[ncl-install] Segmentation fault when compiling NCL from source on Amazon Linux 2 (ARM64)
Ehsan Taghizadeh
ehsantaghizadeh at yahoo.com
Fri Sep 3 09:31:08 MDT 2021
Dear Michael,It might not be your answer directly, however, did you try conda method, including the following commands, for install NCL instead of compiling method:
$ conda update -n root --all$ conda install -c conda-forge ncl
Reference: Installing NCL with "conda"
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Installing NCL with "conda"
How to install NCL using conda
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Sincerely,
Ehsan Taghizadeh On Wednesday, September 1, 2021, 10:07:22 PM GMT+4:30, Michael Graf via ncl-install <ncl-install at mailman.ucar.edu> wrote:
Dear all,
Thanks for adding me to the NCL mailing list.
I am trying to compile the latest NCL Version 6.6.2 from scratch on Amazon
Linux 2 (ARM64 architecture). Everything works fine except that a
segmentation fault occurs when the fontcaps are compiled respectively when
the fontc binary is processing fontcaps (see output below). No other error
occurs. The ncl binary is compiled and it can be started without problems,
but when I run a plotting script a segmentation fault occurs that is
probably related to the compilation error in fontcap.
I also compiled a minimal version with as few dependencies as possible (no
GDAL, HDF5, NETCDF-4 and so on) to rule out that they cause the problem
without any effect. I have also randomly tried different compiler options
for the compilation in the folder fontcap, but the error always remains the
same. I suspect that the compiler is causing the problem, but there is no
alternative on Amazon Linux 2 so far. I'm using gfortran (version 7.3.1) and
gcc (version 7.3.1), but here only Fortran77 code seems to be compiled.
It would be great if somebody has a hint how to overcome this problem. Maybe
there is another option, so that I don't have to build it from scratch. The
installation with conda does not work on ARM64.
Best, Michael
************************************************************************
Making ./common/src/fontcap
make[4]: Entering directory
`/home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap'
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c
cfaamn.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
cfrdln.o cfrdln.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
cfwrit.o cfwrit.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
ffgttk.o ffgttk.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
ffinfo.o ffinfo.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
ffphol.o ffphol.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
ffppkt.o ffppkt.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
ffprcf.o ffprcf.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
ffprsa.o ffprsa.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
fftbkd.o fftbkd.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
fftkin.o fftkin.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
sffndc.o sffndc.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
sfgtin.o sfgtin.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
sfgtkw.o sfgtkw.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
sfprcf.o sfprcf.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
sfskbk.o sfskbk.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -c -o
sftbkd.o sftbkd.f
gfortran -fPIC -fno-second-underscore -fno-range-check -fopenmp -O -o
fontc cfaamn.o cfrdln.o cfwrit.o ffgttk.o ffinfo.o ffphol.o ffppkt.o
ffprcf.o ffprsa.o fftb
kd.o fftkin.o sffndc.o sfgtin.o sfgtkw.o sfprcf.o sfskbk.o sftbkd.o
-L../../.././common/src/libncarg_c -lncarg_c -L/usr/local/ncarg_gdal/lib
-L/usr/local/lib
Processing fontcap font1
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x40001dcb99a3
#1 0x40001dcb888f
#2 0x40001dc90667
#3 0x403bdc
#4 0x403c63
#5 0x4032af
#6 0x400efb
#7 0x401213
#8 0x40001df5ace3
#9 0x400d07
make[4]: *** [font1] Segmentation fault
make[4]: Leaving directory
`/home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap'
************************************************************************
gfortran -g -fbacktrace -Wall -fcheck=all -o fontc cfaamn.o cfrdln.o
cfwrit.o ffgttk.o ffinfo.o ffphol.o ffppkt.o ffprcf.o ffprsa.o
fftbkd.o fftkin.o sffndc.o
sfgtin.o sfgtkw.o sfprcf.o sfskbk.o sftbkd.o
-L../../.././common/src/libncarg_c -lncarg_c -L/usr/local/ncarg/lib
-L/usr/local/lib
Processing fontcap font1
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x40001a29595b in ???
#1 0x40001a29488f in ???
#2 0x40001a26c667 in ???
#3 0x40723c in ???
#4 0x4072e7 in ???
#5 0x405c97 in sfgtwk_
at /home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/sfgtkw.f:95
#6 0x4061cb in sfprcf_
at /home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/sfprcf.f:108
#7 0x40119b in cfaamn
at /home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/cfaamn.f:304
#8 0x401633 in main
at /home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/cfaamn.f:358
make: *** [font1] Segmentation fault
************************************************************************
gfortran -g -fsanitize=address,undefined -o fontc cfaamn.o cfrdln.o
cfwrit.o ffgttk.o ffinfo.o ffphol.o ffppkt.o ffprcf.o ffprsa.o
fftbkd.o fftkin.o sffndc.o
sfgtin.o sfgtkw.o sfprcf.o sfskbk.o sftbkd.o
-L../../.././common/src/libncarg_c -lncarg_c -L/usr/local/ncarg/lib
-L/usr/local/lib
Processing fontcap font1
ASAN:DEADLYSIGNAL
=================================================================
==2477==ERROR: AddressSanitizer: SEGV on unknown address 0x100005104df40 (pc
0x00000040ffd0 bp 0xffffd104daf0 sp 0xffffd104daf0 T0)
==2477==The signal is caused by a READ memory access.
#0 0x40ffcf in gbyte_
(/home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/fontc+0x40ffcf)
#1 0x410057 in gbytes_
(/home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/fontc+0x410057)
#2 0x40deab in sfprcf_
/home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/sfprcf.f:117
#3 0x40213f in cfaamn
/home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/cfaamn.f:304
#4 0x402d7b in main
/home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/cfaamn.f:358
#5 0x40002cbc7ce3 in __libc_start_main (/lib64/libc.so.6+0x1fce3)
#6 0x4018a7
(/home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/fontc+0x4018a7)
AddressSanitizer can not provide additional info.
SUMMARY: AddressSanitizer: SEGV
(/home/ec2-user/wrf/NCL/ncl_ncarg-6.6.2/common/src/fontcap/fontc+0x40ffcf)
in gbyte_
==2477==ABORTING
make: *** [font1] Error 1
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