[OMPI users] openmpi-2.0.1

Discussion:

Professor W P Jones

2016-11-17 13:45:52 UTC

Hi

I am trying to install openmpi-2.0.1 togeter with the version 14.0.2
intel compilers and I an having problems. The configure script with
CC=icc CXX=icpc and FC=ifort runs successfully but when i issue make all
install this fails with the output:

Making all in tools/ompi_info
make[2]: Entering directory
`/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info'
CCLD ompi_info
ld: warning: libimf.so, needed by ../../../ompi/.libs/libmpi.so, not
found (try using -rpath or -rpath-link)
ld: warning: libsvml.so, needed by ../../../ompi/.libs/libmpi.so, not
found (try using -rpath or -rpath-link)
ld: warning: libirng.so, needed by ../../../ompi/.libs/libmpi.so, not
found (try using -rpath or -rpath-link)
ld: warning: libintlc.so.5, needed by ../../../ompi/.libs/libmpi.so, not
found (try using -rpath or -rpath-link)
ld: .libs/ompi_info: hidden symbol `__intel_cpu_features_init_x' in
/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64//libirc.a(cpu_feature_disp.o)
is referenced by DSO
ld: final link failed: Bad value
make[2]: *** [ompi_info] Error 1
make[2]: Leaving directory
`/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi'
make: *** [all-recursive] Error 1

Does anyone have suggestions for fixing this problem?

Thanks
Bill
--
Professor W P Jones, FREng
Department of Mechanical Engineering
Imperial College London
Exhibition Road
London SW7 2AZ
Tel: +44 (0)20 7594 7037/7033
Mobile +44 (0)776 495 9702
Fax: +44 (0)20 7594 5702
E-mail: ***@imperial.ac.uk
web site: http://www.imperial.ac.uk/me

Tim Prince via users

2016-11-17 14:02:56 UTC

Permalink

Post by Professor W P Jones
Hi
I am trying to install openmpi-2.0.1 togeter with the version 14.0.2
intel compilers and I an having problems. The configure script with
CC=icc CXX=icpc and FC=ifort runs successfully but when i issue make
Making all in tools/ompi_info
make[2]: Entering directory
`/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info'
CCLD ompi_info
ld: warning: libimf.so, needed by ../../../ompi/.libs/libmpi.so, not
found (try using -rpath or -rpath-link)
ld: warning: libsvml.so, needed by ../../../ompi/.libs/libmpi.so, not
found (try using -rpath or -rpath-link)
ld: warning: libirng.so, needed by ../../../ompi/.libs/libmpi.so, not
found (try using -rpath or -rpath-link)
ld: warning: libintlc.so.5, needed by ../../../ompi/.libs/libmpi.so,
not found (try using -rpath or -rpath-link)
ld: .libs/ompi_info: hidden symbol `__intel_cpu_features_init_x' in
/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64//libirc.a(cpu_feature_disp.o)
is referenced by DSO
ld: final link failed: Bad value
make[2]: *** [ompi_info] Error 1
make[2]: Leaving directory
`/usr/local/src/openmpi-2.0.1/ompi/tools/ompi_info'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/src/openmpi-2.0.1/ompi'
make: *** [all-recursive] Error 1

Do you have the Intel compilervars.[c]sh sourced (and associated library
files visible) on each node where you expect to install?

--
Tim Prince

Professor W P Jones

2016-11-17 14:20:54 UTC

Permalink

Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version
14.0.2 (gcc version 4.8.0 compatibility)

Bill

Professor W P Jones, FREng
Department of Mechanical Engineering
Imperial College London
Exhibition Road
London SW7 2AZ
Tel: +44 (0)20 7594 7037/7033
Mobile +44 (0)776 495 9702
Fax: +44 (0)20 7594 5702
E-mail: ***@imperial.ac.uk
web site: http://www.imperial.ac.uk/me

Post by Tim Prince via users

Do you have the Intel compilervars.[c]sh sourced (and associated library
files visible) on each node where you expect to install?

Bennet Fauber

2016-11-17 14:33:59 UTC

Permalink

Can you include your entire ./configure line? Also, it would be
useful, perhaps to look at the output of

$ printenv | grep LIBRARY

to make sure that all Intel library paths made it into the appropriate
variables.

When I build 1.10.2, I had these:

LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64

LD_LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64_lin

and those sufficed. I have not tried OMPI 2.x.

-- bennet

On Thu, Nov 17, 2016 at 9:20 AM, Professor W P Jones

Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version 14.0.2
(gcc version 4.8.0 compatibility)
Bill
Professor W P Jones, FREng
Department of Mechanical Engineering
Imperial College London
Exhibition Road
London SW7 2AZ
Tel: +44 (0)20 7594 7037/7033
Mobile +44 (0)776 495 9702
Fax: +44 (0)20 7594 5702
web site: http://www.imperial.ac.uk/me

Post by Tim Prince via users

Do you have the Intel compilervars.[c]sh sourced (and associated library
files visible) on each node where you expect to install?

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

Professor W P Jones

2016-11-17 14:44:09 UTC

Permalink

The .configure is:

./configure PREFIX=/opt/openmpi-2.0.1-intel-14.0.2 CC=icc CXX=icpc
F77=ifort FC=ifort

and the output from printenv | grep LIBRARY is:

LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4
MIC_LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic
LD_LIBRARY_PATH=/opt/lf6481/lib64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4:/opt/lf6481/lib64:/usr/StorMan:/usr/StorMan/ssl/lib:/usr/StorMan/pegasus/lib:
MIC_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic

Bill

Professor W P Jones, FREng
Department of Mechanical Engineering
Imperial College London
Exhibition Road
London SW7 2AZ
Tel: +44 (0)20 7594 7037/7033
Mobile +44 (0)776 495 9702
Fax: +44 (0)20 7594 5702
E-mail: ***@imperial.ac.uk
web site: http://www.imperial.ac.uk/me

Post by Bennet Fauber
Can you include your entire ./configure line? Also, it would be
useful, perhaps to look at the output of
$ printenv | grep LIBRARY
to make sure that all Intel library paths made it into the appropriate
variables.
LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64
LD_LIBRARY_PATH=/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/sw/arcts/centos7/intel/2013.1.046/composer_xe_2013_sp1.2.144/compiler/lib/intel64_lin
and those sufficed. I have not tried OMPI 2.x.
-- bennet
On Thu, Nov 17, 2016 at 9:20 AM, Professor W P Jones

Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version 14.0.2
(gcc version 4.8.0 compatibility)
Bill
Professor W P Jones, FREng
Department of Mechanical Engineering
Imperial College London
Exhibition Road
London SW7 2AZ
Tel: +44 (0)20 7594 7037/7033
Mobile +44 (0)776 495 9702
Fax: +44 (0)20 7594 5702
web site: http://www.imperial.ac.uk/me

Post by Tim Prince via users

Do you have the Intel compilervars.[c]sh sourced (and associated library
files visible) on each node where you expect to install?

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

Bennet Fauber

2016-11-17 15:12:32 UTC

Permalink

That's a stumper. Only thing I can think of is that the
LD_LIBRARY_PATH is being overwritten somewhere inside the Makefile, or
perhaps that it isn't properly exported...?

As a graspable straw, try

$ set -a

to export all variables, then

$ source /opt/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh

(I may have the path to your compilervars.sh wrong). That should
insure that everything is properly exported.

It sure looks to me like the compilers aren't finding the right library paths.

-- bennet

On Thu, Nov 17, 2016 at 9:44 AM, Professor W P Jones

./configure PREFIX=/opt/openmpi-2.0.1-intel-14.0.2 CC=icc CXX=icpc F77=ifort
FC=ifort
LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4
MIC_LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic
MIC_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic
Bill
Professor W P Jones, FREng
Department of Mechanical Engineering
Imperial College London
Exhibition Road
London SW7 2AZ
Tel: +44 (0)20 7594 7037/7033
Mobile +44 (0)776 495 9702
Fax: +44 (0)20 7594 5702
web site: http://www.imperial.ac.uk/me

Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version 14.0.2
(gcc version 4.8.0 compatibility)
Bill
Professor W P Jones, FREng
Department of Mechanical Engineering
Imperial College London
Exhibition Road
London SW7 2AZ
Tel: +44 (0)20 7594 7037/7033
Mobile +44 (0)776 495 9702
Fax: +44 (0)20 7594 5702
web site: http://www.imperial.ac.uk/me

Post by Tim Prince via users

Do you have the Intel compilervars.[c]sh sourced (and associated library
files visible) on each node where you expect to install?

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

Gilles Gouaillardet

2016-11-17 20:43:05 UTC

Permalink

Hi,

at first, you might want to remove path related to Intel MPI runtime
(e.g. /opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64) from
your environment

if you are using bash, double check you
export LD_LIBRARY_PATH
(otherwise echo $LD_LIBRARY_PATH and the linker see different things)

then you can
file ompi/.libs/libmpi.so
file ompi/tools/.libs/ompi_info.o
and they are both 64 bits x86_64 (e.g. no 32 bits, nor MIC binaries)

ldd ompi/.libs/libmpi.so
should resolve all intel runtime libs.

then i recommend you restart configure from a clean directory
if it still does not work, you can
cd ompi/tools
make V=1

and post the output

Cheers,

Gilles

Post by Bennet Fauber
That's a stumper. Only thing I can think of is that the
LD_LIBRARY_PATH is being overwritten somewhere inside the Makefile, or
perhaps that it isn't properly exported...?
As a graspable straw, try
$ set -a
to export all variables, then
$ source /opt/intel/composer_xe_2013_sp1.2.144/bin/compilervars.sh
(I may have the path to your compilervars.sh wrong). That should
insure that everything is properly exported.
It sure looks to me like the compilers aren't finding the right library paths.
-- bennet
On Thu, Nov 17, 2016 at 9:44 AM, Professor W P Jones

Yes, ifort -v and icpc -v give ifort version 14.0.2 and icpc version 14.0.2
(gcc version 4.8.0 compatibility)
Bill
Professor W P Jones, FREng
Department of Mechanical Engineering
Imperial College London
Exhibition Road
London SW7 2AZ
Tel: +44 (0)20 7594 7037/7033
Mobile +44 (0)776 495 9702
Fax: +44 (0)20 7594 5702
web site: http://www.imperial.ac.uk/me

Post by Tim Prince via users

Do you have the Intel compilervars.[c]sh sourced (and associated library
files visible) on each node where you expect to install?

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

Jeff Squyres (jsquyres)

2016-11-18 15:58:49 UTC

Permalink

Post by Gilles Gouaillardet
if it still does not work, you can
cd ompi/tools
make V=1
and post the output

Let me add to that: if that doesn't work, please send all the information listed here:

https://www.open-mpi.org/community/help/

--
Jeff Squyres
***@cisco.com
For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/