Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Jeff Squyres 
On Dec 14, 2011, at 3:48 PM, Prentice Bisbal wrote:

> I realized this after I wrote that and clarified it in a subsequent e-mail. 
> Which you probably just read. ;-)

After I sent the mail, I saw it.  Oops.  :-)

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

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Prentice Bisbal 

On 12/14/2011 03:39 PM, Jeff Squyres wrote:
> On Dec 14, 2011, at 3:21 PM, Prentice Bisbal wrote:
>
>> For example, your configure command,
>>
>> ./configure --prefix=/opt/openmpi/intel CC=gcc CXX=g++ F77=ifort FC=ifort
>>
>> Doesn't tell Open MPI to use ifcort for mpif90 and mpif77.
> Actually, that's not correct.
>
> For Open MPI, our wrapper compilers will default to using the same compilers 
> that were used to build Open MPI.  So in the above case:
>
> mpicc will use gcc
> mpicxx will use g++
> mpif77 will use ifort
> mpif90 will use ifort
>
>

Jeff,

I realized this after I wrote that and clarified it in a subsequent
e-mail. Which you probably just read. ;-)

Prentice

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Prentice Bisbal 
On 12/14/2011 03:29 PM, Micah Sklut wrote:
> Okay thanks Prentice.
>
> I understand what you are saying about specifying the compilers during
> configure.
> Perhaps, that alone would have solved the problem, but removing the
> 1.4.2 ompi installation worked as well.
>
> Micah
>

Well, to clarify my earlier statement, those compilers used during
installation are used to set the defaults in the wrapper files
(mpif90-wrapper--data.txt, etc.), but those
can easily be changed, either by editing those files, or by defining
environment variables.

Anywhow, we're all glad you were finally able to solve your problem.

--
Prentice

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Micah Sklut 
Okay thanks Prentice.

I understand what you are saying about specifying the compilers during
configure.
Perhaps, that alone would have solved the problem, but removing the 1.4.2
ompi installation worked as well.

Micah

On Wed, Dec 14, 2011 at 3:24 PM, Prentice Bisbal  wrote:

>
> On 12/14/2011 01:20 PM, Fernanda Oliveira wrote:
> > Hi Micah,
> >
> > I do not know if it is exactly what you need but I know that there are
> > environment variables to use with intel mpi. They are: I_MPI_CC,
> > I_MPI_CXX, I_MPI_F77, I_MPI_F90. So, you can set this using 'export'
> > for bash, for instance or directly when you run.
> >
> > I use in my bashrc:
> >
> > export I_MPI_CC=icc
> > export I_MPI_CXX=icpc
> > export I_MPI_F77=ifort
> > export I_MPI_F90=ifort
>
> Those environment variables are for Intel MPI.  For OpenMPI, the
> equivalent variables would be OMPI_CC, OMPI_CXX, OMPI_F77, and OMPI_FC,
> respectively.
>
> --
> Prentice
> ___
> users mailing list
> us...@open-mpi.org
>
>

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Prentice Bisbal 

On 12/14/2011 01:20 PM, Fernanda Oliveira wrote:
> Hi Micah,
>
> I do not know if it is exactly what you need but I know that there are
> environment variables to use with intel mpi. They are: I_MPI_CC,
> I_MPI_CXX, I_MPI_F77, I_MPI_F90. So, you can set this using 'export'
> for bash, for instance or directly when you run.
>
> I use in my bashrc:
>
> export I_MPI_CC=icc
> export I_MPI_CXX=icpc
> export I_MPI_F77=ifort
> export I_MPI_F90=ifort

Those environment variables are for Intel MPI.  For OpenMPI, the
equivalent variables would be OMPI_CC, OMPI_CXX, OMPI_F77, and OMPI_FC,
respectively.

--
Prentice

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Prentice Bisbal 

On 12/14/2011 12:21 PM, Micah Sklut wrote:
> Hi Gustav,
>
> I did read Price's email:
>
> When I do "which mpif90", i get:
> /opt/openmpi/intel/bin/mpif90
> which is the desired directory/binary
>
> As I mentioned, the config log file indicated it was using ifort, and
> had no mention of gfortran.
> Below is the output from ompi_info. It shows reference to the correct
> ifort compiler. But, yet the mpif90 compiler, still yeilds a gfortran
> compiler.

Micah,

You are confusing the compilers users to build Open MPI  itself with the
compilers used by Open MPI to compile other codes with the proper build
environment.

For example, your configure command,

./configure --prefix=/opt/openmpi/intel CC=gcc CXX=g++ F77=ifort FC=ifort

Doesn't tell Open MPI to use ifcort for mpif90 and mpif77. It tell the
build process to use ifort to compile the Fortran sections of the Open
MPI source code. To tell mpif90 and mpif77 which compilers you'd like to
use to compile Fortran programs that use Open MPI, you must set the
environment variables OMPI_F77 and OMPI_F90. To illustrate, when I want
to use the gnu compilers, I set the following in my .bashrc:

export OMPI_CC=gcc
export OMPI_CXX=g++
export OMPI_F77=gfortran
export OMPI_FC=gfortran

If I wanted to use Intel compilers, swap the above 4 lines for this:

export OMPI_CC=pgcc
export OMPI_CXX=pgCC
export OMPI_F77=pgf77
export OMPI_FC=pgf95

You can verify which compiler is set using the --showme switch to mpif90:

$ mpif90 --showme
pgf95 -I/usr/local/openmpi-1.2.8/pgi-8.0/x86_64/include
-I/usr/local/openmpi-1.2.8/pgi-8.0/x86_64/lib -L/usr/lib64
-L/usr/local/openmpi-1.2.8/pgi/x86_64/lib
-L/usr/local/openmpi-1.2.8/pgi-8.0/x86_64/lib -lmpi_f90 -lmpi_f77 -lmpi
-lopen-rte -lopen-pal -libverbs -lrt -lnuma -ldl -Wl,--export-dynamic
-lnsl -lutil -lpthread -ldl

I suspect if you run the command ' env | grep OMPI_FC', you'll see that
you have it set to gfortran. I can verify that mine is set to pgf97 this
way:

$ env | grep OMPI_FC
OMPI_FC=pgf95

Of course, a simple echo would work, too:

$ echo $OMPI_FC
pgf95

You can also change these setting by editing the file
mpif90-wrapper-data.txt in your Open MPI installation directory.

Full details on setting these variables (and others) can be found in the
FAQ:

http://www.open-mpi.org/faq/?category=mpi-apps#override-wrappers-after-v1.0

--
Prentice



> -->
> barells@ip-10-17-153-123:~> ompi_info
>  Package: Open MPI barells@ip-10-17-148-204 Distribution
> Open MPI: 1.4.4
>Open MPI SVN revision: r25188
>Open MPI release date: Sep 27, 2011
> Open RTE: 1.4.4
>Open RTE SVN revision: r25188
>Open RTE release date: Sep 27, 2011
> OPAL: 1.4.4
>OPAL SVN revision: r25188
>OPAL release date: Sep 27, 2011
> Ident string: 1.4.4
>   Prefix: /usr/lib64/mpi/gcc/openmpi
>  Configured architecture: x86_64-unknown-linux-gnu
>   Configure host: ip-10-17-148-204
>Configured by: barells
>Configured on: Wed Dec 14 14:22:43 UTC 2011
>   Configure host: ip-10-17-148-204
> Built by: barells
> Built on: Wed Dec 14 14:27:56 UTC 2011
>   Built host: ip-10-17-148-204
>   C bindings: yes
> C++ bindings: yes
>   Fortran77 bindings: yes (all)
>   Fortran90 bindings: yes
>  Fortran90 bindings size: small
>   C compiler: gcc
>  C compiler absolute: /usr/bin/gcc
> C++ compiler: g++
>C++ compiler absolute: /usr/bin/g++
>   Fortran77 compiler: ifort
>   Fortran77 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
>   Fortran90 compiler: ifort
>   Fortran90 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
>  C profiling: yes
>C++ profiling: yes
>  Fortran77 profiling: yes
>  Fortran90 profiling: yes
>   C++ exceptions: no
>   Thread support: posix (mpi: no, progress: no)
>Sparse Groups: no
>   Internal debug support: no
>  MPI parameter check: runtime
> Memory profiling support: no
> Memory debugging support: no
>  libltdl support: yes
>Heterogeneous support: no
>  mpirun default --prefix: no
>  MPI I/O support: yes
>MPI_WTIME support: gettimeofday
> Symbol visibility support: yes
>FT Checkpoint support: no  (checkpoint thread: no)
>MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.4.2)
>   MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.4.2)
>MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.4.2)
>MCA carto: auto_detect (MCA v2.0, API v2.0, Component
> v1.4.2)
>MCA carto: file (MCA v2.0, API v2.0, Component v1.4.2)
>MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.4.2)
>MCA timer: linux (MCA v2.0, API v2.0, Component v1.4.2)
>  MCA installdirs: env (MCA v2.0, API v2.0,

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Micah Sklut 
I uninstalled 1.4.2 with rpm -e ompi, and now my existing mpi binaries are
working.

Thanks so much for everyone's help.

On Wed, Dec 14, 2011 at 3:12 PM, Tim Prince  wrote:

> On 12/14/2011 12:52 PM, Micah Sklut wrote:
>
>> Hi Gustavo,
>>
>> Here is the output of :
>> barells@ip-10-17-153-123:~> /opt/openmpi/intel/bin/mpif90 -showme
>> gfortran -I/usr/lib64/mpi/gcc/openmpi/**include -pthread
>> -I/usr/lib64/mpi/gcc/openmpi/**lib64 -L/usr/lib64/mpi/gcc/openmpi/**lib64
>> -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl
>> -Wl,--export-dynamic -lnsl -lutil -lm -ldl
>>
>> This points to gfortran.
>>
>> I do see what you are saying about the 1.4.2 and 1.4.4 components.
>> I'm not sure why that is, but there seems to be some conflict with the
>> existing openmpi, before recently installed 1.4.4 and trying to install
>> with ifort.
>>
>>  This is one of the reasons for recommending complete removal (rpm -e if
> need be) of any MPI which is on a default path (and setting a clean path)
> before building a new one, as well as choosing a unique install path for
> the new one.
>
> --
> Tim Prince
>
> __**_
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/**mailman/listinfo.cgi/users
>



-- 
Micah Sklut

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Tim Prince 

On 12/14/2011 12:52 PM, Micah Sklut wrote:

Hi Gustavo,

Here is the output of :
barells@ip-10-17-153-123:~> /opt/openmpi/intel/bin/mpif90 -showme
gfortran -I/usr/lib64/mpi/gcc/openmpi/include -pthread
-I/usr/lib64/mpi/gcc/openmpi/lib64 -L/usr/lib64/mpi/gcc/openmpi/lib64
-lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl
-Wl,--export-dynamic -lnsl -lutil -lm -ldl

This points to gfortran.

I do see what you are saying about the 1.4.2 and 1.4.4 components.
I'm not sure why that is, but there seems to be some conflict with the
existing openmpi, before recently installed 1.4.4 and trying to install
with ifort.

This is one of the reasons for recommending complete removal (rpm -e if 
need be) of any MPI which is on a default path (and setting a clean 
path) before building a new one, as well as choosing a unique install 
path for the new one.


--
Tim Prince

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Tim Prince 

On 12/14/2011 1:20 PM, Fernanda Oliveira wrote:

Hi Micah,

I do not know if it is exactly what you need but I know that there are
environment variables to use with intel mpi. They are: I_MPI_CC,
I_MPI_CXX, I_MPI_F77, I_MPI_F90. So, you can set this using 'export'
for bash, for instance or directly when you run.

I use in my bashrc:

export I_MPI_CC=icc
export I_MPI_CXX=icpc
export I_MPI_F77=ifort
export I_MPI_F90=ifort


Let me know if it helps.
Fernanda Oliveira




I didn't see any indication that Intel MPI was in play here.  Of course, 
that's one of the first thoughts, as under Intel MPI,

mpif90 uses gfortran
mpiifort uses ifort
mpicc uses gcc
mpiCC uses g++
mpiicc uses icc
mpiicpc uses icpc
and all the Intel compilers use g++ to find headers and libraries.
The advice to try 'which mpif90' would show whether you fell into this 
bunker.
If you use Intel cluster checker, you will see noncompliance if anyone's 
MPI is on the default paths.  You must set paths explicitly according to 
the MPI you want.  Admittedly, that tool didn't gain a high level of 
adoption.


--
Tim Prince

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Jeff Squyres 
On Dec 14, 2011, at 12:52 PM, Micah Sklut wrote:

> I do see what you are saying about the 1.4.2 and 1.4.4 components. 
> I'm not sure why that is, but there seems to be some conflict with the 
> existing openmpi, before recently installed 1.4.4 and trying to install with 
> ifort. 

Did you install 1.4.4 with ifort over a prior 1.4.2 installation that used 
gfortran?

Can you send the output from "make install"?  (please compress)

That should show exactly where the wrapper data file (that specifies things 
like gfortran vs. ifort) was installed.

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

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Fernanda Oliveira 
Hi Micah,

I do not know if it is exactly what you need but I know that there are
environment variables to use with intel mpi. They are: I_MPI_CC,
I_MPI_CXX, I_MPI_F77, I_MPI_F90. So, you can set this using 'export'
for bash, for instance or directly when you run.

I use in my bashrc:

export I_MPI_CC=icc
export I_MPI_CXX=icpc
export I_MPI_F77=ifort
export I_MPI_F90=ifort


Let me know if it helps.
Fernanda Oliveira


2011/12/14 Micah Sklut :
> Hi Gustavo,
>
> Here is the output of :
> barells@ip-10-17-153-123:~> /opt/openmpi/intel/bin/mpif90 -showme
> gfortran -I/usr/lib64/mpi/gcc/openmpi/include -pthread
> -I/usr/lib64/mpi/gcc/openmpi/lib64 -L/usr/lib64/mpi/gcc/openmpi/lib64
> -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic
> -lnsl -lutil -lm -ldl
>
> This points to gfortran.
>
> I do see what you are saying about the 1.4.2 and 1.4.4 components.
> I'm not sure why that is, but there seems to be some conflict with the
> existing openmpi, before recently installed 1.4.4 and trying to install with
> ifort.
>
>
> On Wed, Dec 14, 2011 at 12:43 PM, Gustavo Correa 
> wrote:
>>
>> How about the output of this?
>>
>> /opt/openmpi/intel/bin/mpif90 -showme
>>
>> Anyway, something seems to be wrong with your OpenMPI installation.
>> Just read the output of your ompi_info in your email below.
>> You will see that the OpenMPI version is 1.4.4.
>> However, most components are version 1.4.2.
>> Do you agree?
>>
>> I would download the OpenMPI 1.4.4 tarball again and start fresh.
>> Untar the tarball in a brand new directory, don't overwrite old stuff.
>> Also, every time your OpenMPI build fails, or if you want to change
>> compilers
>> [say from gfortran to ifort],
>> do a 'make distclean' to cleanup any leftovers of previous builds,
>> and change the destination directory in --prefix= , to install in a
>> different location.
>>
>> I hope this helps,
>> Gus Correa
>>
>> On Dec 14, 2011, at 12:21 PM, Micah Sklut wrote:
>>
>> > Hi Gustav,
>> >
>> > I did read Price's email:
>> >
>> > When I do "which mpif90", i get:
>> > /opt/openmpi/intel/bin/mpif90
>> > which is the desired directory/binary
>> >
>> > As I mentioned, the config log file indicated it was using ifort, and
>> > had no mention of gfortran.
>> > Below is the output from ompi_info. It shows reference to the correct
>> > ifort compiler. But, yet the mpif90 compiler, still yeilds a gfortran
>> > compiler.
>> > -->
>> > barells@ip-10-17-153-123:~> ompi_info
>> >                  Package: Open MPI barells@ip-10-17-148-204 Distribution
>> >                 Open MPI: 1.4.4
>> >    Open MPI SVN revision: r25188
>> >    Open MPI release date: Sep 27, 2011
>> >                 Open RTE: 1.4.4
>> >    Open RTE SVN revision: r25188
>> >    Open RTE release date: Sep 27, 2011
>> >                     OPAL: 1.4.4
>> >        OPAL SVN revision: r25188
>> >        OPAL release date: Sep 27, 2011
>> >             Ident string: 1.4.4
>> >                   Prefix: /usr/lib64/mpi/gcc/openmpi
>> >  Configured architecture: x86_64-unknown-linux-gnu
>> >           Configure host: ip-10-17-148-204
>> >            Configured by: barells
>> >            Configured on: Wed Dec 14 14:22:43 UTC 2011
>> >           Configure host: ip-10-17-148-204
>> >                 Built by: barells
>> >                 Built on: Wed Dec 14 14:27:56 UTC 2011
>> >               Built host: ip-10-17-148-204
>> >               C bindings: yes
>> >             C++ bindings: yes
>> >       Fortran77 bindings: yes (all)
>> >       Fortran90 bindings: yes
>> >  Fortran90 bindings size: small
>> >               C compiler: gcc
>> >      C compiler absolute: /usr/bin/gcc
>> >             C++ compiler: g++
>> >    C++ compiler absolute: /usr/bin/g++
>> >       Fortran77 compiler: ifort
>> >   Fortran77 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
>> >       Fortran90 compiler: ifort
>> >   Fortran90 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
>> >              C profiling: yes
>> >            C++ profiling: yes
>> >      Fortran77 profiling: yes
>> >      Fortran90 profiling: yes
>> >           C++ exceptions: no
>> >           Thread support: posix (mpi: no, progress: no)
>> >            Sparse Groups: no
>> >   Internal debug support: no
>> >      MPI parameter check: runtime
>> > Memory profiling support: no
>> > Memory debugging support: no
>> >          libltdl support: yes
>> >    Heterogeneous support: no
>> >  mpirun default --prefix: no
>> >          MPI I/O support: yes
>> >        MPI_WTIME support: gettimeofday
>> > Symbol visibility support: yes
>> >    FT Checkpoint support: no  (checkpoint thread: no)
>> >            MCA backtrace: execinfo (MCA v2.0, API v2.0, Component
>> > v1.4.2)
>> >               MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component
>> > v1.4.2)
>> >            MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.4.2)
>> >                MCA carto: auto_detect (MCA v2.0, API v2.0, Component
>> >

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Micah Sklut 
Hi Gustavo,

Here is the output of :
barells@ip-10-17-153-123:~> /opt/openmpi/intel/bin/mpif90 -showme
gfortran -I/usr/lib64/mpi/gcc/openmpi/include -pthread
-I/usr/lib64/mpi/gcc/openmpi/lib64 -L/usr/lib64/mpi/gcc/openmpi/lib64
-lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic
-lnsl -lutil -lm -ldl

This points to gfortran.

I do see what you are saying about the 1.4.2 and 1.4.4 components.
I'm not sure why that is, but there seems to be some conflict with the
existing openmpi, before recently installed 1.4.4 and trying to install
with ifort.


On Wed, Dec 14, 2011 at 12:43 PM, Gustavo Correa wrote:

> How about the output of this?
>
> /opt/openmpi/intel/bin/mpif90 -showme
>
> Anyway, something seems to be wrong with your OpenMPI installation.
> Just read the output of your ompi_info in your email below.
> You will see that the OpenMPI version is 1.4.4.
> However, most components are version 1.4.2.
> Do you agree?
>
> I would download the OpenMPI 1.4.4 tarball again and start fresh.
> Untar the tarball in a brand new directory, don't overwrite old stuff.
> Also, every time your OpenMPI build fails, or if you want to change
> compilers
> [say from gfortran to ifort],
> do a 'make distclean' to cleanup any leftovers of previous builds,
> and change the destination directory in --prefix= , to install in a
> different location.
>
> I hope this helps,
> Gus Correa
>
> On Dec 14, 2011, at 12:21 PM, Micah Sklut wrote:
>
> > Hi Gustav,
> >
> > I did read Price's email:
> >
> > When I do "which mpif90", i get:
> > /opt/openmpi/intel/bin/mpif90
> > which is the desired directory/binary
> >
> > As I mentioned, the config log file indicated it was using ifort, and
> had no mention of gfortran.
> > Below is the output from ompi_info. It shows reference to the correct
> ifort compiler. But, yet the mpif90 compiler, still yeilds a gfortran
> compiler.
> > -->
> > barells@ip-10-17-153-123:~> ompi_info
> >  Package: Open MPI barells@ip-10-17-148-204 Distribution
> > Open MPI: 1.4.4
> >Open MPI SVN revision: r25188
> >Open MPI release date: Sep 27, 2011
> > Open RTE: 1.4.4
> >Open RTE SVN revision: r25188
> >Open RTE release date: Sep 27, 2011
> > OPAL: 1.4.4
> >OPAL SVN revision: r25188
> >OPAL release date: Sep 27, 2011
> > Ident string: 1.4.4
> >   Prefix: /usr/lib64/mpi/gcc/openmpi
> >  Configured architecture: x86_64-unknown-linux-gnu
> >   Configure host: ip-10-17-148-204
> >Configured by: barells
> >Configured on: Wed Dec 14 14:22:43 UTC 2011
> >   Configure host: ip-10-17-148-204
> > Built by: barells
> > Built on: Wed Dec 14 14:27:56 UTC 2011
> >   Built host: ip-10-17-148-204
> >   C bindings: yes
> > C++ bindings: yes
> >   Fortran77 bindings: yes (all)
> >   Fortran90 bindings: yes
> >  Fortran90 bindings size: small
> >   C compiler: gcc
> >  C compiler absolute: /usr/bin/gcc
> > C++ compiler: g++
> >C++ compiler absolute: /usr/bin/g++
> >   Fortran77 compiler: ifort
> >   Fortran77 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
> >   Fortran90 compiler: ifort
> >   Fortran90 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
> >  C profiling: yes
> >C++ profiling: yes
> >  Fortran77 profiling: yes
> >  Fortran90 profiling: yes
> >   C++ exceptions: no
> >   Thread support: posix (mpi: no, progress: no)
> >Sparse Groups: no
> >   Internal debug support: no
> >  MPI parameter check: runtime
> > Memory profiling support: no
> > Memory debugging support: no
> >  libltdl support: yes
> >Heterogeneous support: no
> >  mpirun default --prefix: no
> >  MPI I/O support: yes
> >MPI_WTIME support: gettimeofday
> > Symbol visibility support: yes
> >FT Checkpoint support: no  (checkpoint thread: no)
> >MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.4.2)
> >   MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component
> v1.4.2)
> >MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.4.2)
> >MCA carto: auto_detect (MCA v2.0, API v2.0, Component
> v1.4.2)
> >MCA carto: file (MCA v2.0, API v2.0, Component v1.4.2)
> >MCA maffinity: first_use (MCA v2.0, API v2.0, Component
> v1.4.2)
> >MCA timer: linux (MCA v2.0, API v2.0, Component v1.4.2)
> >  MCA installdirs: env (MCA v2.0, API v2.0, Component v1.4.2)
> >  MCA installdirs: config (MCA v2.0, API v2.0, Component v1.4.2)
> >  MCA dpm: orte (MCA v2.0, API v2.0, Component v1.4.2)
> >   MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.4.2)
> >MCA allocator: basic (MCA v2.0, API v2.0, Component v1.4.2)
> >

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Gustavo Correa 
How about the output of this?

/opt/openmpi/intel/bin/mpif90 -showme

Anyway, something seems to be wrong with your OpenMPI installation.
Just read the output of your ompi_info in your email below.
You will see that the OpenMPI version is 1.4.4.
However, most components are version 1.4.2.
Do you agree?

I would download the OpenMPI 1.4.4 tarball again and start fresh.
Untar the tarball in a brand new directory, don't overwrite old stuff.
Also, every time your OpenMPI build fails, or if you want to change compilers 
[say from gfortran to ifort],
do a 'make distclean' to cleanup any leftovers of previous builds,
and change the destination directory in --prefix= , to install in a different 
location.

I hope this helps,
Gus Correa

On Dec 14, 2011, at 12:21 PM, Micah Sklut wrote:

> Hi Gustav, 
> 
> I did read Price's email: 
> 
> When I do "which mpif90", i get: 
> /opt/openmpi/intel/bin/mpif90
> which is the desired directory/binary
> 
> As I mentioned, the config log file indicated it was using ifort, and had no 
> mention of gfortran. 
> Below is the output from ompi_info. It shows reference to the correct ifort 
> compiler. But, yet the mpif90 compiler, still yeilds a gfortran compiler.
> -->
> barells@ip-10-17-153-123:~> ompi_info
>  Package: Open MPI barells@ip-10-17-148-204 Distribution
> Open MPI: 1.4.4
>Open MPI SVN revision: r25188
>Open MPI release date: Sep 27, 2011
> Open RTE: 1.4.4
>Open RTE SVN revision: r25188
>Open RTE release date: Sep 27, 2011
> OPAL: 1.4.4
>OPAL SVN revision: r25188
>OPAL release date: Sep 27, 2011
> Ident string: 1.4.4
>   Prefix: /usr/lib64/mpi/gcc/openmpi
>  Configured architecture: x86_64-unknown-linux-gnu
>   Configure host: ip-10-17-148-204
>Configured by: barells
>Configured on: Wed Dec 14 14:22:43 UTC 2011
>   Configure host: ip-10-17-148-204
> Built by: barells
> Built on: Wed Dec 14 14:27:56 UTC 2011
>   Built host: ip-10-17-148-204
>   C bindings: yes
> C++ bindings: yes
>   Fortran77 bindings: yes (all)
>   Fortran90 bindings: yes
>  Fortran90 bindings size: small
>   C compiler: gcc
>  C compiler absolute: /usr/bin/gcc
> C++ compiler: g++
>C++ compiler absolute: /usr/bin/g++
>   Fortran77 compiler: ifort
>   Fortran77 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
>   Fortran90 compiler: ifort
>   Fortran90 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
>  C profiling: yes
>C++ profiling: yes
>  Fortran77 profiling: yes
>  Fortran90 profiling: yes
>   C++ exceptions: no
>   Thread support: posix (mpi: no, progress: no)
>Sparse Groups: no
>   Internal debug support: no
>  MPI parameter check: runtime
> Memory profiling support: no
> Memory debugging support: no
>  libltdl support: yes
>Heterogeneous support: no
>  mpirun default --prefix: no
>  MPI I/O support: yes
>MPI_WTIME support: gettimeofday
> Symbol visibility support: yes
>FT Checkpoint support: no  (checkpoint thread: no)
>MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.4.2)
>   MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.4.2)
>MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.4.2)
>MCA carto: auto_detect (MCA v2.0, API v2.0, Component v1.4.2)
>MCA carto: file (MCA v2.0, API v2.0, Component v1.4.2)
>MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.4.2)
>MCA timer: linux (MCA v2.0, API v2.0, Component v1.4.2)
>  MCA installdirs: env (MCA v2.0, API v2.0, Component v1.4.2)
>  MCA installdirs: config (MCA v2.0, API v2.0, Component v1.4.2)
>  MCA dpm: orte (MCA v2.0, API v2.0, Component v1.4.2)
>   MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.4.2)
>MCA allocator: basic (MCA v2.0, API v2.0, Component v1.4.2)
>MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: basic (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: inter (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: self (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: sm (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: sync (MCA v2.0, API v2.0, Component v1.4.2)
> MCA coll: tuned (MCA v2.0, API v2.0, Component v1.4.2)
>   MCA io: romio (MCA v2.0, API v2.0, Component v1.4.2)
>MCA mpool: fake (MCA v2.0, API v2.0, Component v1.4.2)
>MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.4.2)
>MCA mpool: sm (MCA v2.0, API

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Micah Sklut 
Hi Gustav,

I did read Price's email:

When I do "which mpif90", i get:
/opt/openmpi/intel/bin/mpif90
which is the desired directory/binary

As I mentioned, the config log file indicated it was using ifort, and had
no mention of gfortran.
Below is the output from ompi_info. It shows reference to the correct ifort
compiler. But, yet the mpif90 compiler, still yeilds a gfortran compiler.
-->
barells@ip-10-17-153-123:~> ompi_info
 Package: Open MPI barells@ip-10-17-148-204 Distribution
Open MPI: 1.4.4
   Open MPI SVN revision: r25188
   Open MPI release date: Sep 27, 2011
Open RTE: 1.4.4
   Open RTE SVN revision: r25188
   Open RTE release date: Sep 27, 2011
OPAL: 1.4.4
   OPAL SVN revision: r25188
   OPAL release date: Sep 27, 2011
Ident string: 1.4.4
  Prefix: /usr/lib64/mpi/gcc/openmpi
 Configured architecture: x86_64-unknown-linux-gnu
  Configure host: ip-10-17-148-204
   Configured by: barells
   Configured on: Wed Dec 14 14:22:43 UTC 2011
  Configure host: ip-10-17-148-204
Built by: barells
Built on: Wed Dec 14 14:27:56 UTC 2011
  Built host: ip-10-17-148-204
  C bindings: yes
C++ bindings: yes
  Fortran77 bindings: yes (all)
  Fortran90 bindings: yes
 Fortran90 bindings size: small
  C compiler: gcc
 C compiler absolute: /usr/bin/gcc
C++ compiler: g++
   C++ compiler absolute: /usr/bin/g++
  Fortran77 compiler: ifort
  Fortran77 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
  Fortran90 compiler: ifort
  Fortran90 compiler abs: /opt/intel/fce/9.1.040/bin/ifort
 C profiling: yes
   C++ profiling: yes
 Fortran77 profiling: yes
 Fortran90 profiling: yes
  C++ exceptions: no
  Thread support: posix (mpi: no, progress: no)
   Sparse Groups: no
  Internal debug support: no
 MPI parameter check: runtime
Memory profiling support: no
Memory debugging support: no
 libltdl support: yes
   Heterogeneous support: no
 mpirun default --prefix: no
 MPI I/O support: yes
   MPI_WTIME support: gettimeofday
Symbol visibility support: yes
   FT Checkpoint support: no  (checkpoint thread: no)
   MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.4.2)
  MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.4.2)
   MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.4.2)
   MCA carto: auto_detect (MCA v2.0, API v2.0, Component v1.4.2)
   MCA carto: file (MCA v2.0, API v2.0, Component v1.4.2)
   MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.4.2)
   MCA timer: linux (MCA v2.0, API v2.0, Component v1.4.2)
 MCA installdirs: env (MCA v2.0, API v2.0, Component v1.4.2)
 MCA installdirs: config (MCA v2.0, API v2.0, Component v1.4.2)
 MCA dpm: orte (MCA v2.0, API v2.0, Component v1.4.2)
  MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.4.2)
   MCA allocator: basic (MCA v2.0, API v2.0, Component v1.4.2)
   MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.4.2)
MCA coll: basic (MCA v2.0, API v2.0, Component v1.4.2)
MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.4.2)
MCA coll: inter (MCA v2.0, API v2.0, Component v1.4.2)
MCA coll: self (MCA v2.0, API v2.0, Component v1.4.2)
MCA coll: sm (MCA v2.0, API v2.0, Component v1.4.2)
MCA coll: sync (MCA v2.0, API v2.0, Component v1.4.2)
MCA coll: tuned (MCA v2.0, API v2.0, Component v1.4.2)
  MCA io: romio (MCA v2.0, API v2.0, Component v1.4.2)
   MCA mpool: fake (MCA v2.0, API v2.0, Component v1.4.2)
   MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.4.2)
   MCA mpool: sm (MCA v2.0, API v2.0, Component v1.4.2)
 MCA pml: cm (MCA v2.0, API v2.0, Component v1.4.2)
 MCA pml: csum (MCA v2.0, API v2.0, Component v1.4.2)
 MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.4.2)
 MCA pml: v (MCA v2.0, API v2.0, Component v1.4.2)
 MCA bml: r2 (MCA v2.0, API v2.0, Component v1.4.2)
  MCA rcache: vma (MCA v2.0, API v2.0, Component v1.4.2)
 MCA btl: ofud (MCA v2.0, API v2.0, Component v1.4.2)
 MCA btl: openib (MCA v2.0, API v2.0, Component v1.4.2)
 MCA btl: self (MCA v2.0, API v2.0, Component v1.4.2)
 MCA btl: sm (MCA v2.0, API v2.0, Component v1.4.2)
 MCA btl: tcp (MCA v2.0, API v2.0, Component v1.4.2)
 MCA btl: udapl (MCA v2.0, API v2.0, Component v1.4.2)
MCA topo: unity (MCA v2.0, API v2.0, Component v1.4.2)
 MCA osc: pt2pt (MCA v2.0, API

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Gustavo Correa 
Hi Micah

Did you read Tim Prince's email to you?  Check it out.

Best thing is to set your environment variables [PATH, LD_LIBRARY_PATH, intel 
setup] 
in your initialization file, .profile/.bashrc or .[t]cshrc.

What is the output of 'ompi_info'? [From your ifort-built OpenMPI.]
Does it show ifort or gfortran?

I hope this helps,
Gus Correa

On Dec 14, 2011, at 11:21 AM, Micah Sklut wrote:

> Thanks for your thoughts, 
> 
> It would certainly appear that it is a PATH issue, but I still haven't 
> figured it out. 
> 
> When I type the ifort command, ifort does run. 
> The intel path is in my PATH and is the first directory listed. 
> 
> Looking at the configure.log, there is nothing indicating use or mentioning 
> of "gfortran".  
> 
> gfortran is in the /usr/bin directory, which is in the PATH as well. 
> 
> Any other suggestions of things to look for? 
> 
> Thank you, 
> 
> On Wed, Dec 14, 2011 at 11:05 AM, Gustavo Correa  
> wrote:
> Hi Micah
> 
> Is  ifort in your PATH?
> If not, the OpenMPI configure script will use any fortran compiler it finds 
> first, which may be gfortran.
> You need to run the Intel compiler startup script before you run the OpenMPI 
> configure.
> The easy thing to do is to source the Intel script inside your 
> .profile/.bashrc or .[t]cshrc file.
> I hope this helps,
> 
> Gus Correa
> 
> On Dec 14, 2011, at 9:49 AM, Micah Sklut wrote:
> 
> > Hi All,
> >
> > I have installed openmpi for gfortran, but am now attempting to install 
> > openmpi as ifort.
> >
> > I have run the following configuration:
> > ./configure --prefix=/opt/openmpi/intel CC=gcc CXX=g++ F77=ifort FC=ifort
> >
> > The install works successfully, but when I run 
> > /opt/openmpi/intel/bin/mpif90, it runs as gfortran.
> > Oddly, when I am user: root, the same mpif90 runs as ifort.
> >
> > Can someone please alleviate my confusion as to why I mpif90 is not running 
> > as ifort?
> >
> > Thank you for your suggestions,
> >
> > --
> > Micah
> >
> >
> > ___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> 
> 
> -- 
> Micah Sklut
> 
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Gustavo Correa 
Hi Micah

Is  ifort in your PATH?
If not, the OpenMPI configure script will use any fortran compiler it finds 
first, which may be gfortran.
You need to run the Intel compiler startup script before you run the OpenMPI 
configure.
The easy thing to do is to source the Intel script inside your .profile/.bashrc 
or .[t]cshrc file.
I hope this helps,

Gus Correa

On Dec 14, 2011, at 9:49 AM, Micah Sklut wrote:

> Hi All, 
> 
> I have installed openmpi for gfortran, but am now attempting to install 
> openmpi as ifort. 
> 
> I have run the following configuration: 
> ./configure --prefix=/opt/openmpi/intel CC=gcc CXX=g++ F77=ifort FC=ifort
> 
> The install works successfully, but when I run /opt/openmpi/intel/bin/mpif90, 
> it runs as gfortran. 
> Oddly, when I am user: root, the same mpif90 runs as ifort. 
> 
> Can someone please alleviate my confusion as to why I mpif90 is not running 
> as ifort? 
> 
> Thank you for your suggestions, 
> 
> -- 
> Micah
> 
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] openmpi - gfortran and ifort conflict

2011-12-14 Thread Tim Prince 

On 12/14/2011 9:49 AM, Micah Sklut wrote:


I have installed openmpi for gfortran, but am now attempting to install
openmpi as ifort.

I have run the following configuration:
./configure --prefix=/opt/openmpi/intel CC=gcc CXX=g++ F77=ifort FC=ifort

The install works successfully, but when I run
/opt/openmpi/intel/bin/mpif90, it runs as gfortran.
Oddly, when I am user: root, the same mpif90 runs as ifort.

Can someone please alleviate my confusion as to why I mpif90 is not
running as ifort?



You might check your configure logs to be certain that ifort was found 
before gfortran at all stages (did you set paths according to sourcing 
the ifortvars or compilervars scripts which come with ifort?).
'which mpif90' should tell you whether you are executing the one from 
your installation.  You may have another mpif90 coming first on your 
PATH.  You won't be able to override your PATH and LD_LIBRARY_PATH 
correctly simply by specifying absolute path to mpif90.



--
Tim Prince