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Bug #1546

Updated by Mark Abraham over 5 years ago

Backtrace for latest master branch code

<pre>

[code]
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'
Reading frame 1 time 0.000 -> frame 1 time 0.000
Program received signal SIGBUS, Bus error.
0xb682b6e0 in quantize_float (x=0x24, x@entry=0x87543, natoms=natoms@entry=3, nframes=nframes@entry=1, precision=0.000999999931, quant=0x1, quant@entry=0x8efa0)
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)
(gdb) bt
#0 0xb682b6e0 in quantize_float (x=0x24, x@entry=0x87543, natoms=natoms@entry=3, nframes=nframes@entry=1, precision=0.000999999931, quant=0x1, quant@entry=0x8efa0)
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=0x87543, natoms=3, nframes=nframes@entry=1, desired_precision=desired_precision@entry=0.00100000005, speed=speed@entry=0,
algo=0x8b6f8, nitems=0xbeffc5bc) 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=0x87543, natoms=<optimized out>, nframes=nframes@entry=1, desired_precision=desired_precision@entry=0.00100000005,
speed=speed@entry=0, algo=0x8b6f8, nitems=0xbeffc5bc, nitems@entry=0xbeffc5b4) at /home/alexxy/Develop/gromacs/src/external/tng_io/src/compression/tng_compress.c:1279
#3 0xb6847cd4 in tng_compress (start_pos=<optimized out>, type=2 '\002', n_particles=1, n_frames=2468575403623720, block=0x88f00, tng_data=0x88f00)
at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:4837
#4 tng_particle_data_block_write (tng_data=0x88f00, tng_data@entry=0x8c528, block=0x88f00, 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=0x8c528, hash_mode=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:13107
#6 0xb686190c in tng_util_generic_write (tng_data=tng_data@entry=0x8c528, frame_nr=<optimized out>, values=values@entry=0x8bf50, n_values_per_frame=n_values_per_frame@entry=3,
block_id=block_id@entry=268435457, block_name=0xb6f0c810 "POSITIONS", block_name@entry=0x10000001 <error: Cannot access memory at address 0x10000001>, particle_dependency=1 '\001',
particle_dependency@entry=0 '\000', compression=2 '\002', compression@entry=16 '\020') at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:18151
#7 0xb68626f4 in tng_util_generic_with_time_write (tng_data=0x8c528, frame_nr=<optimized out>, time=0, values=0x8bf50, n_values_per_frame=3, block_id=268435457,
block_name=0xb6f0c810 "POSITIONS", particle_dependency=1 '\001', compression=2 '\002') at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:18662
#8 0xb6b44204 in gmx_fwrite_tng (tng=0x8c528, bUseLossyCompression=<optimized out>, step=1, elapsedPicoSeconds=<optimized out>, lambda=2.80259693e-45,
box=0x854b8 <__stack_chk_guard@@GLIBC_2.4>, nAtoms=3, x=0x8bf50, v=0x8b5c0, f=0x0) at /home/alexxy/Develop/gromacs/src/gromacs/fileio/tngio.cpp:796
#9 0xb6b3c6f8 in gmx_write_tng_from_trxframe (output=<optimized out>, frame=frame@entry=0xbeffcb90, natoms=3, natoms@entry=-1)
at /home/alexxy/Develop/gromacs/src/gromacs/fileio/tngio_for_tools.cpp:198
#10 0xb6b4a360 in write_tng_frame (status=<optimized out>, frame=frame@entry=0xbeffcb90) at /home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c:510
#11 0xb6c21ae4 in gmx_trjconv (argc=-1224967432, argv=<optimized out>) at /home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c:1748
#12 0x00029638 in runTest (fileName=0x703a0 "spc2-traj.trr", this=<optimized out>) at /home/alexxy/Develop/gromacs/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp:117
#13 (anonymous namespace)::TrjconvWithIndexGroupSubset_WithDifferentInputFormats_Test::TestBody (this=<optimized out>)
at /home/alexxy/Develop/gromacs/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp:128
#14 0x0006f254 in HandleSehExceptionsInMethodIfSupported<testing::Test, void> (location=0x761ac "the test body", method=&virtual testing::Test::TestBody(), object=0x8bec8)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2078
#15 testing::internal::HandleExceptionsInMethodIfSupported<testing::Test, void> (object=object@entry=0x8bec8, method=&virtual testing::Test::TestBody(),
location=location@entry=0x761ac "the test body") at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2114
#16 0x00065dd4 in testing::Test::Run (this=0x8bec8) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2151
#17 0x00065fa0 in testing::TestInfo::Run (this=0x87958) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2326
#18 0x000660e0 in Run (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2301
#19 testing::TestCase::Run (this=0x879d8) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2444
#20 0x000665b0 in Run (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2430
#21 testing::internal::UnitTestImpl::RunAllTests (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:4315
#22 0x000667fc 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
#23 HandleExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool> (location=0x76318 "auxiliary test code (environments or event listeners)",
method=(bool (testing::internal::UnitTestImpl::*)(testing::internal::UnitTestImpl * const)) 0x661bc <testing::internal::UnitTestImpl::RunAllTests()>, object=0x86ca8)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2114
#24 testing::UnitTest::Run (this=<optimized out>) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:3929
#25 0x00028428 in RUN_ALL_TESTS () at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/include/gtest/gtest.h:2288
#26 main (argc=164904, argv=0xbeffef04) at /home/alexxy/Develop/gromacs/src/testutils/unittest_main.cpp:63
(gdb) up
#1 0xb682c7c0 in tng_compress_pos_float (pos=pos@entry=0x87543, natoms=3, nframes=nframes@entry=1, desired_precision=desired_precision@entry=0.00100000005, speed=speed@entry=0,
algo=0x8b6f8, nitems=0xbeffc5bc) 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=0x87543, natoms=<optimized out>, nframes=nframes@entry=1, desired_precision=desired_precision@entry=0.00100000005,
speed=speed@entry=0, algo=0x8b6f8, nitems=0xbeffc5bc, nitems@entry=0xbeffc5b4) 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 0xb6847cd4 in tng_compress (start_pos=<optimized out>, type=2 '\002', n_particles=1, n_frames=2468575403623720, block=0x88f00, tng_data=0x88f00)
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=0x88f00, tng_data@entry=0x8c528, block=0x88f00, 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=0x8c528, 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 0xb686190c in tng_util_generic_write (tng_data=tng_data@entry=0x8c528, frame_nr=<optimized out>, values=values@entry=0x8bf50, n_values_per_frame=n_values_per_frame@entry=3,
block_id=block_id@entry=268435457, block_name=0xb6f0c810 "POSITIONS", block_name@entry=0x10000001 <error: Cannot access memory at address 0x10000001>, particle_dependency=1 '\001',
particle_dependency@entry=0 '\000', compression=2 '\002', compression@entry=16 '\020') at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:18151
18151 stat = tng_frame_set_write(tng_data, TNG_USE_HASH);
(gdb) up
#7 0xb68626f4 in tng_util_generic_with_time_write (tng_data=0x8c528, frame_nr=<optimized out>, time=0, values=0x8bf50, n_values_per_frame=3, block_id=268435457,
block_name=0xb6f0c810 "POSITIONS", particle_dependency=1 '\001', compression=2 '\002') at /home/alexxy/Develop/gromacs/src/external/tng_io/src/lib/tng_io.c:18662
18662 stat = tng_util_generic_write(tng_data, frame_nr, values, n_values_per_frame,
(gdb) up
#8 0xb6b44204 in gmx_fwrite_tng (tng=0x8c528, bUseLossyCompression=<optimized out>, step=1, elapsedPicoSeconds=<optimized out>, lambda=2.80259693e-45,
box=0x854b8 <__stack_chk_guard@@GLIBC_2.4>, nAtoms=3, x=0x8bf50, v=0x8b5c0, f=0x0) at /home/alexxy/Develop/gromacs/src/gromacs/fileio/tngio.cpp:796
796 compression) != TNG_SUCCESS)
(gdb) up
#9 0xb6b3c6f8 in gmx_write_tng_from_trxframe (output=<optimized out>, frame=frame@entry=0xbeffcb90, natoms=3, natoms@entry=-1)
at /home/alexxy/Develop/gromacs/src/gromacs/fileio/tngio_for_tools.cpp:198
198 (const rvec *) frame->f);
(gdb) up
#10 0xb6b4a360 in write_tng_frame (status=<optimized out>, frame=frame@entry=0xbeffcb90) at /home/alexxy/Develop/gromacs/src/gromacs/fileio/trxio.c:510
510 gmx_write_tng_from_trxframe(status->tng, frame, -1);
(gdb) up
#11 0xb6c21ae4 in gmx_trjconv (argc=-1224967432, argv=<optimized out>) at /home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_trjconv.c:1748
1748 write_tng_frame(trxout, &frout);
(gdb) up
#12 0x00029638 in runTest (fileName=0x703a0 "spc2-traj.trr", this=<optimized out>) at /home/alexxy/Develop/gromacs/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp:117
117 return gmx_trjconv(caller.argc(), caller.argv());
(gdb) up
#13 (anonymous namespace)::TrjconvWithIndexGroupSubset_WithDifferentInputFormats_Test::TestBody (this=<optimized out>)
at /home/alexxy/Develop/gromacs/src/gromacs/gmxana/legacytests/gmx_traj_tests.cpp:128
128 runTest(GetParam());
(gdb) up
#14 0x0006f254 in HandleSehExceptionsInMethodIfSupported<testing::Test, void> (location=0x761ac "the test body", method=&virtual testing::Test::TestBody(), object=0x8bec8)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2078
2078 return (object->*method)();
(gdb) up
#15 testing::internal::HandleExceptionsInMethodIfSupported<testing::Test, void> (object=object@entry=0x8bec8, method=&virtual testing::Test::TestBody(),
location=location@entry=0x761ac "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
#16 0x00065dd4 in testing::Test::Run (this=0x8bec8) 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
#17 0x00065fa0 in testing::TestInfo::Run (this=0x87958) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2326
2326 test->Run();
(gdb) up
#18 0x000660e0 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
#19 testing::TestCase::Run (this=0x879d8) at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2444
2444 GetMutableTestInfo(i)->Run();
(gdb) up
#20 0x000665b0 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
#21 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
#22 0x000667fc 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
#23 HandleExceptionsInMethodIfSupported<testing::internal::UnitTestImpl, bool> (location=0x76318 "auxiliary test code (environments or event listeners)",
method=(bool (testing::internal::UnitTestImpl::*)(testing::internal::UnitTestImpl * const)) 0x661bc <testing::internal::UnitTestImpl::RunAllTests()>, object=0x86ca8)
at /home/alexxy/Develop/gromacs/src/external/gmock-1.7.0/gtest/src/gtest.cc:2114
2114 return HandleSehExceptionsInMethodIfSupported(object, method, location);
(gdb) up
#24 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
#25 0x00028428 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
#26 main (argc=164904, argv=0xbeffef04) 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.

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