Miguel
Can you look at https://trac.einsteintoolkit.org/ticket/1800? Can you try replacing "reflevel" in line 816 of the file CarpetIOHDF5/src/Output.cc with "refinementlevel", and see whether this avoids the problem?
-erik
On Wed, Aug 5, 2015 at 8:11 PM, Miguel Zilhão mzilhao@ffn.ub.es wrote:
hi all,
i'm running latest ET Hilbert on openSUSE tumbleweed and i'm having the following issue. upon trying to run a simple head-on collision configuration with McLachlan (attached parameter file), i get the error
INFO (CarpetIOHDF5):
INFO (CarpetIOHDF5): Dumping initial checkpoint at iteration 0, simulation time 0 INFO (CarpetIOHDF5):
terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check: __n (which is 1) >= this->size() (which is 1) Rank 1 with PID 5958 received signal 6
when writing the checkpoint file. this only happens if i run with more than one MPI process; with a single processor it runs fine.
i'm compiling with gcc-5, but i find the same problem with gcc-4.8. i was running this very same configuration just fine a couple of months ago, so it must have been some update i've made in the meantime (either to my OS or to ET). i've also tried with different configurations and the outcome is the same.
i've ran this through gdb, here's the relevant output:
#6 0x00007ffff4f6d4d5 in std::__throw_out_of_range_fmt(char const*, ...) () from /usr/lib64/libstdc++.so.6 #7 0x00000000005bb398 in _M_range_check (__n=<optimized out>, this=<optimized out>) at /usr/include/c++/5/bits/stl_vector.h:803 #8 at (__n=<optimized out>, this=<optimized out>) at /usr/include/c++/5/bits/stl_vector.h:824 #9 CarpetIOHDF5::AddAttributes (cctkGH=cctkGH@entry=0x1b507d0, fullname=fullname@entry=0x3f2434a0 "ML_BSSN::cA", vdim=3, refinementlevel=refinementlevel@entry=0, request=request@entry =0x3df96370, bbox=..., dataset=83886080, is_index=false) at /home/mzilhao/Trabalho/projectos/ET/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:899 #10 0x00000000005bdea4 in CarpetIOHDF5::WriteVarChunkedParallel ( cctkGH=cctkGH@entry=0x1b507d0, outfile=outfile@entry=16777216, io_bytes=@0x7fffffffc980: 1110772, request=0x3df96370, called_from_checkpoint=called_from_checkpoint@entry =true,indexfile=indexfile@entry=-1) at /home/mzilhao/Trabalho/projectos/ET/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:706 #11 0x00000000005a233e in CarpetIOHDF5::Checkpoint (cctkGH=0x1b507d0, called_from=0) at /home/mzilhao/Trabalho/projectos/ET/Cactus/arrangements/Carpet/CarpetIOHDF5/src/CarpetIOHDF5.cc:1277 #12 0x000000000041f0d5 in CCTK_CallFunction ( function=function@entry=0x5a2da0 CarpetIOHDF5::CarpetIOHDF5_InitialDataCheckpoint(cGH*), fdata=fdata@entry=0x1b4a4e8, data=data@entry=0x1b507d0) at /home/mzilhao/Trabalho/projectos/ET/Cactus/src/main/ScheduleInterface.c:312 #13 0x0000000000ef6499 in Carpet::CallScheduledFunction ( time_and_mode=time_and_mode@entry=0x1174842 "Meta mode", function=function@entry=0x5a2da0 CarpetIOHDF5::CarpetIOHDF5_InitialDataCheckpoint(cGH*), attribute=attribute@entry=0x1b4a4e8, data=data@entry=0x1b507d0, user_timer=...) at /home/mzilhao/Trabalho/projectos/ET/Cactus/arrangements/Carpet/Carpet/src/CallFunction.cc:380
so the relevant bits of code seem to be in CarpetIOHDF5/src/Output.cc:706 and CarpetIOHDF5/src/Output.cc:899
this seems to be triggered when writing hdf5 output in parallel. if i remove checkpointing the run goes fine, and i do get regular 2D hdf5 output. this does not seem to be written in parallel, though, as i get only one file per grid function/group. so it seems to be the parallel output that triggers the crash.
i have also tried removing all my hdf5 libs and configuring ET with HDF5_DIR=BUILD, but the outcome was the same.
has anyone seen such an error before? anything else i could provide to help diagnose this?
thanks, Miguel
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