Development/General compiler usage

Description	Content
module load	compiler/gnu|intel|pgi|...
License	Intel: Commercial | GNU: GPL | PGI: Commercial

Description

The basic operations can be performed with the same commands for all available compilers. For advanced usage such as optimization and profiling you should consult the best practice guide of the compiler you intend to use (GCC, Intel Suite).

More information about the MPI versions of the GNU and Intel Compilers is available here:

• Best Practices Guide for Parallel Programming.

Versions and Availability

A list of versions currently available compilers on the bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS

GNU

{{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/compiler/gnu |width=99% |height=750 }}

Intel

{{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/compiler/intel |width=99% |height=700 }}

PGI

{{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/compiler/pgi |width=99% |height=400 }} On the command line interface of any bwHPC cluster you'll get a list of available versions by using the command
'module avail compiler'.

$ : bwUniCluster
$ module avail compiler
---------------------- /opt/bwhpc/common/modulefiles -----------------------
compiler/gnu/4.5             compiler/intel/12.1
compiler/gnu/4.7(default)    compiler/intel/13.1
compiler/gnu/4.8             compiler/intel/14.0
compiler/gnu/4.9             compiler/intel/15.0(default)
compiler/gnu/5.2
$ : bwForCluster (Justus)
$ module avail compiler
---------------------- /opt/bwhpc/common/modulefiles -----------------------
compiler/gnu/4.5             compiler/intel/15.0(default)
compiler/gnu/4.7(default)    compiler/pgi/12.10(default)
compiler/gnu/4.8             compiler/pgi/12.10_static
compiler/gnu/4.9             compiler/pgi/13.7
compiler/gnu/5.2             compiler/pgi/13.7_static
compiler/intel/12.1          compiler/pgi/14.10
compiler/intel/13.1          compiler/pgi/14.10_static
compiler/intel/14.0

Loading the module

Default Version

You can load the default version of the a compiler with the command
module load compiler/name-of-the-compiler-suite.
Example with Intel on bwUniCluster

$ module avail compiler/intel
---------------------- /opt/bwhpc/common/modulefiles -----------------------
compiler/intel/12.1          compiler/intel/14.0
compiler/intel/13.1          compiler/intel/15.0(default)
$ module load compiler/intel
$ module list
Currently Loaded Modulefiles:
  1) compiler/intel/15.0(default)

Here, we got the "default" version 15.0 (example).
The module will try to load modules it needs to function. If loading the module fails, check if you have already loaded the module with 'module list'.

Specific (newer or older) Version

If you wish to load a specific compiler version and release (if available), you can do so using
module load compiler/name-of-the-compiler-suite/version-of-the-compiler-suite
to load the version you desires.
Example with Intel compiler, version 14.0 on bwUniCluster

$ module avail compiler/intel
---------------------- /opt/bwhpc/common/modulefiles -----------------------
compiler/intel/12.1          compiler/intel/14.0
compiler/intel/13.1          compiler/intel/15.0(default)
$ module load compiler/intel/14.0
$ module list
Currently Loaded Modulefiles:
  1) compiler/intel/14.0

Intel C-Compiler "version 14.0" is loaded now (example).

All Intel, GCC and PGI have compilers for different languages which will be available after the module is loaded.

Linux Original Compiler

The original Compiler installed on all compute nodes is GNU.

• Don't get distracted with the available compiler modules.
• Only the modules are loading the complete environments needed.

Example

$ module clear                     # unload all modules
Are you sure you want to clear all loaded modules!? [n] y
$ module list                      # control
No Modulefiles Currently Loaded.
$ gcc --version                    # see version of default Linux GNU compiler
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
[...]
$ module load compiler/gnu         # load default GNU compiler module
$ module list                      # control
Currently Loaded Modulefiles:
  1) compiler/gnu/4.7(default)
$ gcc --version                    # now, check the current (loaded) module
gcc (GCC) 4.7.3 
[...]

Synoptical Tables

Compilers (no MPI)

Compiler Suite	Language	Command
Intel Composer • Best Practice Guides on Intel Compiler Software	C	icc
	C++	icpc
	Fortran	ifort
GCC • Best Practice Guides on GNU Compiler Software	C	gcc
	C++	g++
	Fortran	gfortran
PGI	C	pgcc
	C++	pgCC
	Fortran 77/90	pgf77 or pgf90

MPI compiler and Underlying Compilers

The following table lists available MPI compiler commands and the underlying compilers, compiler families, languages, and application binary interfaces (ABIs) that they support.

MPI Compiler Command	Default Compiler	Supported Language(s)	Supported ABI's
Generic Compilers
mpicc	gcc, cc	C	32/64 bit
mpicxx	g++	C/C++	32/64 bit
mpifc	gfortran	Fortran77/Fortran 95	32/64 bit
GNU Compiler Versions 3 and higher
mpigcc	gcc	C	32/64 bit
mpigxx	g++	C/C++	32/64 bit
mpif77	g77	Fortran 77	32/64 bit
mpif90	gfortran	Fortran 95	32/64 bit
Intel Fortran, C++ Compilers Versions 13.1 through 14.0 and Higher
mpiicc	icc	C	32/64 bit
mpiicpc	icpc	C++	32/64 bit
impiifort	ifort	Fortran77/Fortran 95	32/64 bit

How to use

The following compiler commands work for all the compilers in the list above even though the examples will be for icc only.

Commands

When hello.c is a C source code file such as

#include <stdio.h>
int main() {
    printf("Hello world\n");
    return 0;
}

it can be compiled and linked with the single command

$ icc hello.c -o hello

to produce an executable named hello.

This process can be divided into two steps:

$ icc -c hello.c
$ icc hello.o -o hello

When using libraries you must sometimes specify where the

• include files are (option -I) and where the
• library files are (option -L).

In addition you have to tell the compiler which

• library you want to use (option -l).

For example after loading the module numlib/fftw you can compile code for fftw using

$ icc -c hello.c -I$FFTW_INC_DIR
$ icc hello.o -o hello -L$FFTW_LIB_DIR -lfftw3

When the program crashes or doesn't produce the expected output the compiler can help you by printing warning messages:

$ icc -Wall hello.c -o hello

Debugger

If the problem can't be solved this way you can inspect what exactly your program does using a debugger.
To use the debugger properly with your program you have to compile it with debug information (option -g):
Example

$ icc -g hello.c -o hello

Although -Wall should always be set, the -g option should only be stated when you want to find bugs, since it may slow down execution and enlarges the binary due to debugging symbols.

Optimization

The usual and common way to compile your source is to apply compiler optimization.
Since there are many optimization options, as a stzart for now the optimization level -O2 is recommended:

$ icc -O2 hello.c -o hello

Beware: The optimization-flag used is a capital-O (like Otto) and not a 0 (Zero)!

Both compilers offer a multitude of options (with regard to the above and others), one may check the complete list of options with short explanation on GCC and Intel Suite using option -v --help:

$ icc -v --help hello.c -o hello

Makefile

If you're working in a project that already uses make, there should be a file called Makefile in the top-level directory. Running:

$ make

should build the project from source.

What is make?

Make is a tool designed to manage dependencies in a build process.

Simple Makefile for hello.c

For instance, if you have a source file called hello.c and you need to build the binary/executable hello, then you might have a Makefile in the same directory that looks like this:

 
# define the C compiler to use
# you do not need this if you load the compiler module first
# # CC      = icc 

# define any compile-time flags
#    -g    # adds debugging information to the executable file
#    -O2   # optimization level 2
#    -Wall # turns on most, but not all, compiler warnings
CFLAGS  = -g -O2 -Wall

# unix/linux removal command used for 'make clean'
RM      = rm -f

# the build target executable
# use a variable if you'd like to rename the binary later
TARGET = hello

# default action when make was invoked without options
default: all

# starts section beginning with :hello  -> :hello = :$(TARGET)
all: $(TARGET)

# main build section of this Makefile
# same as: hello: hello.c
#    $(CC) $(CFLAGS) -o hello hello.c
$(TARGET): $(TARGET).c
      $(CC) $(CFLAGS) -o $(TARGET) $(TARGET).c

# clean all garbage with 'make clean' oder 'make veryclean'
clean veryclean:
      $(RM) $(TARGET) $(TARGET).o

# run the programm with 'make run'
run:
      ./$(TARGET)

When ordered to build a file, make will ensure that all dependencies are up to date, and it will not rebuild any those which need not be rebuilt.

Load Compiler Environments

Another makefile (using makedepend and more advanced make syntax). Here we use the GNU-C-Compiler.

$module load compiler/gnu
$ module list
Currently Loaded Modulefiles:
  1) compiler/gnu/4.7(default)

A list of all defined environments set by the 'module load'-command can be displayed by: 'module show compiler/gnu' (e.g. GNU compiler).

$ module show compiler/gnu
-------------------------------------------------------------------
/opt/bwhpc/common/modulefiles/compiler/gnu/4.7:
[...]
setenv		 GNU_VERSION 4.7.3 
setenv		 GNU_HOME /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64 
setenv		 GNU_BIN_DIR /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64/bin 
setenv		 GNU_MAN_DIR /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64/share/man 
setenv		 GNU_LIB_DIR /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64/lib64 
prepend-path	 PATH /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64/bin 
prepend-path	 MANPATH /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64/share/man 
prepend-path	 LD_RUN_PATH /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64/lib 
prepend-path	 LD_LIBRARY_PATH /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64/lib 
prepend-path	 LD_RUN_PATH /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64/lib64 
prepend-path	 LD_LIBRARY_PATH /opt/bwhpc/common/compiler/gnu/4.7.3/x86_64/lib64 
setenv		 CC gcc 
setenv		 CXX g++ 
setenv		 F77 gfortran 
setenv		 FC gfortran 
setenv		 F90 gfortran 
[...]

Advaneced Makefile Examples

This envs may be used in your local Makefile.

 
#
# 'make depend' uses makedepend to automatically generate dependencies 
#               (dependencies are added to end of Makefile)
# 'make'        build executable file 'mycc'
# 'make clean'  removes all .o and executable files
#

# define the C compiler to use. 
# CC is set by the 'module load'-command so it's unnecessary here.
# # CC = gcc

# define any compile-time flags
CFLAGS = -Wall -g -O2

# define any directories containing header files other than /usr/include
#
INCLUDES = -I/home/newhall/include 
#  -I../include -I$(GNU_INC_DIR)  (example)

# define library paths in addition to /usr/lib
#   if I wanted to include libraries not in /usr/lib I'd specify
#   their path using -Lpath, something like:
LFLAGS = -L/home/newhall/lib  -L../lib

# define any libraries to link into executable:
#   if I want to link in libraries (libx.so or libx.a) I use the -llibname 
#   option, something like (this will link in libmylib.so and libm.so:
LIBS = -l$(GNU_LIB_DIR) -lmylib -lm 

# define the C source files (examples only)
SRCS = emitter.c error.c init.c lexer.c main.c symbol.c parser.c

# define the C object files 
#
# This uses Suffix Replacement within a macro:
#   $(name:string1=string2)
#         For each word in 'name' replace 'string1' with 'string2'
# Below we are replacing the suffix .c of all words in the macro SRCS
# with the .o suffix
#
OBJS = $(SRCS:.c=.o)

# define the executable file 
MAIN = mycc

#
# The following part of the makefile is generic; it can be used to 
# build any executable just by changing the definitions above and by
# deleting dependencies appended to the file from 'make depend'
#

.PHONY: depend clean

all:    $(MAIN)
        @echo  Simple compiler named mycc has been compiled

$(MAIN): $(OBJS) 
        $(CC) $(CFLAGS) $(INCLUDES) -o $(MAIN) $(OBJS) $(LFLAGS) $(LIBS)

# this is a suffix replacement rule for building .o's from .c's
# it uses automatic variables $<: the name of the prerequisite of
# the rule(a .c file) and $@: the name of the target of the rule (a .o file) 
# (see the gnu make manual section about automatic variables)
.c.o:
        $(CC) $(CFLAGS) $(INCLUDES) -c $<  -o $@

clean:
        $(RM) *.o *~ $(MAIN)

depend: $(SRCS)
        makedepend $(INCLUDES) $^

# DO NOT DELETE THIS LINE -- make depend needs it

This is an excerpt from the CIS makefile to show how you can do branchings in a makefile.
We use the shell-command $(shell uname -s) to determine the machine is a Linux.

 
[...]
#
# LINUX system
#
UNAME_S := $(shell uname -s)
ifeq ($(UNAME_S),Linux)
   LDFLAGS=-g -m32  -lm -lcrypt
   CFLAGS=-g -Wimplicit -Wunused -Wformat -Werror -Wreturn-type \
   -Wmissing-prototypes -m32 -funsigned-char -Wno-parentheses \
   -D_XOPEN_SOURCE -D_GNU_SOURCE -Wno-pointer-sign -Wno-unused-but-set-variable
endif
#
# MAC-OS
#
ifeq ($(UNAME_S),Darwin)
....... 
[...]
OBJ=db/db.o db/app.o db/w3tool.o db/w3lib.o db/maildecode.o
ALL=.dependent db.c w3dbs cis svnout x tools
SRC=db.c app.c w3tool.c w3lib.c  cis.c x.c maildecode.c

db/%.o: %.c
   @echo "compile $< ..."
   @$(CC) $(CFLAGS) -c $< -o $@

[...]

all: $(ALL)
clean:
   @echo "cleaning ..."
   @rm -rf *.o $(ALL) core tags db.h db.c html/model.html a.out gmon.out core.* x tools svnout w3lib.tgz *.dSYM *.gcno *.gcda *.gcov g* .dependent $(OBJ)

cis: db/cis.o $(OBJ)
   @echo "building cis ..."

Makefile structure

Makefiles contain definitions and rules.

• A definition has the form:
  

VAR=value

• A rule has the form:
  

output files: input files
<TAB><TAB>commands to turn inputs to outputs

• All commands must be tab-indented.
• # are marking the beginning of a comment. Rest of the line will be ignored.
• To reference the variable VAR, surround it with $(VAR).
• Try running 'man make' for more details.

<TAB> = Tabulator