[gradsusr] issues with memory overload when computing some fields

Tue Oct 27 16:34:13 EDT 2015

I am trying to compute ensemble spread from a 10 member ensemble
(convective scale configuration). The field for which I am trying to
compute standard deviation includes thermodynamic indices like CAPE and
CIN. Since I am doing this for cases featuring rather high amounts of CAPE,
I suspect this is the reason my script is overloading on memory and
crashing. I know this because I have the script setup to easily compute
ensemble standard deviation for just about any field, and I have had no
troubles computing spread for temperature, moisture, and wind. Yet, just
changing the name of the field causes the script to crash.

Is there anything that can be done to get around this? I have attached the
script code to this email.

Here is some output from the jobs running the script:
/home/jdduda/grads_scripts
Tue Oct 27 15:06:13 CDT 2015

Grid Analysis and Display System (GrADS) Version 2.1.a3
Copyright (C) 1988-2015 by the Institute for Global Environment and Society
(IGES)
GrADS comes with ABSOLUTELY NO WARRANTY
See file COPYRIGHT for more information

Config: v2.1.a3 little-endian readline grib2 netcdf hdf4-sds hdf5
opendap-grids,stn geotiff shapefile cairo
Issue 'q config' command for more detailed configuration information
GX Package Initialization: Size = 11 8.5
Running in Batch mode
All files closed; all defined objects released;
All GrADS attributes have been reinitialized
Notice: Implied interpolation for file
/work/jdduda/analysis/FLSM/WRFPRS_FLSM.ctl
 Interpolation will be performed on any data displayed from this file
Notice: Implied interpolation for file
/work/jdduda/analysis/MLSM/WRFPRS_MLSM.ctl
 Interpolation will be performed on any data displayed from this file
Notice: Implied interpolation for file
/work/jdduda/analysis/LSMO/WRFPRS_LSMO.ctl
 Interpolation will be performed on any data displayed from this file
Data Request Warning:  Request is completely outside file limits
Data Request Warning:  Request is completely outside file limits
Define Error:  Unable to allocate data memory
  Size of request was -18950400 grid elements
Abort (core dumped)
Tue Oct 27 15:22:30 CDT 2015

*** glibc detected *** /home/jdduda/grads-2.1.a3/bin/grads: double free or
corruption (!prev): 0x0000000005f12580 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3000475e66]
/lib64/libc.so.6[0x30004789b3]
/home/jdduda/grads-2.1.a3/bin/grads(gree+0x2bb)[0x4fb4b2]
/home/jdduda/grads-2.1.a3/bin/grads(gadef+0x1597)[0x51921a]
/home/jdduda/grads-2.1.a3/bin/grads(gacmd+0x2074)[0x52e93c]
/home/jdduda/grads-2.1.a3/bin/grads(gagsdo+0x33)[0x5301d3]
/home/jdduda/grads-2.1.a3/bin/grads(gsstmt+0x6e)[0x4f5fc5]
/home/jdduda/grads-2.1.a3/bin/grads(gsruns+0x4f)[0x4f610e]
/home/jdduda/grads-2.1.a3/bin/grads(gsrund+0xdd)[0x4f6679]
/home/jdduda/grads-2.1.a3/bin/grads(gsruns+0x8c)[0x4f614b]
/home/jdduda/grads-2.1.a3/bin/grads(gsruni+0x95)[0x4f6557]
/home/jdduda/grads-2.1.a3/bin/grads(gsruns+0x11b)[0x4f61da]
/home/jdduda/grads-2.1.a3/bin/grads(gsrund+0xdd)[0x4f6679]
/home/jdduda/grads-2.1.a3/bin/grads(gsruns+0x8c)[0x4f614b]
/home/jdduda/grads-2.1.a3/bin/grads(gsrund+0xdd)[0x4f6679]
/home/jdduda/grads-2.1.a3/bin/grads(gsruns+0x8c)[0x4f614b]
/home/jdduda/grads-2.1.a3/bin/grads(gsrunf+0x2e9)[0x4f69e2]
/home/jdduda/grads-2.1.a3/bin/grads(gsfile+0x290)[0x4f6d7d]
/home/jdduda/grads-2.1.a3/bin/grads(gacmd+0x1162)[0x52da2a]
/home/jdduda/grads-2.1.a3/bin/grads(main+0x962)[0x4a5e59]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x300041ed5d]
/home/jdduda/grads-2.1.a3/bin/grads[0x4a4a09]
======= Memory map: ========
00400000-00dea000 r-xp 00000000 00:31 196231175
/home/jdduda/grads-2.1.a3/bin/grads
00fe9000-0106c000 rw-p 009e9000 00:31 196231175
/home/jdduda/grads-2.1.a3/bin/grads
0106c000-04368000 rw-p 00000000 00:00 0
05eb9000-0b20e000 rw-p 00000000 00:00 0
[heap]
3000000000-3000020000 r-xp 00000000 fd:00 182476
/lib64/ld-2.12.so
300021f000-3000220000 r--p 0001f000 fd:00 182476
/lib64/ld-2.12.so
3000220000-3000221000 rw-p 00020000 fd:00 182476
/lib64/ld-2.12.so
3000221000-3000222000 rw-p 00000000 00:00 0
3000400000-300058a000 r-xp 00000000 fd:00 182477
/lib64/libc-2.12.so
300058a000-300078a000 ---p 0018a000 fd:00 182477
/lib64/libc-2.12.so
300078a000-300078e000 r--p 0018a000 fd:00 182477
/lib64/libc-2.12.so
300078e000-300078f000 rw-p 0018e000 fd:00 182477
/lib64/libc-2.12.so
300078f000-3000794000 rw-p 00000000 00:00 0
3000800000-3000817000 r-xp 00000000 fd:00 182479
/lib64/libpthread-2.12.so
3000817000-3000a17000 ---p 00017000 fd:00 182479
/lib64/libpthread-2.12.so
3000a17000-3000a18000 r--p 00017000 fd:00 182479
/lib64/libpthread-2.12.so
3000a18000-3000a19000 rw-p 00018000 fd:00 182479
/lib64/libpthread-2.12.so
3000a19000-3000a1d000 rw-p 00000000 00:00 0
3000c00000-3000c83000 r-xp 00000000 fd:00 143874
/lib64/libm-2.12.so
3000c83000-3000e82000 ---p 00083000 fd:00 143874
/lib64/libm-2.12.so
3000e82000-3000e83000 r--p 00082000 fd:00 143874
/lib64/libm-2.12.so
3000e83000-3000e84000 rw-p 00083000 fd:00 143874
/lib64/libm-2.12.so
3001000000-3001002000 r-xp 00000000 fd:00 182478
/lib64/libdl-2.12.so
3001002000-3001202000 ---p 00002000 fd:00 182478
/lib64/libdl-2.12.so
3001202000-3001203000 r--p 00002000 fd:00 182478
/lib64/libdl-2.12.so
3001203000-3001204000 rw-p 00003000 fd:00 182478
/lib64/libdl-2.12.so
3001800000-3001807000 r-xp 00000000 fd:00 182480
/lib64/librt-2.12.so
3001807000-3001a06000 ---p 00007000 fd:00 182480
/lib64/librt-2.12.so
3001a06000-3001a07000 r--p 00006000 fd:00 182480
/lib64/librt-2.12.so
3001a07000-3001a08000 rw-p 00007000 fd:00 182480
/lib64/librt-2.12.so
3001c00000-3001c16000 r-xp 00000000 fd:00 144099
/lib64/libgcc_s-4.4.7-20120601.so.1
3001c16000-3001e15000 ---p 00016000 fd:00 144099
/lib64/libgcc_s-4.4.7-20120601.so.1
3001e15000-3001e16000 rw-p 00015000 fd:00 144099
/lib64/libgcc_s-4.4.7-20120601.so.1
3002800000-30028e8000 r-xp 00000000 fd:00 182510
/usr/lib64/libstdc++.so.6.0.13
30028e8000-3002ae8000 ---p 000e8000 fd:00 182510
/usr/lib64/libstdc++.so.6.0.13
3002ae8000-3002aef000 r--p 000e8000 fd:00 182510
/usr/lib64/libstdc++.so.6.0.13
3002aef000-3002af1000 rw-p 000ef000 fd:00 182510
/usr/lib64/libstdc++.so.6.0.13
3002af1000-3002b06000 rw-p 00000000 00:00 0
3008c00000-3008d37000 r-xp 00000000 fd:00 144301
/usr/lib64/libX11.so.6.3.0
3008d37000-3008f37000 ---p 00137000 fd:00 144301
/usr/lib64/libX11.so.6.3.0
3008f37000-3008f3d000 rw-p 00137000 fd:00 144301
/usr/lib64/libX11.so.6.3.0
3009000000-3009002000 r-xp 00000000 fd:00 143787
/usr/lib64/libXau.so.6.0.0
3009002000-3009202000 ---p 00002000 fd:00 143787
/usr/lib64/libXau.so.6.0.0
3009202000-3009203000 rw-p 00002000 fd:00 143787
/usr/lib64/libXau.so.6.0.0
3009400000-300941d000 r-xp 00000000 fd:00 143793
/usr/lib64/libxcb.so.1.1.0
300941d000-300961d000 ---p 0001d000 fd:00 143793
/usr/lib64/libxcb.so.1.1.0
300961d000-300961e000 rw-p 0001d000 fd:00 143793
/usr/lib64/libxcb.so.1.1.0
3018800000-3018811000 r-xp 00000000 fd:00 131862
/usr/lib64/libXext.so.6.4.0
3018811000-3018a11000 ---p 00011000 fd:00 131862
/usr/lib64/libXext.so.6.4.0
3018a11000-3018a12000 rw-p 00011000 fd:00 131862
/usr/lib64/libXext.so.6.4.0
2b2ffc989000-2b2ffc98a000 rw-p 00000000 00:00 0
2b2ffc9a4000-2b2ffcf33000 rw-p 00000000 00:00 0
2b2ffcf3b000-2b300019d000 rw-p 00000000 00:00 0
2b3004000000-2b3004021000 rw-p 00000000 00:00 0
2b3004021000-2b3008000000 ---p 00000000 00:00 0
2b3009231000-2b30122c6000 rw-p 00000000 00:00 0
2b301b353000-2b302d57d000 rw-p 00000000 00:00 0
7fff6c227000-7fff6c23d000 rw-p 00000000 00:00 0
[stack]
7fff6c2ec000-7fff6c2ed000 r-xp 00000000 00:00 0
[vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]

Jeff Duda

-- 
Jeff Duda
Graduate research assistant
University of Oklahoma School of Meteorology
Center for Analysis and Prediction of Storms
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