1 Logging in 1. 2 Star-P 2

Transcription

1 Quinn Mahoney March 21, 2006 Contents 1 Logging in 1 2 Star-P 2 3 Cluster Specifications 9 1 Logging in To log in to the beowulf cluster, ssh to beowulf.csail.mit.edu with the username and password you were provided. From Linux, Unix, and Athena: From the prompt, type ssh user@beowulf.csail.mit.edu. To use X11, type ssh -X user@beowulf.csail.mit.edu. From Mac OS X: From Terminal, type ssh user@beowulf.csail.mit.edu From X11.app, type ssh -Y user@beowulf.csail.mit.edu From Windows: With an SSH client, connect to beowulf.csail.mit.edu I recommend SecureCRT, which is available from web.mit.edu/software. To use X11, you must install and configure X-Win32, which is also available through MIT. The first thing you want to do is change your password. Do this with the command yppasswd. (If you use passwd, you will have to wait for NIS to distribute your password to the other nodes.) The beowulf cluster consists of a frontend and 16 compute nodes, all connected by gigabit ethernet. We d like to reserve the frontend for compiling and for running MATLAB as a frontend to Star-P, so please log in to one of the compute nodes to run your MPI programs. Note that the other nodes are only accessible through the frontend. To do this, pick a random node and ssh to it by typing ssh node-# or ssh -X node-#, where # is a number from 0 to 15. You can use jmon to monitor the CPU and memory usage of all the nodes. 1

2 2 Star-P Getting Started First, you will need to log in to the Star-P server and change your password. To do this, log in to starp.csail.mit.edu with your temporary password and run passwd. Please note! To use Star-P, you will run the MATLAB client on beowulf.csail.mit.edu, but the computation will occur on starp.csail.mit.edu. This is why you need an account on both machines. Running Star-P To run Star-P, you ll use a shell script, starp, located in /usr/local/bin. The directory /usr/local/bin should already be in your path, so you can run the script simply by typing starp, as I do on line 4 below. Notice that you must supply your password to beowulf.csail.mit.edu to log in, as on line 2, but to run Star-P, you must supply your password to starp.csail.mit.edu, as on line 5. For this reason, it is best to use one password on both machines. You are then given a MATLAB prompt, denoted by >>. 1 localhost:~ quinn$ ssh qmahoney@beowulf.csail.mit.edu 2 qmahoney@beowulf.csail.mit.edu s password: 4 [qmahoney@a h32 ~]$ starp 5 Password: 6 Warning: Unable to open display, MATLAB is starting without a display. 7 You will not be able to display graphics on the screen. 8 9 < M A T L A B > 10 Copyright The MathWorks, Inc. 11 Version (R14) Service Pack 2 12 January 29, To get started, type one of these: helpwin, helpdesk, or demo. 16 For product information, visit Connecting to Star-P Server with 4 processes Star-P Client. 21 (C) MIT (C) Interactive Supercomputing, Inc All Rights Reserved. 24 Evaluation copy. Not to be redistributed. 25 By using this software you agree to the terms and 26 conditions described in AGREEMENT. Type help AGREEMENT 27 >> 2

3 When you launch Star-P, it uses the default number of processes, which is 4. To launch Star-P with a different number of processes, type starp X, where X is the number of processes. 1 [qmahoney@a h32 ~]$ starp 8 2 Password: 4 Connecting to Star-P Server with 8 processes Star-P Example 1 [qmahoney@a h32 ~]$ starp 2 Password: 4 Connecting to Star-P Server with 4 processes >> np 7 ans = >> A=randn(3000,3000*p) 11 A = 12 ddense object: 3000-by-3000p >> A(2894,477) 15 ans = >> B=randn(3000,3000*p) 19 B = 20 ddense object: 3000-by-3000p >> tic; X=A*B; toc 23 Elapsed time is seconds >> C = sprandn(100,100*p,0.03) 26 C = 27 dsparse object: 100p-by >> quit 30 [qmahoney@a h32 ~]$ Note the difference between a dense random matrix such as on line 10, and a sparse random matrix such as on line 25. Also, note that the n at the end of these functions stands for normally distributed as opposed to uniformly distributed. 3

4 Explicit Data Movement It is often necessary to explicitly move data between the client and the server. To do this, use pp2matlab and matlab2pp. 1 >> A=randn(50,50); 2 >> B=randn(50*p,50) 3 B = 4 ddense object: 50p-by >> ppwhos 7 Your variables are: 8 Name Size Bytes Class 9 A 50x double array 10 B 50px ddense array 11 Grand total is 5000 elements using bytes 12 MATLAB has a total of 2500 elements using bytes 13 Star-P server has a total of 2500 elements using bytes >> A=matlab2pp(A) 16 A = 17 ddense object: 50p-by-50p >> ppwhos 20 Your variables are: 21 Name Size Bytes Class 22 A 50px50p ddense array 23 B 50px ddense array 24 Grand total is 5000 elements using bytes 25 MATLAB has a total of 0 elements using 0 bytes 26 Star-P server has a total of 5000 elements using bytes >> B=pp2matlab(B); >> ppwhos 31 Your variables are: 32 Name Size Bytes Class 33 A 50px50p ddense array 34 B 50x double array 35 Grand total is 5000 elements using bytes 36 MATLAB has a total of 2500 elements using bytes 37 Star-P server has a total of 2500 elements using bytes Remember that the semicolon at the end of a line will prevent MATLAB from printing the result of the line. This is helpful if that result is a matrix of 2500 elements, such as in lines 1 and 28, but is not necessary when the result is a distributed matrix such as in lines 2 and 15. 4

5 Using ppeval When you re performing simple operations on a distributed matrix, you can use the normal MATLAB syntax. However, in certain situations you will need to use ppeval. The arguments to ppeval are treated differently depending on the type. Any argument that is a scalar is broadcast, that is, sent to every processor. By default, an argument that is a matrix is split, or divided up, among the processors by the last dimension. So a 2x2 matrix is split by its columns. A vector is treated as a 1-by-n matrix, so it is also split by columns. If you want a matrix to be broadcast, then you must use the function bcast in order to pass it to ppeval. If you want to split a matrix by a different dimension, then you use the split function. Both of these are demonstrated below. Note that at least one of the arguments to ppeval must be split. In this first example, I wanted to find the maximum values in a matrix. In the first invocation of ppeval on line 11, the array A was divided up by its columns, and Star-P computed max for each column. Then, I decided to find the maximum value in each row instead. I did this in line 15 by explicitly asking Star-P to split A by its rows. Though, as you can see in lines 19 and 23, Star-P supports the use of max without ppeval. 1 >> A=[ ; ; ] 2 A = >> matlab2pp(a) 8 ans = 9 ddense object: 3p-by-4p >> pp2matlab(ppeval( max,a)) 12 ans = >> pp2matlab(ppeval( max,split(a,1))) 16 ans = >> max(a) 20 ans = >> max(max(a)) 24 ans =

6 In this second example, I try to transpose the matrix A using the permute function. (There is a transpose function for 2D matrices, and it doesn t require ppeval, but I m just using permute as an example.) On line 12, I tried to use permute on its own, and got the wrong answer. On line 20, I tried to use ppeval, but I forgot to use bcast on the order argument. On line 24, I finally get it right. 1 >> A 2 A = 3 ddense object: 5p-by-5 4 >> pp2matlab(a) 5 ans = >> pp2matlab(permute(a,[2 1])) 13 ans = >> pp2matlab(ppeval( permute,a,[2 1])) 21??? Error using ==> ppeval 22 Input arguments not conformable >> pp2matlab(ppeval( permute,a,bcast([2 1]))) 25 ans = Note that I had to use the pp2matlab function when I wanted to see the results on the client. 6

7 Enabling and Disabling the MATLAB GUI If you d like to use the full MATLAB GUI, also called the MATLAB Development Environment, then you must log in to beowulf from an X-enabled terminal and you must enable X11 forwarding when you log in. For instance, from an Athena station, you simply add the -X option to ssh: 1 athena% ssh -X qmahoney@beowulf.csail.mit.edu 2 qmahoney@beowulf.csail.mit.edu s password: 4 [qmahoney@a h32 ~]$ starp 5 Password: At this point, the MATLAB Development Environment will launch. You can quit with either the quit command, or Ctrl-Q. If you don t want to use the MATLAB GUI, but still want to use other X11 programs, such as emacs, you can pass the -nogui parameter to the Star-P client: 1 athena% ssh -X qmahoney@beowulf.csail.mit.edu 2 qmahoney@beowulf.csail.mit.edu s password: 4 [qmahoney@a h32 ~]$ starp -nogui 8 5 Password: 6 Warning: Unable to open display, MATLAB is starting without a display. 7 You will not be able to display graphics on the screen Connecting to Star-P Server with 8 processes >> Debugging If you get an error, or Star-P crashes, there are two files where you can look, ~/starpclient.log and ~/ppclient.log. When looking at log files, I normally use the command less +G filename, which will open the file and scroll to the end. I then use b to scroll up and space to scroll back down. 7

8 Timing and Performance Measurement To time a MATLAB operation, you use tic and toc like so: 1 >> A=randn(100,100); 2 >> B=randn(100,100); 3 >> tic;c=a*b;toc 4 Elapsed time is seconds. In Star-P, tic and toc work the same way. However, you can also use pptic and pptoc to monitor communication between client and server: 1 >> pptic 2 >> A=randn(100,100*p) 3 A = 4 ddense object: 100-by-100p 5 >> B=randn(100,100*p) 6 B = 7 ddense object: 100-by-100p 8 >> C=A*B 9 C = 10 ddense object: 100-by-100p 11 >> pptoc 12 Client/server communication info: 13 Send msgs/bytes Recv msgs/bytes Time spent 14 3e+00 / 2.330e+02B 3e+00 / 3.770e+02B 1.324e+01s 15 Server info: 16 execution time on server: 2.625e+00s 17 #ppchangedist calls: 0 8

9 3 Cluster Specifications beowulf.csail.mit.edu The front end has four 2.40 GHz Intel Xeon processors and 3.5GB of RAM. There are 16 compute nodes. Each compute node has two 2.40GHz Intel Xeons and 2GB of RAM. starp.csail.mit.edu starp is an SGI Altix consisting of 6 nodes, each with two 1.3GHz Itanium 2 s and 2GB of RAM, for a total of 12 processors and 12GB of RAM. 9