I don't have access to PGI compilers, so someone that does can hopefully chime in here, but to start, could you please try either 1. manually running example-dbg for the failing example or 2. compile with METHODs=dbg only and run make check again and see if you trip any asserts and can get a stack trace and send to the list.
On Fri, Feb 13, 2015 at 7:10 AM, <[email protected]> wrote: > > > Hello, > > I am using PGI compilers 15.1 on a Ubuntu 14.04 system. > I would like to install the MOOSE framework. In order to do so I am first > trying to install libMesh. > The configuration and compilation steps seem to run fine and they finish. > But when typing 'make check' there is an error at a certain step. > When I compile with METHODS='opt oprof dbg' I get the following error in > make check: > make[3]: `example-dbg' is up to date. > make[3]: `example-opt' is up to date. > CXXLD example-oprof > ../../../.libs/libmesh_oprof.a(libmesh_oprof_la-tree_node.o): In function > `.st50665': > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj]+0x0): > undefined reference to `.LB14852' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj]+0x8): > undefined reference to `.LB14853' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj]+0x10): > undefined reference to `.LB14854' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj]+0x18): > undefined reference to `.LB14855' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj]+0x20): > undefined reference to `.LB14856' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj]+0x28): > undefined reference to `.LB14857' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj]+0x30): > undefined reference to `.LB14858' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj2EE19create_bounding_boxEj]+0x38): > undefined reference to `.LB14859' > ../../../.libs/libmesh_oprof.a(libmesh_oprof_la-tree_node.o): In function > `.st55932': > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj]+0x0): > undefined reference to `.LB15654' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj]+0x8): > undefined reference to `.LB15655' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj]+0x10): > undefined reference to `.LB15656' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj]+0x18): > undefined reference to `.LB15657' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj]+0x20): > undefined reference to `.LB15658' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj]+0x28): > undefined reference to `.LB15659' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj]+0x30): > undefined reference to `.LB15660' > tree_node.C:(.gnu.linkonce.r._ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj[_ZNK7libMesh8TreeNodeILj4EE19create_bounding_boxEj]+0x38): > undefined reference to `.LB15661' > make[3]: *** [example-oprof] Error 2 > > When I compile with METHODS='opt dbg' I get the following message in make > check: > *************************************************************** > * Running Example miscellaneous_ex8: > * example-opt > *************************************************************** > > Generating 100 point cloud...done > bounding box is > (x,y,z)=( 0.11, 0.34, 0.19) > (x,y,z)=( 9.96, 9.65, 9.96) > bounding box is > (x,y,z)=( 0.11, 0.34, 0.19) > (x,y,z)=( 9.96, 9.65, 9.96) > r_bbox = 16.7078 > rbf(r_bbox/2) = 0.1875 > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > [0]PETSC ERROR: or try http://valgrind.org<http://valgrind.org/> on > GNU/linux and Apple Mac OS X to find memory corruption errors > [0]PETSC ERROR: likely location of problem given in stack below > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > [0]PETSC ERROR: INSTEAD the line number of the start of the function > [0]PETSC ERROR: is given. > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Signal received > [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.htmlfor > trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.5.3, Jan, 31, 2015 > [0]PETSC ERROR: ./example-opt on a arch-linux2-c-debug named > artorg-124-197 by bbecsek Fri Feb 13 10:59:47 2015 > [0]PETSC ERROR: Configure options --prefix=/opt/petsc --download-hypre=1 > --with-debugging=yes --with-pic=1 --with-shared-libraries=1 --with-cc=mpicc > --with-cxx=mpicxx --with-fc=mpifort --download-fblaslapack=1 CC=mpicc > CXX=mpicxx FC=mpifort F77=mpifort F90=mpifort CFLAGS="-fPIC -mp" > [0]PETSC ERROR: #1 User provided function() line 0 in unknown file > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with errorcode 59. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > FAIL: run.sh > ==================================================== > 1 of 1 test failed > Please report to [email protected]<mailto: > [email protected]> > ==================================================== > > I built PETSc with the same PGI compilers and it finished building without > errors. How can I build libmesh successfully in order to install MOOSE? > Thank you in advance for your help. > > Sincerely, > > Barna Becsek > > > ________________________________ > Universität Bern > ARTORG Cardiovascular Engineering > Barna Becsek > PhD Student > Murtenstrasse 50<x-apple-data-detectors://7> > 3010 Bern, Switzerland<x-apple-data-detectors://7> > > Tel.: +41 31 632 7585<tel:+41%2031%20632%207585> (direct) > Tel.: +41 31 632 7478<tel:+41%2031%20632%207478> (secretary) > Fax.: +41 31 632 7576<tel:+41%2031%20632%207576> > http://www.artorg.unibe.ch/< > http://www.artorg.unibe.ch/content/research_units/cardiovascular_engineering/group_members/b_becsek > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is > your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Libmesh-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/libmesh-users > ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. 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