[OMPI users] OS X El Capitan 10.11.6 ld: symbol(s) not found for architecture x86_64

[Richard G French]

Hi, all -
I'm trying to build the SPH code Gadget2 (
http://wwwmpa.mpa-garching.mpg.de/gadget/) under OS X 10.11.6 and I am
getting the following type of error:

222 ***@cosmos> make

mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o
init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o
density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o
forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o
longrange.o -g -L/opt/local/lib/mpich-mp -L/usr/local/lib -lgsl
-lgslcblas -lm -L/usr/local/lib -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw
-o Gadget2

Undefined symbols for architecture x86_64:

"_ompi_mpi_byte", referenced from:

_read_parameter_file in begrun.o

_compute_global_quantities_of_system in global.o

_restart in restart.o

_write_file in io.o

_read_file in read_ic.o

_find_files in read_ic.o
_density in density.o

......

I built the mpich library using

cd openmpi-2.0.0/

./configure

sudo make all install

which installed the libraries in

/opt/local/lib/mpich-mp


I can't seem to track down the library that contains ompi_mpi_byte.


Any suggestions would be welcome. Thanks!

Dick French
--
Richard G. French

McDowell and Whiting Professor of Astrophysics

Chair of the Astronomy Department, Wellesley College

Director of the Whitin Observatory

Cassini Mission to Saturn Radio Science Team Leader

Wellesley, MA 02481-8203

[phone]

[Douglas L Reeder]

Richard,

It looks like you need to add some -lxxxx arguments to the the specific openmpi libraries hat you need (e.g., -lmpi -lmpi_cxx)

Doug

Post by Richard G French
Hi, all -
mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o longrange.o -g -L/opt/local/lib/mpich-mp -L/usr/local/lib -lgsl -lgslcblas -lm -L/usr/local/lib -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw -o Gadget2
_read_parameter_file in begrun.o
_compute_global_quantities_of_system in global.o
_restart in restart.o
_write_file in io.o
_read_file in read_ic.o
_find_files in read_ic.o
_density in density.o
......
I built the mpich library using
cd openmpi-2.0.0/
./configure
sudo make all install
which installed the libraries in
/opt/local/lib/mpich-mp
I can't seem to track down the library that contains ompi_mpi_byte.
Any suggestions would be welcome. Thanks!
Dick French
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

[Richard G French]

Thanks for the suggestion, Doug - but I can't seem to find the missing
function ompi_mpi_byte in any of those other libraries. I'll keep looking!
I wonder if I failed to configure mpich properly when I built it.
Dick

Post by Douglas L Reeder
Richard,
It looks like you need to add some -lxxxx arguments to the the specific
openmpi libraries hat you need (e.g., -lmpi -lmpi_cxx)
Doug
Hi, all -
I'm trying to build the SPH code Gadget2 (http://wwwmpa.mpa-garching.
mpg.de/gadget/) under OS X 10.11.6 and I am getting the following type of
mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o
init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o
density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o
forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o
longrange.o -g -L/opt/local/lib/mpich-mp -L/usr/local/lib -lgsl
-lgslcblas -lm -L/usr/local/lib -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw
-o Gadget2
_read_parameter_file in begrun.o
_compute_global_quantities_of_system in global.o
_restart in restart.o
_write_file in io.o
_read_file in read_ic.o
_find_files in read_ic.o
_density in density.o
......
I built the mpich library using
cd openmpi-2.0.0/
./configure
sudo make all install
which installed the libraries in
/opt/local/lib/mpich-mp
I can't seem to track down the library that contains ompi_mpi_byte.
Any suggestions would be welcome. Thanks!
Dick French
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

--
Richard G. French

McDowell and Whiting Professor of Astrophysics

Chair of the Astronomy Department, Wellesley College

Director of the Whitin Observatory

Cassini Mission to Saturn Radio Science Team Leader

Wellesley, MA 02481-8203

[phone]

[r***@open-mpi.org]

I’m confused - you keep talking about MPICH, but the symbol you are looking for is from OMPI. You cannot mix the two MPI libraries - is that what you are trying to do?

Thanks for the suggestion, Doug - but I can't seem to find the missing function ompi_mpi_byte in any of those other libraries. I'll keep looking! I wonder if I failed to configure mpich properly when I built it.
Dick
Richard,
It looks like you need to add some -lxxxx arguments to the the specific openmpi libraries hat you need (e.g., -lmpi -lmpi_cxx)
Doug

Post by Richard G French
Hi, all -
mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o longrange.o -g -L/opt/local/lib/mpich-mp -L/usr/local/lib -lgsl -lgslcblas -lm -L/usr/local/lib -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw -o Gadget2
_read_parameter_file in begrun.o
_compute_global_quantities_of_system in global.o
_restart in restart.o
_write_file in io.o
_read_file in read_ic.o
_find_files in read_ic.o
_density in density.o
......
I built the mpich library using
cd openmpi-2.0.0/
./configure
sudo make all install
which installed the libraries in
/opt/local/lib/mpich-mp
I can't seem to track down the library that contains ompi_mpi_byte.
Any suggestions would be welcome. Thanks!
Dick French
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone] <tel:%28781%29%20283-3747>
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users <https://rfd.newmexicoconsortium.org/mailman/listinfo/users>

_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users <https://rfd.newmexicoconsortium.org/mailman/listinfo/users>
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

[Douglas L Reeder]

Dick,

In the openmpi library directory you can do

nm library_file_name|grep ompi_mpi_byte

And that wil tell you if that library contains ompi_mpi_byte

Doug

Thanks for the suggestion, Doug - but I can't seem to find the missing function ompi_mpi_byte in any of those other libraries. I'll keep looking! I wonder if I failed to configure mpich properly when I built it.
Dick
Richard,
It looks like you need to add some -lxxxx arguments to the the specific openmpi libraries hat you need (e.g., -lmpi -lmpi_cxx)
Doug

Post by Richard G French
Hi, all -
mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o longrange.o -g -L/opt/local/lib/mpich-mp -L/usr/local/lib -lgsl -lgslcblas -lm -L/usr/local/lib -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw -o Gadget2
_read_parameter_file in begrun.o
_compute_global_quantities_of_system in global.o
_restart in restart.o
_write_file in io.o
_read_file in read_ic.o
_find_files in read_ic.o
_density in density.o
......
I built the mpich library using
cd openmpi-2.0.0/
./configure
sudo make all install
which installed the libraries in
/opt/local/lib/mpich-mp
I can't seem to track down the library that contains ompi_mpi_byte.
Any suggestions would be welcome. Thanks!
Dick French
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone] <tel:%28781%29%20283-3747>
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users <https://rfd.newmexicoconsortium.org/mailman/listinfo/users>

_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users <https://rfd.newmexicoconsortium.org/mailman/listinfo/users>
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

[Richard G French]

It sounds like I need to understand what flavor of MPI I need for this
project. I'll do some homework to try to understand the differences.
Thanks for the leads.
Dick

Post by Douglas L Reeder
Dick,
In the openmpi library directory you can do
nm library_file_name|grep ompi_mpi_byte
And that wil tell you if that library contains ompi_mpi_byte
Doug
Thanks for the suggestion, Doug - but I can't seem to find the missing
function ompi_mpi_byte in any of those other libraries. I'll keep looking!
I wonder if I failed to configure mpich properly when I built it.
Dick

Post by Douglas L Reeder
Richard,
It looks like you need to add some -lxxxx arguments to the the specific
openmpi libraries hat you need (e.g., -lmpi -lmpi_cxx)
Doug
Hi, all -
I'm trying to build the SPH code Gadget2 (http://wwwmpa.mpa-garching.mp
g.de/gadget/) under OS X 10.11.6 and I am getting the following type of
mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o
init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o
density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o
forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o
longrange.o -g -L/opt/local/lib/mpich-mp -L/usr/local/lib -lgsl
-lgslcblas -lm -L/usr/local/lib -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw
-o Gadget2
_read_parameter_file in begrun.o
_compute_global_quantities_of_system in global.o
_restart in restart.o
_write_file in io.o
_read_file in read_ic.o
_find_files in read_ic.o
_density in density.o
......
I built the mpich library using
cd openmpi-2.0.0/
./configure
sudo make all install
which installed the libraries in
/opt/local/lib/mpich-mp
I can't seem to track down the library that contains ompi_mpi_byte.
Any suggestions would be welcome. Thanks!
Dick French
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

--
Richard G. French

McDowell and Whiting Professor of Astrophysics

Chair of the Astronomy Department, Wellesley College

Director of the Whitin Observatory

Cassini Mission to Saturn Radio Science Team Leader

Wellesley, MA 02481-8203

[phone]

[Reuti]

Hi,

Post by Richard G French
Hi, all -
mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o longrange.o -g -L/opt/local/lib/mpich-mp -L/usr/local/lib -lgsl -lgslcblas -lm -L/usr/local/lib -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw -o Gadget2

By default the `mpicc` should add all necessary libraries to compile and link the application. But I wonder why you speak about mpich-mp as this is a different implementation of MPI, not Open MPI. Also the default location of Open MPI isn't mpich-mp.

- what does:

$ mpicc -show
$ which mpicc

output?

- which MPI library was used to build the parallel FFTW?

-- Reuti

Post by Richard G French
_read_parameter_file in begrun.o
_compute_global_quantities_of_system in global.o
_restart in restart.o
_write_file in io.o
_read_file in read_ic.o
_find_files in read_ic.o
_density in density.o
......
I built the mpich library using
cd openmpi-2.0.0/
./configure
sudo make all install
which installed the libraries in
/opt/local/lib/mpich-mp
I can't seem to track down the library that contains ompi_mpi_byte.
Any suggestions would be welcome. Thanks!
Dick French
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

[Richard G French]

2415 ***@cosmos> mpicc -show

gcc -I/usr/local/include -L/usr/local/lib -lmpi

2416 ***@cosmos> which mpicc

/usr/local/bin/mpicc


I'll get rid of the mpich-mp stuff and give it another try!

Post by Douglas L Reeder
Hi,

Post by Richard G French
Hi, all -
I'm trying to build the SPH code Gadget2 (http://wwwmpa.mpa-garching.

mpg.de/gadget/) under OS X 10.11.6 and I am getting the following type of

Post by Richard G French
mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o

init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o
density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o
forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o
longrange.o -g -L/opt/local/lib/mpich-mp -L/usr/local/lib -lgsl
-lgslcblas -lm -L/usr/local/lib -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw
-o Gadget2
By default the `mpicc` should add all necessary libraries to compile and
link the application. But I wonder why you speak about mpich-mp as this is
a different implementation of MPI, not Open MPI. Also the default location
of Open MPI isn't mpich-mp.
$ mpicc -show
$ which mpicc
output?
- which MPI library was used to build the parallel FFTW?
-- Reuti

Post by Richard G French
_read_parameter_file in begrun.o
_compute_global_quantities_of_system in global.o
_restart in restart.o
_write_file in io.o
_read_file in read_ic.o
_find_files in read_ic.o
_density in density.o
......
I built the mpich library using
cd openmpi-2.0.0/
./configure
sudo make all install
which installed the libraries in
/opt/local/lib/mpich-mp
I can't seem to track down the library that contains ompi_mpi_byte.
Any suggestions would be welcome. Thanks!
Dick French
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

--
Richard G. French

McDowell and Whiting Professor of Astrophysics

Chair of the Astronomy Department, Wellesley College

Director of the Whitin Observatory

Cassini Mission to Saturn Radio Science Team Leader

Wellesley, MA 02481-8203

[phone]

[Richard G French]

Problem solved! I had to remove a macports directory from my path that had
the improper MPI library, and at last the code is working. Thanks so much
to everyone for your friendly and prompt suggestions - I appreciate it very
much.
Dick

Post by Richard G French
gcc -I/usr/local/include -L/usr/local/lib -lmpi
/usr/local/bin/mpicc
I'll get rid of the mpich-mp stuff and give it another try!

Post by Douglas L Reeder
Hi,

Post by Richard G French
Hi, all -
I'm trying to build the SPH code Gadget2 (http://wwwmpa.mpa-garching.mp

g.de/gadget/) under OS X 10.11.6 and I am getting the following type of

Post by Richard G French
mpicc main.o run.o predict.o begrun.o endrun.o global.o timestep.o

init.o restart.o io.o accel.o read_ic.o ngb.o system.o allocate.o
density.o gravtree.o hydra.o driftfac.o domain.o allvars.o potential.o
forcetree.o peano.o gravtree_forcetest.o pm_periodic.o pm_nonperiodic.o
longrange.o -g -L/opt/local/lib/mpich-mp -L/usr/local/lib -lgsl
-lgslcblas -lm -L/usr/local/lib -lrfftw_mpi -lfftw_mpi -lrfftw -lfftw
-o Gadget2
By default the `mpicc` should add all necessary libraries to compile and
link the application. But I wonder why you speak about mpich-mp as this is
a different implementation of MPI, not Open MPI. Also the default location
of Open MPI isn't mpich-mp.
$ mpicc -show
$ which mpicc
output?
- which MPI library was used to build the parallel FFTW?
-- Reuti

Post by Richard G French
_read_parameter_file in begrun.o
_compute_global_quantities_of_system in global.o
_restart in restart.o
_write_file in io.o
_read_file in read_ic.o
_find_files in read_ic.o
_density in density.o
......
I built the mpich library using
cd openmpi-2.0.0/
./configure
sudo make all install
which installed the libraries in
/opt/local/lib/mpich-mp
I can't seem to track down the library that contains ompi_mpi_byte.
Any suggestions would be welcome. Thanks!
Dick French
--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

--
Richard G. French
McDowell and Whiting Professor of Astrophysics
Chair of the Astronomy Department, Wellesley College
Director of the Whitin Observatory
Cassini Mission to Saturn Radio Science Team Leader
Wellesley, MA 02481-8203
[phone]

--
Richard G. French

McDowell and Whiting Professor of Astrophysics

Chair of the Astronomy Department, Wellesley College

Director of the Whitin Observatory

Cassini Mission to Saturn Radio Science Team Leader

Wellesley, MA 02481-8203

[phone]