[Dock-fans] running dock6 error

Scott Brozell sbrozell at rci.rutgers.edu
Tue May 30 16:44:25 PDT 2017


Hi,

I also reran the tutorial under valgrind with dock 6.8
gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.3) 
Linux 3.13.0-116-generic #163-Ubuntu SMP Fri Mar 31 14:13:22 UTC 2017 x86_64 GNU/Linux
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:     134 seconds
==12240== 
==12240== HEAP SUMMARY:
==12240==     in use at exit: 0 bytes in 0 blocks
==12240==   total heap usage: 7,214,332 allocs, 7,214,332 frees, 480,896,355 bytes allocated
==12240== 
==12240== All heap blocks were freed -- no leaks are possible
==12240== 
==12240== For counts of detected and suppressed errors, rerun with: -v
==12240== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
===

scott

On Thu, May 25, 2017 at 01:47:27PM -0400, Scott Brozell wrote:
> 
> 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]


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