[gmx-users] strange do_dssp error

[rajat desikan]

Update for anyone interested: Installing dssp 2.2.1 solved the above error!
I am not sure why...


On Sun, Feb 9, 2014 at 11:39 AM, rajat desikan <rajatdesikan at gmail.com>wrote:

> Hi All,
> I get this error while running do_dssp. The program reads the whole
> trajectory but fails to write a scount file. gmxcheck on the trajectory
> shows no problems. Any suggestions?
> (P.S. do_dssp worked fine on another simulation trajectory of similar
> size. To make sure that this was not a memory related issue, I ran this on
> my cluster too. Same fault.)
>
> Selected 36: 'HelixA'
> There are 324 residues in your selected group
> dssp cmd='/home/rajatdesikan/Desktop/dssp-2.0.4-linux-i386 -i ddT5iGbw -o
> ddOpjxP3 > /dev/null 2> /dev/null'
> Reading frame       0 time    0.000
> Back Off! I just backed up ddT5iGbw to ./#ddT5iGbw.1#
> Reading frame   20000 time 100000.000
>
>
> Back Off! I just backed up SS/protmem_ss_A.xpm to SS/#protmem_ss_A.xpm.1#
> 100%
> Back Off! I just backed up SS/protmem_ssdump_A.dat to
> SS/#protmem_ssdump_A.dat.1#
> *** glibc detected *** do_dssp: double free or corruption (!prev):
> 0x00000000029ad9c0 ***
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f68b0a8db96]
> do_dssp(gmx_do_dssp+0x3146)[0x41d5d6]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f68b0a3076d]
> do_dssp[0x419111]
> ======= Memory map: ========
> 00400000-00877000 r-xp 00000000 08:06 6352669
> /opt/apps/gromacs/4.6.3/gnu/serial/bin/do_dssp
> 00a76000-00a77000 r--p 00476000 08:06 6352669
> /opt/apps/gromacs/4.6.3/gnu/serial/bin/do_dssp
> 00a77000-00a88000 rw-p 00477000 08:06 6352669
> /opt/apps/gromacs/4.6.3/gnu/serial/bin/do_dssp
> 00a88000-00a89000 rw-p 00000000 00:00 0
> 023b5000-0365e000 rw-p 00000000 00:00 0
> [heap]
> 7f68aec20000-7f68aec35000 r-xp 00000000 08:06 3014802
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f68aec35000-7f68aee34000 ---p 00015000 08:06 3014802
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f68aee34000-7f68aee35000 r--p 00014000 08:06 3014802
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f68aee35000-7f68aee36000 rw-p 00015000 08:06 3014802
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f68aee36000-7f68afbf0000 rw-p 00000000 00:00 0
> 7f68afce4000-7f68b0807000 rw-p 00000000 00:00 0
> 7f68b0807000-7f68b080e000 r-xp 00000000 08:06 3014971
> /lib/x86_64-linux-gnu/librt-2.15.so
> 7f68b080e000-7f68b0a0d000 ---p 00007000 08:06 3014971
> /lib/x86_64-linux-gnu/librt-2.15.so
> 7f68b0a0d000-7f68b0a0e000 r--p 00006000 08:06 3014971
> /lib/x86_64-linux-gnu/librt-2.15.so
> 7f68b0a0e000-7f68b0a0f000 rw-p 00007000 08:06 3014971
> /lib/x86_64-linux-gnu/librt-2.15.so
> 7f68b0a0f000-7f68b0bc4000 r-xp 00000000 08:06 3014963
> /lib/x86_64-linux-gnu/libc-2.15.so
> 7f68b0bc4000-7f68b0dc4000 ---p 001b5000 08:06 3014963
> /lib/x86_64-linux-gnu/libc-2.15.so
> 7f68b0dc4000-7f68b0dc8000 r--p 001b5000 08:06 3014963
> /lib/x86_64-linux-gnu/libc-2.15.so
> 7f68b0dc8000-7f68b0dca000 rw-p 001b9000 08:06 3014963
> /lib/x86_64-linux-gnu/libc-2.15.so
> 7f68b0dca000-7f68b0dcf000 rw-p 00000000 00:00 0
> 7f68b0dcf000-7f68bG0ddc000 r-xp 00000000 08:06 4064338
> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
> 7f68b0ddc000-7f68b0fdb000 ---p 0000d000 08:06 4064338
> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
> 7f68b0fdb000-7f68b0fdc000 r--p 0000c000 08:06 4064338
> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
> 7f68b0fdc000-7f68b0fdd000 rw-p 0000d000 08:06 4064338
> /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
> 7f68b0fdd000-7f68b0ff5000 r-xp 00000000 08:06 3014974
> /lib/x86_64-linux-gnu/libpthread-2.15.so
> 7f68b0ff5000-7f68b11f4000 ---p 00018000 08:06 3014974
> /lib/x86_64-linux-gnu/libpthread-2.15.so
> 7f68b11f4000-7f68b11f5000 r--p 00017000 08:06 3014974
> /lib/x86_64-linux-gnu/libpthread-2.15.so
> 7f68b11f5000-7f68b11f6000 rw-p 00018000 08:06 3014974
> /lib/x86_64-linux-gnu/libpthread-2.15.so
> 7f68b11f6000-7f68b11fa000 rw-p 00000000 00:00 0
> 7f68b11fa000-7f68b12f5000 r-xp 00000000 08:06 3014978
> /lib/x86_64-linux-gnu/libm-2.15.so
> 7f68b12f5000-7f68b14f4000 ---p 000fb000 08:06 3014978
> /lib/x86_64-linux-gnu/libm-2.15.so
> 7f68b14f4000-7f68b14f5000 r--p 000fa000 08:06 3014978
> /lib/x86_64-linux-gnu/libm-2.15.so
> 7f68b14f5000-7f68b14f6000 rw-p 000fb000 08:06 3014978
> /lib/x86_64-linux-gnu/libm-2.15.so
> 7f68b14f6000-7f68b1518000 r-xp 00000000 08:06 3014980
> /lib/x86_64-linux-gnu/ld-2.15.so
> 7f68b151b000-7f68b1550000 rw-p 00000000 00:00 0
> 7f68b1624000-7f68b16f5000 rw-p 00000000 00:00 0
> 7f68b1712000-7f68b1718000 rw-p 00000000 00:00 0
> 7f68b1718000-7f68b1719000 r--p 00022000 08:06 3014980
> /lib/x86_64-linux-gnu/ld-2.15.so
> 7f68b1719000-7f68b171b000 rw-p 00023000 08:06 3014980
> /lib/x86_64-linux-gnu/ld-2.15.so
> 7fff6c5e2000-7fff6c603000 rw-p 00000000 00:00 0
> [stack]
> 7fff6c657000-7fff6c658000 r-xp 00000000 00:00 0
> [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
> [vsyscall]
> Aborted (core dumped)
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore