Working with IITJ HPC Environment

Transcription

1 Working with IITJ HPC Environment by

2 Training Agenda for 23 Dec Understanding Directory structure of IITJ HPC 2. User vs root 3. What is bash_profile 4. How to install any source code in your user account 5. What is makefile 6. Lets know MPI routines 7. Example of serial program.vs. parallel program 8. Job Submission on IITJ_HPC using msub (Serial/parallel)

3 Directory Structure

4 The root user Most UNIX machines have an account called root root can see everything, change everything, delete everything, including other users work You usually need root access to install programs in the default location. But you can put them in your home directory instead.

5 Startup files sh,ksh: /etc/profile (out-of-the-box login shell settings) /etc/profile.local (addtnl. local system settings) ~/.profile (addtnl. user customized settings) ~/.kcshrc (non-login shell user customization) bash: /etc/profile (out-of-the-box login shell settings) /etc/bash.bashrc (out-of-box non-login settings) /etc/bash.bashrc.local (global non-login settings) ~/.bash_p profile (login shell user customization) ~/.bashrc (non-login shell user customization) ~/.bash_logout (user exits from interactive login shell) csh/tcsh: /etc/login (out-of-the-box login shell settings) /etc/csh.login (non-login shell customizations) /etc/csh.login.local (global non-login settings) ~/.login: (login shell user customizations) ~/.cshrc: (non-login shell user customizations) ~/.cshrc.logout: (non-login shells at logout) ~/.logout: (read by login shells at logout)

6 .bash_profile

7 Permission All of files and directories have owner and permission. There are three types of permission, readable, writeable and executable. Permissions are given to three kinds of group. owner, group member and others. Example: ls l.bash_profile rw r r 1 cnotred cnotred 191 Jan 4 13:1111.bash_profile r:readable, w:writable, x: executable

8 Important Directories /bin This contains files that are essential for correct operation of the system. These are available for use by all users. /home This is where user home directories are stored. /var This directory is used to store files which change frequently, and must be available to be written to. /etc Various system configuration files are stored here. /dev This contains various devices as files, e.g. hard disk, CD ROM drive, etc. /sbin Binaries which are only expected to be used by the super user. /tmp Temporary files.

9 install program Any source code can be compile & install in your user account ~]$ tar zxvf program.tar.gz ~]$ cd program ~]$./configure ~]$ make make install

10 Install Software from Source Code Unix system has a de facto standard d way to install a software. configure, make & make install Typical software installation ti procedure as following. 1. Download source code. Usually, it s archived with tar command and compressed with gzip command. 2. configure command creates Makefile automatically which is used to compile the source. 3. Program compilation is written in Makefile.

11 Makefiles Provide a way for separate compilation. Describe the dependencies among the project files. The make utility.

12 Using makefiles Naming: makefile or Makefile are standard other name can be also used Running make make make f filename if the name of your file is not makefile or Makefile make target_name if you want to make a target that is not the first one

13 makefiles content Makefiles content rules : implicit, explicit variables (macros) directives (conditionals) # sign comments everything till the end of the line \sign to separate one command line on two rows

14 Sample makefile Makefiles main element is called a rule: target : dependencies TAB commands #shell commands Example: my_prog : eval.o main.o g++ -o my_prog eval.o main.o eval.o : eval.c eval.h g++ -c eval.c main.o : main.c eval.h g++ -c main.c # -o to specify executable file name # -c to compile only (no linking)

15 Defining implicit rules %.o : %.c $(C) -c g $< C = g++ OBJS = eval.o main.o HDRS = eval.h my_prog : eval.o main.o $(C) -o my_prog $(OBJS) $(OBJS) : $(HDRS) Avoiding implicit rules empty pycommands target: ; #Implicit rules will not apply for this target.

16 Automatic variables Automatic variables are used to refer to specific part of rule components. target : dependencies TAB commands #shell commands eval.o : eval.c eval.h g++ -c eval.c $@ The name of the target of the rule e(eval.o). a $< The name of the first dependency (eval.c). $^ The names of all the dependencies (eval.c eval.h). $? The names of all dependencies that are newer than the target

17 make options make options: -f filename - when the makefile kfil name is not standard d -t - (touch) mark the targets as up to date -q - (question) are the targets up to date, exits with 0 if true -n - print the commands to execute but do not execute them / -t, -q, and -n, cannot be used together / -s - silent mode -k - keep going compile all the prerequisites even if not able to link them!!

18 Phony targets Phony targets: Targets that have no dependencies. Used only as names for commands that you want to execute. clean : rm $(OBJS) To invoke it: make clean Typical phony targets: t all make all the top level targets or.phony : all all: my_prog1 my_prog2.phony : clean clean: rm $(OBJS) clean delete all files that are normally created by make print print listing of the source files that have changed

19 Variable modifiers C = g++ OBJS = eval.o main.o SRCS = $(OBJS,.o o=.c) #!!! my_prog : $(OBJS) $(C) -g -c $^ %.o : %.c $(C) -g -c S< $(SRCS) : eval.h

20 Conditionals (directives) Possible conditionals are: if ifeq ifneq ifdef ifndef All of them should ldbe closed with endif. Complex conditionals may use elif and else. Example: libs_for_gcc = -lgnu normal_libs lib = ifeq ($(CC),gcc) libs=$(libs_for_gcc) #no tabs at the beginning else libs=$(normal_libs) #no tabs at the beginning endif

21 General MPI Program Structure MPI include file variable declarations Initialize MPI environment Do work and make message passing calls #include <mpi.h> void main (int argc, char *argv[]) { int np, rank, ierr; ierr = MPI_Init(&argc, I &argv); ) MPI_Comm_rank(MPI_COMM_WORLD,&rank); MPI_Comm_size(MPI_COMM_WORLD,&np); /* Do Some Works */ ierr = MPI_Finalize(); } Terminate MPI Environment

22 Sample MPI Program

23 Initialize MPI environment int MPI_Init(int *argc, char **argv[]) *argc **argv[] argument from main() argument from main()

24 Terminate MPI execution environment. int MPI_Finalize(void) Parameters: None.

25 Determine rank of process in communicator int MPI_Comm_rank(MPI_Comm comm, int *rank) Parameters: comm *rank communicator rank (returned)

26 Determine size of group associated with communicator int MPI_Comm_size(MPI_Comm C comm, int *size) Parameters: comm *size communicator size of group p( (returned)

27 Return elapsed time from some point in past, in seconds double MPI_Wtime(void) Parameters: None.

28 Basic MPI Data Types MPI Datatype MPI_CHAR MPI_SHORT MPI_INT MPI_LONG C Type signed char signed short int signed int signed long int MPI_UNSIGNED_CHAR unsigned char MPI_UNSIGNED_SHORT unsigned short int

29 Basic MPI Data Types MPI Datatype MPI_UNSIGNED MPI_UNSIGNED_LONG MPI_FLOAT MPI_DOUBLE C Type unsigned int unsigned long int float double MPI_LONG_DOUBLE long double MPI_BYTE MPI_PACKED (none) (none)

30 Send message (synchronous) int MPI_Ssend(void *buf, int count, MPI_Datatype datatype, int dest, int tag, MPI_Comm comm) Parameters: *buf count datatype dest tag comm send buffer number of entries in buffer data type of entries destination process rank message tag communicator

31 Send message (blocking) int MPI_Send(void *buf, int count, MPI_Datatype datatype, int dest, int tag, MPI_Comm comm) Parameters: *buf count send buffer number of entries in buffer datatype data type of entries dest destination process rank tag messagetag g comm communicator

32 Receive message (blocking) int MPI_Recv(void *buf, int count, MPI_ Datatype datatype, int source, int tag, MPI_Comm comm, MPI_Status *status) Parameters: *buf count datatype source tag comm *status receive buffer (loaded) max number of entries in buffer data type of entries source process rank message tag communicator status (returned)

33 Receive message (blocking) continued MPI_ANY_TAG in tag and MPI_ANY_SOURCE in source matches with anything. Return status is a structure with at least three members: status -> MPI_SOURCErank of source of message status -> MPI_ TAG tag of source message status -> MPI_ERROR potential errors

34 Basic Group Routines

35 Barrier: Block process until all processes have called it int MPI_Barrier(MPI_Comm comm) Parameters: comm communicator

36 Broadcast message from root process to all processes in comm and itself. int MPI_Bcast(void *buf, int count, MPI_Datatype datatype, int root, MPI_Comm comm) Parameters: *buf count datatype root message buffer (loaded) number of entries in buffer data type of buffer rank of root

37 Gather values for group of processes int MPI_Gather(void *sendbuf, int sendcount, MPI_Datatype sendtype, void *recvbuf, int recvcount, MPI_Datatype recvtype, int root, MPI_Comm comm) Parameters: *sendbuf send buffer sendcount number of send buffer elements sendtype data type of send elements *recvbuf receive buffer (loaded) recvcount number of elements each receive recvtype data type of receive elements root rank of receiving process comm communicator

38 Scatter a buffer from root in parts to group of processes int MPI_Scatter(void *sendbuf, int sendcount, MPI_Datatype sendtype, void *recvbuf, int recvcount, MPI_Datatype recvtype, int root, MPI Comm comm) Parameters: *sendbuf sendcount sendtype *recvbuf recvcount recvtype root comm send buffer number of elements send, each process data type of elements receive buffer (loaded) number of recv buffer elements typeof recv elements root process rank communicator

39 Combine values on all processes to single value int MPI_Reduce(void *sendbuf, void *recvbuf, int count, MPI_Datatype datatype, MPI_Op op, int root, MPI_Comm comm) Parameters: *sendbuf *recvbuf count datatype op root comm send buffer address receive buffer address number of send buffer elements data type of send elements reduce operation. Several operations, including MPI_MAX Maximum MPI_MIN Minimum MPI_SUM Sum MPI_PROD Product root process rank for result communicator

40 Combine values on all processes to single value int MPI_Reduce(void *sendbuf, void *recvbuf, int count, MPI_Datatype datatype, MPI_Op op, int root, MPI_Comm comm) Parameters: *sendbuf *recvbuf count datatype op root comm send buffer address receive buffer address number of send buffer elements data type of send elements reduce operation. Several operations, including MPI_MAX Maximum MPI_MIN Minimum MPI_SUM Sum MPI_PROD Product root process rank for result communicator