GROMACS

Can you add a stacktrace?

Both tests fail with "Bus error".

With the LegacyToolsTests the crash happens at the 6th test:

[----------] 5 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
[ RUN      ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
Will write tng: Trajectory file (tng format)
Select group for output
Group     0 (         System) has     6 elements
Group     1 (FirstWaterMolecule) has     3 elements
Group     2 (SecondWaterMolecule) has     3 elements
Select a group: Selected 2: 'SecondWaterMolecule'
Bus errorrame       1 time    0.000    ->  frame      1 time    0.000      

The MdrunTest fails right after the following output:

starting mdrun 'spc-and-methanol'
6 steps,      0.0 ps.

I suspect that both of these may be related to TNG, but let me get some backtraces to confirm.

Below is the bactrace for mdrun-test. This indicates that the issue is in the TNG compression function and based on the SIGBUS, my guess is that this is perhaps an alignment issue.

Program received signal SIGBUS, Bus error.
0x005e78f2 in quantize_float (x=0x25b6323, natoms=3, nframes=2, precision=0.000999999931, quant=0x25b6370)
    at /home/pszilard/data/gromacs-5.0/src/external/tng_io/src/compression/tng_compress.c:91
91              quant[iframe*natoms*3+i*3+j]=(int)floor((x[iframe*natoms*3+i*3+j]/precision)+0.5);
(gdb) (gdb) (gdb) 
(gdb) 
(gdb) bt
#0  0x005e78f2 in quantize_float (x=0x25b6323, natoms=3, nframes=2, precision=0.000999999931, quant=0x25b6370)
    at /home/pszilard/data/gromacs-5.0/src/external/tng_io/src/compression/tng_compress.c:91
#1  0x005e9d34 in tng_compress_pos_float (pos=0x25b6323, natoms=3, nframes=2, desired_precision=0.00100000005, speed=0, algo=0x16129e8, nitems=0xbe7c11ec)
    at /home/pszilard/data/gromacs-5.0/src/external/tng_io/src/compression/tng_compress.c:1248
#2  0x005e9e2e in tng_compress_pos_float_find_algo (pos=0x25b6323, natoms=3, nframes=2, desired_precision=0.00100000005, speed=0, algo=0x16129e8, 
    nitems=0xbe7c11ec) at /home/pszilard/data/gromacs-5.0/src/external/tng_io/src/compression/tng_compress.c:1279
#3  0x005b691a in tng_compress (tng_data=0x24ee4c8, block=0x26d7450, n_frames=2, n_particles=3, type=2 '\002', start_pos=0x25b6323)
    at /home/pszilard/data/gromacs-5.0/src/external/tng_io/src/lib/tng_io.c:4837
#4  0x005b901e in tng_particle_data_block_write (tng_data=0x24ee4c8, block=0x26d7450, block_index=0, mapping=0x0, hash_mode=1 '\001')
    at /home/pszilard/data/gromacs-5.0/src/external/tng_io/src/lib/tng_io.c:6311
#5  0x005c7622 in tng_frame_set_write (tng_data=0x24ee4c8, hash_mode=1 '\001')
    at /home/pszilard/data/gromacs-5.0/src/external/tng_io/src/lib/tng_io.c:13153
#6  0x005c76f4 in tng_frame_set_premature_write (tng_data=0x24ee4c8, hash_mode=1 '\001')
    at /home/pszilard/data/gromacs-5.0/src/external/tng_io/src/lib/tng_io.c:13192
#7  0x00442948 in fflush_tng (tng=0x24ee4c8) at /home/pszilard/data/gromacs-5.0/src/gromacs/fileio/tngio.cpp:866
#8  0x00195f7a in mdoutf_write_to_trajectory_files (fplog=0x2458c58, cr=0x15a2be0, of=0x24ecaa0, mdof_flags=19, top_global=0x17cfb70, step=6, 
    t=0.0060000000000000001, state_local=0x1613170, state_global=0x2458fd8, f_local=0x16117b0, f_global=0x16117b0)
    at /home/pszilard/data/gromacs-5.0/src/gromacs/fileio/mdoutf.c:298
#9  0x0018e40c in do_md_trajectory_writing (fplog=0x2458c58, cr=0x15a2be0, nfile=35, fnm=0xbe7c26a8, step=6, step_rel=6, t=0.0060000000000000001, 
    ir=0x17cf800, state=0x1613170, state_global=0x2458fd8, top_global=0x17cfb70, fr=0x24f1790, outf=0x24ecaa0, mdebin=0x16112a0, ekind=0x2460bf0, 
    f=0x16117b0, f_global=0x16117b0, wcycle=0x0, nchkpt=0xbe7c1928, bCPT=1, bRerunMD=0, bLastStep=1, bDoConfOut=4096, bSumEkinhOld=0)
    at /home/pszilard/data/gromacs-5.0/src/gromacs/fileio/trajectory_writing.c:146
#10 0x00101452 in do_md (fplog=0x2458c58, cr=0x15a2be0, nfile=35, fnm=0xbe7c26a8, oenv=0x189dae0, bVerbose=0, bCompact=1, nstglobalcomm=5, vsite=0x0, 
    constr=0x24ec380, stepout=100, ir=0x17cf800, top_global=0x17cfb70, fcd=0x24592c8, state_global=0x2458fd8, mdatoms=0x24ec928, nrnb=0x24f13c0, 
    wcycle=0x0, ed=0x0, fr=0x24f1790, repl_ex_nst=0, repl_ex_nex=0, repl_ex_seed=-1, membed=0x0, cpt_period=15, max_hours=-1, deviceOptions=0x6be7bc "", 
    imdport=8888, Flags=1055744, walltime_accounting=0x24ec888) at /home/pszilard/data/gromacs-5.0/src/programs/mdrun/md.c:1320
#11 0x000fa61e in mdrunner (hw_opt=0xbe7c29f0, fplog=0x2458c58, cr=0x15a2be0, nfile=35, fnm=0xbe7c26a8, oenv=0x189dae0, bVerbose=0, bCompact=1, 
    nstglobalcomm=-1, ddxyz=0xbe7c2a7c, dd_node_order=1, rdd=0, rconstr=0, dddlb_opt=0x6c4c74 "auto", dlb_scale=0.800000012, ddcsx=0x0, ddcsy=0x0, 
    ddcsz=0x0, nbpu_opt=0x6c4c74 "auto", nstlist_cmdline=0, nsteps_cmdline=-2, nstepout=100, resetstep=-1, nmultisim=0, repl_ex_nst=0, repl_ex_nex=0, 
    repl_ex_seed=-1, pforce=-1, cpt_period=15, max_hours=-1, deviceOptions=0x6be7bc "", imdport=8888, Flags=1055744)
    at /home/pszilard/data/gromacs-5.0/src/programs/mdrun/runner.c:1774
#12 0x00109af0 in gmx_mdrun (argc=1, argv=0x17d4f20) at /home/pszilard/data/gromacs-5.0/src/programs/mdrun/mdrun.cpp:789
#13 0x000f1938 in gmx::test::MdrunTestFixture::callMdrun (this=0x25ad0f0, callerRef=...)
    at /home/pszilard/data/gromacs-5.0/src/programs/mdrun/tests/moduletest.cpp:209
...
[13 more frames left out]

Update:
It is an alignment issue:

$ dmesg | tail -n4
[364077.687276] Switched to NOHz mode on CPU #1
[364078.447618] Alignment trap: not handling instruction ed937a00 at [<005e78ee>]
[364078.460748] Unhandled fault: alignment exception (0x001) at 0x016913f3
[364079.950780] CPU1: shutdown

Gerrit received a related patchset '1' for Issue #1542.
Uploader: Magnus Lundborg (magnus.lundborg@scilifelab.se)
Change-Id: I96e0704d3858264ca918603bf1d7e3b27b4db7ea
Gerrit URL: https://gerrit.gromacs.org/3799