ABySS install : mpi.h not found

[Florence]

Hi !

I try to install ABySS, with MPI, on a cluster.
However, I have a problem.
I can configure, make, make install without mpi, without problem, but
when I want to specify the mpi directory with the "with-mpi" configure
option, "./configure" runs fine, apparently also the "./make", but it
does not generate the ABYSS-P executable ...
I got the following messages during the "./configure":

checking whether we are cross compiling... no
checking for gcc option to accept ISO C89... none needed
checking whether byte ordering is bigendian... no
checking vfork.h usability... no
checking vfork.h presence... no
checking for vfork.h... no
checking for _doprnt... no
checking google/sparse_hash_map usability... no
checking google/sparse_hash_map presence... no
checking for google/sparse_hash_map... no
checking unordered_map usability... no
checking unordered_map presence... no
checking for unordered_map... no
warning: ABySS should be compiled with Google sparsehash to
reduce memory usage. It may be downloaded here:
http://code.google.com/p/google-sparsehash

So "mpi.h" seems to have been found...
during the "make", nothing special...
and make -C Parallel:

make: entrant dans le répertoire « /.projets_2/grisbi/abyss-1.2.6/
Parallel »
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../
DataLayer -Wall -Wextra -Werror -g -O2 -MT ABYSS_P-parallelAbyss.o -
MD -MP -MF .deps/ABYSS_P-parallelAbyss.Tpo -c -o ABYSS_P-
parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo
'./'`parallelAbyss.cpp
In file included from NetworkSequenceCollection.h:7:0,
from parallelAbyss.cpp:3:
CommLayer.h:5:17: erreur fatale: mpi.h : Aucun fichier ou dossier de
ce type
compilation terminée.
make: *** [ABYSS_P-parallelAbyss.o] Erreur 1
make: quittant le répertoire « /.projets_2/grisbi/abyss-1.2.6/Parallel
»

mpi.h isn't found anymore!
I look in the directory I gave with the --with-mpi otption, and it
contains the include/mpi.h...
Please, can you help me?

Thank you in advance.

Florence

[Alejandro Sanchez]

Hi Florence,

Just from the log message from the configue that you posted, it seems I
can't see openMPI being detected and also, is not using google sparse hash.

I would suggest to search for the proper location of both, openMPI and
google sparse hash. For openMPI do:

which mpirun

That would tell you where is installed and if is in your path. Once you
find the location you can write to your .cshrc or .bashrc or whatever
shell you're using the enviromental variables for MPI. In my case, I use
tcsh and looks something like this:

setenv MPI_HOME /software/openmpi-1.3.3/
prepend_path LD_LIBRARY_PATH $MPI_HOME/lib
prepend_path PATH $MPI_HOME/bin
prepend_path MANPATH $MPI_HOME/share/man

Then, I usually run the configure like this (in one line):

./configure --prefix=/path_to/abyss_bin_1.2.7
--with-mpi=/path_to/openmpi-1.3.3/
CPPFLAGS=-I/path_to/sparsehash/include --enable-maxk=96
CC=/path_to/gcc-4.5.1/bin/gcc CXX=/path_to/gcc-4.5.1/bin/g++

As you can see, I also define other location for the compilers since the
GCC libraries and compilers installed in our cluster are a bit old...

Hope this will help you.

Cheers.

> make: entrant dans le r�pertoire � /.projets_2/grisbi/abyss-1.2.6/

> Parallel �
> g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../
> DataLayer -Wall -Wextra -Werror -g -O2 -MT ABYSS_P-parallelAbyss.o -
> MD -MP -MF .deps/ABYSS_P-parallelAbyss.Tpo -c -o ABYSS_P-
> parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo
> './'`parallelAbyss.cpp
> In file included from NetworkSequenceCollection.h:7:0,
> from parallelAbyss.cpp:3:
> CommLayer.h:5:17: erreur fatale: mpi.h : Aucun fichier ou dossier de
> ce type

> compilation termin�e.

> make: *** [ABYSS_P-parallelAbyss.o] Erreur 1

> make: quittant le r�pertoire � /.projets_2/grisbi/abyss-1.2.6/Parallel

> �
>
> mpi.h isn't found anymore!
> I look in the directory I gave with the --with-mpi otption, and it
> contains the include/mpi.h...
> Please, can you help me?
>
> Thank you in advance.
>
> Florence

--
Alejandro Sanchez-Flores
Team133 Parasite Genomics
Wellcome Trust Sanger Institute
Cambridge, UK.

--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

[Steve]

I found these instructions by another poster very good for getting up
and running with abyss and openmpi. Also for upgrading the gcc
compiler to avoid problems with openmp.

http://groups.google.com/group/abyss-users/browse_thread/thread/d1e0e60a600c2734/ea9b9c6055a0dbcc?lnk=gst&q=attached+guide+install+with+openmpi+and+gcc#ea9b9c6055a0dbcc

[Florence]

Thank you! I'll try this!

[Fabrice T]

I add the same problem: openmpi installed but not detected and no ABYSS-P created...
I was on ubuntu 10.04.

I installed

libopenmpi-dev

and tried to compile again. It works now. I have ABYSS-P.
Best regards
Fabrice

[Illinu]

Hi,

I have the same problem. Maybe someone can help me. First issue is, I am working on a cluster and I do not have rights or permissions to touch any installation. MPI is already installed but I might not be hitting the right path and I always get these lines:
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... no
Therefore not getting the ABYSS-P executable created.

I can see mpi.h in /usr/include/openmpi-x86_64/
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... no

When I do which mpirun I get
/usr/lib64/openmpi/bin/mpirun

So I've also tried:
--with-mpi=/usr/lib64/openmpi
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... yes

--with-mpi=/usr/lib64/openmpi/bin
--with-mpi=/media/vol1/ompi/openmpi-1.6.4
--with-mpi=/media/vol1/ompi/openmpi-1.6.4/ompi
--with-mpi=/media/vol1/ompi/openmpi-1.6.4/ompi/include
all these give
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
checking for MPI_Init in -lmpi... no

Can someone help me?
Thanks

[Tony Raymond]

Hi,

Is there an mpi.h in your /usr/lib64/openmpi/include folder?

Tony

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[Illinu]

There is no include/ folder in /usr/lib64/openmpi/ only these bin/  lib/  share/
I've checked inside each folder and subfolder and mpi.h is not there

[Tony Raymond]

Hi,

You'll need to reinstall openMPI so that there is a an include folder, which is how it is installed by default. This may mean you need to install openMPI to your home directory if you don't have root permission.

Let me know if you have a hard time, I'll try to help as much as I can.

Tony