[CIG-SHORT] Problem running user compiled version of Relax
Oliver Boyd
olboyd at usgs.gov
Sun Jul 5 10:59:16 PDT 2015
Thanks a bunch.
> On Jul 5, 2015, at 5:28 AM, Sylvain Barbot <sylbar.vainbot at gmail.com> wrote:
>
> Dear Jeff,
>
> Thank you for pointing out this problem. This was indeed an error
> introduced recently. A pre-stress array was not allocated properly
> when pre-stress is not used. Sorry about that.
>
> I have fixed the problem now and pushed to the repository. The binary
> versions on geodynamics.org and on fink are not affected. Only the
> development version had this problem.
>
> You can get a clean version with
>
>> git pull
>
> Let me know if you run into any other problem.
>
> Best wishes,
> Sylvain
>
> On Tue, Jun 30, 2015 at 4:32 AM, Sylvain Barbot
> <sylbar.vainbot at gmail.com> wrote:
>> 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> 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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