[gmx-users] glibc detected *** g_sas_d
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). Is there still this issue in the 4.6.*? How it can be resolved? Best Rasoul -- gmx-users mailing listgmx-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
Re: [gmx-users] glibc detected *** g_sas_d
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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] glibc detected *** g_sas_d
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: 0x016dfcd0 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] glibc detected *** g_sas_d
Justin, I just ran this calculations on VERSION 4.6-GPU-dev-20120501-ec56c and I will let you know about the outcomes. 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: 0x016dfcd0 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 jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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
Re: [gmx-users] glibc detected *** g_sas_d
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: 0x016dfcd0 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 jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-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
Re: [gmx-users] meaning of results of g_hbond -ac
* Time
* Ac(hbond) with correction for the fact that a finite system is being
simulated.
* Ac(hbond) without correction
* Cross correlation between hbonds and contacts (see the papers by
LuzarChandler and van der Spoel that are mentioned in the stdout from g_hbond)
* Derivative of second column.
On 18 Jul 2013, at 04:51, Wu Chaofu xiaowu...@gmail.com wrote:
Dear gmxers,
By running the command g_hbond -ac, a resulting .xvg file is generated,
which is attached below. In that file, there are five columns. I guess
that, the first column is time, the second the HB autocorrelation function.
But what are the other columns denoted by s1, s2, s3? Thanks a lot for any
reply.
Yours sincerely,
Chaofu Wu
# This file was created Wed Jul 17 09:49:34 2013
# by the following command:
# g_hbond -f iconf.xtc -s conf.tpr -n -ac ihbac2.xvg
#
# g_hbond is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title Hydrogen Bond Autocorrelation
@xaxis label Time (ps)
@yaxis label C(t)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
0 1 1 -5.79228e-110.902311
1 0.09955770.1001860.1345570.455234
2 0.0895326 0.09016760.126435 0.00815676
3 0.0832442 0.08388360.123311 0.00541426
4 0.0787041 0.07934660.117936 0.00376486
5 0.0757145 0.07635910.116489 0.00198866
6 0.0747267 0.07537210.112655 0.00177937
7 0.0721557 0.07280290.109565 0.00255146
8 0.0696238 0.07027270.107288 0.00241577
9 0.0673242 0.06797470.106287 0.00157028
10 0.0664832 0.06713430.104746 0.0014926
110.064339 0.06499160.101947 0.00148105
12 0.0635211 0.0641743 0.0991141 0.00131835
13 0.0617023 0.06235670.101322 0.00147757
140.060566 0.0612212 0.0965892 0.000719808
.
--
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Re: [gmx-users] glibc detected *** g_sas_d
The error message using 6.4: -- *** glibc detected *** g_sas_d: malloc(): memory corruption: 0x0065c8b0 *** === 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: 0040-00401000 r-xp 00:19 2829145631 /nfs01/y07/y07/gmx/4.6.0-phase3/bin/g_sas_d 0060-00601000 r--p 00:19 2829145631 /nfs01/y07/y07/gmx/4.6.0-phase3/bin/g_sas_d 00601000-00602000 rw-p 1000 00:19 2829145631 /nfs01/y07/y07/gmx/4.6.0-phase3/bin/g_sas_d 00602000-00691000 rw-p 00:00 0 [heap] 7f3b9000-7f3b90021000 rw-p 00:00 0 7f3b90021000-7f3b9400 ---p 00:00 0 7f3b96da-7f3b96db6000 r-xp 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 00:00 0 7f3b971b7000-7f3b971cc000 r-xp 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 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 00:00 0 7f3b9772b000-7f3b97742000 r-xp 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 00:00 0 7f3b97948000-7f3b9799d000 r-xp 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 7f3b97b9e000-7f3b97ba r-xp 00:0f 2285806 /lib64/libdl-2.11.1.so 7f3b97ba-7f3b97da ---p 2000 00:0f 2285806 /lib64/libdl-2.11.1.so 7f3b97da-7f3b97da1000 r--p 2000 00:0f 2285806 /lib64/libdl-2.11.1.so 7f3b97da1000-7f3b97da2000 rw-p 3000 00:0f 2285806 /lib64/libdl-2.11.1.so 7f3b97da2000-7f3b98233000 r-xp 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 00:00 0 7f3b98446000-7f3b98598000 r-xp 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 00:00 0 7f3b987a2000-7f3b98989000 r-xp 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 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 00:19 2309614127
Re: [gmx-users] glibc detected *** g_sas_d
On 7/18/13 11:52 AM, Rasoul Nasiri wrote: The error message using 6.4: -- *** glibc detected *** g_sas_d: malloc(): memory corruption: 0x0065c8b0 *** === 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: 0040-00401000 r-xp 00:19 2829145631 /nfs01/y07/y07/gmx/4.6.0-phase3/bin/g_sas_d 0060-00601000 r--p 00:19 2829145631 /nfs01/y07/y07/gmx/4.6.0-phase3/bin/g_sas_d 00601000-00602000 rw-p 1000 00:19 2829145631 /nfs01/y07/y07/gmx/4.6.0-phase3/bin/g_sas_d 00602000-00691000 rw-p 00:00 0 [heap] 7f3b9000-7f3b90021000 rw-p 00:00 0 7f3b90021000-7f3b9400 ---p 00:00 0 7f3b96da-7f3b96db6000 r-xp 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 00:00 0 7f3b971b7000-7f3b971cc000 r-xp 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 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 00:00 0 7f3b9772b000-7f3b97742000 r-xp 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 00:00 0 7f3b97948000-7f3b9799d000 r-xp 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 7f3b97b9e000-7f3b97ba r-xp 00:0f 2285806 /lib64/libdl-2.11.1.so 7f3b97ba-7f3b97da ---p 2000 00:0f 2285806 /lib64/libdl-2.11.1.so 7f3b97da-7f3b97da1000 r--p 2000 00:0f 2285806 /lib64/libdl-2.11.1.so 7f3b97da1000-7f3b97da2000 rw-p 3000 00:0f 2285806 /lib64/libdl-2.11.1.so 7f3b97da2000-7f3b98233000 r-xp 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 00:00 0 7f3b98446000-7f3b98598000 r-xp 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 00:00 0 7f3b987a2000-7f3b98989000 r-xp 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 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
[gmx-users] segfault with an otherwise stable system when I turn on FEP (complete decoupling)
Dear Users: I have a system with water and a drug (54 total atoms; 27 heavy atoms). The system is stable when I simulate it for 1 ns. However, Once I add the following options to the .mdp file, the run dies after a few ps with a segfault. free-energy = yes init-lambda = 1 couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no couple-moltype = drug I do not get any step files or any lincs warnings. If I look at the .xtc and .edr files, there is no indication of something blowing up before the segfault. I have also verified that the drug runs without any problem in vacuum. I get the same behaviour if I remove constraints and use a timestep of 0.5 fs. The segfault is reproducible with v4.6.1 and v4.6.3. I am using the charmm FF, but I converted all UB angles in my drug to type-1 angles and still got the segfault. I also get the segfault with particle decomposition and/or while running a single thread. I am currently using the SD integrator, but I get the same segfault with md and md-vv. Couple-intramol=yes doesn't resolve it, neither does using separate T-coupling groups for the water and drug. Neither does turning off pressure coupling. Here is the .mdp file that works fine, but gives me a segfault when I add the free energy stuff (above): constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs integrator = sd dt = 0.002 tinit = 0 nsteps = 10 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 500 nstenergy = 500 nstlist = 10 nstlog=0 ; reduce log file size ns_type = grid vdwtype = cut-off rlist = 0.8 rvdw = 0.8 rcoulomb = 0.8 coulombtype = cut-off tc_grps = System tau_t = 1.0 ld_seed = -1 ref_t = 310 gen_temp = 310 gen_vel = yes unconstrained_start = no gen_seed = -1 Pcoupl = berendsen pcoupltype = isotropic tau_p = 4 compressibility = 4.5e-5 ref_p = 1.0 I do realize that some of these settings are not ideal for a production run. I started with the real Charmm cutoffs + PME, etc, (which also gives the segfault) but this is what I am using right now for quick testing. The only thing keeping me from filing a redmine issue is that if I remove my drug and do the FEP on one of the water molecules (using the FEP code listed above), I have no segfault. Therefore it is clearly related to the drug, whose parameters I built so I may have caused the problem somehow. Nevertheless, the drug runs fine in water and in vacuum without the FEP code, so I can't imagine what could be causing this segfault (also, the fact that it's a segfault means that I don;t get any useful info from mdrun as to what might be going wrong). Thank you, Chris. -- gmx-users mailing listgmx-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
Re: [gmx-users] segfault with an otherwise stable system when I turn on FEP (complete decoupling)
Chris, can you post a redmine on this so I can look at the files? Also, does it crash immediately, or after a while? On Thu, Jul 18, 2013 at 2:45 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Dear Users: I have a system with water and a drug (54 total atoms; 27 heavy atoms). The system is stable when I simulate it for 1 ns. However, Once I add the following options to the .mdp file, the run dies after a few ps with a segfault. free-energy = yes init-lambda = 1 couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no couple-moltype = drug I do not get any step files or any lincs warnings. If I look at the .xtc and .edr files, there is no indication of something blowing up before the segfault. I have also verified that the drug runs without any problem in vacuum. I get the same behaviour if I remove constraints and use a timestep of 0.5 fs. The segfault is reproducible with v4.6.1 and v4.6.3. I am using the charmm FF, but I converted all UB angles in my drug to type-1 angles and still got the segfault. I also get the segfault with particle decomposition and/or while running a single thread. I am currently using the SD integrator, but I get the same segfault with md and md-vv. Couple-intramol=yes doesn't resolve it, neither does using separate T-coupling groups for the water and drug. Neither does turning off pressure coupling. Here is the .mdp file that works fine, but gives me a segfault when I add the free energy stuff (above): constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs integrator = sd dt = 0.002 tinit = 0 nsteps = 10 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 500 nstenergy = 500 nstlist = 10 nstlog=0 ; reduce log file size ns_type = grid vdwtype = cut-off rlist = 0.8 rvdw = 0.8 rcoulomb = 0.8 coulombtype = cut-off tc_grps = System tau_t = 1.0 ld_seed = -1 ref_t = 310 gen_temp = 310 gen_vel = yes unconstrained_start = no gen_seed = -1 Pcoupl = berendsen pcoupltype = isotropic tau_p = 4 compressibility = 4.5e-5 ref_p = 1.0 I do realize that some of these settings are not ideal for a production run. I started with the real Charmm cutoffs + PME, etc, (which also gives the segfault) but this is what I am using right now for quick testing. The only thing keeping me from filing a redmine issue is that if I remove my drug and do the FEP on one of the water molecules (using the FEP code listed above), I have no segfault. Therefore it is clearly related to the drug, whose parameters I built so I may have caused the problem somehow. Nevertheless, the drug runs fine in water and in vacuum without the FEP code, so I can't imagine what could be causing this segfault (also, the fact that it's a segfault means that I don;t get any useful info from mdrun as to what might be going wrong). Thank you, Chris. -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] segfault with an otherwise stable system when I turn on FEP (complete decoupling)
Dear Michael: I have uploaded them as http://redmine.gromacs.org/issues/1306 It does not crash immediately. The crash is stochastic, giving a segfault between 200 and 5000 integration steps. That made me think it was a simple exploding system problem, but there are other things (listed in my original post) that make me think otherwise. Most notably, the drug is fine in both water and vacuum. I have also built numerous systems and get the crash in each one. My actual production system also has a protein, but during debugging I found that the error persists in a simple and small water solution. Thank you for your assistance. Chris. -- original message -- Chris, can you post a redmine on this so I can look at the files? Also, does it crash immediately, or after a while? On Thu, Jul 18, 2013 at 2:45 PM, Christopher Neale chris.neale at mail.utoronto.ca wrote: Dear Users: I have a system with water and a drug (54 total atoms; 27 heavy atoms). The system is stable when I simulate it for 1 ns. However, Once I add the following options to the .mdp file, the run dies after a few ps with a segfault. free-energy = yes init-lambda = 1 couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no couple-moltype = drug I do not get any step files or any lincs warnings. If I look at the .xtc and .edr files, there is no indication of something blowing up before the segfault. I have also verified that the drug runs without any problem in vacuum. I get the same behaviour if I remove constraints and use a timestep of 0.5 fs. The segfault is reproducible with v4.6.1 and v4.6.3. I am using the charmm FF, but I converted all UB angles in my drug to type-1 angles and still got the segfault. I also get the segfault with particle decomposition and/or while running a single thread. I am currently using the SD integrator, but I get the same segfault with md and md-vv. Couple-intramol=yes doesn't resolve it, neither does using separate T-coupling groups for the water and drug. Neither does turning off pressure coupling. Here is the .mdp file that works fine, but gives me a segfault when I add the free energy stuff (above): constraints = all-bonds lincs-iter = 1 lincs-order = 6 constraint_algorithm = lincs integrator = sd dt = 0.002 tinit = 0 nsteps = 10 nstcomm = 1 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 500 nstenergy = 500 nstlist = 10 nstlog=0 ; reduce log file size ns_type = grid vdwtype = cut-off rlist = 0.8 rvdw = 0.8 rcoulomb = 0.8 coulombtype = cut-off tc_grps = System tau_t = 1.0 ld_seed = -1 ref_t = 310 gen_temp = 310 gen_vel = yes unconstrained_start = no gen_seed = -1 Pcoupl = berendsen pcoupltype = isotropic tau_p = 4 compressibility = 4.5e-5 ref_p = 1.0 I do realize that some of these settings are not ideal for a production run. I started with the real Charmm cutoffs + PME, etc, (which also gives the segfault) but this is what I am using right now for quick testing. The only thing keeping me from filing a redmine issue is that if I remove my drug and do the FEP on one of the water molecules (using the FEP code listed above), I have no segfault. Therefore it is clearly related to the drug, whose parameters I built so I may have caused the problem somehow. Nevertheless, the drug runs fine in water and in vacuum without the FEP code, so I can't imagine what could be causing this segfault (also, the fact that it's a segfault means that I don;t get any useful info from mdrun as to what might be going wrong). Thank you, Chris. -- gmx-users mailing listgmx-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
[gmx-users] Multi-level parallelization: MPI + OpenMP
Dear all, I'm note a gromacs user, I've installed gromacs 4.6.3 on our cluster and making some test. Each node of our machine has 16 cores and 2 GPU. I'm trying to figure how to submit efficient multiple nodes LSF jobs using the maximum of resources. After reading the documentation http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores on Acceleration and parallelization I got confused and inquire some help. I'm just wondering whether someone with some experiences on this matter. I thank you in advance, Éric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Éric Germaneau http://hpc.sjtu.edu.cn/index.htm Shanghai Jiao Tong University Network Information Center room 205 Minhang Campus 800 Dongchuan Road Shanghai 200240 China View Éric Germaneau's profile on LinkedIn http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986 /Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ -- gmx-users mailing listgmx-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
[gmx-users] g_hbond for trajectory without having box information
Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-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
Re: [gmx-users] g_hbond for trajectory without having box information
On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
Re: [gmx-users] g_hbond for trajectory without having box information
Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-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
