Bug #857

Sequencing rdtsc in cycle-counting funcs

Added by Janne Blomqvist over 8 years ago. Updated about 8 years ago.

Target version:
Affected version - extra info:
Affected version:


The x86 rdtsc instruction is not defined as a serializing instruction, thus the CPU is free to move rdtsc past other instructions in the pipeline. If using the TSC to, say, measure the time spent executing some piece of code, this is probably not what one wants, and the Intel system programming manual advices one to use "lfence;rdtsc" in that case. The AMD manual has similar wording, but instead advices "mfence;rdtsc". Also, an alternative to using a fence is "rdtscp" (which differs from rdtsc in that it is a serializing instr), if the CPU supports it.

This seems to affect at least


(checked on 4.5.5)

FWIW, on current Linux with high-resolution clocks (2.6.24+ or thereabouts IIRC) clock_gettime(CLOCK_MONOTONIC, ...) takes only about a factor of 3 as much time as a "{m,f}fence;rdtsc", so it's not like this particular ASM trickery buys one particularly much, but I digress.

Related issues

Related to GROMACS - Bug #1428: rdtscp and illegal instructionsClosed01/31/2014

Associated revisions

Revision 5ba7125c (diff)
Added by Erik Lindahl about 8 years ago

New CPU detection & AVX/SSE code, removed raw assembly files.

Removed all raw assembly files and deprecated altivec support.
Removed support for NASM and other assemblers, and replaced
previous SSE detection code with a new module using CPUID instead.
Added detection for SSE2, SSE4.1, AVX 128-bit with FMA, and AVX 256-bit.
Added Cmake detection of build platform based on CPUID, and output this
to the log file. The executables now compare the compile-time platform
and selected acceleration with the run-time platform and most suitable
acceleration and warns the user if they do not match. The compiler
detection code has also been reordered slightly to produce more readable
warnings when OpenMP is not available, and correctly disable pragma

Added intrinsics code and math functions for SSE2, SSE4.1, AVX128/256
both in single and double precision. All math functions and permutation
code have been tested & verified. Single precision math functions are
correct apart from the least significant bit, and double precision has
roughly twice the accuracy.

This has forced me to temporarily disable the SSE & Fortran acceleration.
SSE will be added back soon based on new intrinsics-only kernels currently
in testing, and we will test if Fortran still makes sense then.

Finally, the patch includes a modification to gmx_rmsdist where
a regression issue was introduced recently by using sqrtf() for
the norm function. This caused the intel compiler to produce slightly
different results at high optimization leves, which got evident here.

Closes #926 - Raw assembly code has been removed.
Refs #923 - Old kernels removed, new will be added shortly.
Fixes #914 - Cmake now does architecture-speficic optimization.
Fixes #912, #913
Fixes #857 - We detect rdtscp support with CPUID and use it if possible.
Fixes #750
Closes #537, #574 - Altivec is now deprecated.

Change-Id: Icfca5a940762f8d82ae67b59c65b2d2ac683256d


#1 Updated by Szilárd Páll about 8 years ago

Sander/Erik, could you comment on this?

#2 Updated by Erik Lindahl about 8 years ago


The only issues I've seen with RDTSC in practice is when executing it twice within a handful of instructions, and in that case it has usually been resolved through the volatile addition to the inline assembly (so it was probably the compiler moving it then).

The Linux high-resolution timers sound interesting, but we aren't yet ready to restrict support to 2.6.24+, and it would have to be tested to work on every single hardware platform, not only x86.

... but, before spending time on creating 3-4 separate code paths for Intel/AMD/old vs new Linux/rdtscp support, etc: Has there ever been a single example of a Gromacs run not executing as expected (incorrect load balance or whatever) due to this?

#3 Updated by Roland Schulz about 8 years ago

  • Status changed from New to Closed

Fixed by 5ba7125c.

#4 Updated by Teemu Murtola over 6 years ago

  • Related to Bug #1428: rdtscp and illegal instructions added

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