Re: [OMPI users] openmpi-2.0.1

2016-11-17 Thread Professor W P Jones 

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:  w.jo...@imperial.ac.uk
web site: http://www.imperial.ac.uk/me

On 17/11/16 14:33, Bennet Fauber wrote:

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
 wrote:

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:  w.jo...@imperial.ac.uk
web site: http://www.imperial.ac.uk/me

On 17/11/16 14:02, Tim Prince via users wrote:


On 11/17/2016 8:45 AM, Professor W P Jones wrote:

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


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


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[OMPI users] openmpi-2.0.1

2016-11-17 Thread 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 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:  w.jo...@imperial.ac.uk
web site: http://www.imperial.ac.uk/me

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Re: [OMPI users] openmpi-2.0.1

2016-11-17 Thread Tim Prince via users 


On 11/17/2016 8:45 AM, Professor W P Jones wrote:
> 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
>
Do you have the Intel compilervars.[c]sh sourced (and associated library
files visible) on each node where you expect to install?

-- 
Tim Prince

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Re: [OMPI users] openmpi-2.0.1

2016-11-17 Thread 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
 wrote:
> 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:  w.jo...@imperial.ac.uk
> web site: http://www.imperial.ac.uk/me
>
> On 17/11/16 14:33, Bennet Fauber wrote:
>>
>> 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
>>  wrote:
>>>
>>> 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:  w.jo...@imperial.ac.uk
>>> web site: http://www.imperial.ac.uk/me
>>>
>>> On 17/11/16 14:02, Tim Prince via users wrote:


 On 11/17/2016 8:45 AM, Professor W P Jones wrote:
>
> 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

Re: [OMPI users] openmpi-2.0.1

2016-11-17 Thread 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
E-mail:  w.jo...@imperial.ac.uk
web site: http://www.imperial.ac.uk/me

On 17/11/16 14:02, Tim Prince via users wrote:


On 11/17/2016 8:45 AM, Professor W P Jones wrote:

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


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



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Re: [OMPI users] openmpi-2.0.1

2016-11-17 Thread 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.

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
 wrote:
> 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:  w.jo...@imperial.ac.uk
> web site: http://www.imperial.ac.uk/me
>
> On 17/11/16 14:02, Tim Prince via users wrote:
>>
>>
>> On 11/17/2016 8:45 AM, Professor W P Jones wrote:
>>>
>>> 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
>>>
>> Do you have the Intel compilervars.[c]sh sourced (and associated library
>> files visible) on each node where you expect to install?
>>
>
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Re: [OMPI users] openmpi-2.0.1

2016-11-17 Thread Gilles Gouaillardet 
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

On Thu, Nov 17, 2016 at 8:12 AM, Bennet Fauber  wrote:
> 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
>  wrote:
>> 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:  w.jo...@imperial.ac.uk
>> web site: http://www.imperial.ac.uk/me
>>
>> On 17/11/16 14:33, Bennet Fauber wrote:
>>>
>>> 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
>>>  wrote:

 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:  w.jo...@imperial.ac.uk
 web site: http://www.imperial.ac.uk/me

 On 17/11/16 14:02, Tim Prince via users wrote:
>
>
> On 11/17/2016 8:45 AM, Professor W P Jones wrote:
>>
>> 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:

[OMPI users] malloc related crash inside openmpi

2016-11-17 Thread Noam Bernstein 
Hi - we’ve started seeing over the last few days crashes and hangs in openmpi, 
in a code that hasn’t been touched in months, and an openmpi installation (v. 
1.8.5) that also hasn’t been touched in months.  The symptoms are either a 
hang, with a stack trace (from attaching to the one running process that’s got 
0% CPU usage) that looks like this:
(gdb) where
#0  0x00358980f00d in nanosleep () from /lib64/libpthread.so.0
#1  0x2af19a8758de in opal_memory_ptmalloc2_free () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6
#2  0x02bca106 in for__free_vm ()
#3  0x02b8cf62 in for__exit_handler ()
#4  0x02b89782 in for__issue_diagnostic ()
#5  0x02b90a50 in for__signal_handler ()
#6  
#7  0x2af19a8746fc in malloc_consolidate () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6
#8  0x2af19a876e69 in opal_memory_ptmalloc2_int_malloc () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6
#9  0x2af19a877c4f in opal_memory_ptmalloc2_int_memalign () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6
#10 0x2af19a8788a3 in opal_memory_ptmalloc2_memalign () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6
#11 0x2af19a29e0f4 in ompi_free_list_grow () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libmpi.so.1
#12 0x2af1a0718546 in append_frag_to_list () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_pml_ob1.so
#13 0x2af1a0718cbe in match_one () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_pml_ob1.so
#14 0x2af1a07190f3 in mca_pml_ob1_recv_frag_callback_match () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_pml_ob1.so
#15 0x2af19fab4a48 in btl_openib_handle_incoming () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_btl_openib.so
#16 0x2af19fab5e1f in poll_device () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_btl_openib.so
#17 0x2af19fab618c in btl_openib_component_progress () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_btl_openib.so
#18 0x2af19a801f8a in opal_progress () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libopen-pal.so.6
#19 0x2af19a2b7a0d in ompi_request_default_wait_all () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libmpi.so.1
#20 0x2af1a17afef2 in ompi_coll_tuned_sendrecv_nonzero_actual () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_coll_tuned.so
#21 0x2af1a17b7542 in ompi_coll_tuned_alltoallv_intra_pairwise () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/openmpi/mca_coll_tuned.so
#22 0x2af19a2c9419 in PMPI_Alltoallv () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libmpi.so.1
#23 0x2af19a05f2a2 in pmpi_alltoallv__ () from 
/usr/local/openmpi/1.8.5/x86_64/ib/intel/12.1.6/lib/libmpi_mpifh.so.2
#24 0x00416213 in m_alltoall_i (comm=..., xsnd=..., psnd=Cannot access 
memory at address 0x51
) at mpi.F:1906
#25 0x029ca135 in mapset (grid=...) at fftmpi_map.F:267
#26 0x02a15c62 in vamp () at main.F:2002
#27 0x0041281e in main ()
#28 0x00358941ed1d in __libc_start_main () from /lib64/libc.so.6
#29 0x00412729 in _start ()
(gdb) quit

Or segfault that looks like this 

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image  PCRoutineLineSource  
   
vasp.gamma_para.i  02C7B031  Unknown   Unknown  Unknown
vasp.gamma_para.i  02C7916B  Unknown   Unknown  Unknown
vasp.gamma_para.i  02BECFF4  Unknown   Unknown  Unknown
vasp.gamma_para.i  02BECE06  Unknown   Unknown  Unknown
vasp.gamma_para.i  02B89827  Unknown   Unknown  Unknown
vasp.gamma_para.i  02B90A50  Unknown   Unknown  Unknown
libpthread-2.12.s  003FED60F7E0  Unknown   Unknown  Unknown
libopen-pal.so.6.  2AF7775346FC  Unknown   Unknown  Unknown
libopen-pal.so.6.  2AF777536E69  opal_memory_ptmal Unknown  Unknown
libopen-pal.so.6.  2AF777537C4F  opal_memory_ptmal Unknown  Unknown
libopen-pal.so.6.  2AF7775388A3  opal_memory_ptmal Unknown  Unknown
libmlx4-rdmav2.so  2AF77EE87242  Unknown   Unknown  Unknown
libmlx4-rdmav2.so  2AF77EE8979F  Unknown   Unknown  Unknown
libmlx4-rdmav2.so  2AF77EE89AD6  Unknown   Unknown  Unknown
libibverbs.so.1.0  2AF77CBFFDD2  ibv_create_qp Unknown  Unknown
mca_btl_openib.so  2AF77C7D15C5  Unknown   Unknown  Unknown
mca_btl_openib.so  2AF77C7D4088  Unknown   Unknown  Unknown
mca_btl_openib.so  2AF77C7C6CAD  mca_btl_openib_en Unknown  Unknown
mca_pml_ob1.so 2AF77D42D7F6  mca_pml_ob1_send_

[OMPI users] Using custom version of gfortran in mpifort

2016-11-17 Thread Mahmood Naderan 
Hi,
The mpifort wrapper uses the default gfortran compiler on the system. How
can I give it another version of gfortran which has been installed in
another folder?

Regards,
Mahmood
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