[CIG-SHORT] Problem running user compiled version of Relax
Falgout, Jeff
jfalgout at usgs.gov
Mon Jun 29 13:25:14 PDT 2015
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> 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> 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
>
>
>
>
>
>
--
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
Phone: 303-202-4261
Cell: 303-648-1767
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