[gmx-users] Re: g_density fails after calculating for the last snapshot

Rajat Desikan rajatdesikan at gmail.com
Sun Mar 10 09:20:13 CET 2013 

Hi All
Thanks to Christopher Neale for his comments. There was a frame missing.
But the frame was nowhere near the end. I played around with the trajectory
and timestamps, got rid of that frame and obtained the density.
Interestingly, g_density in version 4.5.4 was able to run the .xtc. It
mentioned that there was a frame missing, but it gave me the right output.


On Fri, Mar 8, 2013 at 9:25 PM, Christopher Neale [via GROMACS] <
ml-node+s5086n5006228h13 at n6.nabble.com> wrote:

> What output do you get from gmxcheck -f martin_md_290K_100ns_tau1.xtc ?
> Also, can you extract that problematic frame with trjconv and run g_density
> on that one frame (what happens?). Also, can you make a new .xtc that is
> missing that last frame and see what g_density does?
>
> These will help you to figure out what is going on.
>
> Chris.
>
> -- original message --
>
> Hi All
> I have a 100 ns lipid simulation for which I want the density profile. I
> issued the following command
>
> g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s
> martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 50000
>
> The program fails with the following message
>
> Selected 3: 'Water'
> Last frame      25000 time 100000.000
> *** glibc detected *** g_density: munmap_chunk(): invalid pointer:
> 0x0000000000d655d0 ***
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fb120a73b96]
> /usr/lib/libgmxana.so.6(calc_density+0x30c)[0x7fb120e14bec]
> /usr/lib/libgmxana.so.6(gmx_density+0x42b)[0x7fb120e1541b]
> g_density(main+0x9)[0x400629]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fb120a1676d]
> g_density[0x400659]
> ======= Memory map: ========
> 00400000-00401000 r-xp 00000000 08:06 4099695
>  /usr/bin/g_density
> 00600000-00601000 r--p 00000000 08:06 4099695
>  /usr/bin/g_density
> 00601000-00602000 rw-p 00001000 08:06 4099695
>  /usr/bin/g_density
> 00d57000-00e57000 rw-p 00000000 00:00 0
>  [heap]
> 7fb11f003000-7fb11f018000 r-xp 00000000 08:06 3014802
>  /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7fb11f018000-7fb11f217000 ---p 00015000 08:06 3014802
>  /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7fb11f217000-7fb11f218000 r--p 00014000 08:06 3014802
>  /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7fb11f218000-7fb11f219000 rw-p 00015000 08:06 3014802
>  /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7fb11f239000-7fb11f26c000 rw-p 00000000 00:00 0
> 7fb11f26c000-7fb11f282000 r-xp 00000000 08:06 3015169
>  /lib/x86_64-linux-gnu/libz.so.1.2.3.4
> 7fb11f282000-7fb11f481000 ---p 00016000 08:06 3015169
>  /lib/x86_64-linux-gnu/libz.so.1.2.3.4
> 7fb11f481000-7fb11f482000 r--p 00015000 08:06 3015169
>  /lib/x86_64-linux-gnu/libz.so.1.2.3.4
> 7fb11f482000-7fb11f483000 rw-p 00016000 08:06 3015169
>  /lib/x86_64-linux-gnu/libz.so.1.2.3.4
> 7fb11f483000-7fb11f485000 r-xp 00000000 08:06 3014907
>  /lib/x86_64-linux-gnu/libdl-2.15.so
> 7fb11f485000-7fb11f685000 ---p 00002000 08:06 3014907
>  /lib/x86_64-linux-gnu/libdl-2.15.so
> 7fb11f685000-7fb11f686000 r--p 00002000 08:06 3014907
>  /lib/x86_64-linux-gnu/libdl-2.15.so
> 7fb11f686000-7fb11f687000 rw-p 00003000 08:06 3014907
>  /lib/x86_64-linux-gnu/libdl-2.15.so
> 7fb11f687000-7fb11f7d8000 r-xp 00000000 08:06 4070629
>  /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
> 7fb11f7d8000-7fb11f9d7000 ---p 00151000 08:06 4070629
>  /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
> 7fb11f9d7000-7fb11f9df000 r--p 00150000 08:06 4070629
>  /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
> 7fb11f9df000-7fb11f9e1000 rw-p 00158000 08:06 4070629
>  /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
> 7fb11f9e1000-7fb11f9e2000 rw-p 00000000 00:00 0
> 7fb11f9e2000-7fb11fb46000 r-xp 00000000 08:06 4064740
>  /usr/lib/libfftw3f.so.3.3.0
> 7fb11fb46000-7fb11fd45000 ---p 00164000 08:06 4064740
>  /usr/lib/libfftw3f.so.3.3.0
> 7fb11fd45000-7fb11fd51000 r--p 00163000 08:06 4064740
>  /usr/lib/libfftw3f.so.3.3.0
> 7fb11fd51000-7fb11fd52000 rw-p 0016f000 08:06 4064740
>  /usr/lib/libfftw3f.so.3.3.0
> 7fb11fd52000-7fb11fe4d000 r-xp 00000000 08:06 3014916
>  /lib/x86_64-linux-gnu/libm-2.15.so
> 7fb11fe4d000-7fb12004c000 ---p 000fb000 08:06 3014916
>  /lib/x86_64-linux-gnu/libm-2.15.so
> 7fb12004c000-7fb12004d000 r--p 000fa000 08:06 3014916
>  /lib/x86_64-linux-gnu/libm-2.15.so
> 7fb12004d000-7fb12004e000 rw-p 000fb000 08:06 3014916
>  /lib/x86_64-linux-gnu/libm-2.15.so
> 7fb12004e000-7fb120066000 r-xp 00000000 08:06 3014910
>  /lib/x86_64-linux-gnu/libpthread-2.15.so
> 7fb120066000-7fb120265000 ---p 00018000 08:06 3014910
>  /lib/x86_64-linux-gnu/libpthread-2.15.so
> 7fb120265000-7fb120266000 r--p 00017000 08:06 3014910
>  /lib/x86_64-linux-gnu/libpthread-2.15.so
> 7fb120266000-7fb120267000 rw-p 00018000 08:06 3014910
>  /lib/x86_64-linux-gnu/libpthread-2.15.so
> 7fb120267000-7fb12026b000 rw-p 00000000 00:00 0
> 7fb12026b000-7fb1204f9000 r-xp 00000000 08:06 4099651
>  /usr/lib/libgmx.so.6
> 7fb1204f9000-7fb1206f8000 ---p 0028e000 08:06 4099651
>  /usr/lib/libgmx.so.6
> 7fb1206f8000-7fb1206fe000 r--p 0028d000 08:06 4099651
>  /usr/lib/libgmx.so.6
> 7fb1206fe000-7fb120707000 rw-p 00293000 08:06 4099651
>  /usr/lib/libgmx.so.6
> 7fb120707000-7fb120708000 rw-p 00000000 00:00 0
> 7fb120708000-7fb1207f3000 r-xp 00000000 08:06 4099652
>  /usr/lib/libmd.so.6
> 7fb1207f3000-7fb1209f3000 ---p 000eb000 08:06 4099652
>  /usr/lib/libmd.so.6
> 7fb1209f3000-7fb1209f4000 r--p 000eb000 08:06 4099652
>  /usr/lib/libmd.so.6
> 7fb1209f4000-7fb1209f5000 rw-p 000ec000 08:06 4099652
>  /usr/lib/libmd.so.6
> 7fb1209f5000-7fb120baa000 r-xp 00000000 08:06 3014908
>  /lib/x86_64-linux-gnu/libc-2.15.so
> 7fb120baa000-7fb120da9000 ---p 001b5000 08:06 3014908
>  /lib/x86_64-linux-gnu/libc-2.15.so
> 7fb120da9000-7fb120dad000 r--p 001b4000 08:06 3014908
>  /lib/x86_64-linux-gnu/libc-2.15.so
> 7fb120dad000-7fb120daf000 rw-p 001b8000 08:06 3014908
>  /lib/x86_64-linux-gnu/libc-2.15.so
> 7fb120daf000-7fb120db4000 rw-p 00000000 00:00 0
> 7fb120db4000-7fb120f38000 r-xp 00000000 08:06 4099654
>  /usr/lib/libgmxana.so.6
> 7fb120f38000-7fb121138000 ---p 00184000 08:06 4099654
>  /usr/lib/libgmxana.so.6
> 7fb121138000-7fb121139000 r--p 00184000 08:06 4099654
>  /usr/lib/libgmxana.so.6
> 7fb121139000-7fb121144000 rw-p 00185000 08:06 4099654
>  /usr/lib/libgmxana.so.6
> 7fb121144000-7fb121146000 rw-p 00000000 00:00 0
> 7fb121146000-7fb121168000 r-xp 00000000 08:06 3014922
>  /lib/x86_64-linux-gnu/ld-2.15.so
> 7fb121180000-7fb1211c5000 rw-p 00000000 00:00 0
> 7fb1211cd000-7fb1211ef000 rw-p 00000000 00:00 0
> 7fb1211ef000-7fb121288000 rw-p 00000000 00:00 0
> 7fb12129f000-7fb1212c1000 rw-p 00000000 00:00 0
> 7fb1212c1000-7fb121310000 rw-p 00000000 00:00 0
> 7fb12131d000-7fb121346000 rw-p 00000000 00:00 0
> 7fb121362000-7fb121368000 rw-p 00000000 00:00 0
> 7fb121368000-7fb121369000 r--p 00022000 08:06 3014922
>  /lib/x86_64-linux-gnu/ld-2.15.so
> 7fb121369000-7fb12136b000 rw-p 00023000 08:06 3014922
>  /lib/x86_64-linux-gnu/ld-2.15.so
> 7fff7be01000-7fff7be21000 rwxp 00000000 00:00 0
>  [stack]
> 7fff7be21000-7fff7be22000 rw-p 00000000 00:00 0
> 7fff7bf39000-7fff7bf3a000 r-xp 00000000 00:00 0
>  [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>  [vsyscall]
> Aborted (core dumped)
>
> I reinstalled gromacs on my system, but the problem persists. Can somebody
> please help?
>
> Thanks.
> --
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore




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