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Bug #1547

Updated by Mark Abraham about 6 years ago

Also backtrace for mdrun-test

<pre> @
WARNING: Using the slow plain C kernels. This should
not happen during routine usage on supported platforms.

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

Program received signal SIGBUS, Bus error.
0xb682b6e0 in quantize_float (x=0x24, x@entry=0x9591bb, natoms=natoms@entry=3, nframes=1, nframes@entry=2, precision=0.000999999931, quant=0x2, quant@entry=0x959208)
at /home/alexxy/Develop/gromacs/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) bt
#0 0xb682b6e0 in quantize_float (x=0x24, x@entry=0x9591bb, natoms=natoms@entry=3, nframes=1, nframes@entry=2, precision=0.000999999931, quant=0x2, quant@entry=0x959208)
at /home/alexxy/Develop/gromacs/src/external/tng_io/src/compression/tng_compress.c:91
#1 0xb682c7c0 in tng_compress_pos_float (pos=pos@entry=0x9591bb, natoms=3, nframes=2, desired_precision=desired_precision@entry=0.00100000005, speed=speed@entry=0, algo=0x2017728,
nitems=0xbeffc30c) at /home/alexxy/Develop/gromacs/src/external/tng_io/src/compression/tng_compress.c:1248
#2 0xb682c874 in tng_compress_pos_float_find_algo (pos=pos@entry=0x9591bb, natoms=<optimized out>, nframes=<optimized out>, desired_precision=desired_precision@entry=0.00100000005,
speed=speed@entry=0, algo=0x2017728, nitems=0xbeffc30c, nitems@entry=0xbeffc304) at /home/alexxy/Develop/gromacs/src/external/tng_io/src/compression/tng_compress.c:1279
#3 0xb6847cb0 in tng_compress (start_pos=<optimized out>, type=2 '\002', n_particles=2, n_frames=31511178625676096, block=0x9590c8, tng_data=0x9590c8)
at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:4837
#4 tng_particle_data_block_write (tng_data=0x9590c8, tng_data@entry=0x6ff340, block=0x9590c8, block_index=<optimized out>, mapping=mapping@entry=0x0, hash_mode=hash_mode@entry=1 '\001')
at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:6311
#5 0xb685661c in tng_frame_set_write (tng_data=0x6ff340, hash_mode=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:13107
#6 0xb6b5cf60 in mdoutf_write_to_trajectory_files (fplog=0x200a7d0, cr=0x1df1b60, of=0x200ee40, mdof_flags=19, top_global=0x1ffe138, step=6, t=0.0060000000000000001, state_local=0x20101f0,
state_global=0x1df1328, f_local=0x702e08, f_global=0x702e08) at /home/alexxy/Develop/gromacs/src/gromacs/fileio/mdoutf.c:299
#7 0xb6b5c3b8 in do_md_trajectory_writing (fplog=0x1ffe138, cr=0x1df1b60, nfile=7351896, fnm=0x0, step=6, step_rel=6, t=0.0060000000000000001, ir=0x1df0d20, state=0x20101f0,
state_global=0x1df1328, top_global=0x1ffe138, fr=0x200e568, outf=0x200ee40, mdebin=0x701d30, ekind=0x702e58, f=0x702e08, f_global=0x702e08, wcycle=0x0, nchkpt=0xbeffc6c4, bCPT=1,
bRerunMD=0, bLastStep=1, bDoConfOut=4096, bSumEkinhOld=0) at /home/alexxy/Develop/gromacs/src/gromacs/fileio/trajectory_writing.c:146
#8 0x00045078 in do_md (fplog=0x6, cr=0x1df1b60, nfile=0, fnm=0x0, oenv=0x200bcd8, bVerbose=0, bCompact=1, nstglobalcomm=1, vsite=0x0, constr=0x200ede0, stepout=100, ir=0x1df0d20,
top_global=0x1ffe138, fcd=0x1ffe298, state_global=0x1df1328, mdatoms=0x200ed38, nrnb=0x200dba8, wcycle=0x0, ed=0x0, fr=0x200e568, repl_ex_nst=0, repl_ex_nex=0, repl_ex_seed=-1,
membed=0x0, cpt_period=15, max_hours=-1, deviceOptions=0x93f98 "", imdport=8888, Flags=1055744, walltime_accounting=0x696e28)
at /home/alexxy/Develop/gromacs/src/programs/mdrun/md.cpp:1316
#9 0x0004a4dc in mdrunner (hw_opt=<optimized out>, fplog=0x93f98, cr=0x1df1b60, nfile=<optimized out>, fnm=0xbeffcf58, oenv=0x200bcd8, bVerbose=0, bCompact=1, nstglobalcomm=-1,
ddxyz=0xbeffcecc, dd_node_order=1, rdd=<optimized out>, rconstr=0, dddlb_opt=0x94d4c "auto", dlb_scale=0.800000012, ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nbpu_opt=0x94d4c "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=<optimized out>, cpt_period=0, max_hours=-1,
deviceOptions=0x93f98 "", imdport=8888, Flags=606104) at /home/alexxy/Develop/gromacs/src/programs/mdrun/runner.cpp:1762
#10 0x0004f38c in gmx_mdrun (argc=0, argc@entry=17, argv=<optimized out>) at /home/alexxy/Develop/gromacs/src/programs/mdrun/mdrun.cpp:790
#11 0x0003d6b4 in gmx::test::MdrunTestFixture::callMdrun (this=this@entry=0x60cec0, callerRef=...) at /home/alexxy/Develop/gromacs/src/programs/mdrun/tests/moduletest.cpp:211
#12 0x0003d7a4 in gmx::test::MdrunTestFixture::callMdrun (this=this@entry=0x60cec0) at /home/alexxy/Develop/gromacs/src/programs/mdrun/tests/moduletest.cpp:219
#13 0x000378ec in runTest (this=0x60cec0) at /home/alexxy/Develop/gromacs/src/programs/mdrun/tests/trajectory_writing.cpp:76
#14 (anonymous namespace)::Trajectories_ThatDifferInNstxout_Test::TestBody (this=0x60cec0) at /home/alexxy/Develop/gromacs/src/programs/mdrun/tests/trajectory_writing.cpp:105
#15 0x00090114 in HandleSehExceptionsInMethodIfSupported<testing::Test, void> (location=0xa2578 "the test body", method=&virtual testing::Test::TestBody(), object=0x60cec0)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2078
#16 testing::internal::HandleExceptionsInMethodIfSupported<testing::Test, void> (object=object@entry=0x60cec0, method=&virtual testing::Test::TestBody(),
location=location@entry=0xa2578 "the test body") at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2114
#17 0x00086c94 in testing::Test::Run (this=0x60cec0) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2151
#18 0x00086e60 in testing::TestInfo::Run (this=0xb6a60) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2326
#19 0x00086fa0 in Run (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2301
#20 testing::TestCase::Run (this=0xb6b10) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2444
#21 0x00087470 in Run (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2430
#22 testing::internal::UnitTestImpl::RunAllTests (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:4315
#23 0x000876bc in HandleSehExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool> (location=<optimized out>, method=<optimized out>, object=<optimized out>)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2078
#24 HandleExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool> (location=0xa26e4 "auxiliary test code (environments or event listeners)",
method=(bool (testing::internal::UnitTestImpl::*)(testing::internal::UnitTestImpl * const)) 0x8707c <testing::internal::UnitTestImpl::RunAllTests()>, object=0xb4ca8)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2114
#25 testing::UnitTest::Run (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:3929
---Type <return> to continue, or q <return> to quit---
#26 0x0002f558 in RUN_ALL_TESTS () at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/include/gtest/gtest.h:2288
#27 main (argc=193880, argv=0xbeffef14) at /home/alexxy/Develop/gromacs/src/testutils/unittest_main.cpp:63
(gdb) up
#1 0xb682c7c0 in tng_compress_pos_float (pos=pos@entry=0x9591bb, natoms=3, nframes=2, desired_precision=desired_precision@entry=0.00100000005, speed=speed@entry=0, algo=0x2017728,
nitems=0xbeffc30c) at /home/alexxy/Develop/gromacs/src/external/tng_io/src/compression/tng_compress.c:1248
1248 if (quantize_float(pos,natoms,nframes,(float)PRECISION(prec_hi,prec_lo),quant))
(gdb) up
#2 0xb682c874 in tng_compress_pos_float_find_algo (pos=pos@entry=0x9591bb, natoms=<optimized out>, nframes=<optimized out>, desired_precision=desired_precision@entry=0.00100000005,
speed=speed@entry=0, algo=0x2017728, nitems=0xbeffc30c, nitems@entry=0xbeffc304) at /home/alexxy/Develop/gromacs/src/external/tng_io/src/compression/tng_compress.c:1279
1279 return tng_compress_pos_float(pos,natoms,nframes,desired_precision,speed,algo,nitems);
(gdb) up
#3 0xb6847cb0 in tng_compress (start_pos=<optimized out>, type=2 '\002', n_particles=2, n_frames=31511178625676096, block=0x9590c8, tng_data=0x9590c8)
at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:4837
4837 dest = tng_compress_pos_float_find_algo(start_pos, (int)n_particles,
(gdb) up
#4 tng_particle_data_block_write (tng_data=0x9590c8, tng_data@entry=0x6ff340, block=0x9590c8, block_index=<optimized out>, mapping=mapping@entry=0x0, hash_mode=hash_mode@entry=1 '\001')
at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:6311
6311 stat = tng_compress(tng_data, block, frame_step,
(gdb) up
#5 0xb685661c in tng_frame_set_write (tng_data=0x6ff340, hash_mode=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:13107
13107 tng_particle_data_block_write(tng_data, block,
(gdb) up
#6 0xb6b5cf60 in mdoutf_write_to_trajectory_files (fplog=0x200a7d0, cr=0x1df1b60, of=0x200ee40, mdof_flags=19, top_global=0x1ffe138, step=6, t=0.0060000000000000001, state_local=0x20101f0,
state_global=0x1df1328, f_local=0x702e08, f_global=0x702e08) at /home/alexxy/Develop/gromacs/src/gromacs/fileio/mdoutf.c:299
299 fflush_tng(of->tng_low_prec);
(gdb) up
#7 0xb6b5c3b8 in do_md_trajectory_writing (fplog=0x1ffe138, cr=0x1df1b60, nfile=7351896, fnm=0x0, step=6, step_rel=6, t=0.0060000000000000001, ir=0x1df0d20, state=0x20101f0,
state_global=0x1df1328, top_global=0x1ffe138, fr=0x200e568, outf=0x200ee40, mdebin=0x701d30, ekind=0x702e58, f=0x702e08, f_global=0x702e08, wcycle=0x0, nchkpt=0xbeffc6c4, bCPT=1,
bRerunMD=0, bLastStep=1, bDoConfOut=4096, bSumEkinhOld=0) at /home/alexxy/Develop/gromacs/src/gromacs/fileio/trajectory_writing.c:146
146 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
(gdb) up
#8 0x00045078 in do_md (fplog=0x6, cr=0x1df1b60, nfile=0, fnm=0x0, oenv=0x200bcd8, bVerbose=0, bCompact=1, nstglobalcomm=1, vsite=0x0, constr=0x200ede0, stepout=100, ir=0x1df0d20,
top_global=0x1ffe138, fcd=0x1ffe298, state_global=0x1df1328, mdatoms=0x200ed38, nrnb=0x200dba8, wcycle=0x0, ed=0x0, fr=0x200e568, repl_ex_nst=0, repl_ex_nex=0, repl_ex_seed=-1,
membed=0x0, cpt_period=15, max_hours=-1, deviceOptions=0x93f98 "", imdport=8888, Flags=1055744, walltime_accounting=0x696e28)
at /home/alexxy/Develop/gromacs/src/programs/mdrun/md.cpp:1316
1316 bSumEkinhOld);
(gdb) up
#9 0x0004a4dc in mdrunner (hw_opt=<optimized out>, fplog=0x93f98, cr=0x1df1b60, nfile=<optimized out>, fnm=0xbeffcf58, oenv=0x200bcd8, bVerbose=0, bCompact=1, nstglobalcomm=-1,
ddxyz=0xbeffcecc, dd_node_order=1, rdd=<optimized out>, rconstr=0, dddlb_opt=0x94d4c "auto", dlb_scale=0.800000012, ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nbpu_opt=0x94d4c "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=<optimized out>, cpt_period=0, max_hours=-1,
deviceOptions=0x93f98 "", imdport=8888, Flags=606104) at /home/alexxy/Develop/gromacs/src/programs/mdrun/runner.cpp:1762
1762 walltime_accounting);
(gdb) up
#10 0x0004f38c in gmx_mdrun (argc=0, argc@entry=17, argv=<optimized out>) at /home/alexxy/Develop/gromacs/src/programs/mdrun/mdrun.cpp:790
790 pforce, cpt_period, max_hours, deviceOptions, imdport, Flags);
(gdb) up
#11 0x0003d6b4 in gmx::test::MdrunTestFixture::callMdrun (this=this@entry=0x60cec0, callerRef=...) at /home/alexxy/Develop/gromacs/src/programs/mdrun/tests/moduletest.cpp:211
211 return gmx_mdrun(caller.argc(), caller.argv());
(gdb) up
#12 0x0003d7a4 in gmx::test::MdrunTestFixture::callMdrun (this=this@entry=0x60cec0) at /home/alexxy/Develop/gromacs/src/programs/mdrun/tests/moduletest.cpp:219
219 return callMdrun(caller);
(gdb) up
#13 0x000378ec in runTest (this=0x60cec0) at /home/alexxy/Develop/gromacs/src/programs/mdrun/tests/trajectory_writing.cpp:76
76 ASSERT_EQ(0, callMdrun());
(gdb) up
#14 (anonymous namespace)::Trajectories_ThatDifferInNstxout_Test::TestBody (this=0x60cec0) at /home/alexxy/Develop/gromacs/src/programs/mdrun/tests/trajectory_writing.cpp:105
105 runTest();
(gdb) up
#15 0x00090114 in HandleSehExceptionsInMethodIfSupported<testing::Test, void> (location=0xa2578 "the test body", method=&virtual testing::Test::TestBody(), object=0x60cec0)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2078
2078 return (object->*method)();
(gdb) up
#16 testing::internal::HandleExceptionsInMethodIfSupported<testing::Test, void> (object=object@entry=0x60cec0, method=&virtual testing::Test::TestBody(),
location=location@entry=0xa2578 "the test body") at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2114
2114 return HandleSehExceptionsInMethodIfSupported(object, method, location);
(gdb) up
#17 0x00086c94 in testing::Test::Run (this=0x60cec0) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2151
2151 this, &Test::TestBody, "the test body");
(gdb) up
#18 0x00086e60 in testing::TestInfo::Run (this=0xb6a60) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2326
2326 test->Run();
(gdb) up
#19 0x00086fa0 in Run (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2301
2301 if (!should_run_) return;
(gdb) up
#20 testing::TestCase::Run (this=0xb6b10) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2444
2444 GetMutableTestInfo(i)->Run();
(gdb) up
#21 0x00087470 in Run (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2430
2430 if (!should_run_) return;
(gdb) up
#22 testing::internal::UnitTestImpl::RunAllTests (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:4315
4315 GetMutableTestCase(test_index)->Run();
(gdb) up
#23 0x000876bc in HandleSehExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool> (location=<optimized out>, method=<optimized out>, object=<optimized out>)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2078
2078 return (object->*method)();
(gdb) up
#24 HandleExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool> (location=0xa26e4 "auxiliary test code (environments or event listeners)",
method=(bool (testing::internal::UnitTestImpl::*)(testing::internal::UnitTestImpl * const)) 0x8707c <testing::internal::UnitTestImpl::RunAllTests()>, object=0xb4ca8)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2114
2114 return HandleSehExceptionsInMethodIfSupported(object, method, location);
(gdb) up
#25 testing::UnitTest::Run (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:3929
3929 "auxiliary test code (environments or event listeners)") ? 0 : 1;
(gdb) up
#26 0x0002f558 in RUN_ALL_TESTS () at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/include/gtest/gtest.h:2288
2288 return ::testing::UnitTest::GetInstance()->Run();
(gdb) up
#27 main (argc=193880, argv=0xbeffef14) at /home/alexxy/Develop/gromacs/src/testutils/unittest_main.cpp:63
63 int errcode = RUN_ALL_TESTS();
(gdb) up
Initial frame selected; you cannot go up.
(gdb)

</pre>

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