[gmx-users] glibc detected *** g_sas_d
Justin Lemkul
jalemkul at vt.edu
Thu Jul 18 17:54:59 CEST 2013
On 7/18/13 11:52 AM, Rasoul Nasiri wrote:
> 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.
>
It's not really useful to debug old code that may have gotten fixed. If 4.6.3
fails, that's important.
-Justin
>
> 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
>>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/**
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>>>>>
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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
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.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 | (410) 706-7441
==================================================
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