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HYPHY Package >> HyPhy feedback >> Re: problem with MPI install http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1266973821 Message started by Sergei on Feb 23rd, 2010 at 5:49pm |
Title: Re: problem with MPI install Post by Sergei on Feb 23rd, 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 $sh build.sh MPI [/code] Here, /path/to/hyphy/ is where the svn checkout was done (there should be a trunk directory there), and HYPHY is the directory created by buildFromSVN.sh Cheers, Sergei |
Title: Re: problem with MPI install Post by delmotte on Jun 18th, 2010 at 6:58am
I have done :
in HYPHYDIR/trunk/Scripts/ sh buildFromSVN.sh *** everything is built*** now I need MPI so in HYPHYDIR/HYPHY sh build.sh MPI and I get :Linux Checking for curl Curl seems to be present +-----------------------------------------------------------+ |Building a single-threaded HYPHYKernelMPI for MPI | +-----------------------------------------------------------+ COMPILER=g++, gcc COMPILER_FLAGS= -w -c -fsigned-char -O3 -fpermissive -I/usr/remote/hyphy/HYPHY/Source -I/usr/remote/hyphy/HYPHY/Source/SQLite -D INTPTR_TYPE=long -D __UNIX__ -D _SLKP_LFENGINE_REWRITE_ -D __HYPHYMPI__ -D _SLKP_LFENGINE_REWRITE_ Building baseobj.cpp In file included from baseobj.cpp:34: batchlan.h:362:18: error: mpi.h: Aucun fichier ou dossier de ce type baseobj.cpp: In function ‘bool GlobalShutdown()’: baseobj.cpp:228: error: ‘MPI_COMM_WORLD’ was not declared in this scope baseobj.cpp:228: error: ‘MPI_Comm_size’ was not declared in this scope baseobj.cpp:248: error: ‘MPI_Finalize’ was not declared in this scope Error during compilation my mpi.h is in /usr/remote/include How can i explain to the compiler where to look for this directory and find "my" mpi.h? I have already installed for example mpiblast and in that case i used ./configure --prefix=/usr/remote/mpiblast --with-mpi = /usr/remote/include any help will be most welcome merci |
Title: Re: problem with MPI install Post by Sergei on Jun 18th, 2010 at 6:24pm
Hi delmotte,
The HyPhy build.sh script is very primitive and doesn't make use of standard Linux autoconf and automake options. At some point, we'll try to improve the situation, but in the meantime please do the following: Edit line 103 in build.sh, which currently contains: Code (] COMPILER_FLAGS=$COMPILER_FLAGS" -D _SLKP_LFENGINE_REWRITE_ "; [/code):
Cheers, Sergei |
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