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Problem with libscotch in ThirdParty applications

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Old   January 29, 2010, 15:40
Default Problem with libscotch in ThirdParty applications
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Ganesh Vijayakumar
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hi !

I have a Fedora 10 box and am using the OpenFOAM-1.6.x from the git repository. The ThirdParty-1.6 seems to have a problem when using Allwmake.

[root@country ThirdParty-1.6.x]# ./Allwmake
++ '[' -n '' ']'
++ '[' -n '' ']'
++ '[' -n '' ']'
++ '[' -n '' ']'
++ '[' -n '' ']'
++ cd malloc
++ ./Allwmake
+ wmake libso hoard
'/opt/OpenFOAM/OpenFOAM-1.6.x/lib/linuxGccDPOpt/libhoard.so' is up to date.
+ wmake libo fbsdmalloc
'/opt/OpenFOAM/OpenFOAM-1.6.x/lib/linuxGccDPOpt/libfbsdmalloc.o' is up to date.
++ case "$WM_MPLIB" in
++ '[' -r /opt/OpenFOAM/ThirdParty-1.6.x/openmpi-1.3.3/platforms/linuxGccDPOpt/lib/libmpi.so ']'
++ echo 'have OPENMPI shared library'
have OPENMPI shared library
++ cd scotch_5.1
++ wmake libso src/libscotch
SOURCE=parser_yy.y ; bison -v -d -y $SOURCE ; mv y.tab.c Make/linuxGccDPOpt/parser_yy.c ; mv y.tab.h Make/linuxGccDPOpt/parser_yy.h ; gcc -m32 -Dlinux -DWM_DP -Wall -O3 -Drestrict=__restrict -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DCOMMON_TIMING_OLD -DSCOTCH_RENAME -I../../include -DSCOTCH_VERSION=\""5.1"\" -IlnInclude -I. -I/opt/OpenFOAM/OpenFOAM-1.6.x/src/OpenFOAM/lnInclude -I/opt/OpenFOAM/OpenFOAM-1.6.x/src/OSspecific/POSIX/lnInclude -fPIC -c Make/linuxGccDPOpt/parser_yy.c -o Make/linuxGccDPOpt/parser_yy.o
parser_yy.y:69:30: error: parser_yy_scotch.h: No such file or directory
y.tab.c: In function ‘_SCOTCHstratParserParse2’:
y.tab.c:2297: warning: implicit declaration of function ‘_SCOTCHstratParserError’
parser_yy.y: At top level:
parser_yy.y:794: error: static declaration of ‘_SCOTCHstratParserError’ follows non-static declaration
y.tab.c:2297: note: previous implicit declaration of ‘_SCOTCHstratParserError’ was here
make: *** [Make/linuxGccDPOpt/parser_yy.o] Error 1
++ cd metis-5.0pre2
++ wmake libso GKlib
'/opt/OpenFOAM/OpenFOAM-1.6.x/lib/linuxGccDPOpt/libGKlib.so' is up to date.
++ wmake libso libmetis
'/opt/OpenFOAM/OpenFOAM-1.6.x/lib/linuxGccDPOpt/libmetis.so' is up to date.
++ '[' OPENMPI = MPI -o -d /opt/OpenFOAM/ThirdParty-1.6.x/openmpi-1.3.3/platforms/linuxGccDPOpt ']'
++ cd ParMetis-3.1
++ WM_OPTIONS=linuxGccDPOptOPENMPI
++ wmake libso METISLib
'/opt/OpenFOAM/OpenFOAM-1.6.x/lib/linuxGccDPOpt/openmpi-1.3.3/libmetis-parmetis.so' is up to date.
++ wmake libso ParMETISLib
'/opt/OpenFOAM/OpenFOAM-1.6.x/lib/linuxGccDPOpt/openmpi-1.3.3/libparmetis.so' is up to date.
++ wmake libso ParMGridGen-1.0/MGridGen/IMlib
'/opt/OpenFOAM/OpenFOAM-1.6.x/lib/linuxGccDPOpt/libIMlib.so' is up to date.
++ wmake libso ParMGridGen-1.0/MGridGen/Lib
'/opt/OpenFOAM/OpenFOAM-1.6.x/lib/linuxGccDPOpt/libMGridGen.so' is up to date.


Any idea what the problem is ?

ganesh
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Old   January 29, 2010, 21:57
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Bruno Santos
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Greetings Ganesh,

Three hypothesis come to my mind:
  • you didn't install bison, byacc and/or flex (although if wmake did build, then it shouldn't be flex who's missing);
  • the downloaded ThirdParty package is corrupted. Do an md5 checksum to the downloaded file and compare with the value indicated on OpenFOAM's website.
You forgot to mention if you're using the system's gcc (and I don't know which gcc version Fedora 10 comes with), the "built from source" ThirdParty's gcc-4.3.3 or the pre-built ThirdParty's gcc-4.3.3!

Best regards,
Bruno
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Old   January 30, 2010, 03:31
Default Still not working
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Ganesh Vijayakumar
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hi !

I did install bison, byacc and flex and now I checked that they are indeed installed. I am using the version of gcc on the system

[root@country OpenFOAM]# gcc -v
Using built-in specs.
Target: i586-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch=i586 --build=i586-redhat-linux
Thread model: posix
gcc version 4.4.1 20090725 (Red Hat 4.4.1-2) (GCC)

Also I had changed the settings.h in OpenFOAM.1.6.x to use the system gcc. I checked the md5sum against the one on the website. Could anything else be a problem ?


ganesh
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Old   January 30, 2010, 18:17
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Bruno Santos
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Greetings Ganesh!

Uhm, strange... according to your first post, the file parser_yy_scotch.h is missing:
Code:
parser_yy.y:69:30: error: parser_yy_scotch.h: No such file or directory
So it either it wasn't or isn't generated by flex/bison, or the file parser_yy_scotch.h is missing from either one of the following folders:
Code:
ThirdParty-1.6.x/scotch_5.1/src/libscotch
ThirdParty-1.6.x/scotch_5.1/src/libscotch/lnInclude (just a simbolic link to the file in the previous folder)
So:
  • If the file is really in the first folder, and symbolically linked in the second one, then we've got a serious mystery! If so, try
    Code:
    wclean all
    wmake libso
    at the libscotch folder.
  • If it's missing from the first folder, then get it back from the ThirdParty gtgz.
  • If the link is missing from the second folder, then erase the lnInclude folder and do a wmake libso from the libscotch folder. This should rebuild the lnInclude folder and build the libscotch library.
If it still wont build, give us the output of the error again. Oh, and don't forget to use the # button for pasting the output inside the CODE brackets

Best regards and hope this solves it!
Bruno
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Old   January 31, 2010, 03:43
Default It worked
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Ganesh Vijayakumar
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hi !

Thanks Bruno. I had to untar the ThirdParty-1.6.gtgz again and copy the parser_yy_scotch.h manually to the src/libscotch folder again. I don't know how it got deleted. But once that was done it was a smooth ride. The Allwmake command worked in the OpenFOAM-1.6.x folder too.

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