[gmx-developers] Thread affinity in log

[Vedran Miletić]

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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