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valgrind-gmx-trjconv-no-tpr.log

Viveca Lindahl, 02/28/2018 02:26 PM

 
1
==30976== Memcheck, a memory error detector
2
==30976== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
3
==30976== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright info
4
==30976== Command: /home/viveca/programs/gromacs/2018/bin/gmx_debug trjconv -f traj_comp.xtc
5
==30976== 
6
           :-) GROMACS - gmx trjconv, 2018.1-dev-20180227-8223d56 (-:
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8
                            GROMACS is written by:
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     Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par Bjelkmar   
10
 Aldert van Buuren   Rudi van Drunen     Anton Feenstra    Gerrit Groenhof  
11
 Christoph Junghans   Anca Hamuraru    Vincent Hindriksen Dimitrios Karkoulis
12
    Peter Kasson        Jiri Kraus      Carsten Kutzner      Per Larsson    
13
  Justin A. Lemkul    Viveca Lindahl    Magnus Lundborg   Pieter Meulenhoff 
14
   Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk   
15
   Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers  
16
   Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf   
17
                           and the project leaders:
18
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
19

    
20
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
21
Copyright (c) 2001-2017, The GROMACS development team at
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Uppsala University, Stockholm University and
23
the Royal Institute of Technology, Sweden.
24
check out http://www.gromacs.org for more information.
25

    
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GROMACS is free software; you can redistribute it and/or modify it
27
under the terms of the GNU Lesser General Public License
28
as published by the Free Software Foundation; either version 2.1
29
of the License, or (at your option) any later version.
30

    
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GROMACS:      gmx trjconv, version 2018.1-dev-20180227-8223d56
32
Executable:   /home/viveca/programs/gromacs/2018/bin/gmx_debug
33
Data prefix:  /home/viveca/programs/gromacs/2018
34
Working dir:  /data/viveca/awh-use-case/build/test-dihedral-convergence/GCGCGTGCGCG/equil/analysis/wrap-debug/polymer
35
Command line:
36
  gmx_debug trjconv -f traj_comp.xtc
37

    
38
Will write xtc: Compressed trajectory (portable xdr format): xtc
39
Reading frame       0 time    0.000   
Reading frame       0 time    0.000   
40
Precision of traj_comp.xtc is 0.0001 (nm)
41
Using output precision of 0.001 (nm)
42

    
43
Back Off! I just backed up trajout.xtc to ./#trajout.xtc.2#
44
 ->  frame      0 time    0.000      

Reading frame       1 time    0.001    ->  frame      1 time    0.001      

Last frame          1 time    0.001   
45

    
46
==30976== Conditional jump or move depends on uninitialised value(s)
47
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
48
==30976==    by 0x4C71CA: void gmx_sfree_impl<int>(char const*, char const*, int, int*) (smalloc.h:273)
49
==30976==    by 0x4C5375: done_top(t_topology*) (topology.cpp:176)
50
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
51
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
52
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
53
==30976==    by 0x409C22: main (gmx.cpp:60)
54
==30976== 
55
==30976== Conditional jump or move depends on uninitialised value(s)
56
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
57
==30976==    by 0x4C728A: void gmx_sfree_impl<t_iparams>(char const*, char const*, int, t_iparams*) (smalloc.h:273)
58
==30976==    by 0x4C5394: done_top(t_topology*) (topology.cpp:177)
59
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
60
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
61
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
62
==30976==    by 0x409C22: main (gmx.cpp:60)
63
==30976== 
64
==30976== Conditional jump or move depends on uninitialised value(s)
65
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
66
==30976==    by 0x4C71CA: void gmx_sfree_impl<int>(char const*, char const*, int, int*) (smalloc.h:273)
67
==30976==    by 0x4C53D8: done_top(t_topology*) (topology.cpp:180)
68
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
69
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
70
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
71
==30976==    by 0x409C22: main (gmx.cpp:60)
72
==30976== 
73
==30976== Conditional jump or move depends on uninitialised value(s)
74
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
75
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
76
==30976==    by 0x4C71CA: void gmx_sfree_impl<int>(char const*, char const*, int, int*) (smalloc.h:273)
77
==30976==    by 0x4C53D8: done_top(t_topology*) (topology.cpp:180)
78
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
79
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
80
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
81
==30976==    by 0x409C22: main (gmx.cpp:60)
82
==30976== 
83
==30976== Invalid free() / delete / delete[] / realloc()
84
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
85
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
86
==30976==    by 0x4C71CA: void gmx_sfree_impl<int>(char const*, char const*, int, int*) (smalloc.h:273)
87
==30976==    by 0x4C53D8: done_top(t_topology*) (topology.cpp:180)
88
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
89
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
90
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
91
==30976==    by 0x409C22: main (gmx.cpp:60)
92
==30976==  Address 0x1d1ba04 is not stack'd, malloc'd or (recently) free'd
93
==30976== 
94
==30976== Conditional jump or move depends on uninitialised value(s)
95
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
96
==30976==    by 0x92C147: void gmx_sfree_impl<t_atom>(char const*, char const*, int, t_atom*) (smalloc.h:273)
97
==30976==    by 0x92AA39: done_atom(t_atoms*) (atoms.cpp:86)
98
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
99
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
100
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
101
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
102
==30976==    by 0x409C22: main (gmx.cpp:60)
103
==30976== 
104
==30976== Conditional jump or move depends on uninitialised value(s)
105
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
106
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
107
==30976==    by 0x92C147: void gmx_sfree_impl<t_atom>(char const*, char const*, int, t_atom*) (smalloc.h:273)
108
==30976==    by 0x92AA39: done_atom(t_atoms*) (atoms.cpp:86)
109
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
110
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
111
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
112
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
113
==30976==    by 0x409C22: main (gmx.cpp:60)
114
==30976== 
115
==30976== Invalid free() / delete / delete[] / realloc()
116
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
117
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
118
==30976==    by 0x92C147: void gmx_sfree_impl<t_atom>(char const*, char const*, int, t_atom*) (smalloc.h:273)
119
==30976==    by 0x92AA39: done_atom(t_atoms*) (atoms.cpp:86)
120
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
121
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
122
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
123
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
124
==30976==    by 0x409C22: main (gmx.cpp:60)
125
==30976==  Address 0x404c3f is not stack'd, malloc'd or (recently) free'd
126
==30976== 
127
==30976== Conditional jump or move depends on uninitialised value(s)
128
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
129
==30976==    by 0x92C177: void gmx_sfree_impl<t_resinfo>(char const*, char const*, int, t_resinfo*) (smalloc.h:273)
130
==30976==    by 0x92AA58: done_atom(t_atoms*) (atoms.cpp:87)
131
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
132
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
133
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
134
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
135
==30976==    by 0x409C22: main (gmx.cpp:60)
136
==30976== 
137
==30976== Conditional jump or move depends on uninitialised value(s)
138
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
139
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
140
==30976==    by 0x92C177: void gmx_sfree_impl<t_resinfo>(char const*, char const*, int, t_resinfo*) (smalloc.h:273)
141
==30976==    by 0x92AA58: done_atom(t_atoms*) (atoms.cpp:87)
142
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
143
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
144
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
145
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
146
==30976==    by 0x409C22: main (gmx.cpp:60)
147
==30976== 
148
==30976== Invalid free() / delete / delete[] / realloc()
149
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
150
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
151
==30976==    by 0x92C177: void gmx_sfree_impl<t_resinfo>(char const*, char const*, int, t_resinfo*) (smalloc.h:273)
152
==30976==    by 0x92AA58: done_atom(t_atoms*) (atoms.cpp:87)
153
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
154
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
155
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
156
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
157
==30976==    by 0x409C22: main (gmx.cpp:60)
158
==30976==  Address 0x467 is not stack'd, malloc'd or (recently) free'd
159
==30976== 
160
==30976== Conditional jump or move depends on uninitialised value(s)
161
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
162
==30976==    by 0x92C1A7: void gmx_sfree_impl<char**>(char const*, char const*, int, char***) (smalloc.h:273)
163
==30976==    by 0x92AA77: done_atom(t_atoms*) (atoms.cpp:88)
164
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
165
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
166
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
167
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
168
==30976==    by 0x409C22: main (gmx.cpp:60)
169
==30976== 
170
==30976== Conditional jump or move depends on uninitialised value(s)
171
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
172
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
173
==30976==    by 0x92C1A7: void gmx_sfree_impl<char**>(char const*, char const*, int, char***) (smalloc.h:273)
174
==30976==    by 0x92AA77: done_atom(t_atoms*) (atoms.cpp:88)
175
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
176
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
177
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
178
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
179
==30976==    by 0x409C22: main (gmx.cpp:60)
180
==30976== 
181
==30976== Invalid free() / delete / delete[] / realloc()
182
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
183
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
184
==30976==    by 0x92C1A7: void gmx_sfree_impl<char**>(char const*, char const*, int, char***) (smalloc.h:273)
185
==30976==    by 0x92AA77: done_atom(t_atoms*) (atoms.cpp:88)
186
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
187
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
188
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
189
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
190
==30976==    by 0x409C22: main (gmx.cpp:60)
191
==30976==  Address 0x6c9ddc8 is not stack'd, malloc'd or (recently) free'd
192
==30976== 
193
==30976== Conditional jump or move depends on uninitialised value(s)
194
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
195
==30976==    by 0x92C1A7: void gmx_sfree_impl<char**>(char const*, char const*, int, char***) (smalloc.h:273)
196
==30976==    by 0x92AA96: done_atom(t_atoms*) (atoms.cpp:89)
197
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
198
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
199
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
200
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
201
==30976==    by 0x409C22: main (gmx.cpp:60)
202
==30976== 
203
==30976== Conditional jump or move depends on uninitialised value(s)
204
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
205
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
206
==30976==    by 0x92C1A7: void gmx_sfree_impl<char**>(char const*, char const*, int, char***) (smalloc.h:273)
207
==30976==    by 0x92AA96: done_atom(t_atoms*) (atoms.cpp:89)
208
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
209
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
210
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
211
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
212
==30976==    by 0x409C22: main (gmx.cpp:60)
213
==30976== 
214
==30976== Invalid free() / delete / delete[] / realloc()
215
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
216
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
217
==30976==    by 0x92C1A7: void gmx_sfree_impl<char**>(char const*, char const*, int, char***) (smalloc.h:273)
218
==30976==    by 0x92AA96: done_atom(t_atoms*) (atoms.cpp:89)
219
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
220
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
221
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
222
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
223
==30976==    by 0x409C22: main (gmx.cpp:60)
224
==30976==  Address 0x400c90 is not stack'd, malloc'd or (recently) free'd
225
==30976== 
226
==30976== Conditional jump or move depends on uninitialised value(s)
227
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
228
==30976==    by 0x92C1A7: void gmx_sfree_impl<char**>(char const*, char const*, int, char***) (smalloc.h:273)
229
==30976==    by 0x92AAB5: done_atom(t_atoms*) (atoms.cpp:90)
230
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
231
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
232
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
233
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
234
==30976==    by 0x409C22: main (gmx.cpp:60)
235
==30976== 
236
==30976== Conditional jump or move depends on uninitialised value(s)
237
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
238
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
239
==30976==    by 0x92C1A7: void gmx_sfree_impl<char**>(char const*, char const*, int, char***) (smalloc.h:273)
240
==30976==    by 0x92AAB5: done_atom(t_atoms*) (atoms.cpp:90)
241
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
242
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
243
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
244
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
245
==30976==    by 0x409C22: main (gmx.cpp:60)
246
==30976== 
247
==30976== Invalid free() / delete / delete[] / realloc()
248
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
249
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
250
==30976==    by 0x92C1A7: void gmx_sfree_impl<char**>(char const*, char const*, int, char***) (smalloc.h:273)
251
==30976==    by 0x92AAB5: done_atom(t_atoms*) (atoms.cpp:90)
252
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
253
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
254
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
255
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
256
==30976==    by 0x409C22: main (gmx.cpp:60)
257
==30976==  Address 0x100000000 is not stack'd, malloc'd or (recently) free'd
258
==30976== 
259
==30976== Conditional jump or move depends on uninitialised value(s)
260
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
261
==30976==    by 0x92C1D7: void gmx_sfree_impl<t_pdbinfo>(char const*, char const*, int, t_pdbinfo*) (smalloc.h:273)
262
==30976==    by 0x92AAD4: done_atom(t_atoms*) (atoms.cpp:91)
263
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
264
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
265
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
266
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
267
==30976==    by 0x409C22: main (gmx.cpp:60)
268
==30976== 
269
==30976== Conditional jump or move depends on uninitialised value(s)
270
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
271
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
272
==30976==    by 0x92C1D7: void gmx_sfree_impl<t_pdbinfo>(char const*, char const*, int, t_pdbinfo*) (smalloc.h:273)
273
==30976==    by 0x92AAD4: done_atom(t_atoms*) (atoms.cpp:91)
274
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
275
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
276
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
277
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
278
==30976==    by 0x409C22: main (gmx.cpp:60)
279
==30976== 
280
==30976== Invalid free() / delete / delete[] / realloc()
281
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
282
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
283
==30976==    by 0x92C1D7: void gmx_sfree_impl<t_pdbinfo>(char const*, char const*, int, t_pdbinfo*) (smalloc.h:273)
284
==30976==    by 0x92AAD4: done_atom(t_atoms*) (atoms.cpp:91)
285
==30976==    by 0x4C5442: done_top(t_topology*) (topology.cpp:185)
286
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
287
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
288
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
289
==30976==    by 0x409C22: main (gmx.cpp:60)
290
==30976==  Address 0xffeffe738 is on thread 1's stack
291
==30976==  in frame #5, created by gmx_trjconv (gmx_trjconv.cpp:592)
292
==30976== 
293
==30976== Conditional jump or move depends on uninitialised value(s)
294
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
295
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
296
==30976==    by 0x92AB17: done_atomtypes(t_atomtypes*) (atoms.cpp:98)
297
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
298
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
299
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
300
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
301
==30976==    by 0x409C22: main (gmx.cpp:60)
302
==30976== 
303
==30976== Conditional jump or move depends on uninitialised value(s)
304
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
305
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
306
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
307
==30976==    by 0x92AB17: done_atomtypes(t_atomtypes*) (atoms.cpp:98)
308
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
309
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
310
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
311
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
312
==30976==    by 0x409C22: main (gmx.cpp:60)
313
==30976== 
314
==30976== Invalid free() / delete / delete[] / realloc()
315
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
316
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
317
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
318
==30976==    by 0x92AB17: done_atomtypes(t_atomtypes*) (atoms.cpp:98)
319
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
320
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
321
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
322
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
323
==30976==    by 0x409C22: main (gmx.cpp:60)
324
==30976==  Address 0x42241c8 is not stack'd, malloc'd or (recently) free'd
325
==30976== 
326
==30976== Conditional jump or move depends on uninitialised value(s)
327
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
328
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
329
==30976==    by 0x92AB36: done_atomtypes(t_atomtypes*) (atoms.cpp:99)
330
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
331
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
332
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
333
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
334
==30976==    by 0x409C22: main (gmx.cpp:60)
335
==30976== 
336
==30976== Conditional jump or move depends on uninitialised value(s)
337
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
338
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
339
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
340
==30976==    by 0x92AB36: done_atomtypes(t_atomtypes*) (atoms.cpp:99)
341
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
342
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
343
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
344
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
345
==30976==    by 0x409C22: main (gmx.cpp:60)
346
==30976== 
347
==30976== Invalid free() / delete / delete[] / realloc()
348
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
349
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
350
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
351
==30976==    by 0x92AB36: done_atomtypes(t_atomtypes*) (atoms.cpp:99)
352
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
353
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
354
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
355
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
356
==30976==    by 0x409C22: main (gmx.cpp:60)
357
==30976==  Address 0x400aa31 is in the Text segment of /lib/x86_64-linux-gnu/ld-2.19.so
358
==30976==    at 0x400AA31: _dl_lookup_symbol_x (dl-lookup.c:740)
359
==30976== 
360
==30976== Conditional jump or move depends on uninitialised value(s)
361
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
362
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
363
==30976==    by 0x92AB55: done_atomtypes(t_atomtypes*) (atoms.cpp:100)
364
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
365
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
366
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
367
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
368
==30976==    by 0x409C22: main (gmx.cpp:60)
369
==30976== 
370
==30976== Conditional jump or move depends on uninitialised value(s)
371
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
372
==30976==    by 0x92C237: void gmx_sfree_impl<int>(char const*, char const*, int, int*) (smalloc.h:273)
373
==30976==    by 0x92AB74: done_atomtypes(t_atomtypes*) (atoms.cpp:101)
374
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
375
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
376
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
377
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
378
==30976==    by 0x409C22: main (gmx.cpp:60)
379
==30976== 
380
==30976== Conditional jump or move depends on uninitialised value(s)
381
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
382
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
383
==30976==    by 0x92AB93: done_atomtypes(t_atomtypes*) (atoms.cpp:102)
384
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
385
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
386
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
387
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
388
==30976==    by 0x409C22: main (gmx.cpp:60)
389
==30976== 
390
==30976== Conditional jump or move depends on uninitialised value(s)
391
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
392
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
393
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
394
==30976==    by 0x92AB93: done_atomtypes(t_atomtypes*) (atoms.cpp:102)
395
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
396
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
397
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
398
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
399
==30976==    by 0x409C22: main (gmx.cpp:60)
400
==30976== 
401
==30976== Invalid free() / delete / delete[] / realloc()
402
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
403
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
404
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
405
==30976==    by 0x92AB93: done_atomtypes(t_atomtypes*) (atoms.cpp:102)
406
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
407
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
408
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
409
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
410
==30976==    by 0x409C22: main (gmx.cpp:60)
411
==30976==  Address 0x404bab8 is not stack'd, malloc'd or (recently) free'd
412
==30976== 
413
==30976== Conditional jump or move depends on uninitialised value(s)
414
==30976==    at 0x4E3644: save_free (smalloc.cpp:243)
415
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
416
==30976==    by 0x92ABB2: done_atomtypes(t_atomtypes*) (atoms.cpp:103)
417
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
418
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
419
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
420
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
421
==30976==    by 0x409C22: main (gmx.cpp:60)
422
==30976== 
423
==30976== Conditional jump or move depends on uninitialised value(s)
424
==30976==    at 0x4C2BDA2: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
425
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
426
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
427
==30976==    by 0x92ABB2: done_atomtypes(t_atomtypes*) (atoms.cpp:103)
428
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
429
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
430
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
431
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
432
==30976==    by 0x409C22: main (gmx.cpp:60)
433
==30976== 
434
==30976== Invalid free() / delete / delete[] / realloc()
435
==30976==    at 0x4C2BDEC: free (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
436
==30976==    by 0x4E3651: save_free (smalloc.cpp:245)
437
==30976==    by 0x92C207: void gmx_sfree_impl<float>(char const*, char const*, int, float*) (smalloc.h:273)
438
==30976==    by 0x92ABB2: done_atomtypes(t_atomtypes*) (atoms.cpp:103)
439
==30976==    by 0x4C5454: done_top(t_topology*) (topology.cpp:188)
440
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
441
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
442
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
443
==30976==    by 0x409C22: main (gmx.cpp:60)
444
==30976==  Address 0x1 is not stack'd, malloc'd or (recently) free'd
445
==30976== 
446
==30976== Conditional jump or move depends on uninitialised value(s)
447
==30976==    at 0x931219: done_symtab (symtab.cpp:224)
448
==30976==    by 0x4C5466: done_top(t_topology*) (topology.cpp:190)
449
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
450
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
451
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
452
==30976==    by 0x409C22: main (gmx.cpp:60)
453
==30976== 
454
==30976== Use of uninitialised value of size 8
455
==30976==    at 0x9311A3: done_symtab (symtab.cpp:226)
456
==30976==    by 0x4C5466: done_top(t_topology*) (topology.cpp:190)
457
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
458
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
459
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
460
==30976==    by 0x409C22: main (gmx.cpp:60)
461
==30976== 
462
==30976== Invalid read of size 4
463
==30976==    at 0x9311A3: done_symtab (symtab.cpp:226)
464
==30976==    by 0x4C5466: done_top(t_topology*) (topology.cpp:190)
465
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
466
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
467
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
468
==30976==    by 0x409C22: main (gmx.cpp:60)
469
==30976==  Address 0x1d8 is not stack'd, malloc'd or (recently) free'd
470
==30976== 
471
==30976== 
472
==30976== Process terminating with default action of signal 11 (SIGSEGV)
473
==30976==  Access not within mapped region at address 0x1D8
474
==30976==    at 0x9311A3: done_symtab (symtab.cpp:226)
475
==30976==    by 0x4C5466: done_top(t_topology*) (topology.cpp:190)
476
==30976==    by 0x675842: gmx_trjconv (gmx_trjconv.cpp:1981)
477
==30976==    by 0x436FB2: gmx::(anonymous namespace)::CMainCommandLineModule::run(int, char**) (cmdlinemodulemanager.cpp:133)
478
==30976==    by 0x43896A: gmx::CommandLineModuleManager::run(int, char**) (cmdlinemodulemanager.cpp:589)
479
==30976==    by 0x409C22: main (gmx.cpp:60)
480
==30976==  If you believe this happened as a result of a stack
481
==30976==  overflow in your program's main thread (unlikely but
482
==30976==  possible), you can try to increase the size of the
483
==30976==  main thread stack using the --main-stacksize= flag.
484
==30976==  The main thread stack size used in this run was 8388608.
485
==30976== 
486
==30976== HEAP SUMMARY:
487
==30976==     in use at exit: 134,516 bytes in 1,164 blocks
488
==30976==   total heap usage: 3,465 allocs, 2,354 frees, 351,592 bytes allocated
489
==30976== 
490
==30976== LEAK SUMMARY:
491
==30976==    definitely lost: 0 bytes in 0 blocks
492
==30976==    indirectly lost: 0 bytes in 0 blocks
493
==30976==      possibly lost: 15,781 bytes in 476 blocks
494
==30976==    still reachable: 118,735 bytes in 688 blocks
495
==30976==         suppressed: 0 bytes in 0 blocks
496
==30976== Rerun with --leak-check=full to see details of leaked memory
497
==30976== 
498
==30976== For counts of detected and suppressed errors, rerun with: -v
499
==30976== Use --track-origins=yes to see where uninitialised values come from
500
==30976== ERROR SUMMARY: 214 errors from 40 contexts (suppressed: 0 from 0)