[mvapich-discuss] Compilation error

[Jonathan Perkins]

This looks like a problem related to MKL.  I'm not very sure yet but I
think this may be a problem with the installation of the mvapich2
library.  Can you pass along the config.log created when building
mvapich2.

As a work around, can you try adding `-liomp5 -lpthread' to your
command to see if it resolves it?

On Fri, Jul 22, 2011 at 11:51 AM, Jim Bungener <jbungener at zee.aero> wrote:
> Hello,
> I am trying to compile the latest version of the NASA Fun3D CFD code on a
> CENTOS cluster running infiniband.
> Before inifiniband we were using MPI and it compiled/ran fine.
> Now that we are running infiniband we are using MVAPICH2 and I get the
> following compilation error:
> Any suggestions on where I could find the missing libraries?
> /apps/MVAPICH2//bin/mpif90 -I ..//libcore -I ..//libturb -I ..//libsmemrd -I
> ..//LibF90 -I ..//PHYSICS_DUMMY -I ..//PHYSICS_DEPS -I ..//libdesign -I
> ../FuncLib90 -I ../ -O2 -ip -align -fno-als -g -traceback -vec-report0    -o
> dual_mpi  cut_rad.o getgrad_driver.o gmres_matvec.o init_adjs.o main.o
> precond_bc_element_based.o precond_bc.o precond_bci.o precond_inviscid.o
> precond_lamir.o precond_laminari.o precond_nonin.o precond.o
> precond_turbpart.o precond_turbparti.o precond_turbulent.o
> precond_turbulenti.o radp.o relax_adjoint.o residual_bc_element_based.o
> residual_bc residual_bci.o residual_cut.o residual_drdq.o
> residual_inviscid.o residual_inviscidi.o residual_laminar.o
> residual_laminari.o residual.o residual_nonin.o residual_turbpart.o
> residual_turbpar.o residual_turbulent.o residual_turbulenti.o
> -L..//libdesign -ldesign -L..//PHYSICS_DEPS -lFUN3DPhysicsDeps
> -L..//PHYSICS_DUMMY -lFUN3DPhysics -L..//LibF90 -lFUN3DApp -lFUN3DUtil
> -lFUN3DCapDs -L..//libsmemrd -lsmemrd -L..//libturb -lturb -L..//libcore
> -lcore -L/apps/CFD/ParMetis-3.2.0 -lparmetis -lmetis
> -L/apps/CFD/secure/FUN3D/refine-1.7.1/lib -lrefine -lFAUXGeom
> -L/apps/D/secure/FUN3D/knife-1.2.0/lib -lknife
> -L/apps/CFD/secure/cgnslib_3.1.3/src//lib -lcgns       -Vaxlib -lm   -lm
> ifort: command line remark #10010: option '-Vaxlib' is deprecated and will
> be removed in a future release. See '-help deprecated'
> /apps/MVAPICH2/lib/libmpich.a(dbg_printf.o): In function
> `MPIU_dbglog_vprintf':
> dbg_printf.c:(.text+0x30): undefined reference to `__kmpc_global_thread_num'
> dbg_printf.c:(.text+0x251): undefined reference to
> `__kmpc_for_static_init_4'
> dbg_printf.c:(.text+0x462): undefined reference to `__kmpc_for_static_fini'
> dbg_printf.c:(.text+0x53e): undefined reference to `__kmpc_ok_to_fork'
> dbg_printf.c:(.text+0x573): undefined reference to `__kmpc_fork_call'
> /apps/MVAPICH2/lib/libmpich.a(dbg_printf.o): In function `MPIU_dbg_printf':
> dbg_printf.c:(.text+0x7f8): undefined reference to
> `__kmpc_global_thread_num'
> dbg_printf.c:(.text+0xacc): undefined reference to
> `__kmpc_for_static_init_4'
> dbg_printf.c:(.text+0xcdd): undefined reference to `__kmpc_for_static_fini'
> dbg_printf.c:(.text+0xdc0): undefined reference to `__kmpc_ok_to_fork'
> dbg_printf.c:(.text+0xdf5): undefined reference to `__kmpc_fork_call'
> /apps/MVAPICH2/lib/libmpich.a(dbg_printf.o): In function
> `MPIU_dbglog_printf':
> dbg_printf.c:(.text+0x1078): undefined reference to
> `__kmpc_global_thread_num'
> dbg_printf.c:(.text+0x12fa): undefined reference to
> `__kmpc_for_static_init_4'
> dbg_printf.c:(.text+0x150b): undefined reference to `__kmpc_for_static_fini'
> dbg_printf.c:(.text+0x15ee): undefined reference to `__kmpc_ok_to_fork'
> dbg_printf.c:(.text+0x1623): undefined reference to `__kmpc_fork_call'
> /apps/MVAPICH2/lib/libmpich.a(dbg_printf.o): In function `MPIU_dbg_init':
> dbg_printf.c:(.text+0x1a72): undefined reference to
> `__kmpc_global_thread_num'
> dbg_printf.c:(.text+0x1b63): undefined reference to
> `__kmpc_for_static_init_4'
> dbg_printf.c:(.text+0x1d74): undefined reference to `__kmpc_for_static_fini'
> dbg_printf.c:(.text+0x1ea2): undefined reference to `__kmpc_ok_to_fork'
> dbg_printf.c:(.text+0x1ed7): undefined reference to `__kmpc_fork_call'
> /apps/MVAPICH2/lib/libmpich.a(topology.o): In function
> `hwloc_setup_misc_level_from_distances':
> topology.c:(.text+0xcc): undefined reference to `__kmpc_global_thread_num'
> topology.c:(.text+0xb0b): undefined reference to `__kmpc_for_static_init_4'
> topology.c:(.text+0xe51): undefined reference to `__kmpc_for_static_fini'
> topology.c:(.text+0x1562): undefined reference to `__kmpc_ok_to_fork'
> topology.c:(.text+0x15f8): undefined reference to `__kmpc_fork_call'
> /apps/MVAPICH2/lib/libmpich.a(topology.o): In function
> `hwloc__setup_misc_level_from_distances':
> topology.c:(.text+0x1caf): undefined reference to `__kmpc_global_thread_num'
> topology.c:(.text+0x25f5): undefined reference to `__kmpc_for_static_init_4'
> topology.c:(.text+0x293e): undefined reference to `__kmpc_for_static_fini'
> topology.c:(.text+0x3045): undefined reference to `__kmpc_ok_to_fork'
> topology.c:(.text+0x30d8): undefined reference to `__kmpc_fork_call'
> /apps/MVAPICH2/lib/libmpich.a(topology-linux.o): In function `look_cpuinfo':
> topology-linux.c:(.text+0x3a13): undefined reference to
> `__kmpc_global_thread_num'
> topology-linux.c:(.text+0x3a4a): undefined reference to `__kmpc_ok_to_fork'
> topology-linux.c:(.text+0x3aa1): undefined reference to `__kmpc_fork_call'
> topology-linux.c:(.text+0x3ca8): undefined reference to
> `__kmpc_for_static_init_4'
> topology-linux.c:(.text+0x3db2): undefined reference to
> `__kmpc_for_static_fini'
> make[2]: *** [dual_mpi] Error 1
> make[2]: Leaving directory `/apps/CFD/secure/FUN3D/fun3d-11.6-54779/Adjoint'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/apps/CFD/secure/FUN3D/fun3d-11.6-54779'
> make: *** [all] Error 2
> [root at orange1 fun3d-11.6-54779]#
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>
>



-- 
Jonathan Perkins
http://www.cse.ohio-state.edu/~perkinjo