Buffer overflow when calculating timmin on more than 95665 timesteps
Added by Nick Young almost 5 years ago
Hi,
I keep getting a buffer overflow error when trying to calculate timmin on the attached file. The file has 311,160 timesteps, but the error occurs for any selection greater than 95,665. I am using Ubuntu 16.04.5 LTS. I tried with both cdo 1.7.0 from apt and cdo 1.9.6 which I compiled, and both versions had the same problem.
cdo -V
Climate Data Operators version 1.9.6 (http://mpimet.mpg.de/cdo)
System: x86_64-pc-linux-gnu
CXX Compiler: g++ -std=gnu++11 -g -O2 -fopenmp
CXX version : g++ (Ubuntu 5.4.0-6ubuntu1~16.04.10) 5.4.0 20160609
C Compiler: gcc -g -O2 -fopenmp
C version : gcc (Ubuntu 5.4.0-6ubuntu1~16.04.10) 5.4.0 20160609
F77 Compiler:
Features: 125GB 40threads C++11 DATA PTHREADS OpenMP4 NC4/HDF5 OPeNDAP SSE2
Libraries:
Filetypes: srv ext ieg grb1 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.6
cgribex library version : 1.9.2
NetCDF library version : 4.4.0 of Mar 29 2016 11:41:40 $
hdf5 library version : library undefined
exse library version : 1.4.1
FILE library version : 1.8.3
nyou045@ml:/mnt/ssd2/CAWCR/CgE$ cdo timmin -seltimestep,1/95665 0_0.nc test.nc
cdo(2) seltimestep: Process started
Warning (splitTimevalue): Reset wrong date/time to 0000-01-01 00:00:00!
cdo(2) seltimestep: Processed 95665 values from 1 variable over 95666 timesteps
cdo timmin: Processed 95665 values from 1 variable [6.40s 95MB]
nyou045@ml:/mnt/ssd2/CAWCR/CgE$ cdo timmin -seltimestep,1/95666 0_0.nc test.nc
cdo(2) seltimestep: Process started
Warning (splitTimevalue): Reset wrong date/time to 0000-01-01 00:00:00!
*** buffer overflow detected ***: cdo terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7ff7f5aad7e5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7ff7f5b4f15c]
/lib/x86_64-linux-gnu/libc.so.6(+0x117160)[0x7ff7f5b4d160]
/lib/x86_64-linux-gnu/libc.so.6(+0x1166c9)[0x7ff7f5b4c6c9]
/lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0x80)[0x7ff7f5ab16b0]
/lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0xc90)[0x7ff7f5a83e00]
/lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x84)[0x7ff7f5b4c754]
/lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x7d)[0x7ff7f5b4c6ad]
cdo[0x5115ee]
cdo[0x5ae7e9]
cdo[0x5a8b81]
cdo[0x42677d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7ff7f5a56830]
cdo[0x446819]
======= Memory map: ========
00400000-008ca000 r-xp 00000000 fd:00 17040151 /usr/local/bin/cdo
00aca000-00ad8000 r--p 004ca000 fd:00 17040151 /usr/local/bin/cdo
00ad8000-00ada000 rw-p 004d8000 fd:00 17040151 /usr/local/bin/cdo
00ada000-00afd000 rw-p 00000000 00:00 0
011b3000-01380000 rw-p 00000000 00:00 0 [heap]
7ff7e71fd000-7ff7e79fe000 rw-p 00000000 00:00 0
7ff7e8000000-7ff7e9136000 rw-p 00000000 00:00 0
7ff7e9136000-7ff7ec000000 ---p 00000000 00:00 0
7ff7ec2bc000-7ff7efcb8000 rw-p 00000000 00:00 0
7ff7efcb8000-7ff7efcb9000 ---p 00000000 00:00 0
7ff7efcb9000-7ff7f04b9000 rw-p 00000000 00:00 0
7ff7f04b9000-7ff7f04c2000 r-xp 00000000 fd:00 40112554 /lib/x86_64-linux-gnu/libcrypt-2.23.so
7ff7f04c2000-7ff7f06c1000 ---p 00009000 fd:00 40112554 /lib/x86_64-linux-gnu/libcrypt-2.23.so
7ff7f06c1000-7ff7f06c2000 r--p 00008000 fd:00 40112554 /lib/x86_64-linux-gnu/libcrypt-2.23.so
7ff7f06c2000-7ff7f06c3000 rw-p 00009000 fd:00 40112554 /lib/x86_64-linux-gnu/libcrypt-2.23.so
7ff7f06c3000-7ff7f06f1000 rw-p 00000000 00:00 0
7ff7f06f1000-7ff7f07c0000 r-xp 00000000 fd:00 16777669 /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7ff7f07c0000-7ff7f09bf000 ---p 000cf000 fd:00 16777669 /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7ff7f09bf000-7ff7f09c2000 r--p 000ce000 fd:00 16777669 /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7ff7f09c2000-7ff7f09c4000 rw-p 000d1000 fd:00 16777669 /usr/lib/x86_64-linux-gnu/libsqlite3.so.0.8.6
7ff7f09c4000-7ff7f09c5000 rw-p 00000000 00:00 0
7ff7f09c5000-7ff7f0a0c000 r-xp 00000000 fd:00 16785649 /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7ff7f0a0c000-7ff7f0c0b000 ---p 00047000 fd:00 16785649 /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7ff7f0c0b000-7ff7f0c0d000 r--p 00046000 fd:00 16785649 /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7ff7f0c0d000-7ff7f0c0f000 rw-p 00048000 fd:00 16785649 /usr/lib/x86_64-linux-gnu/libhx509.so.5.0.0
7ff7f0c0f000-7ff7f0c10000 rw-p 00000000 00:00 0
7ff7f0c10000-7ff7f0c1e000 r-xp 00000000 fd:00 16785631 /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7ff7f0c1e000-7ff7f0e1d000 ---p 0000e000 fd:00 16785631 /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7ff7f0e1d000-7ff7f0e1e000 r--p 0000d000 fd:00 16785631 /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7ff7f0e1e000-7ff7f0e1f000 rw-p 0000e000 fd:00 16785631 /usr/lib/x86_64-linux-gnu/libheimbase.so.1.0.0
7ff7f0e1f000-7ff7f0e46000 r-xp 00000000 fd:00 16786308 /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7ff7f0e46000-7ff7f1046000 ---p 00027000 fd:00 16786308 /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7ff7f1046000-7ff7f1047000 r--p 00027000 fd:00 16786308 /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7ff7f1047000-7ff7f1048000 rw-p 00028000 fd:00 16786308 /usr/lib/x86_64-linux-gnu/libwind.so.0.0.0
7ff7f1048000-7ff7f105d000 r-xp 00000000 fd:00 16786049 /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7ff7f105d000-7ff7f125c000 ---p 00015000 fd:00 16786049 /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7ff7f125c000-7ff7f125d000 r--p 00014000 fd:00 16786049 /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7ff7f125d000-7ff7f125e000 rw-p 00015000 fd:00 16786049 /usr/lib/x86_64-linux-gnu/libroken.so.18.1.0
7ff7f125e000-7ff7f128e000 r-xp 00000000 fd:00 16785629 /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7ff7f128e000-7ff7f148e000 ---p 00030000 fd:00 16785629 /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7ff7f148e000-7ff7f148f000 r--p 00030000 fd:00 16785629 /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7ff7f148f000-7ff7f1490000 rw-p 00031000 fd:00 16785629 /usr/lib/x86_64-linux-gnu/libhcrypto.so.4.1.0
7ff7f1490000-7ff7f1491000 rw-p 00000000 00:00 0
7ff7f1491000-7ff7f1530000 r-xp 00000000 fd:00 16785066 /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7ff7f1530000-7ff7f172f000 ---p 0009f000 fd:00 16785066 /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7ff7f172f000-7ff7f1730000 r--p 0009e000 fd:00 16785066 /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7ff7f1730000-7ff7f1733000 rw-p 0009f000 fd:00 16785066 /usr/lib/x86_64-linux-gnu/libasn1.so.8.0.0
7ff7f1733000-7ff7f17b7000 r-xp 00000000 fd:00 16785736 /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7ff7f17b7000-7ff7f19b6000 ---p 00084000 fd:00 16785736 /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7ff7f19b6000-7ff7f19b9000 r--p 00083000 fd:00 16785736 /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7ff7f19b9000-7ff7f19bc000 rw-p 00086000 fd:00 16785736 /usr/lib/x86_64-linux-gnu/libkrb5.so.26.0.0
7ff7f19bc000-7ff7f19bd000 rw-p 00000000 00:00 0
7ff7f19bd000-7ff7f19c5000 r-xp 00000000 fd:00 16785633 /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7ff7f19c5000-7ff7f1bc4000 ---p 00008000 fd:00 16785633 /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7ff7f1bc4000-7ff7f1bc5000 r--p 00007000 fd:00 16785633 /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7ff7f1bc5000-7ff7f1bc6000 rw-p 00008000 fd:00 16785633 /usr/lib/x86_64-linux-gnu/libheimntlm.so.0.1.0
7ff7f1bc6000-7ff7f1bc9000 r-xp 00000000 fd:00 40112605 /lib/x86_64-linux-gnu/libkeyutils.so.1.5
7ff7f1bc9000-7ff7f1dc8000 ---p 00003000 fd:00 40112605 /lib/x86_64-linux-gnu/libkeyutils.so.1.5
7ff7f1dc8000-7ff7f1dc9000 r--p 00002000 fd:00 40112605 /lib/x86_64-linux-gnu/libkeyutils.so.1.5
7ff7f1dc9000-7ff7f1dca000 rw-p 00003000 fd:00 40112605 /lib/x86_64-linux-gnu/libkeyutils.so.1.5
7ff7f1dca000-7ff7f1dd1000 r-xp 00000000 fd:00 16785364 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7ff7f1dd1000-7ff7f1fd0000 ---p 00007000 fd:00 16785364 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7ff7f1fd0000-7ff7f1fd1000 r--p 00006000 fd:00 16785364 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7ff7f1fd1000-7ff7f1fd2000 rw-p 00007000 fd:00 16785364 /usr/lib/x86_64-linux-gnu/libffi.so.6.0.4
7ff7f1fd2000-7ff7f200f000 r-xp 00000000 fd:00 16785552 /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7ff7f200f000-7ff7f220f000 ---p 0003d000 fd:00 16785552 /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7ff7f220f000-7ff7f2210000 r--p 0003d000 fd:00 16785552 /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7ff7f2210000-7ff7f2212000 rw-p 0003e000 fd:00 16785552 /usr/lib/x86_64-linux-gnu/libgssapi.so.3.0.0
7ff7f2212000-7ff7f2213000 rw-p 00000000 00:00 0
7ff7f2213000-7ff7f222c000 r-xp 00000000 fd:00 16786076 /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7ff7f222c000-7ff7f242c000 ---p 00019000 fd:00 16786076 /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7ff7f242c000-7ff7f242d000 r--p 00019000 fd:00 16786076 /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7ff7f242d000-7ff7f242e000 rw-p 0001a000 fd:00 16786076 /usr/lib/x86_64-linux-gnu/libsasl2.so.2.0.25
7ff7f242e000-7ff7f2445000 r-xp 00000000 fd:00 40112696 /lib/x86_64-linux-gnu/libresolv-2.23.so
7ff7f2445000-7ff7f2645000 ---p 00017000 fd:00 40112696 /lib/x86_64-linux-gnu/libresolv-2.23.so
7ff7f2645000-7ff7f2646000 r--p 00017000 fd:00 40112696 /lib/x86_64-linux-gnu/libresolv-2.23.so
7ff7f2646000-7ff7f2647000 rw-p 00018000 fd:00 40112696 /lib/x86_64-linux-gnu/libresolv-2.23.so
7ff7f2647000-7ff7f2649000 rw-p 00000000 00:00 0
7ff7f2649000-7ff7f2653000 r-xp 00000000 fd:00 16780363 /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7ff7f2653000-7ff7f2852000 ---p 0000a000 fd:00 16780363 /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7ff7f2852000-7ff7f2853000 r--p 00009000 fd:00 16780363 /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7ff7f2853000-7ff7f2854000 rw-p 0000a000 fd:00 16780363 /usr/lib/x86_64-linux-gnu/libkrb5support.so.0.1
7ff7f2854000-7ff7f2857000 r-xp 00000000 fd:00 40112553 /lib/x86_64-linux-gnu/libcom_err.so.2.1
7ff7f2857000-7ff7f2a56000 ---p 00003000 fd:00 40112553 /lib/x86_64-linux-gnu/libcom_err.so.2.1
7ff7f2a56000-7ff7f2a57000 r--p 00002000 fd:00 40112553 /lib/x86_64-linux-gnu/libcom_err.so.2.1
7ff7f2a57000-7ff7f2a58000 rw-p 00003000 fd:00 40112553 /lib/x86_64-linux-gnu/libcom_err.so.2.1
7ff7f2a58000-7ff7f2a84000 r-xp 00000000 fd:00 16780365 /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7ff7f2a84000-7ff7f2c83000 ---p 0002c000 fd:00 16780365 /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7ff7f2c83000-7ff7f2c85000 r--p 0002b000 fd:00 16780365 /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7ff7f2c85000-7ff7f2c86000 rw-p 0002d000 fd:00 16780365 /usr/lib/x86_64-linux-gnu/libk5crypto.so.3.1
7ff7f2c86000-7ff7f2c87000 rw-p 00000000 00:00 0
7ff7f2c87000-7ff7f2d4a000 r-xp 00000000 fd:00 16780361 /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7ff7f2d4a000-7ff7f2f4a000 ---p 000c3000 fd:00 16780361 /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7ff7f2f4a000-7ff7f2f57000 r--p 000c3000 fd:00 16780361 /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7ff7f2f57000-7ff7f2f59000 rw-p 000d0000 fd:00 16780361 /usr/lib/x86_64-linux-gnu/libkrb5.so.3.3
7ff7f2f59000-7ff7f2f6a000 r-xp 00000000 fd:00 16786154 /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7ff7f2f6a000-7ff7f316a000 ---p 00011000 fd:00 16786154 /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7ff7f316a000-7ff7f316b000 r--p 00011000 fd:00 16786154 /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7ff7f316b000-7ff7f316c000 rw-p 00012000 fd:00 16786154 /usr/lib/x86_64-linux-gnu/libtasn1.so.6.5.1
7ff7f316c000-7ff7f31c5000 r-xp 00000000 fd:00 16785923 /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7ff7f31c5000-7ff7f33c4000 ---p 00059000 fd:00 16785923 /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7ff7f33c4000-7ff7f33ce000 r--p 00058000 fd:00 16785923 /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7ff7f33ce000-7ff7f33d0000 rw-p 00062000 fd:00 16785923 /usr/lib/x86_64-linux-gnu/libp11-kit.so.0.1.0
7ff7f33d0000-7ff7f344f000 r-xp 00000000 fd:00 16785497 /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7ff7f344f000-7ff7f364e000 ---p 0007f000 fd:00 16785497 /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7ff7f364e000-7ff7f364f000 r--p 0007e000 fd:00 16785497 /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7ff7f364f000-7ff7f3650000 rw-p 0007f000 fd:00 16785497 /usr/lib/x86_64-linux-gnu/libgmp.so.10.3.0
7ff7f3650000-7ff7f3682000 r-xp 00000000 fd:00 16785635 /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7ff7f3682000-7ff7f3881000 ---p 00032000 fd:00 16785635 /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7ff7f3881000-7ff7f3882000 r--p 00031000 fd:00 16785635 /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7ff7f3882000-7ff7f3883000 rw-p 00032000 fd:00 16785635 /usr/lib/x86_64-linux-gnu/libhogweed.so.4.2
7ff7f3883000-7ff7f388a000 r-xp 00000000 fd:00 16787446 /usr/lib/x86_64-linux-gnu/libaec.so.0.0.3
7ff7f388a000-7ff7f3a89000 ---p 00007000 fd:00 16787446 /usr/lib/x86_64-linux-gnu/libaec.so.0.0.3
7ff7f3a89000-7ff7f3a8a000 r--p 00006000 fd:00 16787446 /usr/lib/x86_64-linux-gnu/libaec.so.0.0.3
7ff7f3a8a000-7ff7f3a8b000 rw-p 00007000 fd:00 16787446 /usr/lib/x86_64-linux-gnu/libaec.so.0.0.3
7ff7f3a8b000-7ff7f3ad8000 r-xp 00000000 fd:00 16782418 /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7ff7f3ad8000-7ff7f3cd7000 ---p 0004d000 fd:00 16782418 /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7ff7f3cd7000-7ff7f3cd9000 r--p 0004c000 fd:00 16782418 /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7ff7f3cd9000-7ff7f3cda000 rw-p 0004e000 fd:00 16782418 /usr/lib/x86_64-linux-gnu/libldap_r-2.4.so.2.10.5
7ff7f3cda000-7ff7f3cdc000 rw-p 00000000 00:00 0
7ff7f3cdc000-7ff7f3ce9000 r-xp 00000000 fd:00 16782419 /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7ff7f3ce9000-7ff7f3ee9000 ---p 0000d000 fd:00 16782419 /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7ff7f3ee9000-7ff7f3eea000 r--p 0000d000 fd:00 16782419 /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7ff7f3eea000-7ff7f3eeb000 rw-p 0000e000 fd:00 16782419 /usr/lib/x86_64-linux-gnu/liblber-2.4.so.2.10.5
7ff7f3eeb000-7ff7f3f32000 r-xp 00000000 fd:00 16780148 /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7ff7f3f32000-7ff7f4131000 ---p 00047000 fd:00 16780148 /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7ff7f4131000-7ff7f4133000 r--p 00046000 fd:00 16780148 /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7ff7f4133000-7ff7f4135000 rw-p 00048000 fd:00 16780148 /usr/lib/x86_64-linux-gnu/libgssapi_krb5.so.2.2
7ff7f4135000-7ff7f4258000 r-xp 00000000 fd:00 16785515 /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7ff7f4258000-7ff7f4457000 ---p 00123000 fd:00 16785515 /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7ff7f4457000-7ff7f4462000 r--p 00122000 fd:00 16785515 /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7ff7f4462000-7ff7f4464000 rw-p 0012d000 fd:00 16785515 /usr/lib/x86_64-linux-gnu/libgnutls.so.30.6.2
7ff7f4464000-7ff7f4465000 rw-p 00000000 00:00 0
7ff7f4465000-7ff7f4499000 r-xp 00000000 fd:00 16785860 /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7ff7f4499000-7ff7f4698000 ---p 00034000 fd:00 16785860 /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7ff7f4698000-7ff7f469a000 r--p 00033000 fd:00 16785860 /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7ff7f469a000-7ff7f469b000 rw-p 00035000 fd:00 16785860 /usr/lib/x86_64-linux-gnu/libnettle.so.6.2
7ff7f469b000-7ff7f46b6000 r-xp 00000000 fd:00 16786057 /usr/lib/x86_64-linux-gnu/librtmp.so.1
7ff7f46b6000-7ff7f48b5000 ---p 0001b000 fd:00 16786057 /usr/lib/x86_64-linux-gnu/librtmp.so.1
7ff7f48b5000-7ff7f48b6000 r--p 0001a000 fd:00 16786057 /usr/lib/x86_64-linux-gnu/librtmp.so.1
7ff7f48b6000-7ff7f48b7000 rw-p 0001b000 fd:00 16786057 /usr/lib/x86_64-linux-gnu/librtmp.so.1
7ff7f48b7000-7ff7f48e8000 r-xp 00000000 fd:00 16785684 /usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7ff7f48e8000-7ff7f4ae8000 ---p 00031000 fd:00 16785684 /usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7ff7f4ae8000-7ff7f4ae9000 r--p 00031000 fd:00 16785684 /usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7ff7f4ae9000-7ff7f4aea000 rw-p 00032000 fd:00 16785684 /usr/lib/x86_64-linux-gnu/libidn.so.11.6.15
7ff7f4aea000-7ff7f4b03000 r-xp 00000000 fd:00 40112735 /lib/x86_64-linux-gnu/libz.so.1.2.8
7ff7f4b03000-7ff7f4d02000 ---p 00019000 fd:00 40112735 /lib/x86_64-linux-gnu/libz.so.1.2.8
7ff7f4d02000-7ff7f4d03000 r--p 00018000 fd:00 40112735 /lib/x86_64-linux-gnu/libz.so.1.2.8
7ff7f4d03000-7ff7f4d04000 rw-p 00019000 fd:00 40112735 /lib/x86_64-linux-gnu/libz.so.1.2.8
7ff7f4d04000-7ff7f4d06000 r-xp 00000000 fd:00 16787457 /usr/lib/x86_64-linux-gnu/libsz.so.2.0.1
7ff7f4d06000-7ff7f4f05000 ---p 00002000 fd:00 16787457 /usr/lib/x86_64-linux-gnu/libsz.so.2.0.1
7ff7f4f05000-7ff7f4f06000 r--p 00001000 fd:00 16787457 /usr/lib/x86_64-linux-gnu/libsz.so.2.0.1
7ff7f4f06000-7ff7f4f07000 rw-p 00002000 fd:00 16787457 /usr/lib/x86_64-linux-gnu/libsz.so.2.0.1
7ff7f4f07000-7ff7f4f0a000 r-xp 00000000 fd:00 40112568 /lib/x86_64-linux-gnu/libdl-2.23.so
7ff7f4f0a000-7ff7f5109000 ---p 00003000 fd:00 40112568 /lib/x86_64-linux-gnu/libdl-2.23.so
7ff7f5109000-7ff7f510a000 r--p 00002000 fd:00 40112568 /lib/x86_64-linux-gnu/libdl-2.23.so
7ff7f510a000-7ff7f510b000 rw-p 00003000 fd:00 40112568 /lib/x86_64-linux-gnu/libdl-2.23.so
7ff7f510b000-7ff7f5175000 r-xp 00000000 fd:00 16777446 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4.4.0
7ff7f5175000-7ff7f5374000 ---p 0006a000 fd:00 16777446 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4.4.0
7ff7f5374000-7ff7f5377000 r--p 00069000 fd:00 16777446 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4.4.0
7ff7f5377000-7ff7f5378000 rw-p 0006c000 fd:00 16777446 /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so.4.4.0
7ff7f5378000-7ff7f560c000 r-xp 00000000 fd:00 16785249 /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0
7ff7f560c000-7ff7f580b000 ---p 00294000 fd:00 16785249 /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0
7ff7f580b000-7ff7f5810000 r--p 00293000 fd:00 16785249 /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0
7ff7f5810000-7ff7f5815000 rw-p 00298000 fd:00 16785249 /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0
7ff7f5815000-7ff7f5816000 rw-p 00000000 00:00 0
7ff7f5816000-7ff7f5834000 r-xp 00000000 fd:00 16785440 /usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.10.0.2
7ff7f5834000-7ff7f5a33000 ---p 0001e000 fd:00 16785440 /usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.10.0.2
7ff7f5a33000-7ff7f5a34000 r--p 0001d000 fd:00 16785440 /usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.10.0.2
7ff7f5a34000-7ff7f5a35000 rw-p 0001e000 fd:00 16785440 /usr/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.10.0.2
7ff7f5a35000-7ff7f5a36000 rw-p 00000000 00:00 0
7ff7f5a36000-7ff7f5bf6000 r-xp 00000000 fd:00 40112544 /lib/x86_64-linux-gnu/libc-2.23.so
7ff7f5bf6000-7ff7f5df6000 ---p 001c0000 fd:00 40112544 /lib/x86_64-linux-gnu/libc-2.23.so
7ff7f5df6000-7ff7f5dfa000 r--p 001c0000 fd:00 40112544 /lib/x86_64-linux-gnu/libc-2.23.so
7ff7f5dfa000-7ff7f5dfc000 rw-p 001c4000 fd:00 40112544 /lib/x86_64-linux-gnu/libc-2.23.so
7ff7f5dfc000-7ff7f5e00000 rw-p 00000000 00:00 0
7ff7f5e00000-7ff7f5e18000 r-xp 00000000 fd:00 40112690 /lib/x86_64-linux-gnu/libpthread-2.23.so
7ff7f5e18000-7ff7f6017000 ---p 00018000 fd:00 40112690 /lib/x86_64-linux-gnu/libpthread-2.23.so
7ff7f6017000-7ff7f6018000 r--p 00017000 fd:00 40112690 /lib/x86_64-linux-gnu/libpthread-2.23.so
7ff7f6018000-7ff7f6019000 rw-p 00018000 fd:00 40112690 /lib/x86_64-linux-gnu/libpthread-2.23.so
7ff7f6019000-7ff7f601d000 rw-p 00000000 00:00 0
7ff7f601d000-7ff7f6033000 r-xp 00000000 fd:00 40112582 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff7f6033000-7ff7f6232000 ---p 00016000 fd:00 40112582 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff7f6232000-7ff7f6233000 rw-p 00015000 fd:00 40112582 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff7f6233000-7ff7f6254000 r-xp 00000000 fd:00 16778574 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7ff7f6254000-7ff7f6453000 ---p 00021000 fd:00 16778574 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7ff7f6453000-7ff7f6454000 r--p 00020000 fd:00 16778574 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7ff7f6454000-7ff7f6455000 rw-p 00021000 fd:00 16778574 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7ff7f6455000-7ff7f655d000 r-xp 00000000 fd:00 40112614 /lib/x86_64-linux-gnu/libm-2.23.so
7ff7f655d000-7ff7f675c000 ---p 00108000 fd:00 40112614 /lib/x86_64-linux-gnu/libm-2.23.so
7ff7f675c000-7ff7f675d000 r--p 00107000 fd:00 40112614 /lib/x86_64-linux-gnu/libm-2.23.so
7ff7f675d000-7ff7f675e000 rw-p 00108000 fd:00 40112614 /lib/x86_64-linux-gnu/libm-2.23.so
7ff7f675e000-7ff7f68d0000 r-xp 00000000 fd:00 16778825 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7ff7f68d0000-7ff7f6ad0000 ---p 00172000 fd:00 16778825 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7ff7f6ad0000-7ff7f6ada000 r--p 00172000 fd:00 16778825 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7ff7f6ada000-7ff7f6adc000 rw-p 0017c000 fd:00 16778825 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7ff7f6adc000-7ff7f6ae0000 rw-p 00000000 00:00 0
7ff7f6ae0000-7ff7f6be4000 r-xp 00000000 fd:00 16780396 /usr/lib/x86_64-linux-gnu/libnetcdf.so.11.0.0
7ff7f6be4000-7ff7f6de4000 ---p 00104000 fd:00 16780396 /usr/lib/x86_64-linux-gnu/libnetcdf.so.11.0.0
7ff7f6de4000-7ff7f6e32000 r--p 00104000 fd:00 16780396 /usr/lib/x86_64-linux-gnu/libnetcdf.so.11.0.0
7ff7f6e32000-7ff7f6e34000 rw-p 00152000 fd:00 16780396 /usr/lib/x86_64-linux-gnu/libnetcdf.so.11.0.0
7ff7f6e34000-7ff7f9e43000 rw-p 00000000 00:00 0
7ff7f9e43000-7ff7f9e69000 r-xp 00000000 fd:00 40112516 /lib/x86_64-linux-gnu/ld-2.23.so
7ff7f9ee8000-7ff7f9fea000 rw-p 00000000 00:00 0
7ff7fa02b000-7ff7fa043000 rw-p 00000000 00:00 0
7ff7fa067000-7ff7fa068000 rw-p 00000000 00:00 0
7ff7fa068000-7ff7fa069000 r--p 00025000 fd:00 40112516 /lib/x86_64-linux-gnu/ld-2.23.so
7ff7fa069000-7ff7fa06a000 rw-p 00026000 fd:00 40112516 /lib/x86_64-linux-gnu/ld-2.23.so
7ff7fa06a000-7ff7fa06b000 rw-p 00000000 00:00 0
7ffe75d9c000-7ffe75dbd000 rw-p 00000000 00:00 0 [stack]
7ffe75dc8000-7ffe75dcb000 r--p 00000000 00:00 0 [vvar]
7ffe75dcb000-7ffe75dcd000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)
Replies (2)
RE: Buffer overflow when calculating timmin on more than 95665 timesteps - Added by Karin Meier-Fleischer almost 5 years ago
Hi Nick,
the time dimension in your input file is wrong! It is going backward and forward!!??
cdo timmin -seltimestep,1/95665 0_0.nc test.nc
cdo(2) seltimestep: Process started
Warning (splitTimevalue): Reset wrong date/time to 0000-01-01 00:00:00!
cdo(2) seltimestep: Processed 95665 values from 1 variable over 95666 timesteps
cdo timmin: Processed 95665 values from 1 variable [4.79s 110MB]
cdo sinfov 0_0.nc
Warning (splitTimevalue): Reset wrong date/time to 0000-01-01 00:00:00!
File format : NetCDF4 zip
-1 : Institut Source T Steptype Levels Num Points Num Dtype : Parameter name
1 : unknown unknown v instant 1 1 1 1 F32z : CgE
Grid coordinates :
1 : generic : points=1 (1x1)
Vertical coordinates :
1 : surface : levels=1
Time coordinate : 311160 steps
YYYY-MM-DD hh:mm:ss YYYY-MM-DD hh:mm:ss YYYY-MM-DD hh:mm:ss YYYY-MM-DD hh:mm:ss
0000-01-01 00:00:00 0000-01-01 22:59:52 0000-01-01 22:00:07 0000-01-01 21:00:00
0000-01-01 19:59:52 0000-01-01 19:00:07 0000-01-01 18:00:00 0000-01-01 16:59:52
0000-01-01 16:00:07 0000-01-01 15:00:00 0000-01-01 13:59:52 0000-01-01 13:00:07
0000-01-01 12:00:00 0000-01-01 10:59:52 0000-01-01 10:00:07 0000-01-01 09:00:00
0000-01-01 07:59:52 0000-01-01 07:00:07 0000-01-01 06:00:00 0000-01-01 04:59:52
0000-01-01 04:00:07 0000-01-01 03:00:00 0000-01-01 01:59:52 0000-01-01 01:00:07
0000-01-01 00:00:00 0000-01-01 22:59:52 0000-01-01 22:00:07 0000-01-01 21:00:00
0000-01-01 19:59:52 0000-01-01 19:00:07 0000-01-01 18:00:00 0000-01-01 16:59:52
0000-01-01 16:00:07 0000-01-01 15:00:00 0000-01-01 13:59:52 0000-01-01 13:00:07
0000-01-01 12:00:00 0000-01-01 10:59:52 0000-01-01 10:00:07 0000-01-01 09:00:00
0000-01-01 07:59:52 0000-01-01 07:00:07 0000-01-01 06:00:00 0000-01-01 04:59:52
0000-01-01 04:00:07 0000-01-01 03:00:00 0000-01-01 01:59:52 0000-01-01 01:00:07
0000-01-01 00:00:00 0000-01-01 22:59:52 0000-01-01 22:00:07 0000-01-01 21:00:00
0000-01-01 19:59:52 0000-01-01 19:00:07 0000-01-01 18:00:00 0000-01-01 16:59:52
0000-01-01 16:00:07 0000-01-01 15:00:00 0000-01-01 13:59:52 0000-01-01 13:00:07
................................................................................
................................................................................
................................................................................
................................................................................
.......................
0000-01-01 12:00:00 0000-01-01 13:00:28 0000-01-01 13:59:31 0000-01-01 15:00:00
0000-01-01 16:00:28 0000-01-01 16:59:31 0000-01-01 18:00:00 0000-01-01 19:00:28
0000-01-01 19:59:31 0000-01-01 21:00:00 0000-01-01 22:00:28 0000-01-01 22:59:31
0000-01-01 00:00:00 0000-01-01 01:00:28 0000-01-01 01:59:31 0000-01-01 03:00:00
0000-01-01 04:00:28 0000-01-01 04:59:31 0000-01-01 06:00:00 0000-01-01 07:00:28
0000-01-01 07:59:31 0000-01-01 09:00:00 0000-01-01 10:00:28 0000-01-01 10:59:31
0000-01-01 12:00:00 0000-01-01 13:00:28 0000-01-01 13:59:31 0000-01-01 15:00:00
0000-01-01 16:00:28 0000-01-01 16:59:31 0000-01-01 18:00:00 0000-01-01 19:00:28
0000-01-01 19:59:31 0000-01-01 21:00:00 0000-01-01 22:00:28 0000-01-01 22:59:31
0000-01-01 00:00:00 0000-01-01 01:00:28 0000-01-01 01:59:31 0000-01-01 03:00:00
0000-01-01 04:00:28 0000-01-01 04:59:31 0000-01-01 06:00:00 0000-01-01 07:00:28
0000-01-01 07:59:31 0000-01-01 09:00:00 0000-01-01 10:00:28 0000-01-01 10:59:31
0000-01-01 12:00:00 0000-01-01 13:00:28 0000-01-01 13:59:31 0000-01-01 15:00:00
0000-01-01 16:00:28 0000-01-01 16:59:31 0000-01-01 18:00:00 0000-01-01 19:00:28
0000-01-01 19:59:31 0000-01-01 21:00:00 0000-01-01 22:00:28 0000-01-01 22:59:31
cdo sinfon: Processed 1 variable over 311160 timesteps [2.03s 121MB]
cdo sinfov test.ncFile format : NetCDF4
-1 : Institut Source T Steptype Levels Num Points Num Dtype : Parameter name
1 : unknown unknown v instant 1 1 1 1 F32 : CgE
Grid coordinates :
1 : generic : points=1 (1x1)
Vertical coordinates :
1 : surface : levels=1
Time coordinate : 1 step
YYYY-MM-DD hh:mm:ss YYYY-MM-DD hh:mm:ss YYYY-MM-DD hh:mm:ss YYYY-MM-DD hh:mm:ss
0000-01-01 00:00:00
cdo sinfon: Processed 1 variable over 1 timestep [0.01s 23MB]
I used CDO 1.9.6.
-Karin
RE: Buffer overflow when calculating timmin on more than 95665 timesteps - Added by Nick Young almost 5 years ago
Hi Karin,
Thank you for your quick response. I think cdo was misinterpreting the datetimes due to missing attributes (my colleague stripped all metadata from this file). Compare with the output of ncks 0_0.nc for example:
time: type NC_FLOAT, 1 dimension, 0 attributes, compressed? no, chunked? yes, packed? no
time size (RAM) = 311160*sizeof(NC_FLOAT) = 311160*4 = 1244640 bytes
time dimension 0: time, size = 311160 NC_FLOAT, chunksize = 672 (Record coordinate is time)
time[0]=-3987 lat[0] long[0] CgE[0]=-nan
time[1]=-3986.96 lat[0] long[0] CgE[1]=-nan
time[2]=-3986.92 lat[0] long[0] CgE[2]=-nan
time[3]=-3986.88 lat[0] long[0] CgE[3]=-nan
time[4]=-3986.83 lat[0] long[0] CgE[4]=-nan
time[5]=-3986.79 lat[0] long[0] CgE[5]=-nan
time[6]=-3986.75 lat[0] long[0] CgE[6]=-nan
time[7]=-3986.71 lat[0] long[0] CgE[7]=-nan
time[8]=-3986.67 lat[0] long[0] CgE[8]=-nan
time[9]=-3986.62 lat[0] long[0] CgE[9]=-nan
The attributes for the time dimension should read:
time: type NC_DOUBLE, 1 dimension, 5 attributes, compressed? yes, chunked? yes, packed? no
time compression (Lempel-Ziv with shuffling) level = 1
time size (RAM) = 672*sizeof(NC_DOUBLE) = 672*8 = 5376 bytes
time dimension 0: time, size = 672 NC_DOUBLE, chunksize = 1 (Record coordinate is time)
time attribute 0: long_name, size = 15 NC_CHAR, value = julian day (UT)
time attribute 1: standard_name, size = 4 NC_CHAR, value = time
time attribute 2: units, size = 31 NC_CHAR, value = days since 1990-01-01T00:00:00Z
time attribute 3: conventions, size = 61 NC_CHAR, value = relative julian days with decimal part (as parts of the day )
time attribute 4: axis, size = 1 NC_CHAR, value = T
After adding these attributes back into the file I no longer get the buffer overflow - thanks!
Cheers,
Nick
| 0_0_time_attr_fix.nc (1.57 MB) 0_0_time_attr_fix.nc |