Bug #1270
affinity setting broken with MPI
Description
With the MPI builds (i.e GMX_MPI=ON) the affinity setting seems to be broken. While affinity setting works with the exact same build and launch configuration when compiling with thread_mpi, with MPI I get the warning suggesting that affinity setting is not supported by the current platform.
This means that tMPI_Thread_setaffinity_support() returns TMPI_SETAFFINITY_SUPPORT_NO which suggests that HAVE_PTHREAD_SETAFFINITY is not defined. I suspect a bug in the build system.
As this bug will result in no affinities set in all MPI runs, it will cause considerable performance regression - especially at high parallelization where OpenMP is used.
Related issues
Associated revisions
Comprehensive hwinfo structure concurrency fix.
The hwinfo structure and structures contained therein are inherently
global to any mdrun processes/ranks. This patch makes sure that
- The hwinfo structure is shared among all threads
- Only one thread creates a hwinfo structure
- The hwinfo structure is safe to read for all threads after they
obtain it
In addition, it fixes the detection for pthread_setaffinity in thread_mpi.
This fixes concurrency issues with thread affinity settings with or
without MPI, and makes runner.c slightly easier to read because the
concurrency logic is pushed to gmx_detect_hardware.c
Note that #1254 issue 3 seems to be an OpenMPI bug.
Change-Id: I236e81923324d7873f3d8633889b91c7c02a7843
History
#1 Updated by Szilárd Páll about 4 years ago
The bug was introduced by 972ab1f9 which moved the code that does the HAVE_PTHREAD_SETAFFINITY in to the TMPI_ENABLE macro which is called only with thread_mpi. The solution is moving this check out similarly to the way TMPI_TEST_ATOMICS is done.
#2 Updated by Mark Abraham about 4 years ago
Ugh. Thanks for the diagnosis!
#3 Updated by Sander Pronk about 4 years ago
- Assignee changed from Berk Hess to Sander Pronk
#4 Updated by Rossen Apostolov about 4 years ago
- Status changed from New to Fix uploaded
#5 Updated by Mark Abraham about 4 years ago
- Status changed from Fix uploaded to Resolved
#6 Updated by Sander Pronk about 4 years ago
- % Done changed from 0 to 100
Applied in changeset 78569369348e07a300a03f90e667e61879858025.
#7 Updated by Szilárd Páll almost 4 years ago
- Status changed from Resolved to Closed
Sander Pronk wrote:
Applied in changeset 78569369348e07a300a03f90e667e61879858025.
Closing this issue, but I wanted to note that the change seems to be causing yet another problem, see #1334.