How to Compile Kratos on the Acuario Cluster
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| − | The following tutorial is intended to facilitate the compilation of the Kratos on CIMNE's | + | The following tutorial is intended to facilitate the compilation of the Kratos on CIMNE's cluster "Acuario". |
In the following we will assume that the new_user is a member of the "kratos" group defined on the server, which will provide him with the access to all of the libraries which are needed for a standard compilation. | In the following we will assume that the new_user is a member of the "kratos" group defined on the server, which will provide him with the access to all of the libraries which are needed for a standard compilation. | ||
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#OpenMPI use | #OpenMPI use | ||
| − | module load openmpi | + | module load openmpi/1.6.2 |
#adding kratos common libraries to the library path | #adding kratos common libraries to the library path | ||
| − | export LD_LIBRARY_PATH=/home/kratos_common/compiled_libraries/boost/lib:$LD_LIBRARY_PATH | + | export LD_LIBRARY_PATH=/home/kratos_common/compiled_libraries/boost/lib:${LD_LIBRARY_PATH} |
| − | export PYTHONPATH=/home/kratos_common/compiled_libraries/boost/lib:PYTHONPATH | + | export PYTHONPATH=/home/kratos_common/compiled_libraries/boost/lib:${PYTHONPATH} |
#Trilinos libs | #Trilinos libs | ||
| − | export LD_LIBRARY_PATH=/home/kratos_common/compiled_libraries/trilinos-10.6.4/lib/:$LD_LIBRARY_PATH | + | export LD_LIBRARY_PATH=/home/kratos_common/compiled_libraries/trilinos-10.6.4/lib/:${LD_LIBRARY_PATH} |
| − | + | ||
== Getting Kratos from repository == | == Getting Kratos from repository == | ||
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You can get the last version of kratos from repository using following command: | You can get the last version of kratos from repository using following command: | ||
| − | svn checkout | + | svn checkout https://svn.cimne.upc.edu/p/kratos/kratos |
| − | + | ||
| − | + | ||
| − | + | ||
== Configuration file to be used in the compilation == | == Configuration file to be used in the compilation == | ||
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You should copy this to your cmake_build kratos directory and use it for compilation. Changing to the Kratos/cmake_build directory in your account and type the following command: | You should copy this to your cmake_build kratos directory and use it for compilation. Changing to the Kratos/cmake_build directory in your account and type the following command: | ||
| − | cp /home/kratos_common/acuari_configure.sh | + | cp /home/kratos_common/acuari_configure.sh . |
== Running Examples == | == Running Examples == | ||
| − | Scalar or OpenMP parallel | + | Scalar or OpenMP parallel-application examples can be run "on-line" using the standard compilation commands. For longer jobs it's mandatory to be submitted to the queue. Full details on how to do this are given on the Cluster's webpage http://hpc.cimne.upc.edu |
The following example shows how to run (again in online mode) the MPI example "cantilever2d", which is contained in the directory | The following example shows how to run (again in online mode) the MPI example "cantilever2d", which is contained in the directory | ||
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== Cluster's Documentation == | == Cluster's Documentation == | ||
| − | + | The documentation on how to run programs in Acuario can be found here: | |
| − | + | ||
| + | http://hpc.cimne.upc.edu | ||
| − | + | There is a Quick Howto that explains how to prepare run scripts for OpenMP, MPI and Serial jobs. | |
== Trilinos Compilation == | == Trilinos Compilation == | ||
Latest revision as of 16:06, 14 February 2013
The following tutorial is intended to facilitate the compilation of the Kratos on CIMNE's cluster "Acuario".
In the following we will assume that the new_user is a member of the "kratos" group defined on the server, which will provide him with the access to all of the libraries which are needed for a standard compilation.
Contents |
Customarization needed for the user account
Edit the file ".bashrc" and add at the end of it the following code:
#OpenMPI use
module load openmpi/1.6.2
#adding kratos common libraries to the library path
export LD_LIBRARY_PATH=/home/kratos_common/compiled_libraries/boost/lib:${LD_LIBRARY_PATH}
export PYTHONPATH=/home/kratos_common/compiled_libraries/boost/lib:${PYTHONPATH}
#Trilinos libs
export LD_LIBRARY_PATH=/home/kratos_common/compiled_libraries/trilinos-10.6.4/lib/:${LD_LIBRARY_PATH}
Getting Kratos from repository
You can get the last version of kratos from repository using following command:
svn checkout https://svn.cimne.upc.edu/p/kratos/kratos
Configuration file to be used in the compilation
A standard configuration file, which compiles all of the applications in the Kratos can be found in
/home/kratos_common/acuari_configure.sh
You should copy this to your cmake_build kratos directory and use it for compilation. Changing to the Kratos/cmake_build directory in your account and type the following command:
cp /home/kratos_common/acuari_configure.sh .
Running Examples
Scalar or OpenMP parallel-application examples can be run "on-line" using the standard compilation commands. For longer jobs it's mandatory to be submitted to the queue. Full details on how to do this are given on the Cluster's webpage http://hpc.cimne.upc.edu
The following example shows how to run (again in online mode) the MPI example "cantilever2d", which is contained in the directory
kratos/applications/trilinos_application/test_examples/cantilever2d.gid
running 4 processes, distributed between 2 of the cluster nodes (pez001 and pez002) can be obtained as follows:
mpirun --np 4 --host pez001,pez002 python cantilever_aztec.py
Cluster's Documentation
The documentation on how to run programs in Acuario can be found here:
There is a Quick Howto that explains how to prepare run scripts for OpenMP, MPI and Serial jobs.
Trilinos Compilation
The trilinos has been compiled and installed in
/home/kratos_common/trilinos-9.0.0
in principle the users should NOT recompile it. In any case the script used in configuring it is:
../configure \ --enable-mpi \ --enable-shared \ --with-mpi-compilers=/opt/openmpi/1.2.4/bin \ --with-incdirs="-I/opt/openmpi/1.2.4/include -I/home/kratos_common/SuperLU_DIST_2.3/SRC" \ --with-ldflags="-L/home/kratos_common/SuperLU_DIST_2.3/lib -L/home/kratos_common/ParMetis-3.1" \ --with-libs="-lsuperlu_dist_2.3 -lmetis -lparmetis" \ --prefix=/home/kratos_common/trilinos-9.0.0 \ FFLAGS="-O5 -funroll-all-loops -fPIC" \ CFLAGS="-O3 -fPIC -funroll-loops" \ CXXFLAGS="-O3 -fPIC -funroll-loops -ffast-math" \ --enable-amesos --enable-anasazi --enable-aztecoo \ --enable-epetra --enable-epetraext --enable-ifpack --enable-ml --enable-pytrilinos \ --enable-teuchos --enable-triutils --enable-galeri \ --enable-aztecoo-teuchos --enable-amesos-superludist
