1: [hbond HB out nhb-lip-wat.dat :PC avgout solute_avg-lip-wat.dat solventacceptor :WAT@O solventdonor :WAT solvout solvent_avg-lip-wat.dat bridgeout bridge-lip-wat.dat] Acceptor-only atoms: 1152 Donor/acceptor sites: 0 Donor-only sites: 0 0 solute hydrogens. Solvent sites (3712) 7424 solvent hydrogens, 0 ions. Estimated max potential memory usage: 170.568 kB ----- 05_Prod_1.nc (1-1000, 1) ----- ... ... ... ----- 05_Prod_419.nc (1-1000, 1) ----- ----- 05_Prod_420.nc (1-1000, 1) ----- 100% Complete. Read 420000 frames and processed 420000 frames. TIME: Avg. throughput= 37.9878 frames / second. ACTION OUTPUT: HBOND: Actual memory usage is 128.984 kB 0 solute-solute hydrogen bonds. 1024 solute-solvent hydrogen bonds. 763 unique solute-solvent bridging interactions. TIME: Analyses took 0.0202 seconds. DATASETS (4 total): HB[UU] "HB[UU]" (integer), size is 420000 (1.680 MB) HB[UV] "HB[UV]" (integer), size is 420000 (1.680 MB) HB[Bridge] "HB[Bridge]" (integer), size is 420000 (1.680 MB) HB[ID] "HB[ID]" (string), size is 420000 (343.805 MB) Total data set memory usage is at least 348.845 MB DATAFILES (4 total): nhb-lip-wat.dat (Standard Data File): HB[UU] HB[UV] HB[Bridge] HB[ID] solute_avg-lip-wat.dat (Avg. solute-solute HBonds) solvent_avg-lip-wat.dat (Avg. solute-solvent HBonds) bridge-lip-wat.dat (Solvent bridging info) *** buffer overflow detected ***: cpptraj.OMP terminated ======= Backtrace: ========= /lib/i386-linux-gnu/libc.so.6(+0x67377)[0xb72e4377] /lib/i386-linux-gnu/libc.so.6(__fortify_fail+0x68)[0xb7374708] /lib/i386-linux-gnu/libc.so.6(+0xf58f8)[0xb73728f8] /lib/i386-linux-gnu/libc.so.6(+0xf50d8)[0xb73720d8] /lib/i386-linux-gnu/libc.so.6(_IO_default_xsputn+0x74)[0xb72e82d4] /lib/i386-linux-gnu/libc.so.6(+0x40904)[0xb72bd904] /lib/i386-linux-gnu/libc.so.6(_IO_vfprintf+0x341)[0xb72bf401] /lib/i386-linux-gnu/libc.so.6(__vsprintf_chk+0x8d)[0xb737216d] cpptraj.OMP[0x82e755e] cpptraj.OMP[0x8353a96] cpptraj.OMP[0x8323b92] cpptraj.OMP[0x832d0a0] cpptraj.OMP[0x82f3a8a] cpptraj.OMP[0x82f3c26] cpptraj.OMP[0x82f52de] cpptraj.OMP[0x82f6f3b] cpptraj.OMP[0x82e98cc] cpptraj.OMP[0x82ec94b] cpptraj.OMP[0x845beb1] cpptraj.OMP[0x845c78e] cpptraj.OMP[0x8053e90] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf7)[0xb7295637] cpptraj.OMP[0x8053ecb] ======= Memory map: ======== 08048000-087d4000 r-xp 00000000 08:01 27273684 /home/somdev/software/amber18/bin/cpptraj.OMP 087d5000-087e3000 r--p 0078c000 08:01 27273684 /home/somdev/software/amber18/bin/cpptraj.OMP 087e3000-087e7000 rw-p 0079a000 08:01 27273684 /home/somdev/software/amber18/bin/cpptraj.OMP 087e7000-087ff000 rw-p 00000000 00:00 0 08d6d000-275dc000 rw-p 00000000 00:00 0 [heap] b1d00000-b1d21000 rw-p 00000000 00:00 0 b1d21000-b1e00000 ---p 00000000 00:00 0 b1e00000-b1e21000 rw-p 00000000 00:00 0 b1e21000-b1f00000 ---p 00000000 00:00 0 b1f00000-b1f21000 rw-p 00000000 00:00 0 b1f21000-b2000000 ---p 00000000 00:00 0 b2000000-b2021000 rw-p 00000000 00:00 0 b2021000-b2100000 ---p 00000000 00:00 0 b2100000-b2121000 rw-p 00000000 00:00 0 b2121000-b2200000 ---p 00000000 00:00 0 b2200000-b2221000 rw-p 00000000 00:00 0 b2221000-b2300000 ---p 00000000 00:00 0 b2300000-b2321000 rw-p 00000000 00:00 0 b2321000-b2400000 ---p 00000000 00:00 0 b2503000-b31d6000 rw-p 00000000 00:00 0 b31d6000-b31d7000 ---p 00000000 00:00 0 b31d7000-b39d7000 rw-p 00000000 00:00 0 b39d7000-b39d8000 ---p 00000000 00:00 0 b39d8000-b41d8000 rw-p 00000000 00:00 0 b41d8000-b41d9000 ---p 00000000 00:00 0 b41d9000-b49d9000 rw-p 00000000 00:00 0 b49d9000-b49da000 ---p 00000000 00:00 0 b49da000-b51da000 rw-p 00000000 00:00 0 b51da000-b51db000 ---p 00000000 00:00 0 b51db000-b59db000 rw-p 00000000 00:00 0 b59db000-b59dc000 ---p 00000000 00:00 0 b59dc000-b61dc000 rw-p 00000000 00:00 0 b61dc000-b61dd000 ---p 00000000 00:00 0 b61dd000-b6b5e000 rw-p 00000000 00:00 0 b6b65000-b6d81000 rw-p 00000000 00:00 0 b6d8f000-b71e3000 rw-p 00000000 00:00 0 b71e3000-b71e6000 r-xp 00000000 08:01 27530094 /lib/i386-linux-gnu/libdl-2.23.so b71e6000-b71e7000 r--p 00002000 08:01 27530094 /lib/i386-linux-gnu/libdl-2.23.so b71e7000-b71e8000 rw-p 00003000 08:01 27530094 /lib/i386-linux-gnu/libdl-2.23.so b71e8000-b727a000 r-xp 00000000 08:01 6819281 /usr/lib/i386-linux-gnu/libquadmath.so.0.0.0 b727a000-b727b000 r--p 00091000 08:01 6819281 /usr/lib/i386-linux-gnu/libquadmath.so.0.0.0 b727b000-b727c000 rw-p 00092000 08:01 6819281 /usr/lib/i386-linux-gnu/libquadmath.so.0.0.0 b727c000-b727d000 rw-p 00000000 00:00 0 b727d000-b742d000 r-xp 00000000 08:01 27530092 /lib/i386-linux-gnu/libc-2.23.so b742d000-b742f000 r--p 001af000 08:01 27530092 /lib/i386-linux-gnu/libc-2.23.so b742f000-b7430000 rw-p 001b1000 08:01 27530092 /lib/i386-linux-gnu/libc-2.23.so b7430000-b7433000 rw-p 00000000 00:00 0 b7433000-b744c000 r-xp 00000000 08:01 27530091 /lib/i386-linux-gnu/libpthread-2.23.so b744c000-b744d000 r--p 00018000 08:01 27530091 /lib/i386-linux-gnu/libpthread-2.23.so b744d000-b744e000 rw-p 00019000 08:01 27530091 /lib/i386-linux-gnu/libpthread-2.23.so b744e000-b7450000 rw-p 00000000 00:00 0 b7450000-b746c000 r-xp 00000000 08:01 27526486 /lib/i386-linux-gnu/libgcc_s.so.1 b746c000-b746d000 rw-p 0001b000 08:01 27526486 /lib/i386-linux-gnu/libgcc_s.so.1 b746d000-b748f000 r-xp 00000000 08:01 6816135 /usr/lib/i386-linux-gnu/libgomp.so.1.0.0 b748f000-b7490000 r--p 00021000 08:01 6816135 /usr/lib/i386-linux-gnu/libgomp.so.1.0.0 b7490000-b7491000 rw-p 00022000 08:01 6816135 /usr/lib/i386-linux-gnu/libgomp.so.1.0.0 b7491000-b74e4000 r-xp 00000000 08:01 27530088 /lib/i386-linux-gnu/libm-2.23.so b74e4000-b74e5000 r--p 00052000 08:01 27530088 /lib/i386-linux-gnu/libm-2.23.so b74e5000-b74e6000 rw-p 00053000 08:01 27530088 /lib/i386-linux-gnu/libm-2.23.so b74e6000-b74e7000 rw-p 00000000 00:00 0 b74e7000-b7654000 r-xp 00000000 08:01 6819291 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.21 b7654000-b7655000 ---p 0016d000 08:01 6819291 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.21 b7655000-b765a000 r--p 0016d000 08:01 6819291 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.21 b765a000-b765b000 rw-p 00172000 08:01 6819291 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.21 b765b000-b765e000 rw-p 00000000 00:00 0 b765e000-b7677000 r-xp 00000000 08:01 27526637 /lib/i386-linux-gnu/libz.so.1.2.8 b7677000-b7678000 r--p 00018000 08:01 27526637 /lib/i386-linux-gnu/libz.so.1.2.8 b7678000-b7679000 rw-p 00019000 08:01 27526637 /lib/i386-linux-gnu/libz.so.1.2.8 b7679000-b7689000 r-xp 00000000 08:01 27526447 /lib/i386-linux-gnu/libbz2.so.1.0.4 b7689000-b768a000 r--p 0000f000 08:01 27526447 /lib/i386-linux-gnu/libbz2.so.1.0.4 b768a000-b768b000 rw-p 00010000 08:01 27526447 /lib/i386-linux-gnu/libbz2.so.1.0.4 b768b000-b7798000 r-xp 00000000 08:01 6815773 /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0 b7798000-b7799000 ---p 0010d000 08:01 6815773 /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0 b7799000-b779a000 r--p 0010d000 08:01 6815773 /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0 b779a000-b779b000 rw-p 0010e000 08:01 6815773 /usr/lib/i386-linux-gnu/libgfortran.so.3.0.0 b77bc000-b77be000 rw-p 00000000 00:00 0 b77be000-b77c1000 r--p 00000000 00:00 0 [vvar] b77c1000-b77c2000 r-xp 00000000 00:00 0 [vdso] b77c2000-b77e5000 r-xp 00000000 08:01 27530090 /lib/i386-linux-gnu/ld-2.23.so b77e5000-b77e6000 r--p 00022000 08:01 27530090 /lib/i386-linux-gnu/ld-2.23.so b77e6000-b77e7000 rw-p 00023000 08:01 27530090 /lib/i386-linux-gnu/ld-2.23.so bf88a000-bf8ac000 rw-p 00000000 00:00 0 [stack] Aborted (core dumped)