[gmx-developers] Thread affinity in log

[Vedran Miletić]

Gladly. This one? https://gerrit.gromacs.org/#/c/5820/

V.

pon, 25. tra 2016. u 19:06 Mark Abraham <mark.j.abraham at gmail.com> napisao
je:

> 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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