[gmx-users] gmx wham crashes with buffer overflow

Michail Palaiokostas Avramidis m.palaiokostas at qmul.ac.uk
Mon Apr 18 16:30:44 CEST 2016


Dear gmx users,


I am using gmx wham to analyse umbrella sampling simulations. I have 30 positions along the reaction coordinate and therefore 30 tpr, pullf and pullx files. Each of these files have 100,000 rows, as I save every ps.


When I try to execute wham with the command:

gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -v -min 0 -max 29 -zprof0 29


the program is crashing with the Aborted (core dumped) message and a buffer overflow error. Can this be due to the large number of samples (100,000) per file? Because it crashes even if I add the -b flag to 90000.


I would really appreciate any ideas on the topic.

Thank you very much in advance.


Kind Regards,

Michail


PS. The whole message I get, is:

File /<path_to_file>/npt-res-00.tpr, 1 coordinates, geometry "distance", dimensions [N N Y], (1 dimensions)
        Pull group coordinates expected in pullx files.
        crd 0) k = 1000   position = 0.00115691
*** buffer overflow detected ***: gmx terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7338f)[0x7f3c1edba38f]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f3c1ee51c9c]
/lib/x86_64-linux-gnu/libc.so.6(+0x109b60)[0x7f3c1ee50b60]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(gmx_ffopen+0xfa)[0x7f3c1fc3bf3a]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(gmx_fio_open+0x3c3)[0x7f3c1fc5ca13]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(gmx_fio_fopen+0xb)[0x7f3c1fc5cdbb]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(read_xvg_legend+0x46)[0x7f3c1fc49ba6]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(_Z12read_pull_xfPKcS0_P16t_UmbrellaHeaderP16t_UmbrellaWindowP17t_UmbrellaOptionsiPfS7_P16t_groupselection+0xbc)[0x7f3c1fe5ffac]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(_Z21read_tpr_pullxf_filesPPcS0_iP16t_UmbrellaHeaderP16t_UmbrellaWindowP17t_UmbrellaOptions+0x131)[0x7f3c1fe616b1]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(gmx_wham+0x1018)[0x7f3c1fe677a8]
/usr/local/gromacs/bin/../lib/x86_64-linux-gnu/libgromacs.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x1fa)[0x7f3c1fb0641a]
gmx(main+0x84)[0x40be24]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f3c1ed68ec5]
gmx[0x40bf5e]
======= Memory map: ========
00400000-0043c000 r-xp 00000000 08:12 22415410                           /usr/local/gromacs/bin/gmx
0063c000-0063d000 r--p 0003c000 08:12 22415410                           /usr/local/gromacs/bin/gmx
0063d000-0063e000 rw-p 0003d000 08:12 22415410                           /usr/local/gromacs/bin/gmx
0063e000-0063f000 rw-p 00000000 00:00 0
00e1e000-00ea5000 rw-p 00000000 00:00 0                                  [heap]
7f3c1c103000-7f3c1c13e000 r-xp 00000000 08:12 19923688                   /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f3c1c13e000-7f3c1c33d000 ---p 0003b000 08:12 19923688                   /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f3c1c33d000-7f3c1c33e000 r--p 0003a000 08:12 19923688                   /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f3c1c33e000-7f3c1c33f000 rw-p 0003b000 08:12 19923688                   /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f3c1c33f000-7f3c1c704000 r-xp 00000000 08:12 22413453                   /usr/lib/atlas-base/atlas/libblas.so.3.0
7f3c1c704000-7f3c1c903000 ---p 003c5000 08:12 22413453                   /usr/lib/atlas-base/atlas/libblas.so.3.0
7f3c1c903000-7f3c1c90b000 rw-p 003c4000 08:12 22413453                   /usr/lib/atlas-base/atlas/libblas.so.3.0
7f3c1c90b000-7f3c1ca22000 r-xp 00000000 08:12 19925662                   /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f3c1ca22000-7f3c1cc22000 ---p 00117000 08:12 19925662                   /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f3c1cc22000-7f3c1cc23000 r--p 00117000 08:12 19925662                   /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f3c1cc23000-7f3c1cc25000 rw-p 00118000 08:12 19925662                   /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f3c1cc25000-7f3c1cfb1000 r-xp 00000000 08:12 22413457                   /usr/lib/atlas-base/libatlas.so.3.0
7f3c1cfb1000-7f3c1d1b0000 ---p 0038c000 08:12 22413457                   /usr/lib/atlas-base/libatlas.so.3.0
7f3c1d1b0000-7f3c1d1b8000 rw-p 0038b000 08:12 22413457                   /usr/lib/atlas-base/libatlas.so.3.0
7f3c1d1b8000-7f3c1d1d9000 r-xp 00000000 08:12 22413446                   /usr/lib/atlas-base/libcblas.so.3.0
7f3c1d1d9000-7f3c1d3d8000 ---p 00021000 08:12 22413446                   /usr/lib/atlas-base/libcblas.so.3.0
7f3c1d3d8000-7f3c1d3d9000 rw-p 00020000 08:12 22413446                   /usr/lib/atlas-base/libcblas.so.3.0
7f3c1d3d9000-7f3c1d3e6000 r-xp 00000000 08:12 19924391                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f3c1d3e6000-7f3c1d5e6000 ---p 0000d000 08:12 19924391                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f3c1d5e6000-7f3c1d5e7000 r--p 0000d000 08:12 19924391                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f3c1d5e7000-7f3c1d5e8000 rw-p 0000e000 08:12 19924391                   /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f3c1d5e8000-7f3c1d601000 r-xp 00000000 08:12 13632388                   /lib/x86_64-linux-gnu/libpthread-2.19.so
7f3c1d601000-7f3c1d800000 ---p 00019000 08:12 13632388                   /lib/x86_64-linux-gnu/libpthread-2.19.so
7f3c1d800000-7f3c1d801000 r--p 00018000 08:12 13632388                   /lib/x86_64-linux-gnu/libpthread-2.19.so
7f3c1d801000-7f3c1d802000 rw-p 00019000 08:12 13632388                   /lib/x86_64-linux-gnu/libpthread-2.19.so
7f3c1d802000-7f3c1d806000 rw-p 00000000 00:00 0
7f3c1d806000-7f3c1dd9e000 r-xp 00000000 08:12 23859586                   /usr/lib/lapack/liblapack.so.3.0
7f3c1dd9e000-7f3c1df9d000 ---p 00598000 08:12 23859586                   /usr/lib/lapack/liblapack.so.3.0
7f3c1df9d000-7f3c1df9e000 r--p 00597000 08:12 23859586                   /usr/lib/lapack/liblapack.so.3.0
7f3c1df9e000-7f3c1dfa2000 rw-p 00598000 08:12 23859586                   /usr/lib/lapack/liblapack.so.3.0
7f3c1dfa2000-7f3c1dfc1000 r-xp 00000000 08:12 22413455                   /usr/lib/atlas-base/libf77blas.so.3.0
7f3c1dfc1000-7f3c1e1c1000 ---p 0001f000 08:12 22413455                   /usr/lib/atlas-base/libf77blas.so.3.0
7f3c1e1c1000-7f3c1e1c2000 rw-p 0001f000 08:12 22413455                   /usr/lib/atlas-base/libf77blas.so.3.0
7f3c1e1c2000-7f3c1e1da000 r-xp 00000000 08:12 13635584                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7f3c1e1da000-7f3c1e3d9000 ---p 00018000 08:12 13635584                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7f3c1e3d9000-7f3c1e3da000 r--p 00017000 08:12 13635584                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7f3c1e3da000-7f3c1e3db000 rw-p 00018000 08:12 13635584                   /lib/x86_64-linux-gnu/libz.so.1.2.8
7f3c1e3db000-7f3c1e3e2000 r-xp 00000000 08:12 13633246                   /lib/x86_64-linux-gnu/librt-2.19.so
7f3c1e3e2000-7f3c1e5e1000 ---p 00007000 08:12 13633246                   /lib/x86_64-linux-gnu/librt-2.19.so
7f3c1e5e1000-7f3c1e5e2000 r--p 00006000 08:12 13633246                   /lib/x86_64-linux-gnu/librt-2.19.so
7f3c1e5e2000-7f3c1e5e3000 rw-p 00007000 08:12 13633246                   /lib/x86_64-linux-gnu/librt-2.19.so
7f3c1e5e3000-7f3c1e5e6000 r-xp 00000000 08:12 13631780                   /lib/x86_64-linux-gnu/libdl-2.19.so
7f3c1e5e6000-7f3c1e7e5000 ---p 00003000 08:12 13631780                   /lib/x86_64-linux-gnu/libdl-2.19.so
7f3c1e7e5000-7f3c1e7e6000 r--p 00002000 08:12 13631780                   /lib/x86_64-linux-gnu/libdl-2.19.so
7f3c1e7e6000-7f3c1e7e7000 rw-p 00003000 08:12 13631780                   /lib/x86_64-linux-gnu/libdl-2.19.so
7f3c1e7e7000-7f3c1e8c6000 r-xp 00000000 08:12 22413502                   /usr/lib/nvidia-352/libnvidia-ml.so.352.79
7f3c1e8c6000-7f3c1eac6000 ---p 000df000 08:12 22413502                   /usr/lib/nvidia-352/libnvidia-ml.so.352.79
7f3c1eac6000-7f3c1ead4000 rw-p 000df000 08:12 22413502                   /usr/lib/nvidia-352/libnvidia-ml.so.352.79
7f3c1ead4000-7f3c1eae9000 rw-p 00000000 00:00 0
7f3c1eae9000-7f3c1eb44000 r-xp 00000000 08:12 24641585                   /usr/local/cuda-7.5/targets/x86_64-linux/lib/libcudart.so.7.5.18
7f3c1eb44000-7f3c1ed43000 ---p 0005b000 08:12 24641585                   /usr/local/cuda-7.5/targets/x86_64-linux/lib/libcudart.so.7.5.18
7f3c1ed43000-7f3c1ed47000 rw-p 0005a000 08:12 24641585                   /usr/local/cuda-7.5/targets/x86_64-linux/lib/libcudart.so.7.5.18
7f3c1ed47000-7f3c1ef02000 r-xp 00000000 08:12 13633247                   /lib/x86_64-linux-gnu/libc-2.19.so
7f3c1ef02000-7f3c1f101000 ---p 001bb000 08:12 13633247                   /lib/x86_64-linux-gnu/libc-2.19.so
7f3c1f101000-7f3c1f105000 r--p 001ba000 08:12 13633247                   /lib/x86_64-linux-gnu/libc-2.19.so
7f3c1f105000-7f3c1f107000 rw-p 001be000 08:12 13633247                   /lib/x86_64-linux-gnu/libc-2.19.so
7f3c1f107000-7f3c1f10c000 rw-p 00000000 00:00 0
7f3c1f10c000-7f3c1f122000 r-xp 00000000 08:12 13631653                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f3c1f122000-7f3c1f321000 ---p 00016000 08:12 13631653                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f3c1f321000-7f3c1f322000 rw-p 00015000 08:12 13631653                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f3c1f322000-7f3c1f427000 r-xp 00000000 08:12 13631686                   /lib/x86_64-linux-gnu/libm-2.19.so
7f3c1f427000-7f3c1f626000 ---p 00105000 08:12 13631686                   /lib/x86_64-linux-gnu/libm-2.19.so
7f3c1f626000-7f3c1f627000 r--p 00104000 08:12 13631686                   /lib/x86_64-linux-gnu/libm-2.19.so
7f3c1f627000-7f3c1f628000 rw-p 00105000 08:12 13631686                   /lib/x86_64-linux-gnu/libm-2.19.so
7f3c1f628000-7f3c1f70e000 r-xp 00000000 08:12 19927435                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f3c1f70e000-7f3c1f90d000 ---p 000e6000 08:12 19927435                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f3c1f90d000-7f3c1f915000 r--p 000e5000 08:12 19927435                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f3c1f915000-7f3c1f917000 rw-p 000ed000 08:12 19927435                   /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19
7f3c1f917000-7f3c1f92c000 rw-p 00000000 00:00 0
7f3c1f92c000-7f3c2191e000 r-xp 00000000 08:12 22415395                   /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so.1.1.0
7f3c2191e000-7f3c21b1d000 ---p 01ff2000 08:12 22415395                   /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so.1.1.0
7f3c21b1d000-7f3c21b3e000 r--p 01ff1000 08:12 22415395                   /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so.1.1.0
7f3c21b3e000-7f3c21b62000 rw-p 02012000 08:12 22415395                   /usr/local/gromacs/lib/x86_64-linux-gnu/libgromacs.so.1.1.0
7f3c21b62000-7f3c21b6f000 rw-p 00000000 00:00 0
7f3c21b6f000-7f3c21b92000 r-xp 00000000 08:12 13633239                   /lib/x86_64-linux-gnu/ld-2.19.so
7f3c21cab000-7f3c21d67000 rw-p 00000000 00:00 0
7f3c21d8b000-7f3c21d91000 rw-p 00000000 00:00 0
7f3c21d91000-7f3c21d92000 r--p 00022000 08:12 13633239                   /lib/x86_64-linux-gnu/ld-2.19.so
7f3c21d92000-7f3c21d93000 rw-p 00023000 08:12 13633239                   /lib/x86_64-linux-gnu/ld-2.19.so
7f3c21d93000-7f3c21d94000 rw-p 00000000 00:00 0
7fff29375000-7fff29397000 rw-p 00000000 00:00 0                          [stack]
7fff293cf000-7fff293d1000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)



-------------------------------------------------------------------
Michail (Michalis) Palaiokostas
PhD Student
School of Engineering and Materials Science
Queen Mary University of London
-------------------------------------------------------------------


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