[CIG-SHORT] Problem running user compiled version of Relax
Falgout, Jeff
jfalgout at usgs.gov
Mon Jun 29 13:17:43 PDT 2015
Hi Sylvain -
Here is more info on the problem we ran into with the git version from 29
June 2015 (fingers crossed line doesn't kill me)
$ ifort --version
ifort (IFORT) 15.0.0 20140723
Copyright (C) 1985-2014 Intel Corporation. All rights reserved.
$ FCFLAGS="-check arg_temp_created -gen-interfaces -warn interfaces
-fp-stack-check -check bounds -g -traceback"
$ ./waf distclean
'distclean' finished successfully 0.086s
$ ./waf configure --proj-dir=/usr/bin --gmt-dir=/usr/bin
--gmt-incdir=/usr/include --gmt-libdir=/usr/lib64
--mkl-libdir=/opt/intel/mkl/lib/intel64/ --gmt-libdir=/usr/lib64
--mkl-libdir=/opt/intel/mkl/lib/intel64/ --check-fortran-compiler=ifort
--check-cxx-compiler=icpc
Setting top to :
/home/jfalgout/olboyd/Tools/Relax/relax-git/relax
Setting out to :
/home/jfalgout/olboyd/Tools/Relax/relax-git/relax/build
Checking for 'gcc' (c compiler) : /usr/bin/gcc
Checking for 'ifort' (fortran compiler) : /opt/intel/bin/ifort
Checking for 'icpc' (c++ compiler) : /opt/intel/bin/icpc
Compiling a simple fortran app : yes
Checking for header proj_api.h : yes
Checking for gmt.h in '/usr/include' : yes
Checking for openmp flag -fopenmp : yes
Checking for MKL : yes
Checking preprocessor option -cpp : yes
Checking length option : yes
'configure' finished successfully 35.914s
$ ./waf build
Waf: Entering directory
`/home/jfalgout/olboyd/Tools/Relax/relax-git/relax/build'
[ 3/20] fc: src/ctfft.f -> build/src/ctfft.f.1.o
[ 3/20] fc: src/types.f90 -> build/src/types.f90.1.o build/types.mod
[ 3/20] fc: src/okada/dc3d.f -> build/src/okada/dc3d.f.1.o
[ 4/20] c: src/writevtk.c -> build/src/writevtk.c.1.o
[ 5/20] c: src/writegrd4.2.c -> build/src/writegrd4.2.c.1.o
[ 8/20] c: src/proj.c -> build/src/proj.c.1.o
[ 9/20] fc: src/getdata.f -> build/src/getdata.f.1.o
[ 9/20] fc: src/getopt_m.f90 -> build/src/getopt_m.f90.1.o
build/getopt_m.mod
[ 9/20] fc: src/mkl_dfti.f90 -> build/src/mkl_dfti.f90.1.o
build/mkl_dft_type.mod build/mkl_dfti.mod
[10/20] c: src/papi_prof.c -> build/src/papi_prof.c.1.o
[11/20] fc: src/fourier.f90 -> build/src/fourier.f90.1.o build/fourier.mod
[12/20] fc: src/green.f90 -> build/src/green.f90.1.o build/green.mod
[13/20] fc: src/elastic3d.f90 -> build/src/elastic3d.f90.1.o
build/elastic3d.mod
[14/20] fc: src/okada/green_space.f90 ->
build/src/okada/green_space.f90.1.o build/green_space.mod
[15/20] fc: src/viscoelastic3d.f90 -> build/src/viscoelastic3d.f90.1.o
build/viscoelastic3d.mod
[16/20] fc: src/friction3d.f90 -> build/src/friction3d.f90.1.o
build/friction3d.mod
[17/20] fc: src/export.f90 -> build/src/export.f90.1.o build/export.mod
[18/20] fc: src/input.f90 -> build/src/input.f90.1.o build/input.mod
/home/jfalgout/olboyd/Tools/Relax/relax-git/relax/src/input.f90(323):
remark #8293: Recommended relationship between field width 'W', the number
of fractional digits 'D' and the number of exponential digits 'E' in this
edit descriptor is 'W>=D+E+5'.
PRINT '("# output every ",I3.3," steps, dt scaled by ",ES7.2E1)',
in%skip,in%tscale
-------------------------------------------------------------------------------^
[19/20] fc: src/relax.f90 -> build/src/relax.f90.1.o
/home/jfalgout/olboyd/Tools/Relax/relax-git/relax/src/relax.f90(980):
remark #8293: Recommended relationship between field width 'W', the number
of fractional digits 'D' and the number of exponential digits 'E' in this
edit descriptor is 'W>=D+E+5'.
1101 FORMAT (I3.3,"*",ES9.2E2,3ES9.2E2,ES9.2E2,"/",ES7.2E1,2ES9.2E2)
-------------------------------------------------------------------------------^
/home/jfalgout/olboyd/Tools/Relax/relax-git/relax/src/relax.f90(979):
remark #8293: Recommended relationship between field width 'W', the number
of fractional digits 'D' and the number of exponential digits 'E' in this
edit descriptor is 'W>=D+E+5'.
1100 FORMAT (I3.3," ",ES9.2E2,3ES9.2E2,ES9.2E2,"/",ES7.2E1,2ES9.2E2)
-------------------------------------------------------------------------------^
[20/20] fcprogram: build/src/relax.f90.1.o build/src/ctfft.f.1.o
build/src/types.f90.1.o build/src/fourier.f90.1.o build/src/green.f90.1.o
build/src/okada/green_space.f90.1.o build/src/okada/dc3d.f.1.o
build/src/elastic3d.f90.1.o build/src/friction3d.f90.1.o
build/src/viscoelastic3d.f90.1.o build/src/writevtk.c.1.o
build/src/writegrd4.2.c.1.o build/src/proj.c.1.o build/src/export.f90.1.o
build/src/getdata.f.1.o build/src/getopt_m.f90.1.o build/src/input.f90.1.o
build/src/mkl_dfti.f90.1.o build/src/papi_prof.c.1.o -> build/relax
Waf: Leaving directory
`/home/jfalgout/olboyd/Tools/Relax/relax-git/relax/build'
'build' finished successfully 17.861s
(The arrow is pointing to the 7 in ES7.2E1 in the 3 warnings)
When I run the problem, we get a segfault as follows:
# number of inter-seismic strike-slip segments
0
# number of inter-seismic tensile segments
0
# number of events
1
# number of coseismic strike-slip segments
2
#
----------------------------------------------------------------------------
# n slip xs ys zs length width strike dip rake
#
----------------------------------------------------------------------------
001 5.00E+0 1.89E+1 -1.05E+1 5.10E+0 4.00E+1 1.87E+1 173.2 31.9 90.0
002 6.63E+0 1.91E+1 -8.94E+0 0.00E+0 4.00E+1 5.33E+0 173.2 73.0 90.0
#
----------------------------------------------------------------------------
# number of coseismic tensile segments
0
# number of coseismic dilatation point sources
0
# number of surface loads
0
# max sampling size (hor.,vert.): 1.60E+1 2.13E+0
#
----------------------------------------------------------------------------
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
relax 00000000005AFBC1 Unknown Unknown Unknown
relax 00000000005AE317 Unknown Unknown Unknown
relax 000000000055EDE4 Unknown Unknown Unknown
relax 000000000055EBF6 Unknown Unknown Unknown
relax 000000000050D7D4 Unknown Unknown Unknown
relax 000000000051197D Unknown Unknown Unknown
libpthread.so.0 000000314EC0F710 Unknown Unknown Unknown
relax 0000000000454B07 Unknown Unknown Unknown
relax 0000000000414431 Unknown Unknown Unknown
relax 0000000000410CBE Unknown Unknown Unknown
libc.so.6 000000314E01ED5D Unknown Unknown Unknown
relax 0000000000410BC9 Unknown Unknown Unknown
At one point I had the Segfault spitting out a little more info, but it's
not doing that now ... Let me know if there is anything you want me to do
differently or any debug info I can provide.
Thanks for you help,
Jeff
On Wed, Jun 24, 2015 at 4:34 PM, Oliver Boyd <olboyd at usgs.gov> wrote:
>
> We didn’t fix the problem. We just didn't use the files that came out of
the git repository, but rather used those in the source tar ball from the
CIG website.
>
> From: Sylvain Barbot <sylbar.vainbot at gmail.com>
> Reply-To: <cig-short at geodynamics.org>
> Date: Wednesday, June 24, 2015 3:44 PM
> To: "cig-short at geodynamics.org" <cig-short at geodynamics.org>
> Cc: Walter Landry <wlandry at caltech.edu>
> Subject: Re: [CIG-SHORT] Problem running user compiled version of Relax
>
> Hi Oliver,
>
> Can you and Jeff let us know how you fixed the problem? I'd like to know
if and how I can improve the code.
>
> Thanks,
> Sylvain
>
> On Wednesday, June 24, 2015, Oliver Boyd <olboyd at usgs.gov> wrote:
>>
>> Jeff Falgout at the USGS helped me to get it working. Looks like the
>> libraries are fine, but there may be a problem with the git repository.
>> When I build from the source tarball on the CIG website, it works fine.
>>
>> On 6/18/15 1:32 AM, "Walter Landry" <wlandry at caltech.edu> wrote:
>>
>> >Oliver Boyd <olboyd at usgs.gov> wrote:
>> >> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> >> Image PC Routine Line
>> >>Source
>> >> relax 00000000005AF571 Unknown Unknown
>> >>Unknown
>> >> relax 00000000005ADCC7 Unknown Unknown
>> >>Unknown
>> >> relax 000000000055E794 Unknown Unknown
>> >>Unknown
>> >> relax 000000000055E5A6 Unknown Unknown
>> >>Unknown
>> >> relax 000000000050D184 Unknown Unknown
>> >>Unknown
>> >> relax 000000000051132D Unknown Unknown
>> >>Unknown
>> >> libpthread.so.0 0000003F77C0F710 Unknown Unknown
>> >>Unknown
>> >> relax 0000000000454AB7 Unknown Unknown
>> >>Unknown
>> >> relax 00000000004143E1 Unknown Unknown
>> >>Unknown
>> >> relax 0000000000410C6E Unknown Unknown
>> >>Unknown
>> >> libc.so.6 0000003F7701ED5D Unknown Unknown
>> >>Unknown
>> >> relax 0000000000410B79 Unknown Unknown
>> >>Unknown
>> >> srun: error: compute87: task 0: Exited with exit code 174
>> >
>> >It looks like you might be linking against the wrong library at run
>> >time. In your slurm script, run 'ldd' on the executable and make sure
>> >it links against the right libraries in the right places. If that
>> >does not work, we can try running it in a debugger.
>> >
>> >Cheers,
>> >Walter Landry
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