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

# 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
# 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
  0.500000      -nan
  0.510000      -nan
  0.520000      -nan
  0.530000      -nan
  0.540000      -nan
  0.550000      -nan
  0.560000      -nan
  0.570000      -nan
  0.580000      -nan
  0.590000      -nan
  0.600000      -nan
  0.610000      -nan
  0.620000      -nan
  0.630000      -nan
  0.640000      -nan
  0.650000      -nan
  0.660000      -nan
  0.670000      -nan
  0.680000      -nan
  0.690000      -nan
  0.700000      -nan
  0.710000      -nan
  0.720000      -nan
  0.730000      -nan
  0.740000      -nan
  0.750000      -nan
  0.760000      -nan
  0.770000      -nan
  0.780000      -nan
  0.790000      -nan
  0.800000      -nan
  0.810000      -nan
  0.820000      -nan
  0.830000      -nan
  0.840000      -nan
  0.850000      -nan
  0.860000      -nan
  0.870000      -nan
  0.880000      -nan
  0.890000      -nan
  0.900000      -nan
  0.910000      -nan
  0.920000      -nan
  0.930000      -nan
  0.940000      -nan
  0.950000      -nan
  0.960000      -nan
  0.970000      -nan
  0.980000      -nan
  0.990000      -nan
  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
  1.250000      -nan
  1.260000      -nan
  1.270000      -nan
  1.280000      -nan
  1.290000      -nan
  1.300000      -nan
  1.310000      -nan
  1.320000      -nan
  1.330000      -nan
  1.340000      -nan
  1.350000      -nan
  1.360000      -nan
  1.370000      -nan
  1.380000      -nan
  1.390000      -nan
  1.400000      -nan
  1.410000      -nan
  1.420000      -nan
  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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