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 <rajatdesi...@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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.