mpi_Init

[Patrick Dupre]

Hello,

I installed mpich
and set the path to 
/usr/lib64/mpich/bin
however, it seems that I need
MPI_init

Checking if MPI is available
checking for mpif90... mpif90
checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
configure: error: MPI not found: openmpi

Do you know how I could get this MPI_init ?

Thanks

===========================================================================
 Patrick DUPRÉ                                 | | email: [e-mail]
 Laboratoire interdisciplinaire Carnot de Bourgogne
 9 Avenue Alain Savary, BP 47870, 21078 DIJON Cedex FRANCE
 Tel: [phone]                    | | Room# D114A
===========================================================================

[Samuel Sieb]

On 2021-09-19 11:33 a.m., Patrick Dupre wrote:
> Hello,
>
> I installed mpich
> and set the path to
> /usr/lib64/mpich/bin
> however, it seems that I need
> MPI_init
>
> Checking if MPI is available
> checking for mpif90... mpif90
> checking for MPI_Init... no
> checking for MPI_Init in -lmpi... no
> checking for MPI_Init in -lmpich... no
> configure: error: MPI not found: openmpi
>
> Do you know how I could get this MPI_init ?

Did you install "mpich-devel"?

[Patrick Dupre]

Actually MPI_Init is in
openmpi-devel
but I add to make the path
PATH=/usr/lib64/openmpi/bin:$PATH
for mpicc
which is bizare.

Furthermore, I tried man mpicc

/usr/share/man/mpich-x86_64/man1/mpicc.1.gz
/usr/share/man/openmpi-x86_64/man1/mpicc.1.gz

But it does not work

===========================================================================
 Patrick DUPRÉ                                 | | email: [e-mail]
 Laboratoire interdisciplinaire Carnot de Bourgogne
 9 Avenue Alain Savary, BP 47870, 21078 DIJON Cedex FRANCE
 Tel: [phone]                    | | Room# D114A
===========================================================================
> Sent: Sunday, September 19, 2021 at 10:28 PM
> From: "Samuel Sieb" 
> To: [e-mail]
> Subject: Re: mpi_Init
>
> On 2021-09-19 11:33 a.m., Patrick Dupre wrote:
> > Hello,
> >
> > I installed mpich
> > and set the path to
> > /usr/lib64/mpich/bin
> > however, it seems that I need
> > MPI_init
> >
> > Checking if MPI is available
> > checking for mpif90... mpif90
> > checking for MPI_Init... no
> > checking for MPI_Init in -lmpi... no
> > checking for MPI_Init in -lmpich... no
> > configure: error: MPI not found: openmpi
> >
> > Do you know how I could get this MPI_init ?
>
> Did you install "mpich-devel"?
> _______________________________________________
> users mailing list -- [e-mail]
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[Jonathan Billings]

On Sun, Sep 19, 2021 at 10:42:43PM +0200, Patrick Dupre wrote:
> Actually MPI_Init is in
> openmpi-devel
> but I add to make the path
> PATH=/usr/lib64/openmpi/bin:$PATH
> for mpicc
> which is bizare.
>
> Furthermore, I tried man mpicc
>
> /usr/share/man/mpich-x86_64/man1/mpicc.1.gz
> /usr/share/man/openmpi-x86_64/man1/mpicc.1.gz
>
> But it does not work

You don't wnat to use the OpenMPI headers to compile something with
mpich.  As has been said, install the mpich-devel package, which has
its own headers in /usr/include/mpich-x86_64/ that defined MPI_Init,
and don't forget to load the environment module first!

[Jonathan Billings]

On Sun, Sep 19, 2021 at 08:33:21PM +0200, Patrick Dupre wrote:
> Hello,
>
> I installed mpich
> and set the path to 
> /usr/lib64/mpich/bin
> however, it seems that I need
> MPI_init
>
> Checking if MPI is available
> checking for mpif90... mpif90
> checking for MPI_Init... no
> checking for MPI_Init in -lmpi... no
> checking for MPI_Init in -lmpich... no
> configure: error: MPI not found: openmpi

Rather than setting the PATH, you should have run:

module load mpi/mpich-x86_64

... before compiling.  That loads the mpich environment module, which
defines a bunch of environment modules.  Environment Modules are very
popular on HPC systems, lets you have multiple versions and varieties
of packages without them stepping on each other.  You load the
appropriate module before compiling or running software and it gets
the specific libraries/executables/includes/etc.

For example, here is the module file for mpich:

$ cat /usr/share/modulefiles/mpi/mpich-x86_64
#%Module 1.0
#
#  MPICH module for use with 'environment-modules' package:
#

# Only allow one mpi module to be loaded at a time
conflict mpi

# Define prefix so PATH and MANPATH can be updated.
setenv        MPI_BIN       /usr/lib64/mpich/bin
setenv        MPI_SYSCONFIG /etc/mpich-x86_64
setenv        MPI_FORTRAN_MOD_DIR /usr/lib64/gfortran/modules/mpich
setenv        MPI_INCLUDE   /usr/include/mpich-x86_64
setenv        MPI_LIB       /usr/lib64/mpich/lib
setenv        MPI_MAN       /usr/share/man/mpich-x86_64
setenv        MPI_PYTHON_SITEARCH	%{python2_sitearch}/mpich
setenv        MPI_PYTHON2_SITEARCH	%{python2_sitearch}/mpich
setenv        MPI_PYTHON3_SITEARCH	/usr/lib64/python3.9/site-packages/mpich
setenv        MPI_COMPILER  mpich-x86_64
setenv        MPI_SUFFIX    _mpich
setenv        MPI_HOME      /usr/lib64/mpich
prepend-path  PATH          /usr/lib64/mpich/bin
prepend-path  LD_LIBRARY_PATH /usr/lib64/mpich/lib
prepend-path  MANPATH       :/usr/share/man/mpich-x86_64
prepend-path  PKG_CONFIG_PATH /usr/lib64/mpich/lib/pkgconfig

[Jonathan Billings]

On Sun, Sep 19, 2021 at 04:35:14PM -0400, Jonathan Billings wrote:
> ... before compiling.  That loads the mpich environment module, which
> defines a bunch of environment modules.

Er... I mean it defines a bunch of environment *variables*.
> setenv        MPI_PYTHON_SITEARCH	%{python2_sitearch}/mpich
> setenv        MPI_PYTHON2_SITEARCH	%{python2_sitearch}/mpich
> setenv        MPI_PYTHON3_SITEARCH	/usr/lib64/python3.9/site-packages/mpich

Oops.  Looks like the package references Python 2 but those RPM macros
are gone.  I suppose that's a bug.

[Patrick Dupre]

OK

Very good.

But I get

from process 0 out of 1 on Teucidide

with MPI_Comm_size(MPI_COMM_WORLD, &numprocs);

How can I set numprocs to 2 for example?

===========================================================================
 Patrick DUPRÉ                                 | | email: [e-mail]
 Laboratoire interdisciplinaire Carnot de Bourgogne
 9 Avenue Alain Savary, BP 47870, 21078 DIJON Cedex FRANCE
 Tel: [phone]                    | | Room# D114A
===========================================================================
> Sent: Sunday, September 19, 2021 at 10:35 PM
> From: "Jonathan Billings" 
> To: [e-mail]
> Subject: Re: mpi_Init
>
> On Sun, Sep 19, 2021 at 08:33:21PM +0200, Patrick Dupre wrote:
> > Hello,
> >
> > I installed mpich
> > and set the path to 
> > /usr/lib64/mpich/bin
> > however, it seems that I need
> > MPI_init
> >
> > Checking if MPI is available
> > checking for mpif90... mpif90
> > checking for MPI_Init... no
> > checking for MPI_Init in -lmpi... no
> > checking for MPI_Init in -lmpich... no
> > configure: error: MPI not found: openmpi
>
> Rather than setting the PATH, you should have run:
>
> module load mpi/mpich-x86_64
>
> ... before compiling.  That loads the mpich environment module, which
> defines a bunch of environment modules.  Environment Modules are very
> popular on HPC systems, lets you have multiple versions and varieties
> of packages without them stepping on each other.  You load the
> appropriate module before compiling or running software and it gets
> the specific libraries/executables/includes/etc.
>
> For example, here is the module file for mpich:
>
> $ cat /usr/share/modulefiles/mpi/mpich-x86_64
> #%Module 1.0
> #
> #  MPICH module for use with 'environment-modules' package:
> #
>
> # Only allow one mpi module to be loaded at a time
> conflict mpi
>
> # Define prefix so PATH and MANPATH can be updated.
> setenv        MPI_BIN       /usr/lib64/mpich/bin
> setenv        MPI_SYSCONFIG /etc/mpich-x86_64
> setenv        MPI_FORTRAN_MOD_DIR /usr/lib64/gfortran/modules/mpich
> setenv        MPI_INCLUDE   /usr/include/mpich-x86_64
> setenv        MPI_LIB       /usr/lib64/mpich/lib
> setenv        MPI_MAN       /usr/share/man/mpich-x86_64
> setenv        MPI_PYTHON_SITEARCH	%{python2_sitearch}/mpich
> setenv        MPI_PYTHON2_SITEARCH	%{python2_sitearch}/mpich
> setenv        MPI_PYTHON3_SITEARCH	/usr/lib64/python3.9/site-packages/mpich
> setenv        MPI_COMPILER  mpich-x86_64
> setenv        MPI_SUFFIX    _mpich
> setenv        MPI_HOME      /usr/lib64/mpich
> prepend-path  PATH          /usr/lib64/mpich/bin
> prepend-path  LD_LIBRARY_PATH /usr/lib64/mpich/lib
> prepend-path  MANPATH       :/usr/share/man/mpich-x86_64
> prepend-path  PKG_CONFIG_PATH /usr/lib64/mpich/lib/pkgconfig
>
> -- 
> Jonathan Billings 
> _______________________________________________
> users mailing list -- [e-mail]
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[Jonathan Billings]

On Sun, Sep 19, 2021 at 10:53:10PM +0200, Patrick Dupre wrote:
> OK
>
> Very good.
>
> But I get
>
> from process 0 out of 1 on Teucidide
>
> with MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
>
> How can I set numprocs to 2 for example?

That's between you and your compiler.  I think MPI support might be
out of scope for the Fedora mailing list.  :)

[George N. White III]

On Sun, 19 Sept 2021 at 15:33, Patrick Dupre  wrote:
> Hello,
>
> I installed mpich
> and set the path to
> /usr/lib64/mpich/bin
> however, it seems that I need
> MPI_init
>
> Checking if MPI is available
> checking for mpif90... mpif90
> checking for MPI_Init... no
> checking for MPI_Init in -lmpi... no
> checking for MPI_Init in -lmpich... no
> configure: error: MPI not found: openmpi

Try "module load mipch-x86_64".

Fedora uses environment modules to switch between MIP
libraries and tools https://docs.fedoraproject.org/en-US/neurofedora/mpi/:

% ls /usr/share/modulefiles/mpi
mpich-x86_64  openmpi-x86_64

I prefer Lmod (lua modules with tcl support) over the original
tcl environment modules.
> Do you know how I could get this MPI_init ?
>
> Thanks
>
> ===========================================================================
>  Patrick DUPRÉ                                 | | email: [e-mail]
>  Laboratoire interdisciplinaire Carnot de Bourgogne
>  9 Avenue Alain Savary, BP 47870, 21078 DIJON Cedex FRANCE
>  Tel: [phone]                    | | Room# D114A
> ===========================================================================
> _______________________________________________
> users mailing list -- [e-mail]
> To unsubscribe send an email to [e-mail]
> Fedora Code of Conduct:
> https://docs.fedoraproject.org/en-US/project/code-of-conduct/
> List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines
> List Archives:
> https://lists.fedoraproject.org/archives/list/[e-mail]
> Do not reply to spam on the list, report it:
> https://pagure.io/fedora-infrastructure