libMesh: A C++ Finite Element Library

Hi,

I updated by libmesh and tried to build it again but I get an error that
the c++ compiler won't work:

~/Software/libmesh$ ./configure
---------------------------------------------
----------- Configuring libMesh -------------
---------------------------------------------
checking for a sed that does not truncate output... /bin/sed
checking Major version... 0
checking Minor version... 8
checking Point version... 0
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for mpicxx... mpicxx
checking whether the C++ compiler works... no
configure: error: in `/home/cory/Software/libmesh':
configure: error: C++ compiler cannot create executables
See `config.log' for more details


Below is the some of the config.log file:

COLLECT_GCC=c++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro
4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
--program-suffix=-4.6 --enable-shared --enable-linker-build-id
--with-system-zlib --libexecdir=/usr/lib --without-included-gettext
--enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6
--libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu
--enable-libstdcxx-debug --enable-libstdcxx-time=yes
--enable-gnu-unique-object --enable-plugin --enable-objc-gc
--disable-werror --with-arch-32=i686 --with-tune=generic
--enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu
--target=x86_64-linux-gnu
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
configure:3228: $? = 0
configure:3217: mpicxx -V >&5
c++: error: unrecognized option '-V'
configure:3228: $? = 1
configure:3217: mpicxx -qversion >&5
c++: error: unrecognized option '-qversion'
configure:3228: $? = 1
configure:3248: checking whether the C++ compiler works
configure:3270: mpicxx    conftest.cpp  >&5
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 0 has invalid symbol index 10
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 1 has invalid symbol index 11
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 2 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 3 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 4 has invalid symbol index 10
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 5 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 6 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 7 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 8 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 9 has invalid symbol index 2
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 10 has invalid symbol index 11
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 11 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 12 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 13 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 14 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 15 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 16 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 17 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 18 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 19 has invalid symbol index 12
/usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
relocation 20 has invalid symbol index 19
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crt1.o: In
function `_start':
(.text+0x12): undefined reference to `__libc_csu_fini'
/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crt1.o: In
function `_start':
(.text+0x19): undefined reference to `__libc_csu_init'
collect2: ld returned 1 exit status
configure:3274: $? = 1
configure:3312: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libmesh"
| #define PACKAGE_TARNAME "libmesh"
| #define PACKAGE_VERSION "0.8.0"
| #define PACKAGE_STRING "libmesh 0.8.0"
| #define PACKAGE_BUGREPORT "libmesh-users@..."
| #define PACKAGE_URL "http://libmesh.sourceforge.net"
| #define CONFIGURE_INFO "./configure run on Wed Sep 19 17:45:09 MDT 2012"
| /* end confdefs.h.  */
|
| int
| main ()
| {
|
|   ;
|   return 0;
| }
configure:3317: error: in `/home/cory/Software/libmesh':
configure:3319: error: C++ compiler cannot create executables


I am at a lose on what to do here.  Thanks

Regards,

Cory

Re: [Libmesh-users] build error From: Paul T. Bauman <ptbauman@gm...> - 2012-09-19 23:52 This smells like mpicxx doesn't point to the g++ that's listed below. Can you double check? On Wed, Sep 19, 2012 at 6:48 PM, Cory Ahrens <coryahrens@...> wrote: > Hi, > > I updated by libmesh and tried to build it again but I get an error that > the c++ compiler won't work: > > ~/Software/libmesh$ ./configure > --------------------------------------------- > ----------- Configuring libMesh ------------- > --------------------------------------------- > checking for a sed that does not truncate output... /bin/sed > checking Major version... 0 > checking Minor version... 8 > checking Point version... 0 > checking build system type... x86_64-unknown-linux-gnu > checking host system type... x86_64-unknown-linux-gnu > checking target system type... x86_64-unknown-linux-gnu > checking for mpicxx... mpicxx > checking whether the C++ compiler works... no > configure: error: in `/home/cory/Software/libmesh': > configure: error: C++ compiler cannot create executables > See `config.log' for more details > > > Below is the some of the config.log file: > > COLLECT_GCC=c++ > COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper > Target: x86_64-linux-gnu > Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro > 4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs > --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr > --program-suffix=-4.6 --enable-shared --enable-linker-build-id > --with-system-zlib --libexecdir=/usr/lib --without-included-gettext > --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 > --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu > --enable-libstdcxx-debug --enable-libstdcxx-time=yes > --enable-gnu-unique-object --enable-plugin --enable-objc-gc > --disable-werror --with-arch-32=i686 --with-tune=generic > --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu > --target=x86_64-linux-gnu > Thread model: posix > gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5) > configure:3228: $? = 0 > configure:3217: mpicxx -V >&5 > c++: error: unrecognized option '-V' > configure:3228: $? = 1 > configure:3217: mpicxx -qversion >&5 > c++: error: unrecognized option '-qversion' > configure:3228: $? = 1 > configure:3248: checking whether the C++ compiler works > configure:3270: mpicxx conftest.cpp >&5 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 0 has invalid symbol index 10 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 1 has invalid symbol index 11 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 2 has invalid symbol index 2 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 3 has invalid symbol index 2 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 4 has invalid symbol index 10 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 5 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 6 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 7 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 8 has invalid symbol index 2 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 9 has invalid symbol index 2 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 10 has invalid symbol index 11 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 11 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 12 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 13 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 14 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 15 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 16 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 17 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 18 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 19 has invalid symbol index 12 > /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): > relocation 20 has invalid symbol index 19 > /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crt1.o: In > function `_start': > (.text+0x12): undefined reference to `__libc_csu_fini' > /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crt1.o: In > function `_start': > (.text+0x19): undefined reference to `__libc_csu_init' > collect2: ld returned 1 exit status > configure:3274: $? = 1 > configure:3312: result: no > configure: failed program was: > | /* confdefs.h */ > | #define PACKAGE_NAME "libmesh" > | #define PACKAGE_TARNAME "libmesh" > | #define PACKAGE_VERSION "0.8.0" > | #define PACKAGE_STRING "libmesh 0.8.0" > | #define PACKAGE_BUGREPORT "libmesh-users@..." > | #define PACKAGE_URL "http://libmesh.sourceforge.net" > | #define CONFIGURE_INFO "./configure run on Wed Sep 19 17:45:09 MDT 2012" > | /* end confdefs.h. */ > | > | int > | main () > | { > | > | ; > | return 0; > | } > configure:3317: error: in `/home/cory/Software/libmesh': > configure:3319: error: C++ compiler cannot create executables > > > I am at a lose on what to do here. Thanks > > Regards, > > Cory > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Libmesh-users mailing list > Libmesh-users@... > https://lists.sourceforge.net/lists/listinfo/libmesh-users >

Re: [Libmesh-users] build error From: Paul T. Bauman <ptbauman@gm...> - 2012-09-20 01:04 On Wed, Sep 19, 2012 at 7:53 PM, Cory Ahrens <coryahrens@...> wrote: > > I find that > > mpicxx points to /usr/bin/mpicxx.mpich2 > > Not sure where to go from here... Do an mpicxx -v and then a g++ -v and make sure they output the same compiler info.

Re: [Libmesh-users] build error From: Paul T. Bauman <ptbauman@gm...> - 2012-09-20 01:29 Please be sure to reply-all so that others may chime in. Check out this thread: http://stackoverflow.com/questions/6656317/cant-link-a-c-program Sounds like your system might've gotten FUBAR'ed. Can you build a simple hello work program with mpicxx?

Re: [Libmesh-users] build error From: Cory Ahrens <coryahrens@gm...> - 2012-09-20 01:51 Hi, If I follow the steps at http://stackoverflow.com/questions/6656317/cant-link-a-c-program and I get the error ld hw.o /usr/lib/libc.so /usr/lib/crt1.o -o hw ld: cannot find /usr/lib/crt1.o: No such file or directory and indeed crt1.o is not there. I can't find it anywhere. However, if I just do gcc hw.c then it compiles and links fine. All of this started after "upgrading" Ubuntu to 12.04 : ( I've tried reinstalling sudo apt-get update sudo apt-get install --reinstall binutils sudo apt-get install --reinstall build-essential sudo apt-get install --reinstall libc6-dev sudo apt-get install --reinstall gcc-4.6 sudo apt-get install --reinstall libboost1.46-all-dev but still no luck. Thanks. --Cory On Wed, Sep 19, 2012 at 7:29 PM, Paul T. Bauman <ptbauman@...> wrote: > Please be sure to reply-all so that others may chime in. > > Check out this thread: > http://stackoverflow.com/questions/6656317/cant-link-a-c-program > > Sounds like your system might've gotten FUBAR'ed. Can you build a simple > hello work program with mpicxx? >

Re: [Libmesh-users] build error From: Roy Stogner <roystgnr@ic...> - 2012-09-20 03:51 On Wed, 19 Sep 2012, Cory Ahrens wrote: > ld: cannot find /usr/lib/crt1.o: No such file or directory > > and indeed crt1.o is not there. I can't find it anywhere. "locate crt1.o" on my Ubuntu 12.04 system finds it in /usr/lib/x86_64-linux-gnu/ But forget weird system-specific stuff; if "gcc hw.c" works then you're halfway there. Do "mpicc hw.c", "g++ hw.C", and "mpicxx hw.C" also work? --- Roy

Re: [Libmesh-users] build error From: Cory Ahrens <coryahrens@gm...> - 2012-09-20 03:59 Hi, I finally found crt1.o also in /usr/lib/x86_64-linux-gnu Both c++ and g++ worked fine on hello world, but mpicc gave the error mpicc hw.c /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 0 has invalid symbol index 10 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 1 has invalid symbol index 11 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 2 has invalid symbol index 2 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 3 has invalid symbol index 2 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 4 has invalid symbol index 10 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 5 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 6 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 7 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 8 has invalid symbol index 2 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 9 has invalid symbol index 2 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 10 has invalid symbol index 11 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 11 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 12 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 13 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 14 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 15 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 16 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 17 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 18 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 19 has invalid symbol index 12 /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info): relocation 20 has invalid symbol index 19 /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crt1.o: In function `_start': (.text+0x12): undefined reference to `__libc_csu_fini' /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crt1.o: In function `_start': (.text+0x19): undefined reference to `__libc_csu_init' collect2: ld returned 1 exit status Thanks. --Cory On Wed, Sep 19, 2012 at 9:51 PM, Roy Stogner <roystgnr@...: > > On Wed, 19 Sep 2012, Cory Ahrens wrote: > > ld: cannot find /usr/lib/crt1.o: No such file or directory >> >> and indeed crt1.o is not there. I can't find it anywhere. >> > > "locate crt1.o" on my Ubuntu 12.04 system finds it in > /usr/lib/x86_64-linux-gnu/ > > But forget weird system-specific stuff; if "gcc hw.c" works then > you're halfway there. Do "mpicc hw.c", "g++ hw.C", and "mpicxx hw.C" > also work? > --- > Roy >

Re: [Libmesh-users] build error From: Roy Stogner <roystgnr@ic...> - 2012-09-20 04:05 On Wed, 19 Sep 2012, Cory Ahrens wrote: > Both c++ and g++ worked fine on hello world, but mpicc gave the error Well, at least it's not a libMesh problem! :-) Try tracking down and reinstalling whichever package is providing your mpicc? That's mpich-bin or openmpi-bin on Ubuntu, I presume. --- Roy

Re: [Libmesh-users] build error From: Cory Ahrens <coryahrens@gm...> - 2012-09-20 04:08 Hi, Ok. Thanks for the help. I'll try our suggestions. Cheers, Cory On Wed, Sep 19, 2012 at 10:05 PM, Roy Stogner <roystgnr@...: > > On Wed, 19 Sep 2012, Cory Ahrens wrote: > > Both c++ and g++ worked fine on hello world, but mpicc gave the error >> > > Well, at least it's not a libMesh problem! :-) > > Try tracking down and reinstalling whichever package is providing your > mpicc? That's mpich-bin or openmpi-bin on Ubuntu, I presume. > --- > Roy >

Re: [Libmesh-users] build error From: Cory Ahrens <coryahrens@gm...> - 2012-09-20 04:34 Hi, Reinstalling mpi did the trick...not sure what got messed up in the upgrade to 12.04 Ubuntu. Thanks again for the help. Cheers, Cory On Wed, Sep 19, 2012 at 10:08 PM, Cory Ahrens <coryahrens@...> wrote: > Hi, > > Ok. Thanks for the help. I'll try our suggestions. > > Cheers, > > Cory > > > > On Wed, Sep 19, 2012 at 10:05 PM, Roy Stogner <roystgnr@...: > >> >> On Wed, 19 Sep 2012, Cory Ahrens wrote: >> >> Both c++ and g++ worked fine on hello world, but mpicc gave the error >>> >> >> Well, at least it's not a libMesh problem! :-) >> >> Try tracking down and reinstalling whichever package is providing your >> mpicc? That's mpich-bin or openmpi-bin on Ubuntu, I presume. >> --- >> Roy >> > >

9 messages have been excluded from this view by a project administrator.