[Llvm-bgq-discuss] On compiling/running Gromacs with bgclang on BG/Q machine

[Mark Abraham]

Hi,

I'm the GROMACS BG/Q maintainer. That diagnostic is from the memory
allocation system, but we'd need a stack trace to speculate about whose
issue it is. I have not tried to compile GROMACS 2018 branch against any
bgclang. Running most of the test suite is awkward, but if you build the
tests and run $builddir/bin/mdrun-mpi-tests with 1 and 2 ranks and the
tests pass, then that would be excellent news.

The last time I got the tests to pass with bgclang was probably GROMACS
version 5.1.5, but the issues I have seen since then do not resemble yours.
And I'm pretty sure my access to vesta expired earlier this year.

Mark

On Wed, Jul 11, 2018 at 8:43 AM Jernej Zidar <jernej.zidar at gmail.com> wrote:

> i there,
>
> I've been trying to run the most recent version of Gromacs on a
> Bluegene/Q machine. This meant I had to install bgclang (opted for the
> stable release r284961) as a regular user, which was easier than
> expected following the instructions here:
> https://trac.alcf.anl.gov/projects/llvm-bgq
>
> The I compiled my own cmake (3.4.1) and FFTW-3.3.6.
>
> I compiled the source like this:
>
> CMAKE_PREFIX_PATH=/home/ihpczidj/scratch/toolkit/fftw-3.3.6-gcc:/home/ihpczidj/scratch/toolkit/zlib-1.2.11-gcc/lib
> \
> cmake ../gromacs-2018.2 \
> -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-bgclang-CXX
> -DCMAKE_C_COMPILER=/home/ihpczidj/scratch/bgclang/mpi/bgclang/bin/mpicc
> -DCMAKE_CXX_COMPILER=/home/ihpczidj/scratch/bgclang/mpi/bgclang/bin/mpicxx
> -DGMX_MPI=ON -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DEFAULT_SUFFIX=OFF
> -DGMX_BINARY_SUFFIX=-mpi-2018.2-bgq-bgclang
> -DCMAKE_INSTALL_PREFIX=/home/ihpczidj/scratch/toolkit/ -DGMX_GPU=OFF
> make
> make install
>
> There were no errors when compiling but when I try to run a short job
> I would get this error:
> mdrun-mpi-2018.2-bgq-bgclang: malloc.c:2357: sysmalloc: Assertion
> `(old_top == (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) -
> __builtin_offsetof (struct malloc_chunk, fd)))) && old_size == 0) ||
> ((unsigned long) (old_size) >= (unsigned long)((((__builtin_offsetof
> (struct malloc_chunk, fd_nextsize))+((4 * (sizeof(size_t))) - 1)) &
> ~((4 * (sizeof(size_t))) - 1))) && ((old_top)->size & 0x1) &&
> ((unsigned long)old_end & pagemask) == 0)' failed.
>
> The above message would be repeated many times and followed by this:
> *** Error in
> `/scratch/home/ihpc/ihpczidj/scratch/mem-bench/./mdrun-mpi-2018.2-bgq-bgclang':
> malloc(): memory corruption: 0x0000001f80846c00 ***
>
> What could be causing this error? Is it the compiler, Gromacs itself
> or even my job file (currently: srun ./mdrun-mpi-2018.2-bgq-bgclang ... )?
>
> Many thanks in advance,
> Jernej
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