[CIG-SHORT] Problem running user compiled version of Relax
Sylvain Barbot
sylbar.vainbot at gmail.com
Mon Jun 29 13:32:41 PDT 2015
Hi Jeff,
Since the error involves stressstruc, can you send the full output message
and/or the input file so we can reproduce the problem?
Thanks,
S.
On Monday, June 29, 2015, Falgout, Jeff <jfalgout at usgs.gov> wrote:
> Hi Sylvain -
>
> As soon as I hit send, I figured out my mistake for getting a useful
> segfault:
>
> $ FCFLAGS="-check arg_temp_created -gen-interfaces -warn interfaces
> -fp-stack-check -check bounds -g -traceback" ./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/
> --mkl-incdir=/opt/intel/mkl/include --check-c-compiler=icc
> --check-fortran-compiler=ifort --check-cxx-compiler=icpc
>
> # number of surface loads
> 0
> # max sampling size (hor.,vert.): 1.60E+1 2.13E+0
> #
> ----------------------------------------------------------------------------
> forrtl: severe (408): fort: (2): Subscript #1 of the array STRESSSTRUC has
> value 1 which is greater than the upper bound of -1
>
> Image PC Routine Line Source
> relax 00000000006B9C60 Unknown Unknown Unknown
> relax 0000000000418795 MAIN__ 292
> relax.f90
> relax 0000000000410D5E Unknown Unknown Unknown
> libc.so.6 000000314E01ED5D Unknown Unknown Unknown
> relax 0000000000410C69 Unknown Unknown Unknown
>
>
> Jeff
>
> On Mon, Jun 29, 2015 at 2:17 PM, Falgout, Jeff <jfalgout at usgs.gov
> <javascript:_e(%7B%7D,'cvml','jfalgout at usgs.gov');>> wrote:
>
>> 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
>> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','sylbar.vainbot at gmail.com');>>
>> > Reply-To: <cig-short at geodynamics.org
>> <javascript:_e(%7B%7D,'cvml','cig-short at geodynamics.org');>>
>> > Date: Wednesday, June 24, 2015 3:44 PM
>> > To: "cig-short at geodynamics.org
>> <javascript:_e(%7B%7D,'cvml','cig-short at geodynamics.org');>" <
>> cig-short at geodynamics.org
>> <javascript:_e(%7B%7D,'cvml','cig-short at geodynamics.org');>>
>> > Cc: Walter Landry <wlandry at caltech.edu
>> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','wlandry at caltech.edu');>> wrote:
>> >>
>> >> >Oliver Boyd <olboyd at usgs.gov
>> <javascript:_e(%7B%7D,'cvml','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
>>
>>
>>
>>
>>
>>
>
>
> --
>
> Jeff Falgout
> US Geological Survey
> Core Science Analytics, Synthesis, and Libraries
> Denver Federal Center
> Building 810, Mail Stop 302
> Denver, CO 80225
> jfalgout at usgs.gov <javascript:_e(%7B%7D,'cvml','jfalgout at usgs.gov');>
> Phone: 303-202-4261
> Cell: 303-648-1767
>
>
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