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Compilers
You can check the complete list of available compiler on GALILEO with the command:
> module available
and checking the "compilers" section.
In general the available compilers are:
- INTEL (ifort, icc, icpc) : ► module load intel
- PGI - Portland Group (pgf77,pgf90,pgf95,pghpf, pgcc, pgCC): ► module load pgi
- GNU (gcc, g77, g95): ► module load gnu
After loading the appropriate module, use the "man" command to get the complete list of the flags supported by the compiler, for example:
> module load intel > man ifort
There are some flags that are common for all these compilers. Others are more specifics. The most common are reported later for each compiler.
- If you want to use a specific library or a particular include file, you have to give their paths, using the following options
-I/path_include_files specify the path of the include files -L/path_lib_files -l<xxx> specify a library lib<xxx>.a in /path_lib_files
- If you want to debug your code you have to turn off optimisation and turn on run time checkings: these flags are described in the following section.
- If you want to compile your code for normal production you have to turn on optimisation by choosing a higher optimisation level
-O2 or -O3 Higher optimisation levels
Other flags are available for specific compilers and are reported later.
INTEL Compiler
Initialize the environment with the module command:
> module load intel
The names of the Intel compilers are:
- ifort: Fortran77 and Fortran90 compiler
- icc: C compiler
- icpc: C++ compiler
The documentation can be obtained with the man command after loading the relevant module:
> man ifort > man icc
Some miscellanous flags are described in the following:
-extend_source Extend over the 77 column F77's limit -free / -fixed Free/Fixed form for Fortran -ip Enables interprocedural optimization for single-file compilation -ipo Enables interprocedural optimization between files - whole program optimisation
PORTLAND Group (PGI)
Initialize the environment with the module command:
> module load profile/advanced
> module load pgi
The name of the PGI compilers are:
- pgf77: Fortran77 compiler
- pgf90: Fortran90 compiler
- pgf95: Fortran95 compiler
- pghpf: High Performance Fortran compiler
- pgcc: C compiler
- pgCC: C++ compiler
The documentation can be obtained with the man command after loading the relevant module:
> man pgf95 > man pgcc
Some miscellanous flags are described in the following:
-Mextend To extend over the 77 column F77's limit -Mfree / -Mfixed Free/Fixed form for Fortran -fast Chooses generally optimal flags for the target platform -fastsse Chooses generally optimal flags for a processor that supports SSE instructions
GNU compilers
The gnu compilers are always available but they are not the best optimizing compilers. The default version is 4.8.2, you do not need to load the module for using them.
For a more recent version of the compiler, initialize the environment with the module command:
> module load gnu
The name of the GNU compilers are:
- g77: Fortran77 compiler
- gfortran: Fortran95 compiler
- gcc: C compiler
- g++: C++ compiler
The documentation can be obtained with the man command:
> man gfortan > man gcc
Some miscellanous flags are described in the following:
-ffixed-line-length-132 To extend over the 77 column F77's limit -ffree-form / -ffixed-form Free/Fixed form for Fortran
Hybrid programming (Intel PHI)
Some of the nodes of the system are equipped with 2 accelerators per node. They can be addressed within C or Fortran programs by means of the Intel compilers suite.
You can find a brief guide on the production and programming environment for the Intel Xeon Phi (MIC) nodes in a separate document here.
Debuggers and Profilers
If at runtime your code dies, then there is a problem. In order to solve it, you can decide to analyze the core file (core not available with PGI compilers) or to run your code using the debugger.
Compiler flags
Whatever your decision, in any case you need enable compiler runtime checks, by putting specific flags during the compilation phase. In the following we describe those flags for the different Fortran compilers: if you are using the C or C++ compiler, please check before because the flags may differ.
The following flags are generally available for all compilers and are mandatory for an easier debuggin session:
-O0 Lower level of optimisation -g Produce debugging information
Other flags are compiler specific and are described in the following.
INTEL Fortran compiler
The following flags are usefull (in addition to "-O0 -g")for debugging your code:
-traceback generate extra information to provide source file traceback at run time -fp-stack-check generate extra code to ensure that the floating-point stack is in the expected state -check bounds enables checking for array subscript expressions -fpe0 allows some control over floating-point exception handling at run-time
PORTLAND Group (PGI) Compilers
The following flags are usefull (in addition to "-O0 -g")for debugging your code:
-C Add array bounds checking
-Ktrap=ovf,divz,inv Controls the behavior of the processor when exceptions occur:
FP overflow, divide by zero, invalid operands
GNU Fortran compilers
The following flags are usefull (in addition to "-O0 -g")for debugging your code:
-Wall Enables warnings pertaining to usage that should be avoided -fbounds-check Checks for array subscripts.
Debuggers available (Totalview, Scalasca, TAU)
We plan to make available on GALILeO the three applications riported above in a short time. Detailed information will be published asap.
In the following we report information about other ways to debug your codes:
IDB (serial debugger for INTEL compilers)
The Intel Debugger (idb) is a source-level, symbolic debugger that lets you:
- Control the execution of individual source lines in a program.
- Set stops (breakpoints) at specific source lines or under various conditions.
- Change the value of variables in your program.
- Refer to program locations by their symbolic names
- Print the values of variables and set tracepoints
- Perform other functions (examining core files, examining the call stack, displaying registers)
The idb debugger has two modes: dbx (default mode) or gdb (optional mode) For complete information about idb, see the online Intel Debugger (IDB) Manual in:
$INTEL_HOME/Documentation/en_US/idb
To use this debugger, you should specify the ifort command and the debugging command-line options described above, then you run your executable inside the "idb" environment:
> module load intel > ifort -O0 -g -traceback -fp-stack-check -check bounds -fpe0 -o myexec myprog.f90 > idb ./myexec
On PLX the debugger runs in GUI mode by default. You can also start the debugger in command line mode on these systems by specifying idbc instead of idb in the command line.
PGI: pgdbg (serial/parallel debugger)
pgdbg is the Portland Group Inc. symbolic source-level debugger for F77, F90, C, C++ and assembly language programs. It is capable of debugging applications that exhibit various levels of parallelism, including:
- Single-thread, serial applications
- Multi-threaded applications
- Distributed MPI applications
- Any combination of the above
There are two forms of the command used to invoke pgdbg. The first is used when debugging non-MPI applications, the second form, using mpirun, is used when debugging MPI applications:
> pgdbg [options] ./myexec [args] > mpirun [options] -dbg=pgdbg ./myexec [args]
More details in the on line documentation, using the "man pgdbg" command after loading the module.
To use this debugger, you should compile your code with one of the pgi compilers and the debugging command-line options described above, then you run your executable inside the "pgdbg" environment:
> module load profile/advanced
> module load pgi > pgf90 -O0 -g -C -Ktrap=ovf,divz,inv -o myexec myprog.f90 > pgdbg ./myexec
By default, pgdbg presents a graphical user interface (GUI). A command-line interface is also provided though the "-text" option.
GNU: gdb (serial debugger)
GDB is the GNU Project debugger and allows you to see what is going on 'inside' your program while it executes -- or what the program was doing at the moment it crashed.
GDB can do four main kinds of things (plus other things in support of these) to help you catch bugs in the act:
- Start your program, specifying anything that might affect its behavior.
- Make your program stop on specified conditions.
- Examine what has happened, when your program has stopped.
- Change things in your program, so you can experiment with correcting the effects of one bug and go on to learn about another.
More details in the on line documentation, using the "man gdb" command.
To use this debugger, you should compile your code with one of the gnu compilers and the debugging command-line options described above, then you run your executable inside the "gdb" environment:
> module load gnu
> gfortran -O0 -g -Wall -fbounds-check -o myexec myprog.f90
> gdb ./myexec
VALGRIND
Valgrind is a framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. The Valgrind distribution currently includes six production-quality tools: a memory error detector, two thread error detectors, a cache and branch-prediction profiler, a call-graph generating cache profiler, and a heap profiler.
Valgrind is Open Source / Free Software, and is freely available under the GNU General Public License, version 2.
To analyse a serial application:
- Load Valgrind module --> module load valgrind
- Load module for the compiler and compile your code with the compiler you prefer (Use -O0 -g flags)
- Run the executable under Valgrind.
If you normally run your program like this:
myprog arg1 arg2
Use this command line:
valgrind (valgrind-options) myprog arg1 arg2
Memcheck is the default tool. You can add the --leak-ceck option that turns on the detailed memory leak detector. Your program will run much slower than normal, and use a lot more memory. Memcheck will issue messages about memory errors and leaks that it detects.
- Load Valgrind module --> module load valgrind
- Load modules for compiler and openmpi libraries (at present only available for intel and gnu)
- Compile your code with the "-O0 -g" flags both at compiling and linking time
- Run the executable under Valgrind (both in interactive than in bacth mode)
mpirun -np 4 valgrind (valgrind-options) myprog arg1 arg2
Core file analysis
In order to understand what problem was affecting you code, you can also try a "Core file" analysis. Since core files are usually quite large, be sure to work in the /scratch area.
There are several steps to follow:
- Increase the limit for possible core dumping
> ulimit -c unlimited (bash) > limit coredumpsize unlimited (csh/tcsh)
- If you are using Intel compilers, set to TRUE the decfort_dump_flag environment variable
> export decfort_dump_flag=TRUE (bash) > setenv decfort_dump_flag TRUE (csh/tcsh)
- Compile your code with the debug flags described above.
- Run your code and create the core file.
- Analyze the core file using different tools depending on the original compiler.
INTEL compilers
> module load intel > ifort -O0 -g -traceback -fp-stack-check -check bounds -fpe0 -o myexec prog.f90 > ulimit -c unlimited > export decfort_dump_flag=TRUE > ./myexec > ls -lrt -rwxr-xr-x 1 aer0 cineca-staff 9652 Apr 6 14:34 myexec -rw------- 1 aer0 cineca-staff 319488 Apr 6 14:35 core.25629 > idbc ./myexec core.25629
PGI compilers
> module load profile/advenced
> module load pgi > pgf90 -O0 -g -C -Ktrap=ovf,divz,inv -o myexec myprog.f90 > ulimit -c unlimited > ./myexec > ls -lrt -rwxr-xr-x 1 aer0 cineca-staff 9652 Apr 6 14:34 myexec -rw------- 1 aer0 cineca-staff 319488 Apr 6 14:35 core.25666 > pgdbg -text -core core.25666 ./myexec
GNU Compilers
> module load gnu
> gfortran -O0 -g -Wall -fbounds-check -o myexec prog.f90 > ulimit -c unlimited > ./myexec > ls -lrt -rwxr-xr-x 1 aer0 cineca-staff 9652 Apr 6 14:34 myexec -rw------- 1 aer0 cineca-staff 319488 Apr 6 14:35 core.25555 > gdb ./myexec core.2555
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