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Re: problem with MPI install (Read 2970 times)

Sergei

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Re: problem with MPI install
Feb 23^rd, 2010 at 5:49pm

Hi Matt,

buildFromSVN.sh is hardwired to compile multi-threaded CLI and GUI versions only; it ignores command line arguments. If you want to build and MPI version try

Code:

$cd /path/to/hyphy/HYPHY
$sh build.sh MPI

Here, /path/to/hyphy/ is where the svn checkout was done (there should be a trunk directory there), and HYPHY is the directory created by buildFromSVN.sh

Cheers,
Sergei

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Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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delmotte

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Re: problem with MPI install
Reply #1 - Jun 18^th, 2010 at 6:58am

I have done :
in
HYPHYDIR/trunk/Scripts/
sh buildFromSVN.sh
*** everything is built***

now I need MPI so
in HYPHYDIR/HYPHY
sh build.sh MPI

and I get :Linux
Checking for curl
Curl seems to be present
+-----------------------------------------------------------+
|Building a single-threaded HYPHYKernelMPI for MPI |
+-----------------------------------------------------------+
COMPILER=g++, gcc
COMPILER_FLAGS= -w -c -fsigned-char -O3 -fpermissive -I/usr/remote/hyphy/HYPHY/Source -I/usr/remote/hyphy/HYPHY/Source/SQLite -D INTPTR_TYPE=long -D __UNIX__ -D _SLKP_LFENGINE_REWRITE_ -D __HYPHYMPI__ -D _SLKP_LFENGINE_REWRITE_
Building baseobj.cpp
In file included from baseobj.cpp:34:
batchlan.h:362:18: error: mpi.h: Aucun fichier ou dossier de ce type
baseobj.cpp: In function ‘bool GlobalShutdown()’:
baseobj.cpp:228: error: ‘MPI_COMM_WORLD’ was not declared in this scope
baseobj.cpp:228: error: ‘MPI_Comm_size’ was not declared in this scope
baseobj.cpp:248: error: ‘MPI_Finalize’ was not declared in this scope
Error during compilation

my mpi.h is in /usr/remote/include
How can i explain to the compiler where to look for this directory and find "my" mpi.h?

I have already installed for example mpiblast and in that case i used
./configure --prefix=/usr/remote/mpiblast --with-mpi = /usr/remote/include

any help will be most welcome

merci

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Sergei

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Re: problem with MPI install
Reply #2 - Jun 18^th, 2010 at 6:24pm

Hi delmotte,

The HyPhy build.sh script is very primitive and doesn't make use of standard Linux autoconf and automake options. At some point, we'll try to improve the situation, but in the meantime please do the following:

Edit line 103 in build.sh, which currently contains:

Code:

COMPILER_FLAGS=$COMPILER_FLAGS" -D _SLKP_LFENGINE_REWRITE_ ";

to

Code:

COMPILER_FLAGS=$COMPILER_FLAGS" -D _SLKP_LFENGINE_REWRITE_ -I/usr/remote/include ";

Cheers,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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