[gmx-users] g_density fails after calculating for the last snapshot
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 5 The program fails with the following message Selected 3: 'Water' Last frame 25000 time 10.000 *** glibc detected *** g_density: munmap_chunk(): invalid pointer: 0x00d655d0 *** === 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: 0040-00401000 r-xp 08:06 4099695 /usr/bin/g_density 0060-00601000 r--p 08:06 4099695 /usr/bin/g_density 00601000-00602000 rw-p 1000 08:06 4099695 /usr/bin/g_density 00d57000-00e57000 rw-p 00:00 0 [heap] 7fb11f003000-7fb11f018000 r-xp 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 00:00 0 7fb11f26c000-7fb11f282000 r-xp 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 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f485000-7fb11f685000 ---p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f685000-7fb11f686000 r--p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f686000-7fb11f687000 rw-p 3000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f687000-7fb11f7d8000 r-xp 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 0015 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 00:00 0 7fb11f9e2000-7fb11fb46000 r-xp 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 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 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 00:00 0 7fb12026b000-7fb1204f9000 r-xp 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 00:00 0 7fb120708000-7fb1207f3000 r-xp 08:06 4099652 /usr/lib/libmd.so.6 7fb1207f3000-7fb1209f3000 ---p 000eb000 08:06 4099652 /usr/lib/libmd.so.6 7fb1209f3000-7fb1209f4000
[gmx-users] g_density fails after calculating for the last snapshot
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 5 The program fails with the following message Selected 3: 'Water' Last frame 25000 time 10.000 *** glibc detected *** g_density: munmap_chunk(): invalid pointer: 0x00d655d0 *** === 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: 0040-00401000 r-xp 08:06 4099695 /usr/bin/g_density 0060-00601000 r--p 08:06 4099695 /usr/bin/g_density 00601000-00602000 rw-p 1000 08:06 4099695 /usr/bin/g_density 00d57000-00e57000 rw-p 00:00 0 [heap] 7fb11f003000-7fb11f018000 r-xp 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 00:00 0 7fb11f26c000-7fb11f282000 r-xp 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 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f485000-7fb11f685000 ---p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f685000-7fb11f686000 r--p 2000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f686000-7fb11f687000 rw-p 3000 08:06 3014907 /lib/x86_64-linux-gnu/libdl-2.15.so 7fb11f687000-7fb11f7d8000 r-xp 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 0015 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 00:00 0 7fb11f9e2000-7fb11fb46000 r-xp 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 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 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 00:00 0 7fb12026b000-7fb1204f9000 r-xp 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
