERIAL calculations |
| 56 | 1 | equemene | # |
| 57 | 1 | equemene | ################################# |
| 58 | 1 | equemene | nodes=`cat $PBS_NODEFILE` |
| 59 | 1 | equemene | nnodes=`wc $PBS_NODEFILE | awk '{print $1}'`
|
| 60 | 1 | equemene | |
| 61 | 1 | equemene | confile=$home_dir/ip.$PBS_JOBID.conf |
| 62 | 1 | equemene | touch $confile |
| 63 | 1 | equemene | j="init" |
| 64 | 1 | equemene | for i in $nodes |
| 65 | 1 | equemene | do |
| 66 | 1 | equemene | if [ $j != $i ] |
| 67 | 1 | equemene | then echo "$i:1" >> $confile |
| 68 | 1 | equemene | else |
| 69 | 1 | equemene | echo "vous calculez sur des noeuds smp" |
| 70 | 1 | equemene | fi |
| 71 | 1 | equemene | j=$i |
| 72 | 1 | equemene | done |
| 73 | 1 | equemene | |
| 74 | 1 | equemene | ############################# |
| 75 | 1 | equemene | # |
| 76 | 1 | equemene | # We create the 'VaspExe' file that Path will use to run the |
| 77 | 1 | equemene | # actual VASP calculations of E and forces |
| 78 | 1 | equemene | # |
| 79 | 1 | equemene | ############################# |
| 80 | 1 | equemene | cd $work_dir |
| 81 | 1 | equemene | echo "$MPIRUN -nolocal -machinefile $confile -np $nnodes $VASP > out_$numb" > ./RunVasp |
| 82 | 1 | equemene | chmod u+x ./RunVasp |
| 83 | 1 | equemene | |
| 84 | 1 | equemene | ############################### |
| 85 | 1 | equemene | # |
| 86 | 1 | equemene | # We launch PATH |
| 87 | 1 | equemene | # |
| 88 | 1 | equemene | ############################### |
| 89 | 1 | equemene | ln -s ${PathExe} .
|
| 90 | 1 | equemene | |
| 91 | 1 | equemene | ./Path.exe ${Job}.path &> ${Job}.out
|