[CIG-SEISMO] SPECFEM2D on mac issues: librt, scotch and clock_gettime

[Dimitri Komatitsch]

Dear Eve, dear all,

This is a known problem that comes from SCOTCH and is unrelated to 
SPECFEM. I mentioned it to François Pellegrini, the author of SCOTCH, a 
couple of years ago. Basically SCOTCH (at least version 5.1) does not 
compile on MAC OS because of that call to clock_gettime().

We mention a trick in the users manual somewhere:

\item [Mac OS] You will probably need to install \texttt{XCODE}.
In addition, the \texttt{clock\_gettime} routine, which is used by the 
\texttt{SCOTCH} library that we use, does not exist in Mac OS.
You may need to replace it with \texttt{clock\_get\_time} if you want to 
use \texttt{SCOTCH}.


(just make that change in the SCOTCH source file and you should be all set).

François, did you fix that in SCOTCH version 6?

I think that Brad also fixed it in a different way, but probably in the 
3D version of SPECFEM only (?).

Thanks,
Dimitri.

On 10/17/2014 01:28 PM, Eve Tsang-Hin-Sun wrote:
> Dear all,
>
> I am trying ti compile SPECFEM2D. It worked well on my ubuntu laptop but
> fails on my iMac 10.8.5. As I understoof from prvious discussion, th
> problem come from incompatibility with librt and mac OS.
>
> Before changing any thing here is the error I got when  trying te make
> command into the src directory of scotch :
>
> 1ldo162:SPECFEM2D_Eve tsanghin$ make
> mkdir -p obj
> mkdir -p bin
> (cd src/meshfem2D; make )
> (echo "Using bundled Scotch")
> Using bundled Scotch
> (cd "scotch_5.1.12b/src"; make)
> (cd libscotch ;      make VERSION=5 RELEASE=1 PATCHLEVEL=12 scotch &&
> make install)
> rm -f *~ *.o lib*.a parser_yy.c parser_ly.h parser_ll.c *scotch.h
> *scotchf.h y.output dummysizes
> make CC="gcc" CCD="gcc"\
> scotch.h\
> scotchf.h\
> libscotch.a\
> libscotcherr.a\
> libscotcherrexit.a
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict -DSCOTCH_VERSION=5
> -DSCOTCH_RELEASE=1 -DSCOTCH_PATCHLEVEL=12 dummysizes.c -o dummysizes -lz
> -lm -lrt -lpthread
> ld: library not found for -lrt
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make[4]: *** [dummysizes] Error 1
> make[3]: *** [scotch] Error 2
> make[2]: *** [scotch] Error 2
> make[1]: *** [scotch] Error 2
> make: *** [xmeshfem2D] Error 2
>
>
> Then, according to the user manual, the clock_gettime routine, that
> calls librt has to be changed to clock_get_time in the common.c script.
> So I did it and also removed -lrt from the Makefil.inc file. Then after
> the new make, here is what I get :
>
>
>
> 1ldo162:src tsanghin$ make
> (cd libscotch ;      make VERSION=5 RELEASE=1 PATCHLEVEL=12 scotch &&
> make install)
> rm -f *~ *.o lib*.a parser_yy.c parser_ly.h parser_ll.c *scotch.h
> *scotchf.h y.output dummysizes
> make CC="gcc" CCD="gcc"\
> scotch.h\
> scotchf.h\
> libscotch.a\
> libscotcherr.a\
> libscotcherrexit.a
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict -DSCOTCH_VERSION=5
> -DSCOTCH_RELEASE=1 -DSCOTCH_PATCHLEVEL=12 dummysizes.c -o dummysizes -lz
> -lm -lpthread
> ./dummysizes library.h scotch.h
> ./dummysizes libraryf.h scotchf.h
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch.c -o arch.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_build.c -o arch_build.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_cmplt.c -o arch_cmplt.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_cmpltw.c -o arch_cmpltw.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_deco.c -o arch_deco.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_hcub.c -o arch_hcub.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_mesh.c -o arch_mesh.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_tleaf.c -o arch_tleaf.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_torus.c -o arch_torus.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_vcmplt.c -o arch_vcmplt.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c arch_vhcub.c -o arch_vhcub.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph.c -o bgraph.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_bipart_bd.c -o
> bgraph_bipart_bd.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_bipart_df.c -o
> bgraph_bipart_df.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_bipart_ex.c -o
> bgraph_bipart_ex.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_bipart_fm.c -o
> bgraph_bipart_fm.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_bipart_gg.c -o
> bgraph_bipart_gg.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_bipart_gp.c -o
> bgraph_bipart_gp.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_bipart_ml.c -o
> bgraph_bipart_ml.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_bipart_st.c -o
> bgraph_bipart_st.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_bipart_zr.c -o
> bgraph_bipart_zr.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_check.c -o bgraph_check.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c bgraph_store.c -o bgraph_store.o
> gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD
> -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER
> -DSCOTCH_PTHREAD -Drestrict=__restrict  -c common.c
> -DSCOTCH_COMMON_RENAME -o common.o
> common.c:107:3: warning: implicit declaration of function
> 'clock_get_time' is invalid in C99 [-Wimplicit-function-declaration]
>    clock_get_time (CLOCK_REALTIME, &tp);            /* Elapsed time */
>    ^
> common.c:107:19: error: use of undeclared identifier 'CLOCK_REALTIME'
>    clock_get_time (CLOCK_REALTIME, &tp);            /* Elapsed time */
>                    ^
> 1 warning and 1 error generated.
> make[2]: *** [common.o] Error 1
> make[1]: *** [scotch] Error 2
> make: *** [scotch] Error 2
>
>
> So I am a little bit confused : it seems that the clock_get_time routine
> is not defined. So where should I get it ?  Moreover, if the librt
> library doesn’t exist for mac OS, isn’t it another way to get the time
> step ? Or maybe the Makefile.Inc is ot well configured for mac ? If you
> have any tips to make it compile, that would be very helpful.
> Regards
>
> --
> Eve Tsang-Hin-Sun
> Doctorante
> Institut Universitaire Européen de la Mer (IUEM)
> Laboratoires Domaines Océaniques (LDO)
> Place Nicolas Copernic - 29280 Plouzané
>
>
>
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>

-- 
Dimitri Komatitsch
CNRS Research Director (DR CNRS), Laboratory of Mechanics and Acoustics,
UPR 7051, Marseille, France    http://komatitsch.free.fr