Valgrind

Valgrind

Valgrind is a powerful debugging tool to detect bad memory usage. It can detect memory leaks, but also access to unallocated or deallocated memory, multiple deallocation or other bad memory usage. If your program ends with a segmentation fault, broken pipe or bus error, you most likely have such a problem in your code. Valgrind is installed on Compute Canada clusters as part of the base software distribution, so there is no need to load a module to use it.

AVX512 Limitations

Note that current versions of Valgrind are unable to handle the AVX512 instructions used on the latest Intel processors, producing an error message like the following,

vex amd64->IR: unhandled instruction bytes: 0x62 0xF1 0xFE 0x8 0x6F 0x8B 0xE8 0xFF 0xFF 0xFF
vex amd64->IR:   REX=0 REX.W=0 REX.R=0 REX.X=0 REX.B=0
vex amd64->IR:   VEX=0 VEX.L=0 VEX.nVVVV=0x0 ESC=NONE
vex amd64->IR:   PFX.66=0 PFX.F2=0 PFX.F3=0
==35839== valgrind: Unrecognised instruction at address 0x4e68448.
==35839==    at 0x4E68448: if_posix_open (in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/openmpi/4.0.3/lib/libopen-pal.so.40.20.3)
==35839==    by 0x4E2C44A: mca_base_framework_components_open (in /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx512/Compiler/gcc9/openmpi/4.0.3/lib/libopen-pal.so.40.20.3)
...

You can circumvent this problem by first loading the AVX2 environment,

[name@server ~]$ module load arch/avx2

and then recompiling your application from scratch to ensure the binary doesn't contain any such instructions.

Preparing your application

To get useful information from Valgrind, you first need to compile your code with debugging information enabled. With the most compilers, you do so by adding a "-g" option during compilation.

Some aggressive optimizations may yield false errors in Valgrind if they result in unsupported operations, which may occur in certain mathematical libraries. Since you don't want to diagnose errors in those libraries, but rather errors in your own code, you should compile and link your code against non-optimized versions of the libraries (such as the Netlib implementation of BLAS/LAPACK) that do not use those operations. This is of course only to diagnose issues; when the time comes to run real simulations, you should link against optimized libraries.

Using Valgrind

Once your code is compiled with the proper options, you execute it within Valgrind with the following command :

[name@server ~]$ valgrind --tool=memcheck --leak-check=yes --show-reachable=yes ./your_program

For more information about Valgrind, we recommend this page.

Words of wisdom

• When you run your code in Valgrind, your application is executed within a virtual machine that validates every memory access. It will therefore run much slower than usual. Choose the size of the problem to test with caution, much smaller than what you would usually run.
• You do not need to run the exact same problem that results in a segmentation fault to detect memory issues in your code. Very frequently, memory access problem, such as reading data outside of the bounds of an array, will go undetected for small size problems, but will cause a segmentation fault for large ones. Valgrind will detect even the slightest access outside of the bounds of an array.

Some typical error messages

Here are some problems that Valgrind will help you detect, and the error messages that it will produce.

Memory leak

The error message for a memory leak will be given at the end of the program execution, and will look like this :

==2116== 100 bytes in 1 blocks are definitely lost in loss record 1 of 1
==2116==    at 0x1B900DD0: malloc (vg_replace_malloc.c:131)
==2116==    by 0x804840F: main (in /home/cprogram/example1)

Invalid pointer access/out of bound errors

If you attempt to read or write to an unallocated pointer or outside of the allocated memory, the error message will look like this:

==9814==  Invalid write of size 1
==9814==    at 0x804841E: main (example2.c:6)
==9814==  Address 0x1BA3607A is 0 bytes after a block of size 10 alloc'd
==9814==    at 0x1B900DD0: malloc (vg_replace_malloc.c:131)
==9814==    by 0x804840F: main (example2.c:5)

Usage of uninitialized variables

If you use an uninitialized variable, you will get an error message such as

==17943== Conditional jump or move depends on uninitialised value(s)
==17943==    at 0x804840A: main (example3.c:6)