close
Warning:
Can't synchronize with repository "(default)" (Unsupported version control system "svn": /usr/lib/python2.7/dist-packages/libsvn/_core.so: failed to map segment from shared object: Cannot allocate memory). Look in the Trac log for more information.
How to run R-MPI on multiple machine with normal user permission
- Reference Configuration Guide:
- Fisrt, login as nornal user. Here we login with user id 'jazz'. Then exchange SSH public key to each computing node.
login as: jazz
jazz@bio-cluster-12's password:
jazz@bio-cluster-12:~$ ssh-keygen -t rsa
Generating public/private rsa key pair.
Enter file in which to save the key (/home/jazz/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/jazz/.ssh/id_rsa.
Your public key has been saved in /home/jazz/.ssh/id_rsa.pub.
The key fingerprint is:
XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX:XX jazz@bio-cluster-12
jazz@bio-cluster-12:~$ for i in 11 10 09 08 07 06; do scp .ssh/id_rsa.pub bio-cluster-$i:.ssh/authorized_keys; done
- setup .mpd.conf for each compute node in $HOME
jazz@bio-cluster-12:~$ echo "MPD_SECRETWORD=${user}$$" > ~/.mpd.conf
jazz@bio-cluster-12:~$ chmod 600 .mpd.conf
jazz@bio-cluster-12:~$ for i in 11 10 09 08 07 06
> do
> scp .mpd.conf bio-cluster-$i:.
> done
.mpd.conf 100% 21 0.0KB/s 00:00
.mpd.conf 100% 21 0.0KB/s 00:00
.mpd.conf 100% 21 0.0KB/s 00:00
.mpd.conf 100% 21 0.0KB/s 00:00
.mpd.conf 100% 21 0.0KB/s 00:00
.mpd.conf 100% 21 0.0KB/s 00:00
- setup mpd.hosts on localhost
jazz@bio-cluster-12:~$ cat > mpd.hosts << EOF
> bio-cluster-11
> bio-cluster-10
> bio-cluster-09
> bio-cluster-08
> bio-cluster-07
> bio-cluster-06
> EOF
- run mpdboot for 7 nodes and use mpdtrace to check the status of mpd process on each compute node. mpdringtest can test the speed of message passing. mpdallexit to terminate all mpd processes.
jazz@bio-cluster-12:~$ mpdboot -n 7
jazz@bio-cluster-12:~$ mpdtrace -l
bio-cluster-12_54092 (10.220.202.219)
bio-cluster-08_38361 (10.220.202.223)
bio-cluster-09_52923 (10.220.202.222)
bio-cluster-11_33377 (10.220.202.220)
bio-cluster-10_33103 (10.220.202.221)
bio-cluster-06_59631 (10.220.202.225)
bio-cluster-07_59533 (10.220.202.224)
jazz@bio-cluster-12:~$ mpdringtest 100
time for 100 loops = 0.0729811191559 seconds
jazz@bio-cluster-12:~$ mpdallexit
Test 1: single mpd and R-MPI in localhost
- run mpd in localhost
jazz@bio-cluster-12:~$ mpd &
[1] 1505
jazz@bio-cluster-12:~$ mpdtrace -l
bio-cluster-12_37007 (10.220.202.219)
- BTW, you can also use mpdboot to run mpd in localhost
jazz@bio-cluster-12:~$ mpdboot
[1]+ Done mpd
jazz@bio-cluster-12:~$ mpdtrace -l
bio-cluster-12_44810 (10.220.202.219)
- run R-MPI with single mpd in localhost
jazz@bio-cluster-12:~$ R
R version 2.4.0 Patched (2006-11-25 r39997)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
> library(Rmpi)
> mpi.spawn.Rslaves()
1 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 2 is running on: bio-cluster-12
slave1 (rank 1, comm 1) of size 2 is running on: bio-cluster-12
> mpi.close.Rslaves()
mpi.close.Rslaves()
[1] 1
> mpi.quit(save="no")
mpi.quit(save="no")
jazz@bio-cluster-12:~$
Test 2: Compile MPICH2 sample program and run in multiple compute nodes
- Sample program from Wade.
jazz@bio-cluster-12:~$ cat > demo1.c << EOF
> /* Program:
> * 每個 node 將自己的 id 印出，並且將所有的參與運動的 node 總數也印出
> * ，顯示出自己的主機名稱。
> * History:
> * 2008-04-09 BETA
> * 2008-06-25 增加顯示主機名稱功能
> */
>
> #include <stdio.h>
> #include "mpi.h"
> int main (int argc, char **argv)
> {
> int rank, size, len;
> char name[MPI_MAX_PROCESSOR_NAME];
> MPI_Init(&argc, &argv);
> int myid, numprocs;
>
> /* 取得 node 總數 */
> MPI_Comm_size(MPI_COMM_WORLD,&numprocs);
>
> /* 取得本身 node id / rank */
> MPI_Comm_rank(MPI_COMM_WORLD,&myid);
>
> /* 取得本身 host name */
> MPI_Get_processor_name(name, &len);
> printf("This is machine %d of %d name = %s\n", myid, numprocs, name);
> MPI_Finalize();
> }
> EOF
jazz@bio-cluster-12:~$ mpicc -I /usr/include/mpich2/ -lmpich demo1.c -o demo1
jazz@bio-cluster-12:~$ for i in 11 10 09 08 07 06
> do
> scp demo1 bio-cluster-$i:.
> done
demo1 100% 557KB 557.3KB/s 00:00
demo1 100% 557KB 557.3KB/s 00:00
demo1 100% 557KB 557.3KB/s 00:00
demo1 100% 557KB 557.3KB/s 00:00
demo1 100% 557KB 557.3KB/s 00:00
demo1 100% 557KB 557.3KB/s 00:00
jazz@bio-cluster-12:~$ mpdboot -n 7
jazz@bio-cluster-12:~$ mpdtrace -l
bio-cluster-12_41632 (10.220.202.219)
bio-cluster-08_33197 (10.220.202.223)
bio-cluster-09_40371 (10.220.202.222)
bio-cluster-10_54199 (10.220.202.221)
bio-cluster-06_54334 (10.220.202.225)
bio-cluster-07_42302 (10.220.202.224)
bio-cluster-11_36534 (10.220.202.220)
jazz@bio-cluster-12:~$ mpiexec -n 7 /home/jazz/demo1
This is machine 0 of 7 name = bio-cluster-12
This is machine 1 of 7 name = bio-cluster-08
This is machine 2 of 7 name = bio-cluster-09
This is machine 3 of 7 name = bio-cluster-10
This is machine 5 of 7 name = bio-cluster-07
This is machine 6 of 7 name = bio-cluster-11
This is machine 4 of 7 name = bio-cluster-06
Test 3: run multiple mpd and R-MPI in multiple compute nodes
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