GROMACS 2024.2 release notes#

This version was released on May 10th, 2024. These release notes document the changes that have taken place in GROMACS since the previous 2024.1 version, to fix known issues. It also incorporates all fixes made in version 2023.5 and earlier, which you can find described in the Release notes.

Fixes where mdrun could behave incorrectly#

Prevent crashes with AdaptiveCpp/hipSYCL#

In some cases, GROMACS could randomly crash on neighbor-search steps with hip_queue: hipMemsetAsync() failed (error code = HIP:1) error. This was caused by a GPU buffer re-allocation while an operation on the buffer was pending. We add an explicit synchronization to avoid it.

Only AdaptiveCpp/hipSYCL builds are affected. This should not have caused any incorrect physics, only the mdrun crash.

Issue 5078

Fixes for gmx tools#

Improve errors and warnings to avoid poor results with gmx msd#

Fail properly if `-trestart` is not divisible by `-dt` or if `-dt` > `-trestart`. A warning is generated if the two values are equal.

Issue 5051

Improve error messages from editconf and trjconv#

Fail properly if a tpr file is not supplied when using the -conect option. Also avoid a “File input/output error:” when no tpr file is supplied when it is required for -pbc options.

Issue 5032

Avoid floating point exception with corrupted xtc files#

Reading a corrupted xtc file could cause a floating point exception. Now the gmx binary will exit with an error message.

Issue 5037

Make Colvars file backup scheme consistent with GROMACS#

Colvars output files in GROMACS versions 2024.0 and 2024.1 were backed up only once, regardless of the value of GMX_MAXBACKUP. This is corrected in 2024.2 and later releases, by letting Colvars back up existing output files consistently with other files produced by GROMACS itself.

Issue 5071

Fixes that affect portability#

Enable usage of Intel compiler with AVX-512 SIMD on AMD Zen 4#

The fix is to use newer style compiler flags for Intel oneAPI DPC++/C++ Compiler and AVX-512. Older style flag -xCORE-AVX512 supports only Intel CPUs, while newer style -march=skylake-avx512 additionally supports AMD CPUs. This fixes building with Intel compiler on AMD CPUs with Zen 4 cores.

Issue 5043

Warn about unsupported compilers sooner#

Now CMake reports that a user’s compiler is broken or unsupported before running into other fatal issues that would have obscured a critical problem.

Issue 5056

Enable specification of custom install rpath during build configuration#

CMake build and installation steps will now append to the CMAKE_INSTALL_RPATH value provided by the user at the configuration time (if any) instead of overwriting it.

Issue 5064

Permit dpcpp to appear in the path to the compiler#

The compiler named dpcpp is no longer supported, so CMake prohibits its use. However previously we inadvertently also prohibited any compiler whose full path also contained the string “dpcpp,” which was not intended.

Issue 4716


NBLIB always used geometric Lennard-Jones combination rules#

Now NBLIB detects the Lennard-Jones combination rules (or none) from the Lennard-Jones parameters set by the user.

Issue 5015

Fix cuFFTMp compilation issue#

The cuFFTMp build is now more likely to compile because the compiler now sees the correct path.

Fix performance regression for some cases on latest NVIDIA GPUs#

In version 2024.0 we included optimizations to non-bonded force calculations on NVIDIA GPUs which improved performance for a range of cases, through loop unrolling tuning. Here, we tweak the optimization to fix a regression in a specific case, which was discovered to be caused by this tuning.

Issue 4867

Address performance regression on ARM with clang and SVE#

The non-bonded CPU SIMD kernels contained loops which were not unrolled, in particular with the LLVM backend of clang on ARM SVE. Other combinations of compilers and architectures might also have been affected. Note that there are still other performance regressions in certain versions of these kernels on multiple platforms.

Issue 5036

Fix crash in NbnxmSetupTest.CanCreateNbnxmGPU#

NbnxmSetupTest.CanCreateNbnxmGPU could crash in GPU builds with an error in freeDeviceBuffer function during pairlist deinitialization.

Issue 4888

Fix incorrect mdp keyword for mass repartitioning in documentation#

The mdp keyword for mass repartitioning was incorrect in the list of mdp options in the documentation.

Issue 5007

Report AdaptiveCpp/hipSYCL compiler path in gmx -version#

In 2024.0 and 2024.1 it was empty.

Issue 5045

Prevented CTest from running racy test cases concurrently#

Issue 4654 Issue 4975