[ET Trac] [Einstein Toolkit] #2117: CarpetIOHDF5 commit 69c73fb1 " CarpetIOHDF5: Add "active" attribute to grid function dataset describing which points are active" break 'IO::out_mode = "onefile"'
Einstein Toolkit
trac-noreply at einsteintoolkit.org
Mon Feb 5 14:07:49 CST 2018
#2117: CarpetIOHDF5 commit 69c73fb1 " CarpetIOHDF5: Add "active" attribute to grid
function dataset describing which points are active" break 'IO::out_mode =
"onefile"'
---------------------+------------------------------------------------------
Reporter: rhaas | Owner: eschnett
Type: defect | Status: new
Priority: major | Milestone:
Component: Carpet | Version: development version
Resolution: | Keywords:
---------------------+------------------------------------------------------
Description changed by rhaas:
Old description:
> Setting
> {{{
> IO::out_mode = "onefile"
> }}}
> in a parfile and running with more than 1 MPI ranks causes and out-of-
> range array access in Output.cc in line 913:
> {{{
> ostringstream buf;
> buf << (vdd.at(Carpet::map)
> ->local_boxes.at(mglevel)
> .at(refinementlevel)
> ----> .at(local_component)
> .active);
> }}}
> due to {{{local_component}}} being -1. This is the backtrace:
> {{{
> #6 0x00007ffff3a03355 in std::__throw_out_of_range_fmt(char const*, ...)
> ()
> from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> #7 0x00005555578f17ee in std::vector<dh::local_dboxes,
> std::allocator<dh::local_dboxes> >::_M_range_check (__n=<optimized out>,
> this=<optimized out>) at /usr/include/c++/7/bits/stl_vector.h:825
> #8 std::vector<dh::local_dboxes, std::allocator<dh::local_dboxes> >::at
> (__n=<optimized out>,
> this=<optimized out>) at /usr/include/c++/7/bits/stl_vector.h:846
> #9 CarpetIOHDF5::AddAttributes (cctkGH=cctkGH at entry=0x55555f829ab0,
> fullname=fullname at entry=0x5555634efb10 "TMUNUBASE::eTxx", vdim=3,
> refinementlevel=<optimized out>,
> refinementlevel at entry=0, request=request at entry=0x5555635801b0,
> bbox=...,
> dataset=360287970189640065, is_index=false)
> at
> /data/rhaas/postdoc/gr/cactus/ET_vanilla/configs/sim/build/CarpetIOHDF5/Output.cc:913
> #10 0x00005555578f2a45 in CarpetIOHDF5::WriteVarChunkedSequential
> (cctkGH=cctkGH at entry=0x55555f829ab0,
> outfile=outfile at entry=72057594037928056, io_bytes=@0x7fffffffb960:
> 62212, request=0x5555635801b0,
> called_from_checkpoint=called_from_checkpoint at entry=true,
> indexfile=indexfile at entry=-1)
> at
> /data/rhaas/postdoc/gr/cactus/ET_vanilla/configs/sim/build/CarpetIOHDF5/Output.cc:513
> #11 0x00005555578d9bdf in CarpetIOHDF5::Checkpoint
> (cctkGH=0x55555f829ab0, called_from=0)
> at
> /data/rhaas/postdoc/gr/cactus/ET_vanilla/configs/sim/build/CarpetIOHDF5/CarpetIOHDF5.cc:1218
> }}}
>
> To reproduce:
>
> {{{
> wget https://einsteintoolkit.org/gallery/ns/tov.par
> OMP_NUM_THREADS=1 mpirun -n 2 exe/cactus_sim tov.par
> }}}
> }}}
New description:
Setting
{{{
IO::out_mode = "onefile"
}}}
in a parfile and running with more than 1 MPI ranks causes and out-of-
range array access in Output.cc in line 913:
{{{
ostringstream buf;
buf << (vdd.at(Carpet::map)
->local_boxes.at(mglevel)
.at(refinementlevel)
----> .at(local_component)
.active);
}}}
due to {{{local_component}}} being -1. This is the backtrace:
{{{
#6 0x00007ffff3a03355 in std::__throw_out_of_range_fmt(char const*, ...)
()
from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#7 0x00005555578f17ee in std::vector<dh::local_dboxes,
std::allocator<dh::local_dboxes> >::_M_range_check (__n=<optimized out>,
this=<optimized out>) at /usr/include/c++/7/bits/stl_vector.h:825
#8 std::vector<dh::local_dboxes, std::allocator<dh::local_dboxes> >::at
(__n=<optimized out>,
this=<optimized out>) at /usr/include/c++/7/bits/stl_vector.h:846
#9 CarpetIOHDF5::AddAttributes (cctkGH=cctkGH at entry=0x55555f829ab0,
fullname=fullname at entry=0x5555634efb10 "TMUNUBASE::eTxx", vdim=3,
refinementlevel=<optimized out>,
refinementlevel at entry=0, request=request at entry=0x5555635801b0,
bbox=...,
dataset=360287970189640065, is_index=false)
at
/data/rhaas/postdoc/gr/cactus/ET_vanilla/configs/sim/build/CarpetIOHDF5/Output.cc:913
#10 0x00005555578f2a45 in CarpetIOHDF5::WriteVarChunkedSequential
(cctkGH=cctkGH at entry=0x55555f829ab0,
outfile=outfile at entry=72057594037928056, io_bytes=@0x7fffffffb960:
62212, request=0x5555635801b0,
called_from_checkpoint=called_from_checkpoint at entry=true,
indexfile=indexfile at entry=-1)
at
/data/rhaas/postdoc/gr/cactus/ET_vanilla/configs/sim/build/CarpetIOHDF5/Output.cc:513
#11 0x00005555578d9bdf in CarpetIOHDF5::Checkpoint (cctkGH=0x55555f829ab0,
called_from=0)
at
/data/rhaas/postdoc/gr/cactus/ET_vanilla/configs/sim/build/CarpetIOHDF5/CarpetIOHDF5.cc:1218
}}}
To reproduce:
{{{
wget https://einsteintoolkit.org/gallery/ns/tov.par
OMP_NUM_THREADS=1 mpirun -n 2 exe/cactus_sim tov.par
}}}
--
--
Ticket URL: <https://trac.einsteintoolkit.org/ticket/2117#comment:1>
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