[CIG-SEISMO] scotch and clock_gettime

Sat Oct 18 10:21:06 PDT 2014

Hi Eve,

Fixed. (it turns out that timing routine is unused when SCOTCH is called 
from SPECFEM, thus I just removed it)

Thus just update to the latest Git version.

Thanks,
Dimitri.

On 10/17/2014 10:56 PM, Dimitri Komatitsch wrote:
>
> Dear François, dear all,
>
> As a patch could I just comment this statement out in the source code of
> SCOTCH? i.e., is that timing routine really crucial or is it used to
> print execution times for information only? (if so, when called from
> SPECFEM we could just ignore the timing information, which we do not use).
>
> Thanks,
> Best regards,
>
> Dimitri.
>
> On 10/17/2014 10:41 PM, Dimitri Komatitsch wrote:
>>
>> 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
>>>
>>>
>>>
>>> _______________________________________________
>>> CIG-SEISMO mailing list
>>> CIG-SEISMO at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-seismo
>>>
>>
>

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