Freezes while building MPI.o

[Nicholas Carl]

Hello,

I am trying to install mpi4py-1.3 for python 2.7 and it freezes while
building MPI.o and the load goes up a ridiculous amount before I
cancel it. I tried building it with openmpi and mpich2, and also tried
mpi4py-1.2.2 and got the same thing. Not sure what I am doing wrong.
Has anyone seen this before? Thanks!

Below is the example output before it stops:

[root@localhost mpi4py-1.3]# python setup.py build
running build
running build_src
running build_py
running build_clib
error: section/s 'mpi-linux2,mpi' not found in file/s 'mpi.cfg'
running build_ext
error: section/s 'mpi-linux2,mpi' not found in file/s 'mpi.cfg'
checking for MPI compile and link ...
checking for header 'mpi.h' ...
/opt/openmpi/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -
O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c _configtest.c
-o _configtest.o
success!
removing: _configtest.c _configtest.o
success!
/opt/openmpi/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -
O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c _configtest.c
-o _configtest.o
success!
removing: _configtest.c _configtest.o
/opt/openmpi/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -
O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c _configtest.c
-o _configtest.o
/opt/openmpi/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-2.7 -o
_configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for missing MPI functions/symbols ...
/opt/openmpi/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -
O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c _configtest.c
-o _configtest.o
success!
removing: _configtest.c _configtest.o
checking for function 'MPI_Type_create_f90_integer' ...
/opt/openmpi/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -
O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c _configtest.c
-o _configtest.o
/opt/openmpi/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-2.7 -o
_configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_real' ...
/opt/openmpi/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -
O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c _configtest.c
-o _configtest.o
/opt/openmpi/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-2.7 -o
_configtest
success!
removing: _configtest.c _configtest.o _configtest
checking for function 'MPI_Type_create_f90_complex' ...
/opt/openmpi/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -
O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c _configtest.c
-o _configtest.o
/opt/openmpi/bin/mpicc _configtest.o -Lbuild/temp.linux-x86_64-2.7 -o
_configtest
success!
removing: _configtest.c _configtest.o _configtest
building 'mpi4py.MPI' extension
/opt/openmpi/bin/mpicc -fPIC -fno-strict-aliasing -DNDEBUG -g -fwrapv -
O3 -Wall -Wstrict-prototypes -I/usr/include/python2.7 -c src/MPI.c -o
build/temp.linux-x86_64-2.7/src/MPI.o

[Aron Ahmadia]

Never seen this before.  Why are you running "build" as root?  

What version of the compilers are you using?  How much free memory does your system have?

A

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[William Scullin]

Are you on a NFS or other shared file system?

- William

[Nicholas Carl]

Hi All,

The test node (2 core 4g ram) I was on must have had something wrong
with the mpi. Tried it on the prod node (24 core 72g ram) and it built
fine.

Thanks!

[cr1...@gmail.com]

The setup step has me stopped at the same place. It just sits there running as if it can't complete this step. Did you ever figure it out?