Hello,
I am trying to compile a thorn arrangement for the qc0-mclachlan.par parameter file, with the einsteintoolkit.th on a macbook pro 10.6.3 intel core i7. I have attached the configuration file I am using and the output of the compilation errors. The errors are of type: Undefined symbols: "_ompi_mpi_comm_null", referenced from: MPI::Cartcomm::Clone() const in libthorn_CarpetSlab.a(mapping.cc.o) etc.... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o) etc.....
please help, Maria
On Wed, May 26, 2010 at 09:34:10AM -0400, Babiuc-Hamilton, Maria wrote:
I am trying to compile a thorn arrangement for the qc0-mclachlan.par parameter file, with the einsteintoolkit.th on a macbook pro 10.6.3 intel core i7. I have attached the configuration file I am using and the output of the compilation errors. The errors are of type: Undefined symbols: "_ompi_mpi_comm_null", referenced from: MPI::Cartcomm::Clone() const in libthorn_CarpetSlab.a(mapping.cc.o) etc.... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o)
ompi_mpi_comm_null is a symbol from openmpi. Your configuration includes MPICH however, but has openmpi commented out. I guess some files are still linked against openmpi. Please delete the whole configuration (under configs/) and start from scratch.
Frank Loeffler
Hello,
Yes, the "_ompi_" errors were because of that. I recompiled with OpenMPI, and those errors were resolved. However, I still have the second errors: Undefined symbols: "MPI::Comm::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Intercomm in libthorn_CarpetSlab.a(mapping.cc.o) etc... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o) etc... ld: symbol(s) not found collect2: ld returned 1 exit status
Do you have any suggestion about this error?
Maria ________________________________________ From: Frank Loeffler [knarf@cct.lsu.edu] Sent: Wednesday, May 26, 2010 12:42 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: [Users] compilation problem on 10.6.3 macbook pro
On Wed, May 26, 2010 at 09:34:10AM -0400, Babiuc-Hamilton, Maria wrote:
I am trying to compile a thorn arrangement for the qc0-mclachlan.par parameter file, with the einsteintoolkit.th on a macbook pro 10.6.3 intel core i7. I have attached the configuration file I am using and the output of the compilation errors. The errors are of type: Undefined symbols: "_ompi_mpi_comm_null", referenced from: MPI::Cartcomm::Clone() const in libthorn_CarpetSlab.a(mapping.cc.o) etc.... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o)
ompi_mpi_comm_null is a symbol from openmpi. Your configuration includes MPICH however, but has openmpi commented out. I guess some files are still linked against openmpi. Please delete the whole configuration (under configs/) and start from scratch.
Frank Loeffler
Maria
Can you post your current configuration options?
Also, which MPI implementation are you using? Can you tell us the name and version number?
-erik
On May 26, 2010, at 15:02 , Babiuc-Hamilton, Maria wrote:
Hello,
Yes, the "_ompi_" errors were because of that. I recompiled with OpenMPI, and those errors were resolved. However, I still have the second errors: Undefined symbols: "MPI::Comm::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Intercomm in libthorn_CarpetSlab.a(mapping.cc.o) etc... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o) etc... ld: symbol(s) not found collect2: ld returned 1 exit status
Do you have any suggestion about this error?
Maria ________________________________________ From: Frank Loeffler [knarf@cct.lsu.edu] Sent: Wednesday, May 26, 2010 12:42 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: [Users] compilation problem on 10.6.3 macbook pro
On Wed, May 26, 2010 at 09:34:10AM -0400, Babiuc-Hamilton, Maria wrote:
I am trying to compile a thorn arrangement for the qc0- mclachlan.par parameter file, with the einsteintoolkit.th on a macbook pro 10.6.3 intel core i7. I have attached the configuration file I am using and the output of the compilation errors. The errors are of type: Undefined symbols: "_ompi_mpi_comm_null", referenced from: MPI::Cartcomm::Clone() const in libthorn_CarpetSlab.a (mapping.cc.o) etc.... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o)
ompi_mpi_comm_null is a symbol from openmpi. Your configuration includes MPICH however, but has openmpi commented out. I guess some files are still linked against openmpi. Please delete the whole configuration (under configs/) and start from scratch.
Frank Loeffler
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Hi,
The MPI implementation is openmpi 1.4.2_0+gcc43 installed with macports.
And it seems that I have it installed in two places
/usr/include/openmpi/ompi/mpi/cxx/ /opt/local/include/openmpi/openmpi/ompi/mpi/cxx/
The configuration is: # macbook-gcc-config # Whenever this version string changes, the application is configured # and rebuilt from scratch
CPP = cpp-mp-4.3 FPP = cpp-mp-4.3 CC = gcc-mp-4.3 CXX = g++-mp-4.3 F77 = gfortran-mp-4.3 F90 = gfortran-mp-4.3
#CPPFLAGS = -DMPICH_IGNORE_CXX_SEEK FPPFLAGS = -traditional CFLAGS = -g3 -fshow-column -mmacosx-version-min=10.5 -m128bit-long-double -std =gnu99 CXXFLAGS = -g3 -fshow-column -mmacosx-version-min=10.5 -m128bit-long-double F77FLAGS = -g3 -fshow-column -mmacosx-version-min=10.5 -m128bit-long-double -fcr ay-pointer F90FLAGS = -g3 -fshow-column -mmacosx-version-min=10.5 -m128bit-long-double -fcr ay-pointer
LDFLAGS = /System/Library/Frameworks/vecLib.framework/vecLib -L/opt/local/lib -lgfortran
C_LINE_DIRECTIVES = yes F_LINE_DIRECTIVES = yes
REAL16_KIND = 10
DEBUG = no CPP_DEBUG_FLAGS = -DCARPET_DEBUG FPP_DEBUG_FLAGS = -DCARPET_DEBUG C_DEBUG_FLAGS = -fbounds-check -ftrapv -fstack-protector-all CXX_DEBUG_FLAGS = -fbounds-check -ftrapv -fstack-protector-all F77_DEBUG_FLAGS = -fbounds-check -ftrapv -fstack-protector-all F90_DEBUG_FLAGS = -fbounds-check -ftrapv -fstack-protector-all
# Changing ANSI C semantics: OPTIMISE = yes C_OPTIMISE_FLAGS = -O2 CXX_OPTIMISE_FLAGS = -O2 F77_OPTIMISE_FLAGS = -O2 F90_OPTIMISE_FLAGS = -O2
PROFILE = no C_PROFILE_FLAGS = -pg CXX_PROFILE_FLAGS = -pg F77_PROFILE_FLAGS = -pg F90_PROFILE_FLAGS = -pg
BLAS_DIR = /System/Library/Frameworks/vecLib.framework BLAS_LIBS = gfortran
FFTW_DIR = /opt/local FFTW_LIBS = drfftw dfftw m
GSL_DIR = /opt/local
HDF5 = yes HDF5_DIR = /opt/local LIBSZ_DIR = /opt/local
LAPACK = yes LAPACK_DIR = /System/Library/Frameworks/vecLib.framework LAPACK_LIBS =
MPI = OpenMPI MPI_LIBS = mpi #mpi_cxx OPENMPI_DIR = /usr #/opt/local #OPENMPI_LIBS = /usr/lib
PTHREADS = yes
SSL_DIR = /opt/local
X_LIB_DIR = /usr/X11R6/lib
________________________________________ From: Erik Schnetter [schnetter@cct.lsu.edu] Sent: Wednesday, May 26, 2010 7:18 PM To: Babiuc-Hamilton, Maria Cc: Frank Loeffler; users@einsteintoolkit.org Subject: Re: [Users] compilation problem on 10.6.3 macbook pro
Maria
Can you post your current configuration options?
Also, which MPI implementation are you using? Can you tell us the name and version number?
-erik
On May 26, 2010, at 15:02 , Babiuc-Hamilton, Maria wrote:
Hello,
Yes, the "_ompi_" errors were because of that. I recompiled with OpenMPI, and those errors were resolved. However, I still have the second errors: Undefined symbols: "MPI::Comm::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Intercomm in libthorn_CarpetSlab.a(mapping.cc.o) etc... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o) etc... ld: symbol(s) not found collect2: ld returned 1 exit status
Do you have any suggestion about this error?
Maria ________________________________________ From: Frank Loeffler [knarf@cct.lsu.edu] Sent: Wednesday, May 26, 2010 12:42 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: [Users] compilation problem on 10.6.3 macbook pro
On Wed, May 26, 2010 at 09:34:10AM -0400, Babiuc-Hamilton, Maria wrote:
I am trying to compile a thorn arrangement for the qc0- mclachlan.par parameter file, with the einsteintoolkit.th on a macbook pro 10.6.3 intel core i7. I have attached the configuration file I am using and the output of the compilation errors. The errors are of type: Undefined symbols: "_ompi_mpi_comm_null", referenced from: MPI::Cartcomm::Clone() const in libthorn_CarpetSlab.a (mapping.cc.o) etc.... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o)
ompi_mpi_comm_null is a symbol from openmpi. Your configuration includes MPICH however, but has openmpi commented out. I guess some files are still linked against openmpi. Please delete the whole configuration (under configs/) and start from scratch.
Frank Loeffler
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
-- Erik Schnetter schnetter@cct.lsu.edu http://www.cct.lsu.edu/~eschnett/
On Thu, May 27, 2010 at 10:31:43AM -0400, Babiuc-Hamilton, Maria wrote:
The MPI implementation is openmpi 1.4.2_0+gcc43 installed with macports.
And it seems that I have it installed in two places
/usr/include/openmpi/ompi/mpi/cxx/ /opt/local/include/openmpi/openmpi/ompi/mpi/cxx/
There is nothing wrong with installing multiple versions, but care should then be taken that they are not mixed up. This is what could be happening here (just a guess).
If you don't really need two installed versions I would first uninstall one of the two and try again, from scratch.
Frank
On May 27, 2010, at 9:31 , Babiuc-Hamilton, Maria wrote:
Hi,
The MPI implementation is openmpi 1.4.2_0+gcc43 installed with macports.
And it seems that I have it installed in two places
/usr/include/openmpi/ompi/mpi/cxx/ /opt/local/include/openmpi/openmpi/ompi/mpi/cxx/
This could be the problem. Even if you select the /opt/local (MacPorts) one, the search paths will still also find the one in /usr, and there's no telling which one will be used.
I use OpenMPI from MacPorts, and I use the options
MPI = OpenMPI OPENMPI_DIR = /opt/local OPENMPI_LIBS = mpi mpi_cxx open-rte open-pal
-erik
On Wed, May 26, 2010 at 04:02:37PM -0400, Babiuc-Hamilton, Maria wrote:
Yes, the "_ompi_" errors were because of that. I recompiled with OpenMPI, and those errors were resolved. However, I still have the second errors: Undefined symbols: "MPI::Comm::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Intercomm in libthorn_CarpetSlab.a(mapping.cc.o) etc... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o) etc... ld: symbol(s) not found collect2: ld returned 1 exit status
Do you have any suggestion about this error?
Add mpi_cxx to the libraries:
OPENMPI_LIBS = mpi mpi_cxx
Frank Loeffler
Hi,
Adding mpi_cxx did not fix it, although I erased the configuration and rebuild everything. What other things should I try?
Maria ________________________________________ From: Frank Loeffler [knarf@cct.lsu.edu] Sent: Wednesday, May 26, 2010 8:47 PM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: [Users] compilation problem on 10.6.3 macbook pro
On Wed, May 26, 2010 at 04:02:37PM -0400, Babiuc-Hamilton, Maria wrote:
Yes, the "_ompi_" errors were because of that. I recompiled with OpenMPI, and those errors were resolved. However, I still have the second errors: Undefined symbols: "MPI::Comm::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Intercomm in libthorn_CarpetSlab.a(mapping.cc.o) etc... "MPI::Win::Set_errhandler(MPI::Errhandler const&)", referenced from: vtable for MPI::Win in libthorn_CarpetSlab.a(mapping.cc.o) etc... ld: symbol(s) not found collect2: ld returned 1 exit status
Do you have any suggestion about this error?
Add mpi_cxx to the libraries:
OPENMPI_LIBS = mpi mpi_cxx
Frank Loeffler
On 27/05/2010 04:57, Babiuc-Hamilton, Maria wrote:
Hi,
Adding mpi_cxx did not fix it, although I erased the configuration and rebuild everything. What other things should I try?
I use the followind MPI options with 10.6.3 and einsteintoolkit.th. You could try these
MPI = OpenMPI MPI_LIBS = mpi OPENMPI_DIR = /usr
Hi,
Interesting, I do have openmpi in two places: /opt/local/include/openmpi/ /usr/include/openmpi/
I tried your suggestion. Still, the same error!
thanks, Maria ________________________________________ From: users-bounces@einsteintoolkit.org [users-bounces@einsteintoolkit.org] On Behalf Of Barry Wardell [barry.wardell@aei.mpg.de] Sent: Thursday, May 27, 2010 2:14 AM To: users@einsteintoolkit.org Subject: Re: [Users] compilation problem on 10.6.3 macbook pro
On 27/05/2010 04:57, Babiuc-Hamilton, Maria wrote:
Hi,
Adding mpi_cxx did not fix it, although I erased the configuration and rebuild everything. What other things should I try?
I use the followind MPI options with 10.6.3 and einsteintoolkit.th. You could try these
MPI = OpenMPI MPI_LIBS = mpi OPENMPI_DIR = /usr
_______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
On 27/05/2010 16:32, Babiuc-Hamilton, Maria wrote:
Interesting, I do have openmpi in two places: /opt/local/include/openmpi/ /usr/include/openmpi/
I tried your suggestion. Still, the same error!
Maybe also try removing the MacPorts version, then remove your config and rebuild. In the past, I've encountered the sort of errors you're reporting when I had the MacPorts version installed.
users@lists.einsteintoolkit.org
-
Babiuc-Hamilton, Maria -
Barry Wardell -
Erik Schnetter -
Frank Loeffler