glibc detected - malloc(): memory corruption:

Discussions related to the use of ARWPost

glibc detected - malloc(): memory corruption:

Postby rleeper » Thu Sep 12, 2013 5:44 pm

When I run ARWpost.exe I get a memory corruption error (see full error message below) which causes ARWpost to stall. I have played around with namelist.ARWpost options and have determined that I do not get this error when I select diagnostic or 3D model variables. Unfortunately, I need 2 meter temperature T2, which is a 2D model variable that is of the variety that causes ARWpost.exe crashes each time with this error. I have compiled ARWpost using gfortran version 4.5.3 x86_64. I wonder if I missed a compiler flag option or a messed up some namelist.ARWpost setting see the namelist and configure files listed below. Any suggestions would be greatly appreciated!! Thanks for your time in advance.


*** glibc detected *** ./ARWpost.exe: malloc(): memory corruption: 0x0000000001f54490 ***


namelist.ARWpost
&datetime
start_date = '2008-08-24_06:00:00',
end_date = '2008-08-25_06:00:00',
interval_seconds = 1800,
tacc = 0,
debug_level = 0,
/

&io
input_root_name = '../../initLatalBundryLyr_study/Aug_2008/Aug_2008_FNL_12km_new.nc'
output_root_name = 'Aug_2008_FNL_12km_new_test'
plot = 'list'
fields = 'td2,u10m,v10m,ws10,T,T2'
mercator_defs = .true.
/

! plot = 'all'
! plot = 'list'
! plot = 'all_list'
! Below is a list of all available diagnostics
! fields = 'height,geopt,theta,tc,tk,td,td2,rh,rh2,umet,vmet,pressure,u10m,v10m,wdir,wspd,wd10,ws10,slp,mcape,mcin,lcl,lfc,cape,cin,dbz,max_dbz,clfr'

&interp
interp_method = 0,
interp_levels = 1000.,950.,900.,850.,800.,750.,700.,650.,600.,550.,500.,450.,400.,350.,300.,250.,200.,150.,100.,
/
extrapolate = .true.

interp_method = 0, ! 0 is model levels, -1 is nice height levels, 1 is user specified pressure/height

interp_levels = 1000.,950.,900.,850.,800.,750.,700.,650.,600.,550.,500.,450.,400.,350.,300.,250.,200.,150.,100.,
interp_levels = 0.25, 0.50, 0.75, 1.00, 2.00, 3.00, 4.00, 5.00, 6.00, 7.00, 8.00, 9.00, 10.0, 11.0, 12.0, 13.0, 14.0, 15.0, 16.0, 17.0, 18.0, 19.0, 20.0,


configure.arwp
# Settings for PC Linux i486 i586 i686 x86_64, gfortran compiler
#
FC = gfortran
FFLAGS = -ffree-form -O -fno-second-underscore -fconvert=big-endian -frecord-marker=4
F77FLAGS = -ffixed-form -O -fno-second-underscore -fconvert=big-endian
FNGFLAGS = $(FFLAGS)
LDFLAGS = -L/home/ronnieleeper/WRFV3/WRFV3/netcdf_links/lib -lnetcdff -lnetcdf
CC = gcc
CFLAGS = -w -03 -c -DLANDREAD_STUB
CPP = /lib/cpp -C -P -traditional
CPPFLAGS = -DIO_NETCDF -DIO_GRIB1 -DIO_BINARY -DRECL4 -Dbytesw
rleeper
 
Posts: 3
Joined: Mon Sep 09, 2013 12:32 pm

Re: glibc detected - malloc(): memory corruption:

Postby akiortagem » Tue Sep 17, 2013 2:22 am

I have the exact same error, is it resolved yet? do anyone have the solution?
akiortagem
 
Posts: 7
Joined: Thu Sep 12, 2013 5:05 am

Re: glibc detected - malloc(): memory corruption:

Postby kserradell » Tue Oct 07, 2014 6:36 am

I'm having the same issue with GNU Fortran (GCC) 4.4.7 20120313

With only one variable it works:

Code: Select all
 plot = 'list'
 fields = 'height'


But with more

Code: Select all
 plot = 'list'
 fields = 'height,T2'


Crashes.

*** glibc detected *** ./ARWpost.exe: malloc(): memory corruption: 0x00000000044b4060 ***

With Ifort never got this problem.
kserradell
 
Posts: 9
Joined: Wed Jan 09, 2013 10:29 am
Location: Barcelona - Spain

Re: glibc detected - malloc(): memory corruption:

Postby tanbir_sagar » Sun Jun 14, 2015 3:31 am

I am having the same problem can any body help with this problem ??
tanbir_sagar
 
Posts: 2
Joined: Sat Jun 13, 2015 2:10 pm

Re: glibc detected - malloc(): memory corruption:

Postby peter » Mon Aug 31, 2015 3:25 pm

I have a similar problem. The only solution that I found was to remove from my list the variables which I detected as being a problem, T2 and HGT. After that I was able to run arwpost and postprocess my remaining variables.
peter
 
Posts: 23
Joined: Tue Apr 15, 2008 10:06 am

Re: glibc detected - malloc(): memory corruption:

Postby Ramchandra » Mon Dec 21, 2015 11:47 am

I am also having the same problem. if any solution is available please kindly respond. I am a begineer to this wrf arw model
!!!!!!!!!!!!!!!!


ARWpost v3.1
!!!!!!!!!!!!!!!!

FOUND the following input files:
/home/fgvy024/Build_WRF/WRFV3/run/wrfout_d01_2010-06-04_12:00:00

START PROCESSING DATA

Processing time --- 2010-06-04_12:00:00
Found the right date - continue
*** glibc detected *** ./ARWpost.exe: malloc(): memory corruption: 0x0000000000a e6790 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x79098)[0x7f1ed0cc9098]
/lib64/libc.so.6(+0x7c04f)[0x7f1ed0ccc04f]
/lib64/libc.so.6(__libc_malloc+0x77)[0x7f1ed0cce1c7]
/usr/lib64/libgfortran.so.3(+0x1d9b9)[0x7f1ed14859b9]
/usr/lib64/libgfortran.so.3(_gfortran_string_trim+0x58)[0x7f1ed15559d8]
./ARWpost.exe[0x410dd1]
./ARWpost.exe[0x4129c7]
./ARWpost.exe[0x4037ca]
./ARWpost.exe[0x45ca1c]
/lib64/libc.so.6(__libc_start_main+0xe6)[0x7f1ed0c6ec36]
./ARWpost.exe[0x4020b5]
======= Memory map: ========
00400000-004eb000 r-xp 00000000 08:03 1720398 /home/f gvy024/Build_WRF/ARWpost/src/ARWpost.exe
006ea000-006eb000 r--p 000ea000 08:03 1720398 /home/f gvy024/Build_WRF/ARWpost/src/ARWpost.exe
006eb000-006ec000 rw-p 000eb000 08:03 1720398 /home/f gvy024/Build_WRF/ARWpost/src/ARWpost.exe
006ec000-00cf3000 rw-p 00000000 00:00 0 [heap]
7f1ecc000000-7f1ecc021000 rw-p 00000000 00:00 0
7f1ecc021000-7f1ed0000000 ---p 00000000 00:00 0
7f1ed0a18000-7f1ed0a4d000 r-xp 00000000 08:01 2289168 /usr/li b64/libquadmath.so.0.0.0
7f1ed0a4d000-7f1ed0c4c000 ---p 00035000 08:01 2289168 /usr/li b64/libquadmath.so.0.0.0
7f1ed0c4c000-7f1ed0c4d000 r--p 00034000 08:01 2289168 /usr/li b64/libquadmath.so.0.0.0
7f1ed0c4d000-7f1ed0c4e000 rw-p 00035000 08:01 2289168 /usr/li b64/libquadmath.so.0.0.0
7f1ed0c50000-7f1ed0dc2000 r-xp 00000000 08:01 2528069 /lib64/ libc-2.11.3.so
7f1ed0dc2000-7f1ed0fc2000 ---p 00172000 08:01 2528069 /lib64/ libc-2.11.3.so
7f1ed0fc2000-7f1ed0fc6000 r--p 00172000 08:01 2528069 /lib64/ libc-2.11.3.so
7f1ed0fc6000-7f1ed0fc7000 rw-p 00176000 08:01 2528069 /lib64/ libc-2.11.3.so
7f1ed0fc7000-7f1ed0fcc000 rw-p 00000000 00:00 0
7f1ed0fd0000-7f1ed0fe5000 r-xp 00000000 08:01 2528159 /lib64/ libgcc_s.so.1
7f1ed0fe5000-7f1ed11e4000 ---p 00015000 08:01 2528159 /lib64/ libgcc_s.so.1
7f1ed11e4000-7f1ed11e5000 r--p 00014000 08:01 2528159 /lib64/ libgcc_s.so.1
7f1ed11e5000-7f1ed11e6000 rw-p 00015000 08:01 2528159 /lib64/ libgcc_s.so.1
7f1ed11e8000-7f1ed1243000 r-xp 00000000 08:01 2528098 /lib64/ libm-2.11.3.so
7f1ed1243000-7f1ed1442000 ---p 0005b000 08:01 2528098 /lib64/ libm-2.11.3.so
7f1ed1442000-7f1ed1443000 r--p 0005a000 08:01 2528098 /lib64/ libm-2.11.3.so
7f1ed1443000-7f1ed1461000 rw-p 0005b000 08:01 2528098 /lib64/ libm-2.11.3.so
7f1ed1468000-7f1ed157c000 r-xp 00000000 08:01 2289255 /usr/li b64/libgfortran.so.3.0.0
7f1ed157c000-7f1ed177b000 ---p 00114000 08:01 2289255 /usr/li b64/libgfortran.so.3.0.0
7f1ed177b000-7f1ed177c000 r--p 00113000 08:01 2289255 /usr/li b64/libgfortran.so.3.0.0
7f1ed177c000-7f1ed177e000 rw-p 00114000 08:01 2289255 /usr/li b64/libgfortran.so.3.0.0
7f1ed1780000-7f1ed179f000 r-xp 00000000 08:01 2530929 /lib64/ ld-2.11.3.so
7f1ed195e000-7f1ed1960000 rw-p 00000000 00:00 0
7f1ed199f000-7f1ed19a0000 r--p 0001f000 08:01 2530929 /lib64/ ld-2.11.3.so
7f1ed19a0000-7f1ed19a1000 rw-p 00020000 08:01 2530929 /lib64/ ld-2.11.3.so
7f1ed19a1000-7f1ed19a3000 rw-p 00000000 00:00 0
7f1ed19a3000-7f1ed19a5000 rw-p 00000000 00:00 0
7ffeb2505000-7ffeb2526000 rw-p 00000000 00:00 0 [stack]
7ffeb2550000-7ffeb2551000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsysca ll]

namelist.arwpost
&datetime
start_date = '2010-06-04_12:00:00',
end_date = '2010-06-05_12:00:00',
interval_seconds = 10800,
tacc = 0,
debug_level = 0,
/

&io
input_root_name = '/home/fgvy024/Build_WRF/WRFV3/run/wrfout_d01_2010-06-04_12:00:00'
output_root_name = './test'
plot = 'all_list'
fields = 'height,pressure,tk,tc'
mercator_defs = .true.
/
split_output = .true.
frames_per_outfile = 2


plot = 'all'
plot = 'list'
plot = 'all_list'
! Below is a list of all available diagnostics
fields = 'height,geopt,theta,tc,tk,td,td2,rh,rh2,umet,vmet,pressure,u10m,v10m,wdir,wspd,wd10,ws10,slp,mcape,mcin,lcl,lfc,cape,cin,dbz,max_dbz,clfr'


&interp
interp_method = 0,
interp_levels = 1000.,950.,900.,850.,800.,750.,700.,650.,600.,550.,500.,450.,400.,350.,300.,250.,200.,150.,100.,
/
extrapolate = .true.

interp_method = 0, ! 0 is model levels, -1 is nice height levels, 1 is user specified pressure/height

interp_levels = 1000.,950.,900.,850.,800.,750.,700.,650.,600.,550.,500.,450.,400.,350.,300.,250.,200.,150.,100.,
interp_levels = 0.25, 0.50, 0.75, 1.00, 2.00, 3.00, 4.00, 5.00, 6.00, 7.00, 8.00, 9.00, 10.0, 11.0, 12.0, 13.0, 14.0, 15.0, 16.0, 17.0, 18.0, 19.0, 20.0,
Ramchandra
 
Posts: 4
Joined: Mon Dec 21, 2015 11:12 am

Re: glibc detected - malloc(): memory corruption:

Postby Jipson Johnson » Fri Sep 23, 2016 12:39 am

I also have the same kind of problem.

!!!!!!!!!!!!!!!!
ARWpost v3.1
!!!!!!!!!!!!!!!!

FOUND the following input files:
/home/ranjith/Documents/Jips/Build_WRF/WRF_OUT/2016_05_10/d01/wrfout_d01_2016-05-10_12:00:00

START PROCESSING DATA

Processing time --- 2016-05-10_12:00:00
Found the right date - continue
*** glibc detected *** ./ARWpost.exe: malloc(): memory corruption: 0x0000000002571430 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7ba9a)[0x7fea1e45ca9a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_malloc+0x6e)[0x7fea1e45f03e]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(+0x167c9)[0x7fea1ec2a7c9]
/usr/lib/x86_64-linux-gnu/libgfortran.so.3(_gfortran_string_trim+0x58)[0x7fea1ecd3108]
./ARWpost.exe[0x411fe9]
./ARWpost.exe[0x413d83]
./ARWpost.exe[0x403636]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)[0x7fea1e3ffeff]
./ARWpost.exe[0x401e69]
======= Memory map: ========
00400000-004e6000 r-xp 00000000 08:05 13420281 /home/ranjith/Documents/Jips/Build_WRF/ARWpost/src/ARWpost.exe
006e6000-006e7000 r--p 000e6000 08:05 13420281 /home/ranjith/Documents/Jips/Build_WRF/ARWpost/src/ARWpost.exe
006e7000-006e8000 rw-p 000e7000 08:05 13420281 /home/ranjith/Documents/Jips/Build_WRF/ARWpost/src/ARWpost.exe
006e8000-0071e000 rw-p 00000000 00:00 0
01f6f000-02668000 rw-p 00000000 00:00 0 [heap]
7fea18000000-7fea18021000 rw-p 00000000 00:00 0
7fea18021000-7fea1c000000 ---p 00000000 00:00 0
7fea1e344000-7fea1e3e1000 rw-p 00000000 00:00 0
7fea1e3e1000-7fea1e56e000 r-xp 00000000 08:03 262156 /lib/x86_64-linux-gnu/libc-2.13.so
7fea1e56e000-7fea1e76e000 ---p 0018d000 08:03 262156 /lib/x86_64-linux-gnu/libc-2.13.so
7fea1e76e000-7fea1e772000 r--p 0018d000 08:03 262156 /lib/x86_64-linux-gnu/libc-2.13.so
7fea1e772000-7fea1e773000 rw-p 00191000 08:03 262156 /lib/x86_64-linux-gnu/libc-2.13.so
7fea1e773000-7fea1e779000 rw-p 00000000 00:00 0
7fea1e779000-7fea1e78e000 r-xp 00000000 08:03 265950 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fea1e78e000-7fea1e98d000 ---p 00015000 08:03 265950 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fea1e98d000-7fea1e98e000 r--p 00014000 08:03 265950 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fea1e98e000-7fea1e98f000 rw-p 00015000 08:03 265950 /lib/x86_64-linux-gnu/libgcc_s.so.1
7fea1e98f000-7fea1ea13000 r-xp 00000000 08:03 262308 /lib/x86_64-linux-gnu/libm-2.13.so
7fea1ea13000-7fea1ec12000 ---p 00084000 08:03 262308 /lib/x86_64-linux-gnu/libm-2.13.so
7fea1ec12000-7fea1ec13000 r--p 00083000 08:03 262308 /lib/x86_64-linux-gnu/libm-2.13.so
7fea1ec13000-7fea1ec14000 rw-p 00084000 08:03 262308 /lib/x86_64-linux-gnu/libm-2.13.so
7fea1ec14000-7fea1ecf5000 r-xp 00000000 08:03 531503 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fea1ecf5000-7fea1eef5000 ---p 000e1000 08:03 531503 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fea1eef5000-7fea1eef6000 r--p 000e1000 08:03 531503 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fea1eef6000-7fea1eef7000 rw-p 000e2000 08:03 531503 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7fea1eef7000-7fea1eef8000 rw-p 00000000 00:00 0
7fea1eef8000-7fea1ef19000 r-xp 00000000 08:03 262309 /lib/x86_64-linux-gnu/ld-2.13.so
7fea1f0ef000-7fea1f0f3000 rw-p 00000000 00:00 0
7fea1f116000-7fea1f118000 rw-p 00000000 00:00 0
7fea1f118000-7fea1f119000 r--p 00020000 08:03 262309 /lib/x86_64-linux-gnu/ld-2.13.so
7fea1f119000-7fea1f11b000 rw-p 00021000 08:03 262309 /lib/x86_64-linux-gnu/ld-2.13.so
7fffadc6b000-7fffadc8c000 rw-p 00000000 00:00 0 [stack]
7fffadcac000-7fffadcad000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted

can anybody solve this ????
Thanks in advance....
Jipson Johnson
 
Posts: 24
Joined: Thu Jan 08, 2015 2:15 pm


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