[gmx-users] gmx sans crashes or return nan's
Jakub Krajniak
jakub.krajniak at cs.kuleuven.be
Thu Sep 22 10:47:03 CEST 2016
Hi,
I've tried to run gmx sans tool on our trajectory but unfortunately it
crashes or returns -nan.
The crash is when it is compiled in Release mode. I have used the latest
2016 release.
GROMACS: gmx sans, version 2016
gmx_mpi sans -f traj_comp.xtc -s topol.tpr -dt 10 -nt 10
Select a group: 0
Selected 0: 'System'
Reading frame 0 time 0.000 Segmentation fault (core dumped)
With CMAKE_BUILD_TYPE=Debug, the run does not cause the segmentation
fault error but the sq.xvg and pr.xvg contain -nan ; This
is independent of selected groups.
Maybe someone know what could be the reason of such behavior? Here are
the .tpr and .xtc files:
https://www.dropbox.com/s/29ftayq9uhfipjz/sans_50_50.zip?dl=0
Best regards,
Jakub
--
Jakub Krajniak
KU Leuven, Dept. Computer Science lokaal: 01.41
+32 477 68 84 04 / +32 16 37 39 92
-------------- next part --------------
# This file was created Thu Sep 22 09:28:16 2016
# Created by:
# :-) GROMACS - gmx sans, 2016 (-:
#
# Executable: /user/leuven/307/vsc30783/vsc_data/software/2015a/GROMACS/2016/bin/gmx_mpi
# Data prefix: /user/leuven/307/vsc30783/vsc_data/software/2015a/GROMACS/2016
# Working dir: /ddn1/vol1/site_scratch/leuven/307/vsc30783/sans_50_50
# Command line:
# gmx_mpi sans -f traj_comp.xtc -s topol.tpr -dt 10 -nt 10 -sq /user/leuven/307/vsc30783/sq.xvg -pr /user/leuven/307/vsc30783/pr.xvg
# gmx sans is part of G R O M A C S:
#
# Green Red Orange Magenta Azure Cyan Skyblue
#
@ title "G(r)"
@ xaxis label "Distance (nm)"
@ yaxis label "Probability"
@TYPE xy
0.100000 -nan
0.300000 -nan
0.500000 -nan
0.700000 -nan
0.900000 -nan
1.100000 -nan
1.300000 -nan
1.500000 -nan
1.700000 -nan
1.900000 -nan
2.100000 -nan
2.300000 -nan
2.500000 -nan
2.700000 -nan
2.900000 -nan
3.100000 -nan
3.300000 -nan
3.500000 -nan
3.700000 -nan
3.900000 -nan
4.100000 -nan
4.300000 -nan
4.500000 -nan
4.700000 -nan
4.900000 -nan
5.100000 -nan
5.300000 -nan
5.500000 -nan
5.700000 -nan
5.900000 -nan
6.100000 -nan
6.300000 -nan
6.500000 -nan
6.700000 -nan
6.900000 -nan
7.100000 -nan
7.300000 -nan
7.500000 -nan
7.700000 -nan
7.900000 -nan
8.100000 -nan
8.300000 -nan
8.500000 -nan
8.700000 -nan
8.900000 -nan
9.100000 -nan
9.300000 -nan
9.500000 -nan
9.700000 -nan
9.900000 -nan
10.100000 -nan
10.300000 -nan
10.500000 -nan
10.700000 -nan
10.900000 -nan
11.100000 -nan
11.300000 -nan
11.500000 -nan
11.700000 -nan
11.900000 -nan
12.100000 -nan
12.300000 -nan
12.500000 -nan
12.700000 -nan
12.900000 -nan
13.100000 -nan
13.300000 -nan
13.500000 -nan
13.700000 -nan
13.900000 -nan
14.100000 -nan
14.300000 -nan
14.500000 -nan
14.700000 -nan
14.900000 -nan
15.100000 -nan
15.300000 -nan
15.500000 -nan
15.700000 -nan
15.900000 -nan
16.100000 -nan
16.300000 -nan
16.500000 -nan
16.700000 -nan
16.900000 -nan
17.100000 -nan
17.300000 -nan
17.500000 -nan
17.700000 -nan
17.900000 -nan
18.100000 -nan
18.300000 -nan
18.500000 -nan
18.700000 -nan
18.900000 -nan
19.100000 -nan
19.300000 -nan
19.500000 -nan
19.700000 -nan
19.900000 -nan
-------------- next part --------------
# This file was created Thu Sep 22 09:28:16 2016
# Created by:
# :-) GROMACS - gmx sans, 2016 (-:
#
# Executable: /user/leuven/307/vsc30783/vsc_data/software/2015a/GROMACS/2016/bin/gmx_mpi
# Data prefix: /user/leuven/307/vsc30783/vsc_data/software/2015a/GROMACS/2016
# Working dir: /ddn1/vol1/site_scratch/leuven/307/vsc30783/sans_50_50
# Command line:
# gmx_mpi sans -f traj_comp.xtc -s topol.tpr -dt 10 -nt 10 -sq /user/leuven/307/vsc30783/sq.xvg -pr /user/leuven/307/vsc30783/pr.xvg
# gmx sans is part of G R O M A C S:
#
# God Rules Over Mankind, Animals, Cosmos and Such
#
@ title "I(q)"
@ xaxis label "q (nm^-1)"
@ yaxis label "s(q)/s(0)"
@TYPE xy
0.000000 1.000000
0.010000 -nan
0.020000 -nan
0.030000 -nan
0.040000 -nan
0.050000 -nan
0.060000 -nan
0.070000 -nan
0.080000 -nan
0.090000 -nan
0.100000 -nan
0.110000 -nan
0.120000 -nan
0.130000 -nan
0.140000 -nan
0.150000 -nan
0.160000 -nan
0.170000 -nan
0.180000 -nan
0.190000 -nan
0.200000 -nan
0.210000 -nan
0.220000 -nan
0.230000 -nan
0.240000 -nan
0.250000 -nan
0.260000 -nan
0.270000 -nan
0.280000 -nan
0.290000 -nan
0.300000 -nan
0.310000 -nan
0.320000 -nan
0.330000 -nan
0.340000 -nan
0.350000 -nan
0.360000 -nan
0.370000 -nan
0.380000 -nan
0.390000 -nan
0.400000 -nan
0.410000 -nan
0.420000 -nan
0.430000 -nan
0.440000 -nan
0.450000 -nan
0.460000 -nan
0.470000 -nan
0.480000 -nan
0.490000 -nan
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0.510000 -nan
0.520000 -nan
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0.660000 -nan
0.670000 -nan
0.680000 -nan
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0.710000 -nan
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0.760000 -nan
0.770000 -nan
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0.870000 -nan
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0.920000 -nan
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0.950000 -nan
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0.970000 -nan
0.980000 -nan
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1.000000 -nan
1.010000 -nan
1.020000 -nan
1.030000 -nan
1.040000 -nan
1.050000 -nan
1.060000 -nan
1.070000 -nan
1.080000 -nan
1.090000 -nan
1.100000 -nan
1.110000 -nan
1.120000 -nan
1.130000 -nan
1.140000 -nan
1.150000 -nan
1.160000 -nan
1.170000 -nan
1.180000 -nan
1.190000 -nan
1.200000 -nan
1.210000 -nan
1.220000 -nan
1.230000 -nan
1.240000 -nan
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1.290000 -nan
1.300000 -nan
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1.330000 -nan
1.340000 -nan
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1.360000 -nan
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1.430000 -nan
1.440000 -nan
1.450000 -nan
1.460000 -nan
1.470000 -nan
1.480000 -nan
1.490000 -nan
1.500000 -nan
1.510000 -nan
1.520000 -nan
1.530000 -nan
1.540000 -nan
1.550000 -nan
1.560000 -nan
1.570000 -nan
1.580000 -nan
1.590000 -nan
1.600000 -nan
1.610000 -nan
1.620000 -nan
1.630000 -nan
1.640000 -nan
1.650000 -nan
1.660000 -nan
1.670000 -nan
1.680000 -nan
1.690000 -nan
1.700000 -nan
1.710000 -nan
1.720000 -nan
1.730000 -nan
1.740000 -nan
1.750000 -nan
1.760000 -nan
1.770000 -nan
1.780000 -nan
1.790000 -nan
1.800000 -nan
1.810000 -nan
1.820000 -nan
1.830000 -nan
1.840000 -nan
1.850000 -nan
1.860000 -nan
1.870000 -nan
1.880000 -nan
1.890000 -nan
1.900000 -nan
1.910000 -nan
1.920000 -nan
1.930000 -nan
1.940000 -nan
1.950000 -nan
1.960000 -nan
1.970000 -nan
1.980000 -nan
1.990000 -nan
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