From: Minq Q <mi...@gm...> - 2013-07-10 22:56:00
|
Hi, I am trying to compile libmesh on Cray XE6. Using GNU compiler. Then I got an error: CC ncgentab.o CCLD ncgen3 /usr/bin/ld: attempted static link of dynamic object `../liblib/.libs/libnetcdf.so' Do you know, how can fix it? Thank you, / Ming Q. ---- My configure command is: CC=cc CXX=CC FC=ftn ./configure --enable-everything Result is: Library Features: adaptive mesh refinement......... : yes blocked matrix/vector storage.... : yes complex variables................ : no example suite.................... : yes ghosted vectors.................. : yes high-order shape functions....... : yes id size (boundaries)............. : 2 bytes id size (dofs)................... : 4 bytes id size (processors)............. : 2 bytes id size (subdomains)............. : 2 bytes infinite elements................ : yes Dirichlet constraints............ : yes node constraints................. : yes parallel mesh.................... : no performance logging.............. : yes periodic boundary conditions..... : yes reference counting............... : yes shape function 2nd derivatives... : yes stack trace files................ : yes variational smoother............. : yes xdr binary I/O................... : yes providing libMesh::CommWorld..... : yes ***LEGACY FEATURE*** Optional Packages: boost............................ : yes cppunit.......................... : no eigen............................ : yes exodus........................... : yes version....................... : v5.22 fparser.......................... : yes build from version............ : release glpk............................. : no gmv.............................. : yes gzstream......................... : yes hdf5............................. : no laspack.......................... : yes libhilbert....................... : yes metis............................ : yes mpi.............................. : yes nanoflann........................ : yes nemesis.......................... : yes version....................... : v5.22 netcdf........................... : yes version....................... : 4 openmp........................... : yes parmetis......................... : yes petsc............................ : yes version....................... : 3.3.0 sfcurves......................... : yes slepc............................ : no tbb.............................. : no c++ threads...................... : no c++ rtti ........................ : yes tecio............................ : yes tecplot...(vendor binaries)...... : no tetgen........................... : yes triangle......................... : yes trilinos......................... : no vtk.............................. : no |
From: Jim F. <jef...@gm...> - 2013-08-20 18:28:09
|
Hi Minq, Did you ever get this resolved? I am facing the same problem. Thanks, Jim On Wed, Jul 10, 2013 at 5:55 PM, Minq Q <mi...@gm...> wrote: > Hi, > > I am trying to compile libmesh on Cray XE6. Using GNU compiler. > > Then I got an error: > > CC ncgentab.o > CCLD ncgen3 > /usr/bin/ld: attempted static link of dynamic object > `../liblib/.libs/libnetcdf.so' > > Do you know, how can fix it? > > Thank you, > / Ming Q. > > ---- > My configure command is: > CC=cc CXX=CC FC=ftn ./configure --enable-everything > > Result is: > Library Features: > adaptive mesh refinement......... : yes > blocked matrix/vector storage.... : yes > complex variables................ : no > example suite.................... : yes > ghosted vectors.................. : yes > high-order shape functions....... : yes > id size (boundaries)............. : 2 bytes > id size (dofs)................... : 4 bytes > id size (processors)............. : 2 bytes > id size (subdomains)............. : 2 bytes > infinite elements................ : yes > Dirichlet constraints............ : yes > node constraints................. : yes > parallel mesh.................... : no > performance logging.............. : yes > periodic boundary conditions..... : yes > reference counting............... : yes > shape function 2nd derivatives... : yes > stack trace files................ : yes > variational smoother............. : yes > xdr binary I/O................... : yes > providing libMesh::CommWorld..... : yes ***LEGACY FEATURE*** > > Optional Packages: > boost............................ : yes > cppunit.......................... : no > eigen............................ : yes > exodus........................... : yes > version....................... : v5.22 > fparser.......................... : yes > build from version............ : release > glpk............................. : no > gmv.............................. : yes > gzstream......................... : yes > hdf5............................. : no > laspack.......................... : yes > libhilbert....................... : yes > metis............................ : yes > mpi.............................. : yes > nanoflann........................ : yes > nemesis.......................... : yes > version....................... : v5.22 > netcdf........................... : yes > version....................... : 4 > openmp........................... : yes > parmetis......................... : yes > petsc............................ : yes > version....................... : 3.3.0 > sfcurves......................... : yes > slepc............................ : no > tbb.............................. : no > c++ threads...................... : no > c++ rtti ........................ : yes > tecio............................ : yes > tecplot...(vendor binaries)...... : no > tetgen........................... : yes > triangle......................... : yes > trilinos......................... : no > vtk.............................. : no > > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > _______________________________________________ > Libmesh-users mailing list > Lib...@li... > https://lists.sourceforge.net/lists/listinfo/libmesh-users > -- Jim Fonseca, PhD Research Scientist Network for Computational Nanotechnology Purdue University 765-496-6495 www.jimfonseca.com |
From: John P. <jwp...@gm...> - 2013-08-20 18:46:20
|
Are you wanting to build statically on the Cray? (That is, are you already configuring with --enable-static --disable-shared?) If so, this might be related to a similar problem we faced on BG/Q, and there is an -all-static flag that can be passed to the link mode of libtool that might help out. http://www.gnu.org/software/libtool/manual/html_node/Link-mode.html There currently isn't a clean way of passing such an arg to libmesh's configure. What you do is: Run configure _without_ setting LDFLAGS. Then do: LDFLAGS=-all-static make Can you try that and see if it helps? If so, I'll try to work up a patch that adds a --enable-all-static flag to our configure. -- John On Tue, Aug 20, 2013 at 12:27 PM, Jim Fonseca <jef...@gm...> wrote: > Hi Minq, > Did you ever get this resolved? I am facing the same problem. > Thanks, > Jim > > > On Wed, Jul 10, 2013 at 5:55 PM, Minq Q <mi...@gm...> wrote: > > > Hi, > > > > I am trying to compile libmesh on Cray XE6. Using GNU compiler. > > > > Then I got an error: > > > > CC ncgentab.o > > CCLD ncgen3 > > /usr/bin/ld: attempted static link of dynamic object > > `../liblib/.libs/libnetcdf.so' > > > > Do you know, how can fix it? > > > > Thank you, > > / Ming Q. > > > > ---- > > My configure command is: > > CC=cc CXX=CC FC=ftn ./configure --enable-everything > > > > Result is: > > Library Features: > > adaptive mesh refinement......... : yes > > blocked matrix/vector storage.... : yes > > complex variables................ : no > > example suite.................... : yes > > ghosted vectors.................. : yes > > high-order shape functions....... : yes > > id size (boundaries)............. : 2 bytes > > id size (dofs)................... : 4 bytes > > id size (processors)............. : 2 bytes > > id size (subdomains)............. : 2 bytes > > infinite elements................ : yes > > Dirichlet constraints............ : yes > > node constraints................. : yes > > parallel mesh.................... : no > > performance logging.............. : yes > > periodic boundary conditions..... : yes > > reference counting............... : yes > > shape function 2nd derivatives... : yes > > stack trace files................ : yes > > variational smoother............. : yes > > xdr binary I/O................... : yes > > providing libMesh::CommWorld..... : yes ***LEGACY FEATURE*** > > > > Optional Packages: > > boost............................ : yes > > cppunit.......................... : no > > eigen............................ : yes > > exodus........................... : yes > > version....................... : v5.22 > > fparser.......................... : yes > > build from version............ : release > > glpk............................. : no > > gmv.............................. : yes > > gzstream......................... : yes > > hdf5............................. : no > > laspack.......................... : yes > > libhilbert....................... : yes > > metis............................ : yes > > mpi.............................. : yes > > nanoflann........................ : yes > > nemesis.......................... : yes > > version....................... : v5.22 > > netcdf........................... : yes > > version....................... : 4 > > openmp........................... : yes > > parmetis......................... : yes > > petsc............................ : yes > > version....................... : 3.3.0 > > sfcurves......................... : yes > > slepc............................ : no > > tbb.............................. : no > > c++ threads...................... : no > > c++ rtti ........................ : yes > > tecio............................ : yes > > tecplot...(vendor binaries)...... : no > > tetgen........................... : yes > > triangle......................... : yes > > trilinos......................... : no > > vtk.............................. : no > > > > > ------------------------------------------------------------------------------ > > See everything from the browser to the database with AppDynamics > > Get end-to-end visibility with application monitoring from AppDynamics > > Isolate bottlenecks and diagnose root cause in seconds. > > Start your free trial of AppDynamics Pro today! > > > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > > _______________________________________________ > > Libmesh-users mailing list > > Lib...@li... > > https://lists.sourceforge.net/lists/listinfo/libmesh-users > > > > > > -- > Jim Fonseca, PhD > Research Scientist > Network for Computational Nanotechnology > Purdue University > 765-496-6495 > www.jimfonseca.com > > ------------------------------------------------------------------------------ > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk > _______________________________________________ > Libmesh-users mailing list > Lib...@li... > https://lists.sourceforge.net/lists/listinfo/libmesh-users > |
From: Jim F. <jef...@gm...> - 2013-08-20 19:06:56
|
Hi John, No, we are doing dynamic linking. Blue Waters supports dynamic linking and in our development phase, it seems to cause us fewer headaches, so we are not concerned about advantages of static linking right now. I'm pretty sure I was able to do this same configuration with a libmesh development build in the spring before 0.9 came out but I'm looking into that. Related questions: is netcdf required? I am trying with it disabled now. Also, why does the netcdf shared library end up in (contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7) when all other libraries seems to be .libs or contrib/.libs? Thanks, Jim On Tue, Aug 20, 2013 at 1:45 PM, John Peterson <jwp...@gm...> wrote: > Are you wanting to build statically on the Cray? (That is, are you > already configuring with --enable-static --disable-shared?) > > If so, this might be related to a similar problem we faced on BG/Q, and > there is an -all-static flag that can be passed to the link mode of libtool > that might help out. > > http://www.gnu.org/software/libtool/manual/html_node/Link-mode.html > > There currently isn't a clean way of passing such an arg to libmesh's > configure. What you do is: > > Run configure _without_ setting LDFLAGS. > > Then do: > > LDFLAGS=-all-static make > > Can you try that and see if it helps? If so, I'll try to work up a patch > that adds a --enable-all-static flag to our configure. > > -- > John > > > On Tue, Aug 20, 2013 at 12:27 PM, Jim Fonseca <jef...@gm...> wrote: > >> Hi Minq, >> Did you ever get this resolved? I am facing the same problem. >> Thanks, >> Jim >> >> >> On Wed, Jul 10, 2013 at 5:55 PM, Minq Q <mi...@gm...> wrote: >> >> > Hi, >> > >> > I am trying to compile libmesh on Cray XE6. Using GNU compiler. >> > >> > Then I got an error: >> > >> > CC ncgentab.o >> > CCLD ncgen3 >> > /usr/bin/ld: attempted static link of dynamic object >> > `../liblib/.libs/libnetcdf.so' >> > >> > Do you know, how can fix it? >> > >> > Thank you, >> > / Ming Q. >> > >> > ---- >> > My configure command is: >> > CC=cc CXX=CC FC=ftn ./configure --enable-everything >> > >> > Result is: >> > Library Features: >> > adaptive mesh refinement......... : yes >> > blocked matrix/vector storage.... : yes >> > complex variables................ : no >> > example suite.................... : yes >> > ghosted vectors.................. : yes >> > high-order shape functions....... : yes >> > id size (boundaries)............. : 2 bytes >> > id size (dofs)................... : 4 bytes >> > id size (processors)............. : 2 bytes >> > id size (subdomains)............. : 2 bytes >> > infinite elements................ : yes >> > Dirichlet constraints............ : yes >> > node constraints................. : yes >> > parallel mesh.................... : no >> > performance logging.............. : yes >> > periodic boundary conditions..... : yes >> > reference counting............... : yes >> > shape function 2nd derivatives... : yes >> > stack trace files................ : yes >> > variational smoother............. : yes >> > xdr binary I/O................... : yes >> > providing libMesh::CommWorld..... : yes ***LEGACY FEATURE*** >> > >> > Optional Packages: >> > boost............................ : yes >> > cppunit.......................... : no >> > eigen............................ : yes >> > exodus........................... : yes >> > version....................... : v5.22 >> > fparser.......................... : yes >> > build from version............ : release >> > glpk............................. : no >> > gmv.............................. : yes >> > gzstream......................... : yes >> > hdf5............................. : no >> > laspack.......................... : yes >> > libhilbert....................... : yes >> > metis............................ : yes >> > mpi.............................. : yes >> > nanoflann........................ : yes >> > nemesis.......................... : yes >> > version....................... : v5.22 >> > netcdf........................... : yes >> > version....................... : 4 >> > openmp........................... : yes >> > parmetis......................... : yes >> > petsc............................ : yes >> > version....................... : 3.3.0 >> > sfcurves......................... : yes >> > slepc............................ : no >> > tbb.............................. : no >> > c++ threads...................... : no >> > c++ rtti ........................ : yes >> > tecio............................ : yes >> > tecplot...(vendor binaries)...... : no >> > tetgen........................... : yes >> > triangle......................... : yes >> > trilinos......................... : no >> > vtk.............................. : no >> > >> > >> ------------------------------------------------------------------------------ >> > See everything from the browser to the database with AppDynamics >> > Get end-to-end visibility with application monitoring from AppDynamics >> > Isolate bottlenecks and diagnose root cause in seconds. >> > Start your free trial of AppDynamics Pro today! >> > >> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk >> > _______________________________________________ >> > Libmesh-users mailing list >> > Lib...@li... >> > https://lists.sourceforge.net/lists/listinfo/libmesh-users >> > >> >> >> >> -- >> Jim Fonseca, PhD >> Research Scientist >> Network for Computational Nanotechnology >> Purdue University >> 765-496-6495 >> www.jimfonseca.com >> >> ------------------------------------------------------------------------------ >> Introducing Performance Central, a new site from SourceForge and >> AppDynamics. Performance Central is your source for news, insights, >> analysis and resources for efficient Application Performance Management. >> Visit us today! >> >> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk >> >> _______________________________________________ >> Libmesh-users mailing list >> Lib...@li... >> https://lists.sourceforge.net/lists/listinfo/libmesh-users >> > > > > -- Jim Fonseca, PhD Research Scientist Network for Computational Nanotechnology Purdue University 765-496-6495 www.jimfonseca.com |
From: Kirk, B. (JSC-EG311) <ben...@na...> - 2013-08-20 19:10:23
|
On Aug 20, 2013, at 2:06 PM, Jim Fonseca <jef...@gm...> wrote: > Related questions: is netcdf required? I am trying with it disabled now. > Also, why does the netcdf shared library end up in > (contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7) when all other libraries > seems to be .libs or contrib/.libs? > > Thanks, > Jim Are you doing 'make install?' netcdf is required by Exodus, and we are treating it as a nested package, so that's where its build system puts it before doing make install. -Ben |
From: Jim F. <jef...@gm...> - 2013-08-20 21:02:17
|
yes, we are doing make install. but your explanation helped to resolve that issue--thanks! Unfortunately I see I've created a problem with two different discussions on the same thread but at least that first one is solved. Still looking into the dynamic build issue...trying to narrow it down... Jim On Tue, Aug 20, 2013 at 2:10 PM, Kirk, Benjamin (JSC-EG311) < ben...@na...> wrote: > On Aug 20, 2013, at 2:06 PM, Jim Fonseca <jef...@gm...> > wrote: > > > Related questions: is netcdf required? I am trying with it disabled now. > > Also, why does the netcdf shared library end up in > > (contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7) when all other libraries > > seems to be .libs or contrib/.libs? > > > > Thanks, > > Jim > > Are you doing 'make install?' > > netcdf is required by Exodus, and we are treating it as a nested package, > so that's where its build system puts it before doing make install. > > -Ben > > > -- Jim Fonseca, PhD Research Scientist Network for Computational Nanotechnology Purdue University 765-496-6495 www.jimfonseca.com |
From: Jim F. <jef...@gm...> - 2013-08-21 14:42:08
|
Thanks Ben, Could you please take a look at where it is failing (config.log attached). For 0.9.2.1 Here is the line that's failing from make -n and the output when I run it. I've $ /bin/sh ./libtool --silent --tag=CXX --mode=link CC -O2 -felide-constructors -funroll-loops -fstrict-aliasing -Wdisabled-optimization -fopenmp -o getpot_parse-opt src/apps/getpot_parse_opt-getpot_parse.o libmesh_opt.la-L/opt/cray/hdf5-parallel/1.8.9/cray/81/lib -L/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys -Wl,-rpath,/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib -lsuperlu_dist_3.3 -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis -Wl,-rpath,/opt/cray/hdf5-parallel/1.8.9/cray/81/lib -lhdf5_fortran -lhdf5_hl -lhdf5 -L/opt/cray/papi/5.1.0.2/perf_events/no-cuda/lib-L/opt/cray/udreg/2.3.2-1.0401.5929.3.3.gem/lib64 -L/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/lib64 -L/opt/cray/pmi/4.0.1-1.0000.9421.73.3.gem/lib64 -L/opt/cray/dmapp/3.2.1-1.0401.5983.4.5.gem/lib64 -L/opt/cray/xpmem/0.1-2.0401.36790.4.3.gem/lib64 -L/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/lib64 -L/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib -L/opt/cray/libsci/12.0.01/gnu/47/interlagos/lib -L/opt/fftw/ 3.3.0.2/interlagos/lib -L/opt/cray/hdf5-parallel/1.8.9/gnu/47/lib -L/opt/cray/xe-sysroot/4.1.40/usr/lib64 -L/opt/cray/xe-sysroot/4.1.40/lib64 -L/opt/cray/xe-sysroot/4.1.40/usr/lib/alps -L/usr/lib/alps -L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2 -L/opt/gcc/4.7.2/snos/lib64 -L/opt/gcc/4.7.2/snos/lib -L/opt/cray/atp/1.6.2/lib -lhdf5hl_fortran_gnu_parallel -lhdf5_fortran_gnu_parallel -lmpichf90_gnu_47 -lquadmath -lm -lmpichcxx_gnu_47 -lpapi -lrca -lAtpSigHCommData -lAtpSigHandler -lgfortran -lhdf5_hl_gnu_parallel -lhdf5_gnu_parallel -lz -lscicpp_gnu -lsci_gnu_mp -lstdc++ -lfftw3_mpi -lfftw3f_mpi -lfftw3_threads -lfftw3f_threads -lfftw3 -lfftw3f -lmpich_gnu_47 -lmpl -lrt -lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil -ludreg -lpthread -lgomp -lgcc_eh -ldl /usr/bin/ld: attempted static link of dynamic object `./.libs/libmesh_opt.so' collect2: error: ld returned 1 exit status I was able to build 0.9.2-rc1 previously (config.log is attached for that). Still looking into what may be different. Thanks, Jim On Tue, Aug 20, 2013 at 4:05 PM, Kirk, Benjamin (JSC-EG311) < ben...@na...> wrote: > On Aug 20, 2013, at 4:01 PM, Jim Fonseca <jef...@gm...> > wrote: > > > yes, we are doing make install. but your explanation helped to resolve > that issue--thanks! > > > > Unfortunately I see I've created a problem with two different > discussions on the same thread but at least that first one is solved. Still > looking into the dynamic build issue...trying to narrow it down... > > > > Jim > > Good! > > Consider this an open request to get access to troubling machines - be it > this Cray or the previously mentioned Blue Gene - I'm happy to see what I > can do to make things work. > > -Ben > > -- Jim Fonseca, PhD Research Scientist Network for Computational Nanotechnology Purdue University 765-496-6495 www.jimfonseca.com |
From: John P. <jwp...@gm...> - 2013-08-21 14:49:49
|
This could be an email parsing bug, but I noticed: On Wed, Aug 21, 2013 at 8:41 AM, Jim Fonseca <jef...@gm...> wrote: > > $ /bin/sh ./libtool --silent --tag=CXX --mode=link CC -O2 > -felide-constructors -funroll-loops -fstrict-aliasing > -Wdisabled-optimization -fopenmp -o getpot_parse-opt > src/apps/getpot_parse_opt-getpot_parse.o > libmesh_opt.la-L/opt/cray/hdf5-parallel/1.8.9/cray/81/lib > There's no space here between "libmesh_opt.la" and "-L/opt/cray". Could you verify if that is indeed the case? -- John |
From: Jim F. <jef...@gm...> - 2013-08-21 15:08:00
|
Hi John, Yes, it's an email issue. Screenshot attached. Thanks, Jim On Wed, Aug 21, 2013 at 9:49 AM, John Peterson <jwp...@gm...> wrote: > This could be an email parsing bug, but I noticed: > > > On Wed, Aug 21, 2013 at 8:41 AM, Jim Fonseca <jef...@gm...> wrote: > >> >> $ /bin/sh ./libtool --silent --tag=CXX --mode=link CC -O2 >> -felide-constructors -funroll-loops -fstrict-aliasing >> -Wdisabled-optimization -fopenmp -o getpot_parse-opt >> src/apps/getpot_parse_opt-getpot_parse.o >> libmesh_opt.la-L/opt/cray/hdf5-parallel/1.8.9/cray/81/lib >> > > There's no space here between "libmesh_opt.la" and "-L/opt/cray". > > Could you verify if that is indeed the case? > > -- > John > -- Jim Fonseca, PhD Research Scientist Network for Computational Nanotechnology Purdue University 765-496-6495 www.jimfonseca.com |
From: John P. <jwp...@gm...> - 2013-08-21 16:04:41
|
On Wed, Aug 21, 2013 at 9:07 AM, Jim Fonseca <jef...@gm...> wrote: > Hi John, > Yes, it's an email issue. Screenshot attached. > I see. I think it might help if we could see the actual output of libtool, so would you try running 'make V=1' and sending the output? On my machine, for instance, that prints: libtool: link: mpicxx -O2 -felide-constructors -funroll-loops -fstrict-aliasing -Wdisabled-optimization -fopenmp -o .libs/getpot_parse-opt src/apps/getpot_parse_opt-getpot_parse.o -Wl,-bind_at_load ./.libs/libmesh_opt.dylib -L/opt/packages/tbb/lib etc... so you can see exactly what linking command it's using. -- John |
From: Jim F. <jef...@gm...> - 2013-08-21 17:42:57
|
Hi John, >From make V=1 make[1]: Entering directory `/mnt/b/projects/sciteam/jna/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/libmesh/libmesh' /bin/sh ./libtool --tag=CXX --mode=link CC -O2 -felide-constructors -funroll-loops -fstrict-aliasing -Wdisabled-optimization -fopenmp -o getpot_parse-opt src/apps/getpot_parse_opt-getpot_parse.o libmesh_opt.la-L/opt/cray/hdf5-parallel/1.8.9/cray/81/lib -L/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys -Wl,-rpath,/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib -lsuperlu_dist_3.3 -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis -Wl,-rpath,/opt/cray/hdf5-parallel/1.8.9/cray/81/lib -lhdf5_fortran -lhdf5_hl -lhdf5 -L/opt/cray/papi/5.1.0.2/perf_events/no-cuda/lib-L/opt/cray/udreg/2.3.2-1.0401.5929.3.3.gem/lib64 -L/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/lib64 -L/opt/cray/pmi/4.0.1-1.0000.9421.73.3.gem/lib64 -L/opt/cray/dmapp/3.2.1-1.0401.5983.4.5.gem/lib64 -L/opt/cray/xpmem/0.1-2.0401.36790.4.3.gem/lib64 -L/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/lib64 -L/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib -L/opt/cray/libsci/12.0.01/gnu/47/interlagos/lib -L/opt/fftw/ 3.3.0.2/interlagos/lib -L/opt/cray/hdf5-parallel/1.8.9/gnu/47/lib -L/opt/cray/xe-sysroot/4.1.40/usr/lib64 -L/opt/cray/xe-sysroot/4.1.40/lib64 -L/opt/cray/xe-sysroot/4.1.40/usr/lib/alps -L/usr/lib/alps -L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2 -L/opt/gcc/4.7.2/snos/lib64 -L/opt/gcc/4.7.2/snos/lib -L/opt/cray/atp/1.6.2/lib -lhdf5hl_fortran_gnu_parallel -lhdf5_fortran_gnu_parallel -lmpichf90_gnu_47 -lquadmath -lm -lmpichcxx_gnu_47 -lpapi -lrca -lAtpSigHCommData -lAtpSigHandler -lgfortran -lhdf5_hl_gnu_parallel -lhdf5_gnu_parallel -lz -lscicpp_gnu -lsci_gnu_mp -lstdc++ -lfftw3_mpi -lfftw3f_mpi -lfftw3_threads -lfftw3f_threads -lfftw3 -lfftw3f -lmpich_gnu_47 -lmpl -lrt -lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil -ludreg -lpthread -lgomp -lgcc_eh -ldl libtool: link: CC -O2 -felide-constructors -funroll-loops -fstrict-aliasing -Wdisabled-optimization -fopenmp -o .libs/getpot_parse-opt src/apps/getpot_parse_opt-getpot_parse.o -Wl,-rpath -Wl,/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib -Wl,-rpath -Wl,/opt/cray/hdf5-parallel/1.8.9/cray/81/lib ./.libs/libmesh_opt.so -L/opt/cray/hdf5-parallel/1.8.9/cray/81/lib -L/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib -L/opt/cray/udreg/2.3.2-1.0401.5929.3.3.gem/lib64 -L/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/lib64 -L/opt/cray/dmapp/3.2.1-1.0401.5983.4.5.gem/lib64 -L/opt/cray/xpmem/0.1-2.0401.36790.4.3.gem/lib64 -L/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/lib64 -L/opt/cray/xe-sysroot/4.1.40/usr/lib64 -L/opt/cray/xe-sysroot/4.1.40/lib64 -L/opt/cray/xe-sysroot/4.1.40/usr/lib/alps -L/opt/gcc/4.7.2/snos/lib64 -L/opt/gcc/4.7.2/snos/lib -L/opt/cray/atp/1.6.2/lib -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys -lsuperlu_dist_3.3 -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis -lmetis -lhdf5_fortran -lhdf5_hl -lhdf5 -L/opt/cray/papi/ 5.1.0.2/perf_events/no-cuda/lib-L/opt/cray/pmi/4.0.1-1.0000.9421.73.3.gem/lib64 -L/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib -L/opt/cray/libsci/12.0.01/gnu/47/interlagos/lib -L/opt/fftw/ 3.3.0.2/interlagos/lib -L/opt/cray/hdf5-parallel/1.8.9/gnu/47/lib -L/usr/lib/alps -L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2 -lhdf5hl_fortran_gnu_parallel -lhdf5_fortran_gnu_parallel -lmpichf90_gnu_47 -lmpichcxx_gnu_47 -lpapi -lrca -lAtpSigHCommData -lAtpSigHandler /opt/gcc/4.7.2/snos/lib/../lib64/libgfortran.so /opt/gcc/4.7.2/snos/lib/../lib64/libquadmath.so -lhdf5_hl_gnu_parallel -lhdf5_gnu_parallel -lz -lscicpp_gnu -lsci_gnu_mp /opt/gcc/4.7.2/snos/lib/../lib64/libstdc++.so /opt/fftw/ 3.3.0.2/interlagos/lib/libfftw3_mpi.so /opt/fftw/ 3.3.0.2/interlagos/lib/libfftw3f_mpi.so /opt/fftw/ 3.3.0.2/interlagos/lib/libfftw3_threads.so /opt/fftw/ 3.3.0.2/interlagos/lib/libfftw3f_threads.so /opt/fftw/ 3.3.0.2/interlagos/lib/libfftw3.so /opt/fftw/ 3.3.0.2/interlagos/lib/libfftw3f.so -lm -lcray_memcpy -lmpich_gnu_47 -lmpl -lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil -ludreg -lpthread /opt/gcc/4.7.2/snos/lib/../lib64/libgomp.so -lrt -lgcc_eh -ldl -pthread -fopenmp -Wl,-rpath -Wl,/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/libmesh/lib -Wl,-rpath -Wl,/opt/gcc/4.7.2/snos/lib/../lib64 -Wl,-rpath -Wl,/opt/fftw/ 3.3.0.2/interlagos/lib /usr/bin/ld: attempted static link of dynamic object `./.libs/libmesh_opt.so' collect2: error: ld returned 1 exit status make[1]: *** [getpot_parse-opt] Error 1 Thanks, Jim On Wed, Aug 21, 2013 at 11:04 AM, John Peterson <jwp...@gm...>wrote: > > > > On Wed, Aug 21, 2013 at 9:07 AM, Jim Fonseca <jef...@gm...> wrote: > >> Hi John, >> Yes, it's an email issue. Screenshot attached. >> > > I see. I think it might help if we could see the actual output of libtool, > so would you try running 'make V=1' and sending the output? > > On my machine, for instance, that prints: > > libtool: link: mpicxx -O2 -felide-constructors -funroll-loops > -fstrict-aliasing -Wdisabled-optimization -fopenmp -o > .libs/getpot_parse-opt src/apps/getpot_parse_opt-getpot_parse.o > -Wl,-bind_at_load ./.libs/libmesh_opt.dylib -L/opt/packages/tbb/lib > etc... > > so you can see exactly what linking command it's using. > > -- > John > -- Jim Fonseca, PhD Research Scientist Network for Computational Nanotechnology Purdue University 765-496-6495 www.jimfonseca.com |
From: John P. <jwp...@gm...> - 2013-08-21 18:56:28
|
On Wed, Aug 21, 2013 at 11:42 AM, Jim Fonseca <jef...@gm...> wrote: > Hi John, > From make V=1 > > make[1]: Entering directory > `/mnt/b/projects/sciteam/jna/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/libmesh/libmesh' > /bin/sh ./libtool --tag=CXX --mode=link CC -O2 -felide-constructors > -funroll-loops -fstrict-aliasing -Wdisabled-optimization -fopenmp -o > getpot_parse-opt src/apps/getpot_parse_opt-getpot_parse.o libmesh_opt.la-L/opt/cray/hdf5-parallel/1.8.9/cray/81/lib > -L/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib > -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys > -Wl,-rpath,/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib > -lsuperlu_dist_3.3 -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common > -lpord -lparmetis -lmetis > -Wl,-rpath,/opt/cray/hdf5-parallel/1.8.9/cray/81/lib -lhdf5_fortran > -lhdf5_hl -lhdf5 -L/opt/cray/papi/5.1.0.2/perf_events/no-cuda/lib-L/opt/cray/udreg/2.3.2-1.0401.5929.3.3.gem/lib64 > -L/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/lib64 > -L/opt/cray/pmi/4.0.1-1.0000.9421.73.3.gem/lib64 > -L/opt/cray/dmapp/3.2.1-1.0401.5983.4.5.gem/lib64 > -L/opt/cray/xpmem/0.1-2.0401.36790.4.3.gem/lib64 > -L/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/lib64 > -L/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib > -L/opt/cray/libsci/12.0.01/gnu/47/interlagos/lib -L/opt/fftw/ > 3.3.0.2/interlagos/lib -L/opt/cray/hdf5-parallel/1.8.9/gnu/47/lib > -L/opt/cray/xe-sysroot/4.1.40/usr/lib64 -L/opt/cray/xe-sysroot/4.1.40/lib64 > -L/opt/cray/xe-sysroot/4.1.40/usr/lib/alps -L/usr/lib/alps > -L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2 > -L/opt/gcc/4.7.2/snos/lib64 -L/opt/gcc/4.7.2/snos/lib > -L/opt/cray/atp/1.6.2/lib -lhdf5hl_fortran_gnu_parallel > -lhdf5_fortran_gnu_parallel -lmpichf90_gnu_47 -lquadmath -lm > -lmpichcxx_gnu_47 -lpapi -lrca -lAtpSigHCommData -lAtpSigHandler -lgfortran > -lhdf5_hl_gnu_parallel -lhdf5_gnu_parallel -lz -lscicpp_gnu -lsci_gnu_mp > -lstdc++ -lfftw3_mpi -lfftw3f_mpi -lfftw3_threads -lfftw3f_threads -lfftw3 > -lfftw3f -lmpich_gnu_47 -lmpl -lrt -lxpmem -ldmapp -lugni -lpmi -lalpslli > -lalpsutil -ludreg -lpthread -lgomp -lgcc_eh -ldl > libtool: link: CC -O2 -felide-constructors -funroll-loops > -fstrict-aliasing -Wdisabled-optimization -fopenmp -o > .libs/getpot_parse-opt src/apps/getpot_parse_opt-getpot_parse.o -Wl,-rpath > -Wl,/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib > -Wl,-rpath -Wl,/opt/cray/hdf5-parallel/1.8.9/cray/81/lib > ./.libs/libmesh_opt.so -L/opt/cray/hdf5-parallel/1.8.9/cray/81/lib > -L/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/petsc/build-real/arch-linux2-cxx-opt/lib > -L/opt/cray/udreg/2.3.2-1.0401.5929.3.3.gem/lib64 > -L/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/lib64 > -L/opt/cray/dmapp/3.2.1-1.0401.5983.4.5.gem/lib64 > -L/opt/cray/xpmem/0.1-2.0401.36790.4.3.gem/lib64 > -L/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/lib64 > -L/opt/cray/xe-sysroot/4.1.40/usr/lib64 -L/opt/cray/xe-sysroot/4.1.40/lib64 > -L/opt/cray/xe-sysroot/4.1.40/usr/lib/alps -L/opt/gcc/4.7.2/snos/lib64 > -L/opt/gcc/4.7.2/snos/lib -L/opt/cray/atp/1.6.2/lib -lpetscts -lpetscsnes > -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetscsys -lsuperlu_dist_3.3 > -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lparmetis > -lmetis -lhdf5_fortran -lhdf5_hl -lhdf5 -L/opt/cray/papi/ > 5.1.0.2/perf_events/no-cuda/lib-L/opt/cray/pmi/4.0.1-1.0000.9421.73.3.gem/lib64 > -L/opt/cray/mpt/5.6.4/gni/mpich2-gnu/47/lib > -L/opt/cray/libsci/12.0.01/gnu/47/interlagos/lib -L/opt/fftw/ > 3.3.0.2/interlagos/lib -L/opt/cray/hdf5-parallel/1.8.9/gnu/47/lib > -L/usr/lib/alps -L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2 > -lhdf5hl_fortran_gnu_parallel -lhdf5_fortran_gnu_parallel -lmpichf90_gnu_47 > -lmpichcxx_gnu_47 -lpapi -lrca -lAtpSigHCommData -lAtpSigHandler > /opt/gcc/4.7.2/snos/lib/../lib64/libgfortran.so > /opt/gcc/4.7.2/snos/lib/../lib64/libquadmath.so -lhdf5_hl_gnu_parallel > -lhdf5_gnu_parallel -lz -lscicpp_gnu -lsci_gnu_mp > /opt/gcc/4.7.2/snos/lib/../lib64/libstdc++.so /opt/fftw/ > 3.3.0.2/interlagos/lib/libfftw3_mpi.so /opt/fftw/ > 3.3.0.2/interlagos/lib/libfftw3f_mpi.so /opt/fftw/ > 3.3.0.2/interlagos/lib/libfftw3_threads.so /opt/fftw/ > 3.3.0.2/interlagos/lib/libfftw3f_threads.so /opt/fftw/ > 3.3.0.2/interlagos/lib/libfftw3.so /opt/fftw/ > 3.3.0.2/interlagos/lib/libfftw3f.so -lm -lcray_memcpy -lmpich_gnu_47 > -lmpl -lxpmem -ldmapp -lugni -lpmi -lalpslli -lalpsutil -ludreg -lpthread > /opt/gcc/4.7.2/snos/lib/../lib64/libgomp.so -lrt -lgcc_eh -ldl -pthread > -fopenmp -Wl,-rpath > -Wl,/u/sciteam/jfonseca/group/NEMO5_PETSc3.4_no_MAGMA_new_libmesh/libs/libmesh/lib > -Wl,-rpath -Wl,/opt/gcc/4.7.2/snos/lib/../lib64 -Wl,-rpath -Wl,/opt/fftw/ > 3.3.0.2/interlagos/lib > /usr/bin/ld: attempted static link of dynamic object > `./.libs/libmesh_opt.so' > collect2: error: ld returned 1 exit status > make[1]: *** [getpot_parse-opt] Error 1 > Thanks. So I guess my next question is: what does "CC" do on Cray when you try to use it for linking? Does it need to be passed a '-shared' option? It seems like CC is trying to link "statically" and it freaks out as soon as it sees libmesh_opt.so. BTW, I didn't get a copy of the config.log, would you mind sending me that as well? -- John |
From: John P. <jwp...@gm...> - 2013-08-21 18:59:46
|
On Wed, Aug 21, 2013 at 12:56 PM, John Peterson <jwp...@gm...> wrote: > > > > > On Wed, Aug 21, 2013 at 11:42 AM, Jim Fonseca <jef...@gm...> wrote: >> >> Hi John, >> From make V=1 >> >> > Thanks. > > So I guess my next question is: what does "CC" do on Cray when you try to use it for linking? Does it need to be passed a '-shared' option? > > It seems like CC is trying to link "statically" and it freaks out as soon as it sees libmesh_opt.so. > > BTW, I didn't get a copy of the config.log, would you mind sending me that as well? Not sure it's relevant, but [0] says: "The -dynamic flag instructs the compiler wrappers (i.e., ftn, cc, CC) to prepare a dynamically linked executable. " [0]: http://www.nersc.gov/users/computational-systems/hopper/programming/shared-and-dynamic-libraries/ -- John |
From: John P. <jwp...@gm...> - 2013-08-21 19:03:54
|
On Wed, Aug 21, 2013 at 12:59 PM, John Peterson <jwp...@gm...>wrote: > > > > On Wed, Aug 21, 2013 at 12:56 PM, John Peterson <jwp...@gm...> > wrote: > > > > > > > > > > On Wed, Aug 21, 2013 at 11:42 AM, Jim Fonseca <jef...@gm...> > wrote: > >> > >> Hi John, > >> From make V=1 > >> > >> > > Thanks. > > > > So I guess my next question is: what does "CC" do on Cray when you try > to use it for linking? Does it need to be passed a '-shared' option? > > > > It seems like CC is trying to link "statically" and it freaks out as > soon as it sees libmesh_opt.so. > > > > BTW, I didn't get a copy of the config.log, would you mind sending me > that as well? > > > Not sure it's relevant, but [0] says: > > "The -dynamic flag instructs the compiler wrappers (i.e., ftn, cc, CC) to > prepare a dynamically linked executable. " > > [0]: > http://www.nersc.gov/users/computational-systems/hopper/programming/shared-and-dynamic-libraries/ > And here's a related thread discussing the opposite situation of trying to force static linking: http://lists.dune-project.org/pipermail/dune/2012-November/012060.html Looks like they solved it by passing LD='CC --static' to configure, so you might try LD='CC --dynamic' (not sure if it needs one dash or two). -- John |
From: Jim F. <jef...@gm...> - 2013-08-21 19:24:59
|
Hi John, Here is the config.log. Many thanks for the suggestions--I will look into those. Thanks, Jim On Wed, Aug 21, 2013 at 2:03 PM, John Peterson <jwp...@gm...> wrote: > > > On Wed, Aug 21, 2013 at 12:59 PM, John Peterson <jwp...@gm...>wrote: > >> >> >> >> On Wed, Aug 21, 2013 at 12:56 PM, John Peterson <jwp...@gm...> >> wrote: >> > >> > >> > >> > >> > On Wed, Aug 21, 2013 at 11:42 AM, Jim Fonseca <jef...@gm...> >> wrote: >> >> >> >> Hi John, >> >> From make V=1 >> >> >> >> >> > Thanks. >> > >> > So I guess my next question is: what does "CC" do on Cray when you try >> to use it for linking? Does it need to be passed a '-shared' option? >> > >> > It seems like CC is trying to link "statically" and it freaks out as >> soon as it sees libmesh_opt.so. >> > >> > BTW, I didn't get a copy of the config.log, would you mind sending me >> that as well? >> >> >> Not sure it's relevant, but [0] says: >> >> "The -dynamic flag instructs the compiler wrappers (i.e., ftn, cc, CC) >> to prepare a dynamically linked executable. " >> >> [0]: >> http://www.nersc.gov/users/computational-systems/hopper/programming/shared-and-dynamic-libraries/ >> > > And here's a related thread discussing the opposite situation of trying to > force static linking: > > http://lists.dune-project.org/pipermail/dune/2012-November/012060.html > > Looks like they solved it by passing LD='CC --static' to configure, so > you might try LD='CC --dynamic' (not sure if it needs one dash or two). > > -- > John > -- Jim Fonseca, PhD Research Scientist Network for Computational Nanotechnology Purdue University 765-496-6495 www.jimfonseca.com |
From: Jim F. <jef...@gm...> - 2013-08-22 04:15:30
|
Many thanks for everyone's help with this. It is resolved now and your suggestions sent me down the right path. >From Blue Waters support: Static linking is and has been the default on BW when compiling applications for the CPUs. For the GPUs, when you load the cudatoolkit module, it sets XTPE_LINK_TYPE to dynamic, which changes the default linking behavior. I was trying a new build and not loading that particular module, and so the default linking was therefore static. Thanks again, Jim On Wed, Aug 21, 2013 at 2:24 PM, Jim Fonseca <jef...@gm...> wrote: > Hi John, > Here is the config.log. Many thanks for the suggestions--I will look into > those. > Thanks, > Jim > > > On Wed, Aug 21, 2013 at 2:03 PM, John Peterson <jwp...@gm...>wrote: > >> >> >> On Wed, Aug 21, 2013 at 12:59 PM, John Peterson <jwp...@gm...>wrote: >> >>> >>> >>> >>> On Wed, Aug 21, 2013 at 12:56 PM, John Peterson <jwp...@gm...> >>> wrote: >>> > >>> > >>> > >>> > >>> > On Wed, Aug 21, 2013 at 11:42 AM, Jim Fonseca <jef...@gm...> >>> wrote: >>> >> >>> >> Hi John, >>> >> From make V=1 >>> >> >>> >> >>> > Thanks. >>> > >>> > So I guess my next question is: what does "CC" do on Cray when you try >>> to use it for linking? Does it need to be passed a '-shared' option? >>> > >>> > It seems like CC is trying to link "statically" and it freaks out as >>> soon as it sees libmesh_opt.so. >>> > >>> > BTW, I didn't get a copy of the config.log, would you mind sending me >>> that as well? >>> >>> >>> Not sure it's relevant, but [0] says: >>> >>> "The -dynamic flag instructs the compiler wrappers (i.e., ftn, cc, CC) >>> to prepare a dynamically linked executable. " >>> >>> [0]: >>> http://www.nersc.gov/users/computational-systems/hopper/programming/shared-and-dynamic-libraries/ >>> >> >> And here's a related thread discussing the opposite situation of trying >> to force static linking: >> >> http://lists.dune-project.org/pipermail/dune/2012-November/012060.html >> >> Looks like they solved it by passing LD='CC --static' to configure, so >> you might try LD='CC --dynamic' (not sure if it needs one dash or two). >> >> -- >> John >> > > > > -- > Jim Fonseca, PhD > Research Scientist > Network for Computational Nanotechnology > Purdue University > 765-496-6495 > www.jimfonseca.com > > > -- Jim Fonseca, PhD Research Scientist Network for Computational Nanotechnology Purdue University 765-496-6495 www.jimfonseca.com |