[gmx-developers] Thread affinity in log

[Mark Abraham]

Hi,

Unsure offhand, but there's a fix in gerrit in this area if you want to try
that?

Mark

On Mon, 25 Apr 2016 19:05 Vedran Miletić <rivanvx at gmail.com> wrote:

> Hi,
>
> since fa1360610d6fcf7eb263ce1181d9954074fd5151 "Make thread affinity
> failures always end up in log", I get crashes in mdrun when using tMPI on
> any simulation I tried (does not affect OpenMPI). I am seeing this on two
> machines using Fedora 23 and 24, GCC 5.3 and 6, respectively.
>
> Backtrace is
>
> #0 0x00007ffff78c966f in tMPI_Thread_getspecific (key=...) at
> /home/miletivn/workspace/gromacs/src/external/thread_mpi/src/pthreads.c:571
> #1 0x00007ffff78cff34 in tMPI_Reduce (sendbuf=0x7fffffffa4dc,
> recvbuf=0x7fffffffa4d8, count=1, datatype=0x7ffff7dd6660 <tmpi_int>,
> op=TMPI_LAND, root=0, comm=0x0) at
> /home/miletivn/workspace/gromacs/src/external/thread_mpi/src/reduce.c:247
> #2 0x00007ffff63038a5 in invalidWithinSimulation (cr=0x681bd0,
> invalidLocally=false) at
> /home/miletivn/workspace/gromacs/src/gromacs/mdrunutility/threadaffinity.cpp:73
> #3 0x00007ffff6303c0b in get_thread_affinity_layout (fplog=0x689410,
> cr=0x681bd0, hwinfo=0x680230, threads=8, pin_offset=0,
> pin_stride=0x7fffffffc634, localityOrder=0x7fffffffc638) at
> /home/miletivn/workspace/gromacs/src/gromacs/mdrunutility/threadaffinity.cpp:142
> ...
>
> Variable key looks like
>
> $1 = {initialized = {value = 0, padding = '\000' <repeats 59 times>}, key
> = 0x0}
>
> So key is uninitialized. Any idea why?
>
> Regards,
> Vedran
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