[Dock-fans] running dock6 error

Scott Brozell sbrozell at rci.rutgers.edu
Thu May 25 10:47:27 PDT 2017


Hi,

I reran the tutorial under valgrind with dock 6.8
gcc version 4.8.5 (GCC) 
Linux osc 2.6.32-573.40.1.el6.x86_64 #1 SMP Tue Feb 21 16:47:03 EST 2017 x86_64 GNU/Linux
Red Hat Enterprise Linux Server release 6.7 (Santiago)
and it was clean:
===
                          Grid_Score:          -29.553888
                     Grid_vdw_energy:          -22.534115
                      Grid_es_energy:           -7.019773
           Internal_energy_repulsive:            0.888303


1 Molecules Processed
Total elapsed time:  163 seconds
==30997== 
==30997== HEAP SUMMARY:
==30997==     in use at exit: 0 bytes in 0 blocks
==30997==   total heap usage: 7,214,332 allocs, 7,214,332 frees, 480,896,355 bytes allocated
==30997== 
==30997== All heap blocks were freed -- no leaks are possible
==30997== 
==30997== For counts of detected and suppressed errors, rerun with: -v
==30997== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 5 from 5)
===

What compiler version are you using ?
I don't think i have easy access to an ubuntu machine anymore.
Can you get more clues from building a debug version of dock6 ?
cd install; make dockclean; make dock DOCKBUILDFLAGS=' -g -fsanitize=address'

Do you have valgrind installed ?

thanks,
scott


On Thu, May 25, 2017 at 01:35:25PM +0200, Urszula Uciechowska wrote:
> I regenerated the grid files.
> 
> platform information:
> 
> ares at ares ~ $ uname -a
> Linux ares 4.4.0-21-generic #37-Ubuntu SMP Mon Apr 18 18:33:37 UTC 2016
> x86_64 x86_64 x86_64 GNU/Linux
> 
> ares at ares ~ $ lsb_release -a
> No LSB modules are available.
> Distributor ID:	LinuxMint
> Description:	Linux Mint 18 Sarah
> Release:	18
> Codename:	sarah
> 
> ares at ares ~ $ cat /etc/lsb-release
> DISTRIB_ID=LinuxMint
> DISTRIB_RELEASE=18
> DISTRIB_CODENAME=sarah
> DISTRIB_DESCRIPTION="Linux Mint 18 Sarah"
> 
> 
> 
> Architecture:          x86_64
> CPU op-mode(s):        32-bit, 64-bit
> Byte Order:            Little Endian
> CPU(s):                4
> On-line CPU(s) list:   0-3
> Thread(s) per core:    1
> Core(s) per socket:    4
> Socket(s):             1
> NUMA node(s):          1
> Vendor ID:             GenuineIntel
> CPU family:            6
> Model:                 60
> Model name:            Intel(R) Core(TM) i5-4670K CPU @ 3.40GHz
> Stepping:              3
> CPU MHz:               3497.750
> CPU max MHz:           3800,0000
> CPU min MHz:           800,0000
> BogoMIPS:              6783.69
> Virtualization:        VT-x
> L1d cache:             32K
> L1i cache:             32K
> L2 cache:              256K
> L3 cache:              6144K
> NUMA node0 CPU(s):     0-3
> Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr
> pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe
> syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good
> nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64
> monitor ds_cpl vmx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_1
> sse4_2 movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm
> abm epb tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1
> avx2 smep bmi2 erms invpcid xsaveopt dtherm ida arat pln pts
> 
> 
> Should I try to install older version of dock?
> 
> best
> Urszula
> 
> 
> > I recently did this with dock 6.8 without problems.  This may be a
> > platform dependency.  Please send  and verbatim verbose details
> > including versions of compilers, os, etc. and
> > in particular did you regenerate the grid files or use the downloaded
> > ones?
> >
> > scott
> >
> > On Wed, May 24, 2017 at 02:47:48PM +0200, Urszula Uciechowska wrote:
> >> Dear dock users,
> >>
> >> I am trying to run dock6 on files taken from tutorial. After typing
> >> dock6
> >> -i rigid.in I am getting an error message:
> >>
> >> Initializing Library File Routines...
> >> Initializing Orienting Routines...
> >> Initializing Conformer Generator Routines...
> >> Initializing Grid Score Routines...
> >>  Reading the energy grid from grid.nrg
> >>  Done reading the energy grid.
> >>  Reading the grid box quantifiers from grid.bmp
> >>  Done reading the grid box quantifiers.
> >> *** Error in `/home/ares/Software/dock6/bin/dock6': free(): invalid next
> >> size (fast): 0x00000000021c2580 ***
> >> ======= Backtrace: =========
> >> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f6b3d1867e5]
> >> /lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f6b3d18ee0a]
> >> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f6b3d19298c]
> >> /home/ares/Software/dock6/bin/dock6[0x40e991]
> >> /home/ares/Software/dock6/bin/dock6[0x435774]
> >> /home/ares/Software/dock6/bin/dock6[0x4240cf]
> >> /home/ares/Software/dock6/bin/dock6[0x425320]
> >> /home/ares/Software/dock6/bin/dock6[0x4067a4]
> >> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f6b3d12f830]
> >> /home/ares/Software/dock6/bin/dock6[0x407539]


More information about the Dock-fans mailing list