[gmx-users] valgrind warnigs with git mdrun

Jochen Hub jochen at xray.bmc.uu.se
Thu Jan 28 10:28:59 CET 2010


Hi,

I am implementing some addition stuff to mdrun, but my mdrun (in 
particle decomposition) stops with lincs warings after running fine for 
10 to 50 ps or so. The same system with the git master does not crash 
(with -pd), which, of course, does not mean there is no memory leak as 
well. So I was running my system with the git master mdrun within 
valgrind --leak-check=yes, and got the following warnings (see below), 
which eventually stop in a fatal error:

Program mdrun_debug, VERSION 4.0.99_development_20090927
Source code file: mshift.c, line: 647

Fatal error:
No GREY nodes found while nG=4

I am now wondering if that is a valgrind problem or if mdrun has a 
problem that shows up as crashes in my altered version of mdrun.

Thanks for any hints,

Jochen

ps: I have compiled mdrun on a linux with an intel compiler via:
export LDFLAGS="-L/opt/fftw/3.2/icc11/lib"
export CPPFLAGS=-I/opt/fftw/3.2/icc11/include
source /opt/intel/ictce/3.2.1.015/ictvars.sh
export CC=icc
export I_MPI_CC=icc
export LD=icc
export CFLAGS="-g -O0"
make distclean
./configure --prefix=/home/jhub/src/git/gmx-master/build.debug 
--without-x --enable-mpi --program-suffix=_debug --disable-shared 
--without-xml

During compilation, I get the following warnings. Don't know if they are 
a problem though:

../../../../include/gmx_sse2_single.h(251): warning #167: argument of 
type "__m128i" is incompatible with parameter of type
 "__m128"
        xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base));
                                  ^
../../../../include/gmx_sse2_single.h(251): warning #167: argument of 
type "__m128i" is incompatible with parameter of type
 "__m128"
        xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base));

../../include/gmx_sse2_single.h(251): warning #167: argument of type 
"__m128i" is incompatible with parameter of type "__m1
28"
        xmm2 = _mm_add_epi32(xmm2,gmx_mm_castps_si128(base));
                                  ^
resall.c(488): warning #167: argument of type "const char *" is 
incompatible with parameter of type "char *"
      n=neq_str(key,rtp[i].resname);
                ^
grompp.c(306): warning #592: variable "mbs" is used before its value is set
    mbs;
    ^

valgrind output:
*************

Getting Loaded...
Reading file test.with-normal-grompp.tpr, VERSION 
4.0.99_development_20090927 (single precision)
^[[BLoaded with Money

Getting Loaded...
Reading file test.with-normal-grompp.tpr, VERSION 
4.0.99_development_20090927 (single precision)
Loaded with Money

==6218== Invalid read of size 4
==6218==    at 0x53A866: mk_grey (mshift.c:528)
==6218==    by 0x53B010: mk_mshift (mshift.c:657)
==6218==    by 0x4CA095: low_do_pbc_mtop (sim_util.c:1295)
==6218==    by 0x4CA168: do_pbc_first_mtop (sim_util.c:1314)
==6218==    by 0x412AAD: mdrunner (runner.c:545)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==  Address 0x5add7f8 is 8 bytes inside a block of size 457,016 free'd
==6218==    at 0x4A05F1D: realloc (vg_replace_malloc.c:476)
==6218==    by 0x5547C5: save_realloc (smalloc.c:196)
==6218==    by 0x53996A: compact_graph (mshift.c:260)
==6218==    by 0x539F1D: mk_graph_ilist (mshift.c:364)
==6218==    by 0x4CA03B: low_do_pbc_mtop (sim_util.c:1291)
==6218==    by 0x4CA168: do_pbc_first_mtop (sim_util.c:1314)
==6218==    by 0x412AAD: mdrunner (runner.c:545)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
Getting Loaded...
Reading file test.with-normal-grompp.tpr, VERSION 
4.0.99_development_20090927 (single precision)
^[[BLoaded with Money

==6025== Invalid read of size 4
==6025==    at 0x53A866: mk_grey (mshift.c:528)
==6025==    by 0x53B010: mk_mshift (mshift.c:657)
==6025==    by 0x4CA095: low_do_pbc_mtop (sim_util.c:1295)
==6025==    by 0x4CA168: do_pbc_first_mtop (sim_util.c:1314)
==6025==    by 0x412AAD: mdrunner (runner.c:545)
==6025==    by 0x411972: mdrunner_threads (runner.c:196)
==6025==    by 0x41DAC0: main (mdrun.c:515)
==6025==  Address 0x5add7f8 is 8 bytes inside a block of size 457,016 free'd
==6025==    at 0x4A05F1D: realloc (vg_replace_malloc.c:476)
==6025==    by 0x5547C5: save_realloc (smalloc.c:196)
==6025==    by 0x53996A: compact_graph (mshift.c:260)
==6025==    by 0x539F1D: mk_graph_ilist (mshift.c:364)
==6025==    by 0x4CA03B: low_do_pbc_mtop (sim_util.c:1291)
==6025==    by 0x4CA168: do_pbc_first_mtop (sim_util.c:1314)
==6025==    by 0x412AAD: mdrunner (runner.c:545)
==6025==    by 0x411972: mdrunner_threads (runner.c:196)
==6025==    by 0x41DAC0: main (mdrun.c:515)
==6025==
==6025== Invalid read of size 4
==6025==    at 0x4DDD2C: init_vcm (vcm.c:78)
==6025==    by 0x4CA70E: init_md (sim_util.c:1457)
==6025==    by 0x41617A: do_md (md.c:969)
==6025==    by 0x4133D1: mdrunner (runner.c:669)
==6025==    by 0x411972: mdrunner_threads (runner.c:196)
==6025==    by 0x41DAC0: main (mdrun.c:515)
==6025==  Address 0x57a80d4 is 0 bytes after a block of size 4 alloc'd
==6025==    at 0x4A05140: calloc (vg_replace_malloc.c:418)
==6025==    by 0x5546CA: save_calloc (smalloc.c:157)
==6025==    by 0x560956: do_inputrec (tpxio.c:688)
==6025==    by 0x56F51F: do_tpx (tpxio.c:2085)
==6025==    by 0x56F948: read_tpx_state (tpxio.c:2201)
==6025==    by 0x465B6C: init_single (init.c:155)
==6025==    by 0x411D49: mdrunner (runner.c:324)
==6025==    by 0x411972: mdrunner_threads (runner.c:196)
==6025==    by 0x41DAC0: main (mdrun.c:515)
==6025==

Back Off! I just backed up traj.trr to ./#traj.trr.2#

Back Off! I just backed up traj.xtc to ./#traj.xtc.2#

Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun 'box'
400000 steps,   1600.0 ps.
==6025== Invalid read of size 4
==6025==    at 0x53A866: mk_grey (mshift.c:528)
==6025==    by 0x53B010: mk_mshift (mshift.c:657)
==6025==    by 0x4C69C1: do_force (sim_util.c:568)
==6025==    by 0x419229: do_md (md.c:1657)
==6025==    by 0x4133D1: mdrunner (runner.c:669)
==6025==    by 0x411972: mdrunner_threads (runner.c:196)
==6025==    by 0x41DAC0: main (mdrun.c:515)
==6025==  Address 0x81fa438 is 8 bytes inside a block of size 2,881,592 
free'd
==6025==    at 0x4A05F1D: realloc (vg_replace_malloc.c:476)
==6025==    by 0x5547C5: save_realloc (smalloc.c:196)
==6025==    by 0x53996A: compact_graph (mshift.c:260)
==6025==    by 0x539F1D: mk_graph_ilist (mshift.c:364)
==6025==    by 0x53A14F: mk_graph (mshift.c:395)
==6025==    by 0x416854: do_md (md.c:1062)
==6025==    by 0x4133D1: mdrunner (runner.c:669)
==6025==    by 0x411972: mdrunner_threads (runner.c:==6218== Invalid 
read of size 4
==6218==    at 0x4DDD2C: init_vcm (vcm.c:78)
==6218==    by 0x4CA70E: init_md (sim_util.c:1457)
==6218==    by 0x41617A: do_md (md.c:969)
==6218==    by 0x4133D1: mdrunner (runner.c:669)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==  Address 0x57a8354 is 0 bytes after a block of size 4 alloc'd
==6218==    at 0x4A05140: calloc (vg_replace_malloc.c:418)
==6218==    by 0x5546CA: save_calloc (smalloc.c:157)
==6218==    by 0x560956: do_inputrec (tpxio.c:688)
==6218==    by 0x56F51F: do_tpx (tpxio.c:2085)
==6218==    by 0x56F948: read_tpx_state (tpxio.c:2201)
==6218==    by 0x465B6C: init_single (init.c:155)
==6218==    by 0x411D49: mdrunner (runner.c:324)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==

Back Off! I just backed up traj.trr to ./#traj.trr.3#

Back Off! I just backed up traj.xtc to ./#traj.xtc.3#

Back Off! I just backed up ener.edr to ./#ener.edr.3#
starting mdrun 'box'
400000 steps,   1600.0 ps.
==6218== Invalid read of size 4
==6218==    at 0x53A866: mk_grey (mshift.c:528)
==6218==    by 0x53B010: mk_mshift (mshift.c:657)
==6218==    by 0x4C69C1: do_force (sim_util.c:568)
==6218==    by 0x419229: do_md (md.c:1657)
==6218==    by 0x4133D1: mdrunner (runner.c:669)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==  Address 0x88ff048 is 8 bytes inside a block of size 2,881,592 
free'd
==6218==    at 0x4A05F1D: realloc (vg_replace_malloc.c:476)
==6218==    by 0x5547C5: save_realloc (smalloc.c:196)
==6218==    by 0x53996A: compact_graph (mshift.c:260)
==6218==    by 0x539F1D: mk_graph_ilist (mshift.c:364)
==6218==    by 0x53A14F: mk_graph (mshift.c:395)
==6218==    by 0x416854: do_md (md.c:1062)
==6218==    by 0x4133D1: mdrunner (runner.c:669)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
step 0
-------------------------------------------------------
Program mdrun_debug, VERSION 4.0.99_development_20090927
Source code file: mshift.c, line: 647

Fatal error:
No GREY nodes found while nG=4

For more information and tips for trouble shooting please check the 
GROMACS website at
http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"You Hear Footsteps Coming From Behind" (Colossal Cave)

Halting program mdrun_debug

gcq#184: "You Hear Footsteps Coming From Behind" (Colossal Cave)

[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
==6218==
==6218== HEAP SUMMARY:
==6218==     in use at exit: 93,436,385 bytes in 4,712 blocks
==6218==   total heap usage: 155,351 allocs, 150,639 frees, 458,502,488 
bytes allocated
==6218==
==6218== 4 bytes in 1 blocks are definitely lost in loss record 21 of 1,032
==6218==    at 0x4A05140: calloc (vg_replace_malloc.c:418)
==6218==    by 0x5546CA: save_calloc (smalloc.c:157)
==6218==    by 0x57C85E: init_block (typedefs.c:112)
==6218==    by 0x57CA72: init_mtop (typedefs.c:177)
==6218==    by 0x56D0AF: do_mtop (tpxio.c:1728)
==6218==    by 0x56EE6A: do_tpx (tpxio.c:2034)
==6218==    by 0x56F948: read_tpx_state (tpxio.c:2201)
==6218==    by 0x465B6C: init_single (init.c:155)
==6218==    by 0x411D49: mdrunner (runner.c:324)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== 8 bytes in 1 blocks are definitely lost in loss record 41 of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4D446B4: MPIR_Init_thread (init_coll.h:859)
==6218==    by 0x4D391AE: PMPI_Init (init.c:117)
==6218==    by 0x5437D7: gmx_setup (network.c:92)
==6218==    by 0x5378A2: init_par (main.c:413)
==6218==    by 0x41D27F: main (mdrun.c:393)
==6218==
==6218== 8 bytes in 1 blocks are definitely lost in loss record 42 of 1,032
==6218==    at 0x4A05140: calloc (vg_replace_malloc.c:418)
==6218==    by 0x5546CA: save_calloc (smalloc.c:157)
==6218==    by 0x57DAC7: init_gtc_state (typedefs.c:444)
==6218==    by 0x57DDF7: init_state (typedefs.c:500)
==6218==    by 0x56E5F0: do_tpx (tpxio.c:1968)
==6218==    by 0x56F948: read_tpx_state (tpxio.c:2201)
==6218==    by 0x465B6C: init_single (init.c:155)
==6218==    by 0x411D49: mdrunner (runner.c:324)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== 9 bytes in 1 blocks are definitely lost in loss record 49 of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x3B8A078AC1: strdup (in /lib64/libc-2.5.so)
==6218==    by 0x468C8D: init_mdebin (mdebin.c:412)
==6218==    by 0x4CAB12: init_md (sim_util.c:1517)
==6218==    by 0x41617A: do_md (md.c:969)
==6218==    by 0x4133D1: mdrunner (runner.c:669)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== 12 bytes in 1 blocks are definitely lost in loss record 57 of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x3B8A078AC1: strdup (in /lib64/libc-2.5.so)
==6218==    by 0x4692D2: init_mdebin (mdebin.c:476)
==6218==    by 0x4CAB12: init_md (sim_util.c:1517)
==6218==    by 0x41617A: do_md (md.c:969)
==6218==    by 0x4133D1: mdrunner (runner.c:669)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== 257 bytes in 1 blocks are possibly lost in loss record 830 of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4D4FF9A: ??? (mpid_init.c:387)
==6218==    by 0x4D4F2AB: MPIDD_Init (mpid_init.c:85)
==6218==    by 0x4E0DF82: MPID_Init (wrap_adi3.c:334)
==6218==    by 0x4D414D4: MPIR_Init_thread (initthread.c:277)
==6218==    by 0x4D391AE: PMPI_Init (init.c:117)
==6218==    by 0x5437D7: gmx_setup (network.c:92)
==6218==    by 0x5378A2: init_par (main.c:413)
==6218==    by 0x41D27F: main (mdrun.c:393)
==6218==
==6218== 257 bytes in 1 blocks are possibly lost in loss record 831 of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4D5031C: ??? (mpid_init.c:435)
==6218==    by 0x4D4F2AB: MPIDD_Init (mpid_init.c:85)
==6218==    by 0x4E0DF82: MPID_Init (wrap_adi3.c:334)
==6218==    by 0x4D414D4: MPIR_Init_thread (initthread.c:277)
==6218==    by 0x4D391AE: PMPI_Init (init.c:117)
==6218==    by 0x5437D7: gmx_setup (network.c:92)
==6218==    by 0x5378A2: init_par (main.c:413)
==6218==    by 0x41D27F: main (mdrun.c:393)
==6218==
==6218== 328 bytes in 1 blocks are possibly lost in loss record 842 of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4D2B657: I_MPI_Amalloc (handlemem.c:484)
==6218==    by 0x4D6A47B: MPIDI_PG_Create (mpidi_pg.c:90)
==6218==    by 0x4D501E6: ??? (mpid_init.c:418)
==6218==    by 0x4D4F2AB: MPIDD_Init (mpid_init.c:85)
==6218==    by 0x4E0DF82: MPID_Init (wrap_adi3.c:334)
==6218==    by 0x4D414D4: MPIR_Init_thread (initthread.c:277)
==6218==    by 0x4D391AE: PMPI_Init (init.c:117)
==6218==    by 0x5437D7: gmx_setup (network.c:92)
==6218==    by 0x5378A2: init_par (main.c:413)
==6218==    by 0x41D27F: main (mdrun.c:393)
==6218==
==6218== 488 bytes in 1 blocks are possibly lost in loss record 861 of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4D2B657: I_MPI_Amalloc (handlemem.c:484)
==6218==    by 0x4D6A566: MPIDI_PG_Create (mpidi_pg.c:91)
==6218==    by 0x4D501E6: ??? (mpid_init.c:418)
==6218==    by 0x4D4F2AB: MPIDD_Init (mpid_init.c:85)
==6218==    by 0x4E0DF82: MPID_Init (wrap_adi3.c:334)
==6218==    by 0x4D414D4: MPIR_Init_thread (initthread.c:277)
==6218==    by 0x4D391AE: PMPI_Init (init.c:117)
==6218==    by 0x5437D7: gmx_setup (network.c:92)
==6218==    by 0x5378A2: init_par (main.c:413)
==6218==    by 0x41D27F: main (mdrun.c:393)
==6218==
==6218== 1,352 bytes in 1 blocks are possibly lost in loss record 891 of 
1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4CAB25E: MPIDI_CH3_SHM_Init (ch3_init.c:1668)
==6218==    by 0x4CA5294: MPIDI_CH3_Init (ch3_init.c:189)
==6218==    by 0x4D4F2D8: MPIDD_Init (mpid_init.c:96)
==6218==    by 0x4E0DF82: MPID_Init (wrap_adi3.c:334)
==6218==    by 0x4D414D4: MPIR_Init_thread (initthread.c:277)
==6218==    by 0x4D391AE: PMPI_Init (init.c:117)
==6218==    by 0x5437D7: gmx_setup (network.c:92)
==6218==    by 0x5378A2: init_par (main.c:413)
==6218==    by 0x41D27F: main (mdrun.c:393)
==6218==
==6218== 2,259 bytes in 42 blocks are definitely lost in loss record 905 
of 1,032
==6218==    at 0x4A05140: calloc (vg_replace_malloc.c:418)
==6218==    by 0x5546CA: save_calloc (smalloc.c:157)
==6218==    by 0x555BD3: mk_desc (statutil.c:620)
==6218==    by 0x556C2D: parse_common_args (statutil.c:863)
==6218==    by 0x41D342: main (mdrun.c:412)
==6218==
==6218== 16,032 bytes in 1 blocks are possibly lost in loss record 919 
of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x46246C: make_nbf_tables (forcerec.c:1040)
==6218==    by 0x464ABC: init_forcerec (forcerec.c:1539)
==6218==    by 0x4128C8: mdrunner (runner.c:508)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== 32,048 bytes in 1 blocks are possibly lost in loss record 923 
of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x46242B: make_nbf_tables (forcerec.c:1034)
==6218==    by 0x464ABC: init_forcerec (forcerec.c:1539)
==6218==    by 0x4128C8: mdrunner (runner.c:508)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== 48,064 bytes in 1 blocks are possibly lost in loss record 929 
of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4D4883: make_tables (tables.c:921)
==6218==    by 0x4623CB: make_nbf_tables (forcerec.c:1020)
==6218==    by 0x464ABC: init_forcerec (forcerec.c:1539)
==6218==    by 0x4128C8: mdrunner (runner.c:508)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== 48,064 bytes in 1 blocks are possibly lost in loss record 930 
of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4D4883: make_tables (tables.c:921)
==6218==    by 0x464EF1: init_forcerec (forcerec.c:1574)
==6218==    by 0x4128C8: mdrunner (runner.c:508)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== 262,408 bytes in 1 blocks are possibly lost in loss record 968 
of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4CCC1D4: MPIDI_CH3I_SHM_Get_mem_shm (ch3_shm_memory.c:1015)
==6218==    by 0x4CAC05A: MPIDI_CH3_SHM_Init (ch3_init.c:1894)
==6218==    by 0x4CA5294: MPIDI_CH3_Init (ch3_init.c:189)
==6218==    by 0x4D4F2D8: MPIDD_Init (mpid_init.c:96)
==6218==    by 0x4E0DF82: MPID_Init (wrap_adi3.c:334)
==6218==    by 0x4D414D4: MPIR_Init_thread (initthread.c:277)
==6218==    by 0x4D391AE: PMPI_Init (init.c:117)
==6218==    by 0x5437D7: gmx_setup (network.c:92)
==6218==    by 0x5378A2: init_par (main.c:413)
==6218==    by 0x41D27F: main (mdrun.c:393)
==6218==
==6218== 2,649,952 bytes in 1 blocks are possibly lost in loss record 
1,025 of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4FE31D: gmx_alloc_aligned (fftgrid.c:73)
==6218==    by 0x4FE6AF: mk_fftgrid (fftgrid.c:164)
==6218==    by 0x4B2899: gmx_pme_init (pme.c:1818)
==6218==    by 0x412E3E: mdrunner (runner.c:609)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== 2,649,952 bytes in 1 blocks are possibly lost in loss record 
1,026 of 1,032
==6218==    at 0x4A05E1C: malloc (vg_replace_malloc.c:195)
==6218==    by 0x4FE31D: gmx_alloc_aligned (fftgrid.c:73)
==6218==    by 0x4FE80E: mk_fftgrid (fftgrid.c:181)
==6218==    by 0x4B2899: gmx_pme_init (pme.c:1818)
==6218==    by 0x412E3E: mdrunner (runner.c:609)
==6218==    by 0x411972: mdrunner_threads (runner.c:196)
==6218==    by 0x41DAC0: main (mdrun.c:515)
==6218==
==6218== LEAK SUMMARY:
==6218==    definitely lost: 2,300 bytes in 47 blocks
==6218==    indirectly lost: 0 bytes in 0 blocks
==6218==      possibly lost: 5,709,202 bytes in 12 blocks
==6218==    still reachable: 87,724,883 bytes in 4,653 blocks
==6218==         suppressed: 0 bytes in 0 blocks
==6218== Reachable blocks (those to which a pointer was found) are not 
shown.
==6218== To see them, rerun with: --leak-check=full --show-reachable=yes
==6218==
==6218== For counts of detected and suppressed errors, rerun with: -v
==6218== ERROR SUMMARY: 252186 errors from 21 contexts (suppressed: 4 
from 4)


-- 
---------------------------------------------------
Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
---------------------------------------------------




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