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1 \n \r \![\n \r \](847412/n-r-r-n-r-n-n-n-n-r-r-r-r-0-12-34151-6-7.jpg "\n \r \")
\n \r \r ! " !# # # !$ \n \r\n \n \n \n \r \r\r\r ! " !# # # !$%&'()* + *,- $- " . ., /)0&12%3415167/)0&12%34133 Table of Contents Section 1: Introduction ........................................................ 3Section 2: Accessing The Cluster @ GIKI ......................... 42.1 Linux Client .......................................................................... 42.2 Windows Client .................................................................... 52.2.1 Password-less Authentication ..................................
2 ............... Section 3: Submitting Jo
............... Section 3: Submitting Jobs on the Cluster ........................ 83.1 Running Sequential Jobs .................................................... 83.2 Running Parallel MPI Jobs .................................................. 93.3 Running Parallel MPJ Express Jobs ................................ 10Contact Information ........................................................... 12Contact Address ................................................................ 12 8 ! " "# + " "8 # " + "# + "9+" +" # ! " : !# + 7# + +" - "+ 9$9 # $; 8 # " , !+ # # ;4; 4')# " ! 4'\n + " " # "%; \r
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4 $ ssh u30 @hpc.giki.edu.pk "$ #
$ ssh u30 @hpc.giki.edu.pk "$ # $+ $ ssh u30@ , ! ! ++ " , - +" + 9 "$ "+, "9; "$ "+, "9 "9 " ! ## # "; +, "9, - 9 +$ 9 " #" $" "## ! * , ! ! , ++ "; 9 $ ; " #- " 9-$ 9 !++ # +#B! . ; 9;+. ! ! &' ( \n \r \n \n \n \n \n $% $+ , ! +" + 9+" " @hpc.giki.edu.pk # $+ $ ssh u30@ 192.168.100.21 , ! ! ++ " , - +" + 9 "$ "+, "9; "$ "+, "9 "9 " ! ## #
5 "; +, "9, - 9 +$ 9
"; +, "9, - 9 +$ 9 " #" $" "## ! * , ! ! , ++ "; , " 9 $ ; " #- " 9-$ 9 !++ # +#B! . ; 9;+. &' ( ) , - +" + 9 "$ "+, "9; "$ "+, "9 "9 " ! ## # "; +, "9, - 9 +$ 9 " #" $" , " 9 $ ; " #- " 9-$ 9 !++ # " !#!*+4; "9 " ! ## # " " !, 9 ,# $ # # # ; + "# +" !" #- 9 , 9 9 " +@CC,,,;# ".;!" 9; "!;.CD! C+ $C9 , 9; %; "$ : 9 , 9 9 *
6 "9 " " *9 - E# #.
"9 " " *9 - E# #. 9 $+ , ! 99" C 99" - 7,!#-.#//#! "'\n# ##\n &; # 8 # # $+ 9%% + " - "(; #. + " $ " 5; , - +" + 9 "$ " " ;$+ $ " " 9+" "; "# " ! " 9+, "9*# # '\n( ##\n '; ,$ , - +" + 9 " +, "9;$+ $ "+, "99+" "; +, "9, - 9 +$ 99 #" $" 9 , ! ! , ++ " # !#!# + 0&' " + ! " 8. $+ "; +" : C+- #. $+ ", - 9 # $ "! # ; ! " . $* $+ , ! " @$ ssh-keygen t rsa
7 "9 ! # 9, .$ :
"9 ! # 9, .$ : " @Enter file in which to save the key (/export/home/msuleman/.ssh/id_rsa): (you can press enter here) Enter passphrase (empty for no passphrase): (you can press enter here) Enter same passphrase again: (you can press enter here) $ 7 +, - # +$ +- #. $ " � 9A. $; 9 * $+ , !# 9@$ cd ~ $ cat ./.ssh/id_rsa.pub �� ./.ssh/authorized_keys % " 1 ' "#23 1 4; "9 " # ++ # *#" , ! #" + #!/bin/bash #seq.sh # # --------------------------- # The following will be the name of the Sequential Job. You may change it according to your needs. #$ -N SEQUENTIAL_Job # The output and errors of th
8 e programmes will be written in # SEQUEN
e programmes will be written in # SEQUENTIAL_Job.oJOB_ID and SEQUENTIAL_Job.eJOB_ID respectively. #Path to the executable. /usr/bin/top # End of Script %; 7 # + " #" + $ chmod 755 seq.sh &; ,- $ "# 9-$+ " " ! , !# 9;$ qsub -V seq.sh , $ "F - 9 # # 9 7 # 9(; " , !# 9 : , " - $ "F -;$ qstat 5. 9 $ "" !F - # 9@$ qdel 30 G " &) $ "F - 9 & "#!2 1 4;" , ! #" + "# !++ # #!/bin/bash #mpi.sh # --------------------------- # The following will be the name of the MPI Job. You may change it #according to your needs. #$ -N MPI_Job # The output and errors of the programmes will be written in # MPI_
9 Job.oJOB_ID and MPI_Job.eJOB_ID respecti
Job.oJOB_ID and MPI_Job.eJOB_ID respectively.# Number of slots/cores that need to be utilized are given in the #following line. Currently it shows 2-8 i.e. The number of free cores #will be assigned to the programme. #$ -pe mpi 2-8 #The parallel environment that is being used is mpi# --------------------------- # needs in # $NSLOTS # the number of tasks to be used/cores assigned by grid engine # $TMPDIR/machines # a valid machine file to be passed to mpirun echo "Got $NSLOTS slots." mpirun -np $NSLOTS -mca ras gridengine --hostfile $TMPDIR/machines ./a.out # End of Script %; 7 # + " #" + -$ $+ ! , !# 9$ chmod 755 mpi.sh &; - $ "# 9* $+ , !# 9;$ qsub -V mpi.sh +" F - 9 $ "- 9F -(; : , "
10 $ "F -* " , !# 9$
$ "F -* " , !# 9$ qstat 5; "9 " 9 " !F - $+ , !# 9;$ qdel 30 G " &) $ "F - 9; \n "#"2 14%\n 1 4;" #" + "# !++ # #!/bin/bash #mpjrun_sge.sh # # --------------------------- # The following will be the name of the MPJ Express Job. You may change it according to your needs. #$ -N MPJ_Job # The output and errors of the programmes will be written in # MPJ_Job.oJOB_ID and MPJ_Job.eJOB_ID respectively.# Number of slots/cores that need to be utilized are given in the following line. Currently it shows 2-8 i.e. The number of free cores will be assigned to the programme. #$ -pe mpj 2-8 #The parallel environment that is being used is mpj# --------------------------- # # needs in # $NSLOTS # the num
11 ber of tasks to be used/cores assigned b
ber of tasks to be used/cores assigned by grid engine # $TMPDIR/machines # a valid machine file to be passed to mpirun echo "Got $NSLOTS slots." cat $TMPDIR/machines � `pwd`/machines # if your d_port, s_port and mpj_port are different than default then you have to give them properly in the respective command mpjboot $TMPDIR/machines mpjrun.sh -np $NSLOTS -dev niodev World mpjhalt machines rm `pwd`/machines # End of Script %; 7 # + " #" + $ chmod 755 mpjrun_sge.sh &; ,- $ "# 9-$+ " " ! , !# 9;$ qsub -V mpjrun_sge.sh , +" F - 9 $ "- 9F -;(; " , !# 9 : ,$ "F -H ;$ qstat 5. 9 $ "" !F -* $+ , !# 9$ qdel 30 G " &) $ "F - 9;\r !\n I -
12 !'\n# ##\n 4;" ! #
!'\n# ##\n 4;" ! #" + "# ! ++ # #!/bin/bash #mpi.sh # # --------------------------- # The following will be the name of the MPI Job. You may change it #according to your needs. #$ -N MPI_Job # The output and errors of the programmes will be written in # MPI_Job.oJOB_ID and MPI_Job.eJOB_ID respectively # Number of slots/cores that need to utilized are given in the # following line. Currently it shows 2-8 i.e. The number of free cores # will be assigned to the programme. #$ -pe mpi 2-8 # The parallel environment that is being used is mpi # --------------------------- # # needs in # $NSLOTS # the number of tasks to be used/cores assigned by grid engine # $TMPDIR/machines # a valid machine file to be passed to mpirun echo "Got $NSLOTS slots." mpirun -np $NSLOTS -mca ras gridengin
13 e mca btl mx,sm,self -- hostfile $TMPDI
e mca btl mx,sm,self -- hostfile $TMPDIR/machines ./a.out # You can also you mca mtl mx,sm,self instead of mca btl mx,sm,self # End of Script %; 7 # + " #" + $ chmod 755 mpi.sh 3. ,- $ "# 9-$+ " " ! , !# 9;$ qsub -V mpi.sh , +" F - 9 $ "- 9F -(; " , !# 9 " " : " - $ "F -; ' $ qstat 5; 9 $ "" !F - # 9@$ qdel 30 G " &) $ "F - 9; 5 # "$* 9 "$ @+#B! . ; 9;+. B! . ; 9;+. B! . ; 9;+. & # $ + "# # 9 ! " !* ! " !# # # !$%&'()* + *,- $- " . ., /)0&12%341517/)0&12%34133