[Libmesh-users] Error make checking libmesh

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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 lib...@li...<mailto:lib...@li...>
====================================================

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>

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