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 <jalem...@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 <nasiri1...@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 <jalem...@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@outerbanks.umaryland.****edu <jalemkul@outerbanks.** >>>> umaryland.edu <jalem...@outerbanks.umaryland.edu>>| (410) 706-7441 >>>> >>>> ==============================****==================== >>>> >>>> -- >>>> gmx-users mailing list gmx-users@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/** >>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>>> posting! >>>> >>>> * Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> * Can't post? Read >>>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >>> >>> > -- > ==============================**==================== > > 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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@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/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
