Re: [Libmesh-users] compilation error
I have the --disable-unique-ptr option in my configuration script since it is required by another library I’m using on top of libMesh. Thanks, Simone On Nov 7, 2016, at 11:49, John Peterson mailto:jwpeter...@gmail.com>> wrote: On Mon, Nov 7, 2016 at 9:28 AM, Rossi, Simone mailto:sro...@email.unc.edu>> wrote: Dear all, I’m upgrading to PETSc 3.7.4 and I am now compiling the git version of libMesh. On my workstation (using gcc 5.4 and openmpi 2.0.0) I get a compilation error /not_backed_up/srossi/TPL/libmesh/libmesh-git/src/reduced_basis/rb_eim_assembly.C: In member function ‘virtual void libMesh::RBEIMAssembly::evaluate_basis_function(unsigned int, const libMesh::Elem&, const libMesh::QBase&, std::vector&)’: /not_backed_up/srossi/TPL/libmesh/libmesh-git/src/reduced_basis/rb_eim_assembly.C:72:14: error: no match for ‘operator!=’ (operand types are ‘libMesh::AutoPtr’ and ‘const libmesh_nullptr_t’) if (_qrule != libmesh_nullptr) I solved the error just by changing if (_qrule != libmesh_nullptr) =>if (_qrule.get() != libmesh_nullptr) With this change it compiles fine, but I since ’m not using the rb classes and I cannot say if this is the best way to solve this problem. Thanks, the fix looks OK to me, but I'm wondering how you ended up with a libMesh::AutoPtr here. Did you explicitly configure with --disable-unique-ptr perhaps? -- John -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] compilation error
On Mon, 7 Nov 2016, John Peterson wrote: With this change it compiles fine, but I since ’m not using the rb classes and I cannot say if this is the best way to solve this problem. Thanks, the fix looks OK to me, but I'm wondering how you ended up with a libMesh::AutoPtr here. Did you explicitly configure with --disable-unique-ptr perhaps? Aha! That's why I didn't get the same error; C++11 defines an override of operator==(unique_ptr, nullptr_t). I'm kind of surprised that this only cropped up in one place. --- Roy-- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] compilation error
On Mon, Nov 7, 2016 at 9:28 AM, Rossi, Simone wrote: > Dear all, > I’m upgrading to PETSc 3.7.4 and I am now compiling the git version of > libMesh. > On my workstation (using gcc 5.4 and openmpi 2.0.0) I get a compilation > error > > /not_backed_up/srossi/TPL/libmesh/libmesh-git/src/ > reduced_basis/rb_eim_assembly.C: In member function ‘virtual void > libMesh::RBEIMAssembly::evaluate_basis_function(unsigned int, const > libMesh::Elem&, const libMesh::QBase&, std::vector&)’: > /not_backed_up/srossi/TPL/libmesh/libmesh-git/src/ > reduced_basis/rb_eim_assembly.C:72:14: error: no match for ‘operator!=’ > (operand types are ‘libMesh::AutoPtr’ and ‘const > libmesh_nullptr_t’) >if (_qrule != libmesh_nullptr) > > > I solved the error just by changing >if (_qrule != libmesh_nullptr) =>if (_qrule.get() != > libmesh_nullptr) > > With this change it compiles fine, but I since ’m not using the rb classes > and I cannot say if this is the best way to solve this problem. > Thanks, the fix looks OK to me, but I'm wondering how you ended up with a libMesh::AutoPtr here. Did you explicitly configure with --disable-unique-ptr perhaps? -- John -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] compilation error
On Mon, 7 Nov 2016, Rossi, Simone wrote: I solved the error just by changing if (_qrule != libmesh_nullptr) =>if (_qrule.get() != libmesh_nullptr) With this change it compiles fine, but I since ’m not using the rb classes and I cannot say if this is the best way to solve this problem. This looks correct; I'll put in a patch just as soon as I figure out why my own builds didn't trigger the same compiler failure. I could swear I built a --enable-everything libMesh, using SLEPc, more recently than John's unique_ptr upgrades. --- Roy-- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
[Libmesh-users] compilation error
Dear all, I’m upgrading to PETSc 3.7.4 and I am now compiling the git version of libMesh. On my workstation (using gcc 5.4 and openmpi 2.0.0) I get a compilation error /not_backed_up/srossi/TPL/libmesh/libmesh-git/src/reduced_basis/rb_eim_assembly.C: In member function ‘virtual void libMesh::RBEIMAssembly::evaluate_basis_function(unsigned int, const libMesh::Elem&, const libMesh::QBase&, std::vector&)’: /not_backed_up/srossi/TPL/libmesh/libmesh-git/src/reduced_basis/rb_eim_assembly.C:72:14: error: no match for ‘operator!=’ (operand types are ‘libMesh::AutoPtr’ and ‘const libmesh_nullptr_t’) if (_qrule != libmesh_nullptr) I solved the error just by changing if (_qrule != libmesh_nullptr) =>if (_qrule.get() != libmesh_nullptr) With this change it compiles fine, but I since ’m not using the rb classes and I cannot say if this is the best way to solve this problem. Thanks, Simone -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error
> On Oct 3, 2014, at 11:57 AM, Roy Stogner wrote: > > > > On Fri, 3 Oct 2014, John Peterson wrote: > >>> libtool makes you jump through a bunch of annoying scripts, and >>> unless you need help making your stuff compile on 1990s Unices, the >>> only benefit is that it gets your dependency library flags right. >>> You had ONE JOB to do, libtool! >> >> I don't know, it does make building shared libraries portably across >> different architectures much less of a crap shoot. I can remember >> when there was a new secret linker flag to discover with every OSX >> release... > > Yeah, like I said: "making your stuff compile on 1990s Unices". Oh yeah, *this* is the year of the Linux desktop. Right? -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error
On Fri, 3 Oct 2014, John Peterson wrote: >> libtool makes you jump through a bunch of annoying scripts, and >> unless you need help making your stuff compile on 1990s Unices, the >> only benefit is that it gets your dependency library flags right. >> You had ONE JOB to do, libtool! > > I don't know, it does make building shared libraries portably across > different architectures much less of a crap shoot. I can remember > when there was a new secret linker flag to discover with every OSX > release... Yeah, like I said: "making your stuff compile on 1990s Unices". *rimshot* --- Roy -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error
> On Oct 3, 2014, at 11:51 AM, Roy Stogner wrote: > > >> On Fri, 3 Oct 2014, Dana Christen wrote: >> >> That's interesting: link_all_deplibs is set to "no" on this Ubuntu >> 14.04 machine. However, it is set to "unknown" on a machine running >> Ubuntu 13.04, where everything works fine. > > This might be it, then. While looking through some unrelated code > history I stumbled across: > > https://github.com/grinsfem/grins/pull/6/files > > where I apparently encountered and used a hackish workaround for this > problem before. > > I suppose the long term solution from libMesh's POV is that we should > propagate dependency library flags manually rather than relying on > libtool to do it for us. That's annoying. libtool makes you jump > through a bunch of annoying scripts, and unless you need help making > your stuff compile on 1990s Unices, the only benefit is that it gets > your dependency library flags right. You had ONE JOB to do, libtool! I don't know, it does make building shared libraries portably across different architectures much less of a crap shoot. I can remember when there was a new secret linker flag to discover with every OSX release... -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error
On Fri, 3 Oct 2014, Dana Christen wrote: > That's interesting: link_all_deplibs is set to "no" on this Ubuntu > 14.04 machine. However, it is set to "unknown" on a machine running > Ubuntu 13.04, where everything works fine. This might be it, then. While looking through some unrelated code history I stumbled across: https://github.com/grinsfem/grins/pull/6/files where I apparently encountered and used a hackish workaround for this problem before. I suppose the long term solution from libMesh's POV is that we should propagate dependency library flags manually rather than relying on libtool to do it for us. That's annoying. libtool makes you jump through a bunch of annoying scripts, and unless you need help making your stuff compile on 1990s Unices, the only benefit is that it gets your dependency library flags right. You had ONE JOB to do, libtool! --- Roy -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error
That's interesting: link_all_deplibs is set to "no" on this Ubuntu 14.04 machine. However, it is set to "unknown" on a machine running Ubuntu 13.04, where everything works fine. FYI, uninstalling the system netcdf and starting from a fresh clone didn't work, but Miguel's workaround did. Dana On Fri, Oct 3, 2014 at 5:46 PM, Roy Stogner wrote: > > Hey, here's a question - what does link_all_deplibs get set to in your > ./libtool script? Debian+Ubuntu disable that, but we depend on it. I > *thought* that our practice of distributing the output of bootstrap > was enough to avoid requiring deb users to build their own autotools, > but perhaps that's not the case. > --- > Roy > > > On Fri, 3 Oct 2014, Dana Christen wrote: > > Hi Roy, >> >> Thanks for your reply. Uninstalling the system netcdf doesn't help. >> Running make -n shows that the problematic command is the following: >> >> /bin/bash ./libtool --silent --tag=CXX --mode=link mpicxx -std=gnu++11 >> -O2 -felide-constructors -funroll-loops -fstrict-aliasing >> -Wdisabled-optimization -fopenmp -std=gnu++11 -o meshid-opt >> src/apps/meshid_opt-meshid.o libmesh_opt.la -L/lib -lhdf5 >> -Wl,-rpath,/lib -lz >> -Wl,-rpath,/home/dana/software/libmesh_install/opt_real/slepc///lib >> -L/home/dana/software/libmesh_install/opt_real/slepc///lib -lslepc >> -L/home/dana/software/libmesh_install/opt_real/petsc/lib >> -L/usr/lib/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.7 >> -L/usr/lib/x86_64-linux-gnu >> -L/lib/x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -lpetsc >> -lX11 -Wl,-rpath,/home/dana/software/libmesh_install/opt_real/petsc/lib >> -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis >> -lmetis -lscalapack -lblacs -lHYPRE -Wl,-rpath,/usr/lib/openmpi/lib >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.7 >> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >> -Wl,-rpath,/lib/x86_64-linux-gnu >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8 -lumfpack -lamd -llapack >> -lblas -lmpi_f90 -lmpi_f77 -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ >> -lmpi -lhwloc -lgcc_s -lpthread -ldl >> >> I can work around the problem by manually adding the path to the compiled >> netcdf library (in my case >> /mnt/DATA/dana/software/libmesh_build/opt_real/contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7). >> Note that simply adding -lnetcdf to that command >> works too (in this case the system library is used if it's installed). >> >> I'm going to try Miguel's workaround. I'll keep you posted. >> >> Dana >> >> On Fri, Oct 3, 2014 at 3:51 PM, Roy Stogner >> wrote: >> >> On Fri, 3 Oct 2014, Dana Christen wrote: >> >> Just realized there was a typo in my original message: I >> updated to Ubuntu >> 14.04 (latest long-term-support version). This error occurs >> with GCC 4.7.3, >> GCC 4.8.2, with and without the system netcdf libraries. >> >> >> You're not the first person to run into this: >> >> http://comments.gmane.org/gmane.comp.mathematics.libmesh.user/6345 >> >> But I'm running on Ubuntu 14.04 and have never managed to replicate >> the problem. I've never had the system netcdf installed, though; if >> you can uninstall that and try building from a fresh directory >> hopefully your system will work like mine. >> >> If that doesn't work (and please let us know either way), you can >> try >> the workaround Miguel had success with: configure >> --enable-netcdf=old --enable-exodus=old --enable-nemesis=old >> --- >> Roy >> >> On Fri, Oct 3, 2014 at 12:15 PM, Dana Christen < >> dana.chris...@akselos.com> >> wrote: >> >> Hello, >> >> I updated my workstation to Ubuntu 10.04 and libMesh >> now fails to compile. >> I'm getting the following error while compiling the >> latest revision of a >> fresh libmesh clone: >> >> (...) >> CXXLDmeshid-opt >> /usr/bin/ld: src/apps/meshid_opt-meshid.o: undefined >> reference to symbol >> 'nc_close' >> //mnt/DATA/dana/software/libmesh_build/opt_real/ >> contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7: >> error adding symbols: DSO missing from command line >> collect2: error: ld returned 1 exit status >> make[1]: *** [meshid-opt] Error 1 >> make[1]: Leaving directory `/mnt/DATA/dana/software/ >> libmesh_build/opt_real' >> make: *** [all-recursive] Error 1 >> >> The libnetcdf package is not installed on my system and >> I'm doing an >> out-of-tree build. Here's my configure line: >> >> /mnt/DATA/dana/software/libmesh-src/configure >> --enable-everything >> --enable-slepc --with-metis=PETSc >> --with-subdomain-id-bytes=4 >> --with-boundary-id-bytes=4 --prefix=/mnt/DATA/dana/ >> s
Re: [Libmesh-users] Compilation error
Hey, here's a question - what does link_all_deplibs get set to in your ./libtool script? Debian+Ubuntu disable that, but we depend on it. I *thought* that our practice of distributing the output of bootstrap was enough to avoid requiring deb users to build their own autotools, but perhaps that's not the case. --- Roy On Fri, 3 Oct 2014, Dana Christen wrote: Hi Roy, Thanks for your reply. Uninstalling the system netcdf doesn't help. Running make -n shows that the problematic command is the following: /bin/bash ./libtool --silent --tag=CXX --mode=link mpicxx -std=gnu++11 -O2 -felide-constructors -funroll-loops -fstrict-aliasing -Wdisabled-optimization -fopenmp -std=gnu++11 -o meshid-opt src/apps/meshid_opt-meshid.o libmesh_opt.la -L/lib -lhdf5 -Wl,-rpath,/lib -lz -Wl,-rpath,/home/dana/software/libmesh_install/opt_real/slepc///lib -L/home/dana/software/libmesh_install/opt_real/slepc///lib -lslepc -L/home/dana/software/libmesh_install/opt_real/petsc/lib -L/usr/lib/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.7 -L/usr/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -lpetsc -lX11 -Wl,-rpath,/home/dana/software/libmesh_install/opt_real/petsc/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs -lHYPRE -Wl,-rpath,/usr/lib/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.7 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8 -lumfpack -lamd -llapack -lblas -lmpi_f90 -lmpi_f77 -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ -lmpi -lhwloc -lgcc_s -lpthread -ldl I can work around the problem by manually adding the path to the compiled netcdf library (in my case /mnt/DATA/dana/software/libmesh_build/opt_real/contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7). Note that simply adding -lnetcdf to that command works too (in this case the system library is used if it's installed). I'm going to try Miguel's workaround. I'll keep you posted. Dana On Fri, Oct 3, 2014 at 3:51 PM, Roy Stogner wrote: On Fri, 3 Oct 2014, Dana Christen wrote: Just realized there was a typo in my original message: I updated to Ubuntu 14.04 (latest long-term-support version). This error occurs with GCC 4.7.3, GCC 4.8.2, with and without the system netcdf libraries. You're not the first person to run into this: http://comments.gmane.org/gmane.comp.mathematics.libmesh.user/6345 But I'm running on Ubuntu 14.04 and have never managed to replicate the problem. I've never had the system netcdf installed, though; if you can uninstall that and try building from a fresh directory hopefully your system will work like mine. If that doesn't work (and please let us know either way), you can try the workaround Miguel had success with: configure --enable-netcdf=old --enable-exodus=old --enable-nemesis=old --- Roy On Fri, Oct 3, 2014 at 12:15 PM, Dana Christen wrote: Hello, I updated my workstation to Ubuntu 10.04 and libMesh now fails to compile. I'm getting the following error while compiling the latest revision of a fresh libmesh clone: (...) CXXLD meshid-opt /usr/bin/ld: src/apps/meshid_opt-meshid.o: undefined reference to symbol 'nc_close' //mnt/DATA/dana/software/libmesh_build/opt_real/contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[1]: *** [meshid-opt] Error 1 make[1]: Leaving directory `/mnt/DATA/dana/software/libmesh_build/opt_real' make: *** [all-recursive] Error 1 The libnetcdf package is not installed on my system and I'm doing an out-of-tree build. Here's my configure line: /mnt/DATA/dana/software/libmesh-src/configure --enable-everything --enable-slepc --with-metis=PETSc --with-subdomain-id-bytes=4 --with-boundary-id-bytes=4 --prefix=/mnt/DATA/dana/software/libmesh_install --with-methods=opt --enable-shared The new version of GCC that was installed is the following: gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Any help would be greatly appreciated. Thanks, Dana -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with
Re: [Libmesh-users] Compilation error
Hi Roy, Thanks for your reply. Uninstalling the system netcdf doesn't help. Running make -n shows that the problematic command is the following: /bin/bash ./libtool --silent --tag=CXX --mode=link mpicxx -std=gnu++11 -O2 -felide-constructors -funroll-loops -fstrict-aliasing -Wdisabled-optimization -fopenmp -std=gnu++11 -o meshid-opt src/apps/meshid_opt-meshid.o libmesh_opt.la -L/lib -lhdf5 -Wl,-rpath,/lib -lz -Wl,-rpath,/home/dana/software/libmesh_install/opt_real/slepc///lib -L/home/dana/software/libmesh_install/opt_real/slepc///lib -lslepc -L/home/dana/software/libmesh_install/opt_real/petsc/lib -L/usr/lib/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.7 -L/usr/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -lpetsc -lX11 -Wl,-rpath,/home/dana/software/libmesh_install/opt_real/petsc/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lscalapack -lblacs -lHYPRE -Wl,-rpath,/usr/lib/openmpi/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.7 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.8 -lumfpack -lamd -llapack -lblas -lmpi_f90 -lmpi_f77 -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ -lmpi -lhwloc -lgcc_s -lpthread -ldl I can work around the problem by manually adding the path to the compiled netcdf library (in my case /mnt/DATA/dana/software/libmesh_build/opt_real/contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7). Note that simply adding -lnetcdf to that command works too (in this case the system library is used if it's installed). I'm going to try Miguel's workaround. I'll keep you posted. Dana On Fri, Oct 3, 2014 at 3:51 PM, Roy Stogner wrote: > > On Fri, 3 Oct 2014, Dana Christen wrote: > > Just realized there was a typo in my original message: I updated to Ubuntu >> 14.04 (latest long-term-support version). This error occurs with GCC >> 4.7.3, >> GCC 4.8.2, with and without the system netcdf libraries. >> > > You're not the first person to run into this: > > http://comments.gmane.org/gmane.comp.mathematics.libmesh.user/6345 > > But I'm running on Ubuntu 14.04 and have never managed to replicate > the problem. I've never had the system netcdf installed, though; if > you can uninstall that and try building from a fresh directory > hopefully your system will work like mine. > > If that doesn't work (and please let us know either way), you can try > the workaround Miguel had success with: configure --enable-netcdf=old > --enable-exodus=old --enable-nemesis=old > --- > Roy > > On Fri, Oct 3, 2014 at 12:15 PM, Dana Christen > > >> wrote: >> >> Hello, >>> >>> I updated my workstation to Ubuntu 10.04 and libMesh now fails to >>> compile. >>> I'm getting the following error while compiling the latest revision of a >>> fresh libmesh clone: >>> >>> (...) >>> CXXLDmeshid-opt >>> /usr/bin/ld: src/apps/meshid_opt-meshid.o: undefined reference to symbol >>> 'nc_close' >>> //mnt/DATA/dana/software/libmesh_build/opt_real/ >>> contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7: >>> error adding symbols: DSO missing from command line >>> collect2: error: ld returned 1 exit status >>> make[1]: *** [meshid-opt] Error 1 >>> make[1]: Leaving directory `/mnt/DATA/dana/software/ >>> libmesh_build/opt_real' >>> make: *** [all-recursive] Error 1 >>> >>> The libnetcdf package is not installed on my system and I'm doing an >>> out-of-tree build. Here's my configure line: >>> >>> /mnt/DATA/dana/software/libmesh-src/configure --enable-everything >>> --enable-slepc --with-metis=PETSc --with-subdomain-id-bytes=4 >>> --with-boundary-id-bytes=4 --prefix=/mnt/DATA/dana/ >>> software/libmesh_install >>> --with-methods=opt --enable-shared >>> >>> The new version of GCC that was installed is the following: gcc (Ubuntu >>> 4.8.2-19ubuntu1) 4.8.2 >>> >>> Any help would be greatly appreciated. >>> >>> Thanks, >>> Dana >>> >>> >>> >>> >> -- >> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer >> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports >> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper >> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer >> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&; >> iu=/4140/ostg.clktrk >> ___ >> Libmesh-users mailing list >> Libmesh-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/libmesh-users >> >> >> -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
Re: [Libmesh-users] Compilation error
On Fri, 3 Oct 2014, Dana Christen wrote: > Just realized there was a typo in my original message: I updated to Ubuntu > 14.04 (latest long-term-support version). This error occurs with GCC 4.7.3, > GCC 4.8.2, with and without the system netcdf libraries. You're not the first person to run into this: http://comments.gmane.org/gmane.comp.mathematics.libmesh.user/6345 But I'm running on Ubuntu 14.04 and have never managed to replicate the problem. I've never had the system netcdf installed, though; if you can uninstall that and try building from a fresh directory hopefully your system will work like mine. If that doesn't work (and please let us know either way), you can try the workaround Miguel had success with: configure --enable-netcdf=old --enable-exodus=old --enable-nemesis=old --- Roy > On Fri, Oct 3, 2014 at 12:15 PM, Dana Christen > wrote: > >> Hello, >> >> I updated my workstation to Ubuntu 10.04 and libMesh now fails to compile. >> I'm getting the following error while compiling the latest revision of a >> fresh libmesh clone: >> >> (...) >> CXXLDmeshid-opt >> /usr/bin/ld: src/apps/meshid_opt-meshid.o: undefined reference to symbol >> 'nc_close' >> //mnt/DATA/dana/software/libmesh_build/opt_real/contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7: >> error adding symbols: DSO missing from command line >> collect2: error: ld returned 1 exit status >> make[1]: *** [meshid-opt] Error 1 >> make[1]: Leaving directory `/mnt/DATA/dana/software/libmesh_build/opt_real' >> make: *** [all-recursive] Error 1 >> >> The libnetcdf package is not installed on my system and I'm doing an >> out-of-tree build. Here's my configure line: >> >> /mnt/DATA/dana/software/libmesh-src/configure --enable-everything >> --enable-slepc --with-metis=PETSc --with-subdomain-id-bytes=4 >> --with-boundary-id-bytes=4 --prefix=/mnt/DATA/dana/software/libmesh_install >> --with-methods=opt --enable-shared >> >> The new version of GCC that was installed is the following: gcc (Ubuntu >> 4.8.2-19ubuntu1) 4.8.2 >> >> Any help would be greatly appreciated. >> >> Thanks, >> Dana >> >> >> > -- > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk > ___ > Libmesh-users mailing list > Libmesh-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/libmesh-users > > -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error
Just realized there was a typo in my original message: I updated to Ubuntu 14.04 (latest long-term-support version). This error occurs with GCC 4.7.3, GCC 4.8.2, with and without the system netcdf libraries. Thanks, Dana On Fri, Oct 3, 2014 at 12:15 PM, Dana Christen wrote: > Hello, > > I updated my workstation to Ubuntu 10.04 and libMesh now fails to compile. > I'm getting the following error while compiling the latest revision of a > fresh libmesh clone: > > (...) > CXXLDmeshid-opt > /usr/bin/ld: src/apps/meshid_opt-meshid.o: undefined reference to symbol > 'nc_close' > //mnt/DATA/dana/software/libmesh_build/opt_real/contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7: > error adding symbols: DSO missing from command line > collect2: error: ld returned 1 exit status > make[1]: *** [meshid-opt] Error 1 > make[1]: Leaving directory `/mnt/DATA/dana/software/libmesh_build/opt_real' > make: *** [all-recursive] Error 1 > > The libnetcdf package is not installed on my system and I'm doing an > out-of-tree build. Here's my configure line: > > /mnt/DATA/dana/software/libmesh-src/configure --enable-everything > --enable-slepc --with-metis=PETSc --with-subdomain-id-bytes=4 > --with-boundary-id-bytes=4 --prefix=/mnt/DATA/dana/software/libmesh_install > --with-methods=opt --enable-shared > > The new version of GCC that was installed is the following: gcc (Ubuntu > 4.8.2-19ubuntu1) 4.8.2 > > Any help would be greatly appreciated. > > Thanks, > Dana > > > -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
[Libmesh-users] Compilation error
Hello, I updated my workstation to Ubuntu 10.04 and libMesh now fails to compile. I'm getting the following error while compiling the latest revision of a fresh libmesh clone: (...) CXXLDmeshid-opt /usr/bin/ld: src/apps/meshid_opt-meshid.o: undefined reference to symbol 'nc_close' //mnt/DATA/dana/software/libmesh_build/opt_real/contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[1]: *** [meshid-opt] Error 1 make[1]: Leaving directory `/mnt/DATA/dana/software/libmesh_build/opt_real' make: *** [all-recursive] Error 1 The libnetcdf package is not installed on my system and I'm doing an out-of-tree build. Here's my configure line: /mnt/DATA/dana/software/libmesh-src/configure --enable-everything --enable-slepc --with-metis=PETSc --with-subdomain-id-bytes=4 --with-boundary-id-bytes=4 --prefix=/mnt/DATA/dana/software/libmesh_install --with-methods=opt --enable-shared The new version of GCC that was installed is the following: gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2 Any help would be greatly appreciated. Thanks, Dana -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] compilation error
Oh, yeah, that looks good, thanks.
This didn't cause any compilation problem for me, not sure why...
David
On 12/06/2013 01:08 PM, Manav Bhatia wrote:
> I ended up adding the a call to the mesh constructor in the RBEIMEvaluation
> constructor with “comm” as the argument.
>
> Not sure if this would be the correct communicator to pass. Maybe David could
> comment.
>
> -Manav
>
>
>RBEIMEvaluation::RBEIMEvaluation(const libMesh::Parallel::Communicator
> &comm)
>:
> RBEvaluation(comm),
> extra_interpolation_point_elem(NULL),
> _previous_N(0),
> _previous_error_bound(-1),
>_interpolation_points_mesh(comm)
> {
>// Indicate that we need to compute the RB
>// inner product matrix in this case
>compute_RB_inner_product = true;
>
>// initialize to the empty RBThetaExpansion object
>set_rb_theta_expansion(_empty_rb_theta_expansion);
>
>// Let's not renumber the _interpolation_points_mesh
>_interpolation_points_mesh.allow_renumbering(false);
> }
>
>
> On Dec 6, 2013, at 12:13 PM, John Peterson wrote:
>
>> On Fri, Dec 6, 2013 at 10:03 AM, Manav Bhatia wrote:
>>> Hi,
>>>
>>> I got the latest libMesh from github, and compilation on Mac OS X with
>>> clang5 gives the following error:
>>>
>>> src/reduced_basis/rb_eim_evaluation.C:37:20: error: constructor for
>>> 'libMesh::RBEIMEvaluation' must explicitly initialize the member
>>> '_interpolation_points_mesh' which does not have a default constructor
>>> RBEIMEvaluation::RBEIMEvaluation(const libMesh::Parallel::Communicator
>>> &comm)
>>>^
>>> ./include/libmesh/rb_eim_evaluation.h:251:14: note: member is declared here
>>> SerialMesh _interpolation_points_mesh;
>>> ^
>>> ./include/libmesh/serial_mesh.h:47:7: note: 'libMesh::SerialMesh' declared
>>> here
>>> class SerialMesh : public UnstructuredMesh
>>> ^
>> Looks like that code is relying on a deprecated constructor which is
>> only available if LIBMESH_DISABLE_COMMWORLD is not defined.
>>
>> Try initializing it with libMesh::CommWorld?
>>
>> --
>> John
> --
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Re: [Libmesh-users] compilation error
I ended up adding the a call to the mesh constructor in the RBEIMEvaluation
constructor with “comm” as the argument.
Not sure if this would be the correct communicator to pass. Maybe David could
comment.
-Manav
RBEIMEvaluation::RBEIMEvaluation(const libMesh::Parallel::Communicator &comm)
:
RBEvaluation(comm),
extra_interpolation_point_elem(NULL),
_previous_N(0),
_previous_error_bound(-1),
_interpolation_points_mesh(comm)
{
// Indicate that we need to compute the RB
// inner product matrix in this case
compute_RB_inner_product = true;
// initialize to the empty RBThetaExpansion object
set_rb_theta_expansion(_empty_rb_theta_expansion);
// Let's not renumber the _interpolation_points_mesh
_interpolation_points_mesh.allow_renumbering(false);
}
On Dec 6, 2013, at 12:13 PM, John Peterson wrote:
> On Fri, Dec 6, 2013 at 10:03 AM, Manav Bhatia wrote:
>> Hi,
>>
>> I got the latest libMesh from github, and compilation on Mac OS X with
>> clang5 gives the following error:
>>
>> src/reduced_basis/rb_eim_evaluation.C:37:20: error: constructor for
>> 'libMesh::RBEIMEvaluation' must explicitly initialize the member
>> '_interpolation_points_mesh' which does not have a default constructor
>> RBEIMEvaluation::RBEIMEvaluation(const libMesh::Parallel::Communicator
>> &comm)
>> ^
>> ./include/libmesh/rb_eim_evaluation.h:251:14: note: member is declared here
>> SerialMesh _interpolation_points_mesh;
>> ^
>> ./include/libmesh/serial_mesh.h:47:7: note: 'libMesh::SerialMesh' declared
>> here
>> class SerialMesh : public UnstructuredMesh
>> ^
>
> Looks like that code is relying on a deprecated constructor which is
> only available if LIBMESH_DISABLE_COMMWORLD is not defined.
>
> Try initializing it with libMesh::CommWorld?
>
> --
> John
--
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Re: [Libmesh-users] compilation error
On Fri, Dec 6, 2013 at 10:03 AM, Manav Bhatia wrote: > Hi, > > I got the latest libMesh from github, and compilation on Mac OS X with > clang5 gives the following error: > > src/reduced_basis/rb_eim_evaluation.C:37:20: error: constructor for > 'libMesh::RBEIMEvaluation' must explicitly initialize the member > '_interpolation_points_mesh' which does not have a default constructor > RBEIMEvaluation::RBEIMEvaluation(const libMesh::Parallel::Communicator > &comm) >^ > ./include/libmesh/rb_eim_evaluation.h:251:14: note: member is declared here > SerialMesh _interpolation_points_mesh; > ^ > ./include/libmesh/serial_mesh.h:47:7: note: 'libMesh::SerialMesh' declared > here > class SerialMesh : public UnstructuredMesh > ^ Looks like that code is relying on a deprecated constructor which is only available if LIBMESH_DISABLE_COMMWORLD is not defined. Try initializing it with libMesh::CommWorld? -- John -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
[Libmesh-users] compilation error
Hi, I got the latest libMesh from github, and compilation on Mac OS X with clang5 gives the following error: src/reduced_basis/rb_eim_evaluation.C:37:20: error: constructor for 'libMesh::RBEIMEvaluation' must explicitly initialize the member '_interpolation_points_mesh' which does not have a default constructor RBEIMEvaluation::RBEIMEvaluation(const libMesh::Parallel::Communicator &comm) ^ ./include/libmesh/rb_eim_evaluation.h:251:14: note: member is declared here SerialMesh _interpolation_points_mesh; ^ ./include/libmesh/serial_mesh.h:47:7: note: 'libMesh::SerialMesh' declared here class SerialMesh : public UnstructuredMesh ^ -Manav -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
[Libmesh-users] Compilation error with libmesh
I have compiled and installed libmesh; when I try to make an example program using Makefile.old I get the following error: Makefile:68: .depend: No such file or directory Compiling C++ (in optimized mode) introduction_ex2.C... Linking introduction_ex2-opt... ld: warning: ignoring file introduction_ex2.x86_64-apple-darwin12.3.0.opt.lo, file was built for unsupported file format ( 0x23 0x20 0x69 0x6e 0x74 0x72 0x6f 0x64 0x75 0x63 0x74 0x69 0x6f 0x6e 0x5f 0x65 ) which is not the architecture being linked (x86_64): introduction_ex2.x86_64-apple-darwin12.3.0.opt.lo Undefined symbols for architecture x86_64: "_main", referenced from: implicit entry/start for main executable ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status make: *** [introduction_ex2-opt] Error 1 I would like to use the old makefile if possible. Any suggestions would be much appreciated, thanks. --- Dr. Gianluca Longoni E-Mail: longo...@comcast.net Website : http://plaza.ufl.edu/longoni/index.html --- -- Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error when compiling Libmesh
I messed around with the programs this morning, uninstalled and reinstalled a few with macports and then manually and finally got it to work. When I reinstalled petsc with macports it installed a few dependancies which I guess I must not have had before. Thanks for the advice! Mike -Original Message- From: Cody Permann To: "Welland, Michael Joshua" Cc: "Paul T. Bauman" , "libmesh-users@lists.sourceforge.net" Subject: Re: [Libmesh-users] Compilation error when compiling Libmesh >Sent from my evil iPhone > >On Jul 27, 2012, at 4:33 PM, "Welland, Michael J." >wrote: > >> Oops, sorry, I should have said 4.2: >> >> ~~~ >> mac-6d-42701:libmesh mwelland$ gcc --version >> i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build >>5658) (LLVM build 2336.9.00) >> Copyright (C) 2007 Free Software Foundation, Inc. >> This is free software; see the source for copying conditions. There is >>NO >> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >>PURPOSE. >> ~~~ >> >> I compiled again with the ‹disable-fparser and it finished, but when I >>tried to test it I got this: >> >> ~~~ >> mac-6d-42701:libmesh mwelland$ make run_examples >> Makefile:66: .depend: No such file or directory >> Compiling C++ (in optimized mode) adaptivity_ex1.C... >> Linking adaptivity_ex1-opt... >> *** >> * Running Example ./adaptivity_ex1-opt >> *** >> >> dyld: Symbol not found: __ZNKSt11logic_error4whatEv >> Referenced from: > >This is odd, a missing symbol that should exist in the standard >library?! There may be something else going on with your system. For >troubleshooting purposes you might try building static libraries. >That will turn your linker errors into compile errors which are easier >to track down (--disable-shared). If that fails to turn up anything >useful, we might try removing the solver as a source of the problem >(--disable-petsc). > >Let us know what you see. >Cody > >> >>/Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmes >>h.dylib >> Expected in: flat namespace >> in >>/Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmes >>h.dylib >> make[2]: *** [run] Trace/BPT trap: 5 >> make[1]: *** [run] Error 1 >> make: *** [run_examples] Error 2 >> mac-6d-42701:libmesh mwelland$ >> ~ >> >> I'm pretty new to Mac, but dyld indicates a problem linking the >>libraries no? I tried recompiling PETSc with the >>"--with-shared-libraries" flag but it still got the same thingŠ >> >> Thanks, >> Mike >> >> From: Cody Permann mailto:codyperm...@gmail.com>> >> To: "Welland, Michael Joshua" >>mailto:mwell...@anl.gov>> >> Cc: "Paul T. Bauman" mailto:ptbau...@gmail.com>>, >>"libmesh-users@lists.sourceforge.net<mailto:libmesh-users@lists.sourcefor >>ge.net>" >>mailto:libmesh-users@lists.sourcefor >>ge.net>> >> Subject: Re: [Libmesh-users] Compilation error when compiling Libmesh >> >> That's an odd version! The Apple version of the GCC compilers have >>been frozen at 4.2.1 for years now. If you are using Fink or Ports you >>should be getting way newer version. Where did you get that compiler >>from? Can you give us the output of "gcc --version"? >> >> Also as a workaround you might consider disabling the fparser >>"--disable-fparser", but it really should work. I'm using the Apple GCC >>compiler (4.2.1) and it works fine for me too. >> >> Cody >> >> On Fri, Jul 27, 2012 at 1:21 PM, Welland, Michael J. >>mailto:mwell...@anl.gov>> wrote: >> HI Paul, >> >> I'm using gcc 4.2.2. I checked out the latest from the svn and tried >>again, but it looks pretty similar: >> >> Linking (in optimized mode) >>util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... >> Creating Bytecode (in optimized mode) util/bytecoderules_parser... >> dyld: Symbol not found: __ZSt4codyld: Symbol not found: __ZSt4ceut >> Referenced from: /Users/mwerr >> Referenced from: >>/Users/mwelland/programs/libmesh/contrib/flland/programs/libmesh/contrib/ >>fparser/util/cpp_compress >> Expecparser/util/bytecoderules_parserted in: flat namespace >> in /User >> Expected in: flat namespace >> s/mwelland/programs/libmesh/contin >&
Re: [Libmesh-users] Compilation error when compiling Libmesh
Sent from my evil iPhone On Jul 27, 2012, at 4:33 PM, "Welland, Michael J." wrote: > Oops, sorry, I should have said 4.2: > > ~~~ > mac-6d-42701:libmesh mwelland$ gcc --version > i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) > (LLVM build 2336.9.00) > Copyright (C) 2007 Free Software Foundation, Inc. > This is free software; see the source for copying conditions. There is NO > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > ~~~ > > I compiled again with the —disable-fparser and it finished, but when I tried > to test it I got this: > > ~~~ > mac-6d-42701:libmesh mwelland$ make run_examples > Makefile:66: .depend: No such file or directory > Compiling C++ (in optimized mode) adaptivity_ex1.C... > Linking adaptivity_ex1-opt... > *** > * Running Example ./adaptivity_ex1-opt > *** > > dyld: Symbol not found: __ZNKSt11logic_error4whatEv > Referenced from: This is odd, a missing symbol that should exist in the standard library?! There may be something else going on with your system. For troubleshooting purposes you might try building static libraries. That will turn your linker errors into compile errors which are easier to track down (--disable-shared). If that fails to turn up anything useful, we might try removing the solver as a source of the problem (--disable-petsc). Let us know what you see. Cody > /Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib > Expected in: flat namespace > in > /Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib > make[2]: *** [run] Trace/BPT trap: 5 > make[1]: *** [run] Error 1 > make: *** [run_examples] Error 2 > mac-6d-42701:libmesh mwelland$ > ~ > > I'm pretty new to Mac, but dyld indicates a problem linking the libraries no? > I tried recompiling PETSc with the "--with-shared-libraries" flag but it > still got the same thing… > > Thanks, > Mike > > From: Cody Permann mailto:codyperm...@gmail.com>> > To: "Welland, Michael Joshua" mailto:mwell...@anl.gov>> > Cc: "Paul T. Bauman" mailto:ptbau...@gmail.com>>, > "libmesh-users@lists.sourceforge.net<mailto:libmesh-users@lists.sourceforge.net>" > > mailto:libmesh-users@lists.sourceforge.net>> > Subject: Re: [Libmesh-users] Compilation error when compiling Libmesh > > That's an odd version! The Apple version of the GCC compilers have been > frozen at 4.2.1 for years now. If you are using Fink or Ports you should be > getting way newer version. Where did you get that compiler from? Can you > give us the output of "gcc --version"? > > Also as a workaround you might consider disabling the fparser > "--disable-fparser", but it really should work. I'm using the Apple GCC > compiler (4.2.1) and it works fine for me too. > > Cody > > On Fri, Jul 27, 2012 at 1:21 PM, Welland, Michael J. > mailto:mwell...@anl.gov>> wrote: > HI Paul, > > I'm using gcc 4.2.2. I checked out the latest from the svn and tried again, > but it looks pretty similar: > > Linking (in optimized mode) > util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... > Creating Bytecode (in optimized mode) util/bytecoderules_parser... > dyld: Symbol not found: __ZSt4codyld: Symbol not found: __ZSt4ceut > Referenced from: /Users/mwerr > Referenced from: > /Users/mwelland/programs/libmesh/contrib/flland/programs/libmesh/contrib/fparser/util/cpp_compress > Expecparser/util/bytecoderules_parserted in: flat namespace > in /User > Expected in: flat namespace > s/mwelland/programs/libmesh/contin > /Users/mwelland/programs/libmrib/fparser/util/cpp_compress > esh/contrib/fparser/util/bytecoderules_parser > /bin/sh: line 1: 24308 Trace/BPT trap: 5 util/bytecoderules_parser < > util/bytecoderules.dat > 24309 | util/cpp_compress >> > extrasrc/fp_opcode_add.inc > make[2]: *** [extrasrc/fp_opcode_add.inc] Error 133 > make[1]: *** [all] Error 2 > make: *** > [/Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib] > Error 2 > > From: "Paul T. Bauman" > mailto:ptbau...@gmail.com><mailto:ptbau...@gmail.com<mailto:ptbau...@gmail.com>>> > To: "Welland, Michael Joshua" > mailto:mwell...@anl.gov><mailto:mwell...@anl.gov<mailto:mwell...@anl.gov>>> > Cc: > "libmesh-users@lists.sourceforge.net<mailto:libmesh-users@lists.sourceforge.net><mailto:libmesh-use
Re: [Libmesh-users] Compilation error when compiling Libmesh
Oops, sorry, I should have said 4.2: ~~~ mac-6d-42701:libmesh mwelland$ gcc --version i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.9.00) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. ~~~ I compiled again with the —disable-fparser and it finished, but when I tried to test it I got this: ~~~ mac-6d-42701:libmesh mwelland$ make run_examples Makefile:66: .depend: No such file or directory Compiling C++ (in optimized mode) adaptivity_ex1.C... Linking adaptivity_ex1-opt... *** * Running Example ./adaptivity_ex1-opt *** dyld: Symbol not found: __ZNKSt11logic_error4whatEv Referenced from: /Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib Expected in: flat namespace in /Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib make[2]: *** [run] Trace/BPT trap: 5 make[1]: *** [run] Error 1 make: *** [run_examples] Error 2 mac-6d-42701:libmesh mwelland$ ~ I'm pretty new to Mac, but dyld indicates a problem linking the libraries no? I tried recompiling PETSc with the "--with-shared-libraries" flag but it still got the same thing… Thanks, Mike From: Cody Permann mailto:codyperm...@gmail.com>> To: "Welland, Michael Joshua" mailto:mwell...@anl.gov>> Cc: "Paul T. Bauman" mailto:ptbau...@gmail.com>>, "libmesh-users@lists.sourceforge.net<mailto:libmesh-users@lists.sourceforge.net>" mailto:libmesh-users@lists.sourceforge.net>> Subject: Re: [Libmesh-users] Compilation error when compiling Libmesh That's an odd version! The Apple version of the GCC compilers have been frozen at 4.2.1 for years now. If you are using Fink or Ports you should be getting way newer version. Where did you get that compiler from? Can you give us the output of "gcc --version"? Also as a workaround you might consider disabling the fparser "--disable-fparser", but it really should work. I'm using the Apple GCC compiler (4.2.1) and it works fine for me too. Cody On Fri, Jul 27, 2012 at 1:21 PM, Welland, Michael J. mailto:mwell...@anl.gov>> wrote: HI Paul, I'm using gcc 4.2.2. I checked out the latest from the svn and tried again, but it looks pretty similar: Linking (in optimized mode) util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... Creating Bytecode (in optimized mode) util/bytecoderules_parser... dyld: Symbol not found: __ZSt4codyld: Symbol not found: __ZSt4ceut Referenced from: /Users/mwerr Referenced from: /Users/mwelland/programs/libmesh/contrib/flland/programs/libmesh/contrib/fparser/util/cpp_compress Expecparser/util/bytecoderules_parserted in: flat namespace in /User Expected in: flat namespace s/mwelland/programs/libmesh/contin /Users/mwelland/programs/libmrib/fparser/util/cpp_compress esh/contrib/fparser/util/bytecoderules_parser /bin/sh: line 1: 24308 Trace/BPT trap: 5 util/bytecoderules_parser < util/bytecoderules.dat 24309 | util/cpp_compress >> extrasrc/fp_opcode_add.inc make[2]: *** [extrasrc/fp_opcode_add.inc] Error 133 make[1]: *** [all] Error 2 make: *** [/Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib] Error 2 From: "Paul T. Bauman" mailto:ptbau...@gmail.com><mailto:ptbau...@gmail.com<mailto:ptbau...@gmail.com>>> To: "Welland, Michael Joshua" mailto:mwell...@anl.gov><mailto:mwell...@anl.gov<mailto:mwell...@anl.gov>>> Cc: "libmesh-users@lists.sourceforge.net<mailto:libmesh-users@lists.sourceforge.net><mailto:libmesh-users@lists.sourceforge.net<mailto:libmesh-users@lists.sourceforge.net>>" mailto:libmesh-users@lists.sourceforge.net><mailto:libmesh-users@lists.sourceforge.net<mailto:libmesh-users@lists.sourceforge.net>>> Subject: Re: [Libmesh-users] Compilation error when compiling Libmesh On Fri, Jul 27, 2012 at 2:01 PM, Welland, Michael J. mailto:mwell...@anl.gov><mailto:mwell...@anl.gov<mailto:mwell...@anl.gov>>> wrote: Hi all, I'm having a problem compiling libmesh on my Mac (version 10.7.4) When it gets to "Building Contributed Packages" it stops after: Compiling C++ (in optimized mode) util/cpp_compress_main.cc... Linking (in optimized mode) util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... Creating Bytecode (in optimized mode) util/bytecoderules_parser... dyld: Symbol not found: __ZSt4cedyld: Symbol not found: __ZSt4corr Referenced from: /Users/mweut Referenced from: /Users/mwelland/programs/libmesh-0.7.3.1/llland/programs/libmesh-0
Re: [Libmesh-users] Compilation error when compiling Libmesh
That's an odd version! The Apple version of the GCC compilers have been frozen at 4.2.1 for years now. If you are using Fink or Ports you should be getting way newer version. Where did you get that compiler from? Can you give us the output of "gcc --version"? Also as a workaround you might consider disabling the fparser "--disable-fparser", but it really should work. I'm using the Apple GCC compiler (4.2.1) and it works fine for me too. Cody On Fri, Jul 27, 2012 at 1:21 PM, Welland, Michael J. wrote: > HI Paul, > > I'm using gcc 4.2.2. I checked out the latest from the svn and tried > again, but it looks pretty similar: > > Linking (in optimized mode) > util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... > Creating Bytecode (in optimized mode) util/bytecoderules_parser... > dyld: Symbol not found: __ZSt4codyld: Symbol not found: __ZSt4ceut > Referenced from: /Users/mwerr > Referenced from: > /Users/mwelland/programs/libmesh/contrib/flland/programs/libmesh/contrib/fparser/util/cpp_compress > Expecparser/util/bytecoderules_parserted in: flat namespace > in /User > Expected in: flat namespace > s/mwelland/programs/libmesh/contin > /Users/mwelland/programs/libmrib/fparser/util/cpp_compress > esh/contrib/fparser/util/bytecoderules_parser > /bin/sh: line 1: 24308 Trace/BPT trap: 5 util/bytecoderules_parser < > util/bytecoderules.dat > 24309 | util/cpp_compress >> > extrasrc/fp_opcode_add.inc > make[2]: *** [extrasrc/fp_opcode_add.inc] Error 133 > make[1]: *** [all] Error 2 > make: *** > [/Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib] > Error 2 > > From: "Paul T. Bauman" mailto:ptbau...@gmail.com>> > To: "Welland, Michael Joshua" mailto:mwell...@anl.gov>> > Cc: "libmesh-users@lists.sourceforge.net libmesh-users@lists.sourceforge.net>" <mailto:libmesh-users@lists.sourceforge.net>> > Subject: Re: [Libmesh-users] Compilation error when compiling Libmesh > > On Fri, Jul 27, 2012 at 2:01 PM, Welland, Michael J. <mailto:mwell...@anl.gov>> wrote: > Hi all, I'm having a problem compiling libmesh on my Mac (version 10.7.4) > > When it gets to "Building Contributed Packages" it stops after: > > Compiling C++ (in optimized mode) util/cpp_compress_main.cc... > Linking (in optimized mode) > util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... > Creating Bytecode (in optimized mode) util/bytecoderules_parser... > dyld: Symbol not found: __ZSt4cedyld: Symbol not found: __ZSt4corr > Referenced from: /Users/mweut > Referenced from: > /Users/mwelland/programs/libmesh-0.7.3.1/llland/programs/libmesh-0.7.3.1/libmesh/contrib/fparser/util/byteibmesh/contrib/fparser/util/cpp_coderules_parser > Expected in: compress > Expected in: flat namflat namespace > in /Users/mwellaespace > in > /Users/mwelland/progrnd/programs/libmesh-0.7.3.1/libmams/libmesh-0.7.3.1/libmesh/contesh/contrib/fparser/util/bytecodrib/fparser/util/cpp_compress > erules_parser > /bin/sh: line 1: 69159 Trace/BPT trap: 5 util/bytecoderules_parser < > util/bytecoderules.dat > 69160 | util/cpp_compress >> > extrasrc/fp_opcode_add.inc > make[2]: *** [extrasrc/fp_opcode_add.inc] Error 133 > make[1]: *** [all] Error 2 > make: *** > [/Users/mwelland/programs/libmesh-0.7.3.1/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib] > Error 2 > > Any hints on how to get around this please? > > What compiler are you using? Also, it appears you're using 0.7.3.1 - I > would reccommend using the latest trunk, which can be checked out from the > public svn repo: > https://libmesh.svn.sourceforge.net/svnroot/libmesh/trunk/libmesh > > The current trunk is working for me on my OS X Lion laptop. > > Best, > > Paul > > > -- > 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@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/libmesh-users > -- 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error when compiling Libmesh
HI Paul, I'm using gcc 4.2.2. I checked out the latest from the svn and tried again, but it looks pretty similar: Linking (in optimized mode) util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... Creating Bytecode (in optimized mode) util/bytecoderules_parser... dyld: Symbol not found: __ZSt4codyld: Symbol not found: __ZSt4ceut Referenced from: /Users/mwerr Referenced from: /Users/mwelland/programs/libmesh/contrib/flland/programs/libmesh/contrib/fparser/util/cpp_compress Expecparser/util/bytecoderules_parserted in: flat namespace in /User Expected in: flat namespace s/mwelland/programs/libmesh/contin /Users/mwelland/programs/libmrib/fparser/util/cpp_compress esh/contrib/fparser/util/bytecoderules_parser /bin/sh: line 1: 24308 Trace/BPT trap: 5 util/bytecoderules_parser < util/bytecoderules.dat 24309 | util/cpp_compress >> extrasrc/fp_opcode_add.inc make[2]: *** [extrasrc/fp_opcode_add.inc] Error 133 make[1]: *** [all] Error 2 make: *** [/Users/mwelland/programs/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib] Error 2 From: "Paul T. Bauman" mailto:ptbau...@gmail.com>> To: "Welland, Michael Joshua" mailto:mwell...@anl.gov>> Cc: "libmesh-users@lists.sourceforge.net<mailto:libmesh-users@lists.sourceforge.net>" mailto:libmesh-users@lists.sourceforge.net>> Subject: Re: [Libmesh-users] Compilation error when compiling Libmesh On Fri, Jul 27, 2012 at 2:01 PM, Welland, Michael J. mailto:mwell...@anl.gov>> wrote: Hi all, I'm having a problem compiling libmesh on my Mac (version 10.7.4) When it gets to "Building Contributed Packages" it stops after: Compiling C++ (in optimized mode) util/cpp_compress_main.cc... Linking (in optimized mode) util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... Creating Bytecode (in optimized mode) util/bytecoderules_parser... dyld: Symbol not found: __ZSt4cedyld: Symbol not found: __ZSt4corr Referenced from: /Users/mweut Referenced from: /Users/mwelland/programs/libmesh-0.7.3.1/llland/programs/libmesh-0.7.3.1/libmesh/contrib/fparser/util/byteibmesh/contrib/fparser/util/cpp_coderules_parser Expected in: compress Expected in: flat namflat namespace in /Users/mwellaespace in /Users/mwelland/progrnd/programs/libmesh-0.7.3.1/libmams/libmesh-0.7.3.1/libmesh/contesh/contrib/fparser/util/bytecodrib/fparser/util/cpp_compress erules_parser /bin/sh: line 1: 69159 Trace/BPT trap: 5 util/bytecoderules_parser < util/bytecoderules.dat 69160 | util/cpp_compress >> extrasrc/fp_opcode_add.inc make[2]: *** [extrasrc/fp_opcode_add.inc] Error 133 make[1]: *** [all] Error 2 make: *** [/Users/mwelland/programs/libmesh-0.7.3.1/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib] Error 2 Any hints on how to get around this please? What compiler are you using? Also, it appears you're using 0.7.3.1 - I would reccommend using the latest trunk, which can be checked out from the public svn repo: https://libmesh.svn.sourceforge.net/svnroot/libmesh/trunk/libmesh The current trunk is working for me on my OS X Lion laptop. Best, Paul -- 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error when compiling Libmesh
On Fri, Jul 27, 2012 at 2:01 PM, Welland, Michael J. wrote: > Hi all, I'm having a problem compiling libmesh on my Mac (version 10.7.4) > > When it gets to "Building Contributed Packages" it stops after: > > Compiling C++ (in optimized mode) util/cpp_compress_main.cc... > Linking (in optimized mode) > util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... > Creating Bytecode (in optimized mode) util/bytecoderules_parser... > dyld: Symbol not found: __ZSt4cedyld: Symbol not found: __ZSt4corr > Referenced from: /Users/mweut > Referenced from: > /Users/mwelland/programs/libmesh-0.7.3.1/llland/programs/libmesh-0.7.3.1/libmesh/contrib/fparser/util/byteibmesh/contrib/fparser/util/cpp_coderules_parser > Expected in: compress > Expected in: flat namflat namespace > in /Users/mwellaespace > in > /Users/mwelland/progrnd/programs/libmesh-0.7.3.1/libmams/libmesh-0.7.3.1/libmesh/contesh/contrib/fparser/util/bytecodrib/fparser/util/cpp_compress > erules_parser > /bin/sh: line 1: 69159 Trace/BPT trap: 5 util/bytecoderules_parser < > util/bytecoderules.dat > 69160 | util/cpp_compress >> > extrasrc/fp_opcode_add.inc > make[2]: *** [extrasrc/fp_opcode_add.inc] Error 133 > make[1]: *** [all] Error 2 > make: *** > [/Users/mwelland/programs/libmesh-0.7.3.1/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib] > Error 2 > > Any hints on how to get around this please? > What compiler are you using? Also, it appears you're using 0.7.3.1 - I would reccommend using the latest trunk, which can be checked out from the public svn repo: https://libmesh.svn.sourceforge.net/svnroot/libmesh/trunk/libmesh The current trunk is working for me on my OS X Lion laptop. Best, Paul -- 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
[Libmesh-users] Compilation error when compiling Libmesh
Hi all, I'm having a problem compiling libmesh on my Mac (version 10.7.4) When it gets to "Building Contributed Packages" it stops after: Compiling C++ (in optimized mode) util/cpp_compress_main.cc... Linking (in optimized mode) util/cpp_compress.x86_64-apple-darwin11.4.0.opt.o... Creating Bytecode (in optimized mode) util/bytecoderules_parser... dyld: Symbol not found: __ZSt4cedyld: Symbol not found: __ZSt4corr Referenced from: /Users/mweut Referenced from: /Users/mwelland/programs/libmesh-0.7.3.1/llland/programs/libmesh-0.7.3.1/libmesh/contrib/fparser/util/byteibmesh/contrib/fparser/util/cpp_coderules_parser Expected in: compress Expected in: flat namflat namespace in /Users/mwellaespace in /Users/mwelland/progrnd/programs/libmesh-0.7.3.1/libmams/libmesh-0.7.3.1/libmesh/contesh/contrib/fparser/util/bytecodrib/fparser/util/cpp_compress erules_parser /bin/sh: line 1: 69159 Trace/BPT trap: 5 util/bytecoderules_parser < util/bytecoderules.dat 69160 | util/cpp_compress >> extrasrc/fp_opcode_add.inc make[2]: *** [extrasrc/fp_opcode_add.inc] Error 133 make[1]: *** [all] Error 2 make: *** [/Users/mwelland/programs/libmesh-0.7.3.1/libmesh/lib/x86_64-apple-darwin11.4.0_opt/libmesh.dylib] Error 2 Any hints on how to get around this please? -- 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@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error in SVN head
fixes it, thanks! On 11/01/2011 03:25 PM, John Peterson wrote: > On Tue, Nov 1, 2011 at 1:20 PM, David Knezevic > wrote: >> I just svn up'd and ./configure'd and I'm getting the compilation error: >> >> Compiling C++ (in debug mode) src/base/dof_map.C... >> In file included from >> /home/dknez/software/libmesh/include/base/dof_map.h:39:0, >> from src/base/dof_map.C:30: >> /home/dknez/software/libmesh/include/parallel/threads_allocators.h:103:13: >> error: ‘ptrdiff_t’ does not name a type >> make: *** [src/base/dof_map.x86_64-unknown-linux-gnu.dbg.o] Error 1 >> >> Seems like a strange thing for the compiler to complain about, no? I'm >> using gcc 4.6.1: >> gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 > We use that in include/parallel/threads_allocators.h > > Maybe we should #include "stddef.h" or #include in that file? > -- RSA® Conference 2012 Save $700 by Nov 18 Register now! http://p.sf.net/sfu/rsa-sfdev2dev1 ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error in SVN head
On Tue, Nov 1, 2011 at 1:20 PM, David Knezevic wrote: > I just svn up'd and ./configure'd and I'm getting the compilation error: > > Compiling C++ (in debug mode) src/base/dof_map.C... > In file included from > /home/dknez/software/libmesh/include/base/dof_map.h:39:0, > from src/base/dof_map.C:30: > /home/dknez/software/libmesh/include/parallel/threads_allocators.h:103:13: > error: ‘ptrdiff_t’ does not name a type > make: *** [src/base/dof_map.x86_64-unknown-linux-gnu.dbg.o] Error 1 > > Seems like a strange thing for the compiler to complain about, no? I'm > using gcc 4.6.1: > gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 We use that in include/parallel/threads_allocators.h Maybe we should #include "stddef.h" or #include in that file? -- John -- RSA® Conference 2012 Save $700 by Nov 18 Register now! http://p.sf.net/sfu/rsa-sfdev2dev1 ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
[Libmesh-users] Compilation error in SVN head
I just svn up'd and ./configure'd and I'm getting the compilation error: Compiling C++ (in debug mode) src/base/dof_map.C... In file included from /home/dknez/software/libmesh/include/base/dof_map.h:39:0, from src/base/dof_map.C:30: /home/dknez/software/libmesh/include/parallel/threads_allocators.h:103:13: error: ‘ptrdiff_t’ does not name a type make: *** [src/base/dof_map.x86_64-unknown-linux-gnu.dbg.o] Error 1 Seems like a strange thing for the compiler to complain about, no? I'm using gcc 4.6.1: gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1 David -- RSA® Conference 2012 Save $700 by Nov 18 Register now! http://p.sf.net/sfu/rsa-sfdev2dev1 ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] compilation error in the file numerics/eigen_solver.C
On Tue, Sep 1, 2009 at 9:06 AM, zeljka wrote: > Hi there! > I am tying to compile the svn version but the following errors occur > > In file included from src/numerics/eigen_solver.C:27: > /home/zeljka/libmesh/include/numerics/eigen_solver.h:200: error: > expected unqualified-id before ‘<<’ token > /home/zeljka/libmesh/include/numerics/eigen_solver.h:208: error: > expected unqualified-id before ‘>>’ token It looks to me like you have an SVN conflict in this file? I don't have any such '<<' or '>>' characters in my version of eigen_solver.h -- John -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
[Libmesh-users] compilation error in the file numerics/eigen_solver.C
Hi there! I am tying to compile the svn version but the following errors occur In file included from src/numerics/eigen_solver.C:27: /home/zeljka/libmesh/include/numerics/eigen_solver.h:200: error: expected unqualified-id before ‘<<’ token /home/zeljka/libmesh/include/numerics/eigen_solver.h:208: error: expected unqualified-id before ‘>>’ token /home/zeljka/libmesh/include/numerics/eigen_solver.h: In member function ‘libMeshEnums::EigenSolverType EigenSolver::eigen_solver_type() const’: /home/zeljka/libmesh/include/numerics/eigen_solver.h:92: error: ‘_eigen_solver_type’ was not declared in this scope /home/zeljka/libmesh/include/numerics/eigen_solver.h: In member function ‘void EigenSolver::set_eigensolver_type(libMeshEnums::EigenSolverType)’: /home/zeljka/libmesh/include/numerics/eigen_solver.h:109: error: ‘_eigen_solver_type’ was not declared in this scope /home/zeljka/libmesh/include/numerics/eigen_solver.h: In constructor ‘EigenSolver::EigenSolver()’: /home/zeljka/libmesh/include/numerics/eigen_solver.h:241: error: class ‘EigenSolver’ does not have any field named ‘_eigen_solver_type’ /home/zeljka/libmesh/include/numerics/slepc_eigen_solver.h: In constructor ‘SlepcEigenSolver::SlepcEigenSolver() [with T = double]’: src/numerics/eigen_solver.C:47: instantiated from ‘static AutoPtr > EigenSolver::build(libMeshEnums::SolverPackage) [with T = double]’ src/numerics/eigen_solver.C:68: instantiated from here /home/zeljka/libmesh/include/numerics/slepc_eigen_solver.h:276: error: ‘class SlepcEigenSolver’ has no member named ‘_eigen_solver_type’ make: *** [src/numerics/eigen_solver.x86_64-unknown-linux-gnu.opt.o] Error 1 (SLEPc version: 3.0.0-p3) Regards, Zeljka. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] compilation error
Charuka Jayarathna wrote: > Hello, > > I tried to compile with gmake. > and got the following error. > > src/mesh/xdr_io.C: In member function `virtual void XdrIO::write(const >std::string&)': > src/mesh/xdr_io.C:150: error: parse error before `,' token > src/mesh/xdr_io.C:152: confused by earlier errors, bailing out > gmake: *** [src/mesh/xdr_io.mips-sgi-irix6.5.opt.o] Error 1 Well, there is some progress. At least this error doesn't seem to be make related. What compiler are you using? Victor. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] compilation error
On Fri, 16 Jan 2009, Charuka Jayarathna wrote: > I am trying to compile libmesh on a system IRIX64 hydra 6.5 07202013 IP2. > > I am getting following error > > 5% make > make: file `Make.common' line 42: Must be a separator (: or ::) for rules > (bu39) Make.common differs from system to system depending on the results of your "./configure" run. Would you post line 42 (and a few lines one each side for context) to the list? Thanks, --- Roy -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
[Libmesh-users] compilation error
Hello, I am trying to compile libmesh on a system IRIX64 hydra 6.5 07202013 IP2. I am getting following error 5% make make: file `Make.common' line 42: Must be a separator (: or ::) for rules (bu39) make: file `Make.common' line 42: Must be a separator (: or ::) for rules (bu39) make: file `Make.common' line 42: Syntax error 6% make run_example make: file `Make.common' line 42: Must be a separator (: or ::) for rules (bu39) make: file `Make.common' line 42: Must be a separator (: or ::) for rules (bu39) make: file `Make.common' line 42: Syntax error Please help me to resolve Thanks charuka -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error with Intel compilers
On Thu, 15 Jan 2009, Mengda Wu wrote: > I am using the version 10.1.008 on a 64bit linux platform. Odd. Both 10.1.017 and the old 7.0 I had lying around worked. > Your solution does fix the problem for that file, but the same error comes > out for other files: Yeah; I did some refactoring and we've got the new assert_cast's all over the place now. I just wanted to see if that workaround was successful for you before trying to put it everywhere myself! It's kind of a wordy workaround, so I'm just going to use two different function names; we don't currently use the reference-casting version anyway. "libmesh_cast_ptr" and "libmesh_cast_ref" it is, unless someone has better naming ideas; I thought being completely accurate with "libmesh_assert_dynamic_cast_ptr" was way too long. Anyway, I've just committed the change to SVN head. Try it now. --- Roy -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error with Intel compilers
I am using the version 10.1.008 on a 64bit linux platform. Your solution does fix the problem for that file, but the same error comes out for other files: Compiling C++ (in optimized mode) src/numerics/petsc_nonlinear_solver.C... src/numerics/petsc_nonlinear_solver.C(90): error: more than one instance of overloaded function "libmesh_assert_cast" ma tches the argument list: function template "Tnew libmesh_assert_cast(Told &)" function template "Tnew libmesh_assert_cast(Told *)" argument types are: (NumericVector *) PetscVector& R_sys = *libmesh_assert_cast*>(sys.rhs); ^ src/numerics/petsc_nonlinear_solver.C(135): error: more than one instance of overloaded function "libmesh_assert_cast" m atches the argument list: function template "Tnew libmesh_assert_cast(Told &)" function template "Tnew libmesh_assert_cast(Told *)" argument types are: (SparseMatrix *) PetscMatrix& Jac_sys = *libmesh_assert_cast*>(sys.matrix); BTW, As suggest by a google search, I need to set the following to compile export libmesh_CXXFLAGS=-DMPICH_SKIP_MPICXX otherwise, I failed at the first file: Compiling C++ (in optimized mode) src/base/dof_map.C... /opt/intel/impi/3.1/include64/mpicxx.h(45): catastrophic error: #error directive: "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h" #error "SEEK_SET is #defined but must not be for the C++ binding of MPI. Include mpi.h before stdio.h" ^ compilation aborted for src/base/dof_map.C (code 4) make: *** [src/base/dof_map.x86_64-unknown-linux-gnu.opt.o] Error 4 Thanks, Mengda 2009/1/15 Roy Stogner > > On Thu, 15 Jan 2009, Mengda Wu wrote: > > I used intel compiler to build the latest svn version of libmesh. >> > > Which version? It compiled fine with icc 10.1.017 for me, but if I've > just inadvertantly broken older Intel compilers I'd definitely like to > fix that. > > I got the following error in the middle. >> >> Compiling C++ (in optimized mode) src/numerics/mesh_function.C... >> src/numerics/mesh_function.C(116): error: more than one instance of >> overloaded function "libmesh_assert_cast" matches th >> e argument list: >> function template "Tnew libmesh_assert_cast(Told &)" >> function template "Tnew libmesh_assert_cast(Told *)" >> argument types are: (const FunctionBase *) >> libmesh_assert_cast(this->_master); >> ^ >> >> compilation aborted for src/numerics/mesh_function.C (code 2) >> > > So the compiler is seeing a "const MeshFunction*" argument, it's > correctly noting that that could also be passed to a function which > takes "const MeshFunction*&", but it looks like it's not correctly > disambiguating the problem by choosing the most specific template > specialization to use. > > Try replacing that line with: > libmesh_assert_cast FunctionBase*>(this->master); > > But even if that works it's pretty ugly, and I'd hate to have to do it > everywhere. Anyone have any ideas for a better workaround? > --- > Roy > -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
Re: [Libmesh-users] Compilation error with Intel compilers
On Thu, 15 Jan 2009, Mengda Wu wrote: > I used intel compiler to build the latest svn version of libmesh. Which version? It compiled fine with icc 10.1.017 for me, but if I've just inadvertantly broken older Intel compilers I'd definitely like to fix that. > I got the following error in the middle. > > Compiling C++ (in optimized mode) src/numerics/mesh_function.C... > src/numerics/mesh_function.C(116): error: more than one instance of > overloaded function "libmesh_assert_cast" matches th > e argument list: >function template "Tnew libmesh_assert_cast(Told &)" >function template "Tnew libmesh_assert_cast(Told *)" >argument types are: (const FunctionBase *) >libmesh_assert_cast(this->_master); >^ > > compilation aborted for src/numerics/mesh_function.C (code 2) So the compiler is seeing a "const MeshFunction*" argument, it's correctly noting that that could also be passed to a function which takes "const MeshFunction*&", but it looks like it's not correctly disambiguating the problem by choosing the most specific template specialization to use. Try replacing that line with: libmesh_assert_cast(this->master); But even if that works it's pretty ugly, and I'd hate to have to do it everywhere. Anyone have any ideas for a better workaround? --- Roy -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
[Libmesh-users] Compilation error with Intel compilers
Hi all, I used intel compiler to build the latest svn version of libmesh. I got the following error in the middle. Compiling C++ (in optimized mode) src/numerics/mesh_function.C... src/numerics/mesh_function.C(116): error: more than one instance of overloaded function "libmesh_assert_cast" matches th e argument list: function template "Tnew libmesh_assert_cast(Told &)" function template "Tnew libmesh_assert_cast(Told *)" argument types are: (const FunctionBase *) libmesh_assert_cast(this->_master); ^ compilation aborted for src/numerics/mesh_function.C (code 2) Could you please help? Thanks, Mengda -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
