[gmx-users] glibc detected *** g_sas_d
Rasoul Nasiri
nasiri1355 at gmail.com
Thu Jul 18 17:52:54 CEST 2013
The error message using 6.4:
----------------------------------------------------------------------------------------------------------------------------------------------------------------------
*** glibc detected *** g_sas_d: malloc(): memory corruption:
0x000000000065c8b0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x75018)[0x7f3b97442018]
/lib64/libc.so.6(+0x77fff)[0x7f3b97444fff]
/lib64/libc.so.6(__libc_calloc+0xc8)[0x7f3b974466b8]
/usr/local/packages/gmx/4.6.0-phase3/lib/libgmx_d.so.6(save_calloc
+0x46)[0x7f3b97e97dc6]
/usr/local/packages/gmx/4.6.0-phase3/lib/libgmxana_d.so.6(sas
_plot+0x4e1)[0x7f3b990ecb61]
/usr/local/packages/gmx/4.6.0-phase3/lib/libgmxana_d.so.6(gmx_sas
+0x4be)[0x7f3b990f0a7e]
g_sas_d(main+0x9)[0x400899]
/lib64/libc.so.6(__libc_start_main+0xe6)[0x7f3b973ebbc6]
g_sas_d[0x4007c9]
======= Memory map: ========
00400000-00401000 r-xp 00000000 00:19 2829145631
/nfs01/y07/y07/gmx/4.6.0-phase3/bin/g_sas_d
00600000-00601000 r--p 00000000 00:19 2829145631
/nfs01/y07/y07/gmx/4.6.0-phase3/bin/g_sas_d
00601000-00602000 rw-p 00001000 00:19 2829145631
/nfs01/y07/y07/gmx/4.6.0-phase3/bin/g_sas_d
00602000-00691000 rw-p 00000000 00:00 0
[heap]
7f3b90000000-7f3b90021000 rw-p 00000000 00:00 0
7f3b90021000-7f3b94000000 ---p 00000000 00:00 0
7f3b96da0000-7f3b96db6000 r-xp 00000000 00:0f 2285586
/lib64/libgcc_s.so.1
7f3b96db6000-7f3b96fb5000 ---p 00016000 00:0f 2285586
/lib64/libgcc_s.so.1
7f3b96fb5000-7f3b96fb6000 r--p 00015000 00:0f 2285586
/lib64/libgcc_s.so.1
7f3b96fb6000-7f3b96fb7000 rw-p 00016000 00:0f 2285586
/lib64/libgcc_s.so.1
7f3b96fb7000-7f3b971b7000 rw-p 00000000 00:00 0
7f3b971b7000-7f3b971cc000 r-xp 00000000 00:0f 2285660
/lib64/libz.so.1.2.3
7f3b971cc000-7f3b973cb000 ---p 00015000 00:0f 2285660
/lib64/libz.so.1.2.3
7f3b973cb000-7f3b973cc000 r--p 00014000 00:0f 2285660
/lib64/libz.so.1.2.3
7f3b973cc000-7f3b973cd000 rw-p 00015000 00:0f 2285660
/lib64/libz.so.1.2.3
7f3b973cd000-7f3b97522000 r-xp 00000000 00:0f 2285709
/lib64/libc-2.11.1.so
7f3b97522000-7f3b97721000 ---p 00155000 00:0f 2285709
/lib64/libc-2.11.1.so
7f3b97721000-7f3b97725000 r--p 00154000 00:0f 2285709
/lib64/libc-2.11.1.so
7f3b97725000-7f3b97726000 rw-p 00158000 00:0f 2285709
/lib64/libc-2.11.1.so
7f3b97726000-7f3b9772b000 rw-p 00000000 00:00 0
7f3b9772b000-7f3b97742000 r-xp 00000000 00:0f 2285826
/lib64/libpthread-2.11.1.so
7f3b97742000-7f3b97942000 ---p 00017000 00:0f 2285826
/lib64/libpthread-2.11.1.so
7f3b97942000-7f3b97943000 r--p 00017000 00:0f 2285826
/lib64/libpthread-2.11.1.so
7f3b97943000-7f3b97944000 rw-p 00018000 00:0f 2285826
/lib64/libpthread-2.11.1.so
7f3b97944000-7f3b97948000 rw-p 00000000 00:00 0
7f3b97948000-7f3b9799d000 r-xp 00000000 00:0f 2285808
/lib64/libm-2.11.1.so
7f3b9799d000-7f3b97b9c000 ---p 00055000 00:0f 2285808
/lib64/libm-2.11.1.so
7f3b97b9c000-7f3b97b9d000 r--p 00054000 00:0f 2285808
/lib64/libm-2.11.1.so
7f3b97b9d000-7f3b97b9e000 rw-p 00055000 00:0f 2285808
/lib64/libm-2.11.1.so
7f3b97b9e000-7f3b97ba0000 r-xp 00000000 00:0f 2285806
/lib64/libdl-2.11.1.so
7f3b97ba0000-7f3b97da0000 ---p 00002000 00:0f 2285806
/lib64/libdl-2.11.1.so
7f3b97da0000-7f3b97da1000 r--p 00002000 00:0f 2285806
/lib64/libdl-2.11.1.so
7f3b97da1000-7f3b97da2000 rw-p 00003000 00:0f 2285806
/lib64/libdl-2.11.1.so
7f3b97da2000-7f3b98233000 r-xp 00000000 00:19 1503619150
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmx_d.so.6
7f3b98233000-7f3b98433000 ---p 00491000 00:19 1503619150
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmx_d.so.6
7f3b98433000-7f3b9843a000 r--p 00491000 00:19 1503619150
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmx_d.so.6
7f3b9843a000-7f3b98445000 rw-p 00498000 00:19 1503619150
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmx_d.so.6
7f3b98445000-7f3b98446000 rw-p 00000000 00:00 0
7f3b98446000-7f3b98598000 r-xp 00000000 00:0f 3760217 /
usr/lib64/libxml2.so.2.7.6
7f3b98598000-7f3b98797000 ---p 00152000 00:0f 3760217 /
usr/lib64/libxml2.so.2.7.6
7f3b98797000-7f3b9879f000 r--p 00151000 00:0f 3760217 /
usr/lib64/libxml2.so.2.7.6
7f3b9879f000-7f3b987a1000 rw-p 00159000 00:0f 3760217 /
usr/lib64/libxml2.so.2.7.6
7f3b987a1000-7f3b987a2000 rw-p 00000000 00:00 0
7f3b987a2000-7f3b98989000 r-xp 00000000 00:0f 8565593
/opt/fftw/3.3.0.0/x86_64/lib/libfftw3.so.3.3.0
7f3b98989000-7f3b98b89000 ---p 001e7000 00:0f 8565593
/opt/fftw/3.3.0.0/x86_64/lib/libfftw3.so.3.3.0
7f3b98b89000-7f3b98b9a000 rw-p 001e7000 00:0f 8565593
/opt/fftw/3.3.0.0/x86_64/lib/libfftw3.so.3.3.0
7f3b98b9a000-7f3b98dbc000 r-xp 00000000 00:19 3521599651
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libmd_d.so.6
7f3b98dbc000-7f3b98fbb000 ---p 00222000 00:19 3521599651
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libmd_d.so.6
7f3b98fbb000-7f3b98fbc000 r--p 00221000 00:19 3521599651
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libmd_d.so.6
7f3b98fbc000-7f3b98fbe000 rw-p 00222000 00:19 3521599651
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libmd_d.so.6
7f3b98fbe000-7f3b99203000 r-xp 00000000 00:19 2309614127
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmxana_d.so.6
7f3b99203000-7f3b99402000 ---p 00245000 00:19 2309614127
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmxana_d.so.6
7f3b99402000-7f3b99403000 r--p 00244000 00:19 2309614127
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmxana_d.so.6
7f3b99403000-7f3b9940c000 rw-p 00245000 00:19 2309614127
/nfs01/y07/y07/gmx/4.6.0-phase3/lib/libgmxana_d.so.6
7f3b9940c000-7f3b9940d000 rw-p 00000000 00:00 0
7f3b9940d000-7f3b9942c000 r-xp 00000000 00:0f 2285702
/lib64/ld-2.11.1.so
7f3b995f7000-7f3b995fd000 rw-p 00000000 00:00 0
7f3b99602000-7f3b9962b000 rw-p 00000000 00:00 0
7f3b9962b000-7f3b9962c000 r--p 0001e000 00:0f 2285702
/lib64/ld-2.11.1.so
7f3b9962c000-7f3b9962d000 rw-p 0001f000 00:0f 2285702
/lib64/ld-2.11.1.so
7f3b9962d000-7f3b9962e000 rw-p 00000000 00:00 0
7fff97796000-7fff977aa000 rwxp 00000000 00:00 0
[stack]
7fff977aa000-7fff977ae000 rw-p 00000000 00:00 0
7fff977ff000-7fff97800000 r-xp 00000000 00:00 0 [
vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [
vsyscall]Aborted
---------------------------------------------------------------------------------------------------------------------------------------------------
If you still think that results of 4.6.3 might be necessary, I will do it.
Rasoul
On Thu, Jul 18, 2013 at 2:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 7/18/13 8:04 AM, Rasoul Nasiri wrote:
>
>> Justin,
>>
>> I just ran this calculations on "VERSION 4.6-GPU-dev-20120501-ec56c" and I
>> will let you know about the outcomes.
>>
>>
> The outcome of 4.6.3 would be more interesting than an outdated
> development version.
>
> -Justin
>
> Rasoul
>>
>>
>> On Thu, Jul 18, 2013 at 1:09 PM, Rasoul Nasiri <nasiri1355 at gmail.com>
>> wrote:
>>
>> Bellow are commands and error message:
>>>
>>> 1- trjconv_d -f traj.xtc -n maxclust.ndx -o traj_out.xtc
>>>
>>> 2- g_sas_d -f traj_out.xtc -n maxclust.ndx -o surface.xvg -nopbc
>>>
>>>
>>> glibc detected *** g_sas_d: malloc(): memory corruption:
>>> 0x00000000016dfcd0
>>>
>>>
>>> Rasoul
>>>
>>>
>>> On Thu, Jul 18, 2013 at 1:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 7/18/13 6:52 AM, Rasoul Nasiri wrote:
>>>>
>>>> Hello all,
>>>>>
>>>>> I'm trying to know how the surface area of a nano-drop changes during
>>>>> the
>>>>> evaporation in the vacuum.
>>>>>
>>>>> When I filter the trajectory of non-evaporated molecules by trjconv and
>>>>> use
>>>>> g_sas for calculation of their surface, it usually crash (I'm using
>>>>> version
>>>>> of 4.5.5).
>>>>>
>>>>>
>>>>> What's the error message? What's your command?
>>>>
>>>>
>>>> Is there still this issue in the 4.6.*? How it can be resolved?
>>>>
>>>>>
>>>>>
>>>>> Have you tried version 4.6? That's the quickest way to know. If
>>>> there
>>>> are still problems, you'll need to provide more information.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==============================****====================
>>>>
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences
>>>> School of Pharmacy
>>>> Health Sciences Facility II, Room 601
>>>> University of Maryland, Baltimore
>>>> 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.****edu <jalemkul at outerbanks.**
>>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>>| (410) 706-7441
>>>>
>>>> ==============================****====================
>>>>
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>
>>>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
>
> ==============================**====================
> --
> gmx-users mailing list gmx-users at gromacs.org
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