memory error -- IEG files
Added by Birgit Mannig about 9 years ago
Hello,
I run CDO version 1.6.2 on a Ubuntu 14.04 (64-bit).
For CDO operations on IEG files I get a memory error ("Speicherzugriffsfehler (Speicherabzug geschrieben)"). The problem seems to be with the library libcdi (see below). I tried the same files with the same CDO and Ubuntu version (but 32-bit), on a different machine, without any errors.
To exclude mistakes, I also tried with a public example file from https://www.unidata.ucar.edu/software/netcdf/examples/files.html (see attached), same problem occurs, I am not able to convert the file to IEG.
Does anybody know a way to fix this?
Running CDO with valgrind delivers:
valgrind cdo -info myfile.ieg ==3849== Invalid read of size 8 ==3849== at 0x4EB5230: iegInqContents (in /usr/lib/x86_64-linux-gnu/libcdi.so.0.0.0) ==3849== by 0x4ECDFAF: ??? (in /usr/lib/x86_64-linux-gnu/libcdi.so.0.0.0) ==3849== by 0x4ED09D6: streamOpen (in /usr/lib/x86_64-linux-gnu/libcdi.so.0.0.0) ==3849== by 0x4ED0A51: streamOpenRead (in /usr/lib/x86_64-linux-gnu/libcdi.so.0.0.0) ==3849== by 0x5010F4: ??? (in /usr/bin/cdo) ==3849== by 0x44C67C: ??? (in /usr/bin/cdo) ==3849== by 0x40BEAF: ??? (in /usr/bin/cdo) ==3849== by 0x607EEC4: (below main) (libc-start.c:287) ==3849== Address 0x5878 is not stack'd, malloc'd or (recently) free'd ==3849== ==3849== ==3849== Process terminating with default action of signal 11 (SIGSEGV) ==3849== Access not within mapped region at address 0x5878 ==3849== at 0x4EB5230: iegInqContents (in /usr/lib/x86_64-linux-gnu/libcdi.so.0.0.0) ==3849== by 0x4ECDFAF: ??? (in /usr/lib/x86_64-linux-gnu/libcdi.so.0.0.0) ==3849== by 0x4ED09D6: streamOpen (in /usr/lib/x86_64-linux-gnu/libcdi.so.0.0.0) ==3849== by 0x4ED0A51: streamOpenRead (in /usr/lib/x86_64-linux-gnu/libcdi.so.0.0.0) ==3849== by 0x5010F4: ??? (in /usr/bin/cdo) ==3849== by 0x44C67C: ??? (in /usr/bin/cdo) ==3849== by 0x40BEAF: ??? (in /usr/bin/cdo) ==3849== by 0x607EEC4: (below main) (libc-start.c:287) ==3849== If you believe this happened as a result of a stack ==3849== overflow in your program's main thread (unlikely but ==3849== possible), you can try to increase the size of the ==3849== main thread stack using the --main-stacksize= flag. ==3849== The main thread stack size used in this run was 67108864. ==3849== ==3849== HEAP SUMMARY: ==3849== in use at exit: 217,828 bytes in 20 blocks ==3849== total heap usage: 26 allocs, 6 frees, 297,767 bytes allocated ==3849== ==3849== LEAK SUMMARY: ==3849== definitely lost: 0 bytes in 0 blocks ==3849== indirectly lost: 0 bytes in 0 blocks ==3849== possibly lost: 0 bytes in 0 blocks ==3849== still reachable: 217,828 bytes in 20 blocks ==3849== suppressed: 0 bytes in 0 blocks ==3849== Rerun with --leak-check=full to see details of leaked memory ==3849==
Replies (2)
RE: memory error -- IEG files - Added by Ralf Mueller about 9 years ago
with 1.7.1 I get
ram@luthien:~/Downloads cdo infov sresa1b_ncar_ccsm3-example.nc
Warning (cdfScanVarAttributes) : NetCDF: Variable not found - height
-1 : Date Time Level Gridsize Miss : Minimum Mean Maximum : Parameter name
1 : 2000-05-16 12:00:00 0 32768 0 : 4.7346e+08 1.5561e+10 2.4346e+10 : area
2 : 2000-05-16 12:00:00 0 32768 0 : 0.0000 0.00061035 1.0000 : msk_rgn
3 : 2000-05-16 12:00:00 0 32768 0 : 2.4460e-26 2.7258e-05 0.00030686 : pr
4 : 2000-05-16 12:00:00 0 32768 0 : 205.24 278.64 309.10 : tas
5 : 2000-05-16 12:00:00 100000 32768 20132 : -14.621 -1.2652 12.228 : ua
6 : 2000-05-16 12:00:00 92500 32768 5340 : -17.808 1.4447 19.665 : ua
7 : 2000-05-16 12:00:00 85000 32768 3381 : -18.704 2.3264 20.983 : ua
8 : 2000-05-16 12:00:00 70000 32768 1769 : -16.946 4.3663 24.866 : ua
9 : 2000-05-16 12:00:00 60000 32768 259 : -13.667 5.8819 27.928 : ua
10 : 2000-05-16 12:00:00 50000 32768 0 : -11.098 7.7648 31.205 : ua
11 : 2000-05-16 12:00:00 40000 32768 0 : -9.0083 10.428 35.412 : ua
12 : 2000-05-16 12:00:00 30000 32768 0 : -9.9183 13.887 39.998 : ua
13 : 2000-05-16 12:00:00 25000 32768 0 : -11.765 15.763 44.598 : ua
14 : 2000-05-16 12:00:00 20000 32768 0 : -12.916 17.281 49.843 : ua
15 : 2000-05-16 12:00:00 15000 32768 0 : -16.155 17.237 49.299 : ua
16 : 2000-05-16 12:00:00 10000 32768 0 : -24.160 13.707 38.365 : ua
17 : 2000-05-16 12:00:00 7000 32768 0 : -19.685 9.2464 39.309 : ua
18 : 2000-05-16 12:00:00 5000 32768 0 : -16.001 6.5147 43.567 : ua
19 : 2000-05-16 12:00:00 3000 32768 0 : -13.673 5.3174 50.794 : ua
20 : 2000-05-16 12:00:00 2000 32768 0 : -13.934 6.0367 56.021 : ua
21 : 2000-05-16 12:00:00 1000 32768 0 : -12.700 9.1144 63.261 : ua
cdo infon: Processed 688128 values from 5 variables over 1 timestep ( 0.00s )
Could you update? Conda might be an option Anaconda
RE: memory error -- IEG files - Added by Birgit Mannig about 9 years ago
that was easy, with the update it works. Thank you!
(I still do not understand why the older version works on the 32-bit system but not on the 64-bit, but whatever...)