Version 1.0

alya/ALYA_Build_README.txt

+In order to build ALYA (Alya.x), please follow these steps:
+
+- Go to: Thirdparties/metis-4.0 and build the Metis library (libmetis.a) using 'make'
+- Go to the directory: Executables/unix
+- Adapt the file: configure-marenostrum-mpi.txt to your own MPI wrappers and paths
+- Execute:
+  ./configure -x -f=configure-marenostrum-mpi.txt nastin parall
+  make

alya/ALYA_Run_README.txt

+In order to run ALYA, you need at least the following input files per execution:
+
+X.dom.dat
+X.typ.dat
+X.geo.dat
+X.bcs.dat
+X.inflow_profile.bcs
+X.ker.dat
+X.nsi.dat
+X.dat
+
+In our case, there are 2 different inputs, so X={1_1p1mill,3_27p3mill}
+To execute a simulation, you must be inside the input directory and you should submit a job like:
+
+mpirun Alya.x 1_1p1mill
+or
+mpirun Alya.x 3_27p3mill

code_saturne/Code_Saturne_README.txt

+Installation:
+-------------
+
+Code_Saturne is open source and the documentation about how to install
+it is to be found under http://www.code-saturne.org
+
+However, the version 3.0.1 has been copied to the current folder.
+
+
+Running - Test case:
+----------------
+
+Running a case is described in the following page:  http://www.code-saturne.org
+
+The test case deals with the flow in a bundle of tubes.
+A larger mesh (51M cells) is built from an original mesh of 13M cells.
+
+The original mesh_input file (already preprocessed for Code_Saturne)
+is to be found under MESH.
+
+The user subroutines are under XE6_INTERLAGOS/SRC
+
+The test case has been set up to run for 10 time-steps.
+
+Contact:
+--------
+
+If you have any question, please contact Charles Moulinec (STFC Daresbury Laboratory)
+at charles.moulinec@stfc.ac.uk

cp2k/CP2K_Build_README.txt

+Build instructions for CP2K.
+2014-04-09 : ntell@iasa.gr
+
+CP2K needs a number of external libraries and a threads enabled MPI implementation.
+These are : BLAS/LAPACK, BLACS/SCALAPACK, LIBINT, FFTW3.
+It is advised to use the vendor optimized versions of these libraries.
+If some of these are not available on your machine,
+there some implementations of these libraries. Some of these are below.
+
+1. 	BLAS/LAPACK : 
+	netlib BLAS/LAPACK : http://netlib.org/lapack/
+	ATLAS              : http://math-atlas.sf.net/
+	GotoBLAS	   : http://www.tacc.utexas.edu/tacc-projects
+	MKL                : refer to your Intel MKL installation, if available
+	ACML	           : refer to your ACML installation if available
+
+2.	BLACS/SCALAPACK	   : http://netlib.org/scalapack/
+			     Intel BLACS/SCALAPACK Implementation
+
+3.	LIBINT		   : http://sourceforge.net/projects/libint/files/v1-releases/
+
+4.	FFTW3		   : http://www.fftw.org/
+			     
+
+In the directory cp2k-VERSION/arch there are some ARCH files with instructions how
+to build CP2K. For each architecture/compiler there are few arch files describing how to build cp2k.
+Select one of the .psmp files that fits your architecture/compiler.
+cd to cp2k-VERSION/makefiles
+If the arch file for your machine is called SOMEARCH_SOMECOMPILER.psmp,
+issue : make ARCH=SOMEARCH_SOMECOMPILER VERSION=psmp
+If everything goes fine, you'll find the executable cp2k.psmp in the directory
+cp2k-VERSION/exe/SOMEARCH_SOMECOMPILER
+
+In most cases you need to create a custom arch file that fits cpu type,
+compiler, and the installation path of external libraries.
+As an example below is the arch file for a machine with mpif90/gcc/gfortran, that supports SSE2, has 
+all the external libraries installed under /usr/local/, uses ATLAS with full
+LAPACK support for BLAS/LAPACK, Scalapack-2 for BLACS/Scalapack, fftw3 FFTW3 and libint-1.1.4:
+
+
+#=======================================================================================================
+CC       = gcc
+CPP      = 
+FC       = mpif90 -fopenmp
+LD       = mpif90 -fopenmp
+AR       = ar -r
+DFLAGS   =  -D__GFORTRAN -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK -D__FFTW3 -D__LIBINT  -I/usr/local/fftw3/include -I/usr/local/libint-1.1.4/include 
+CPPFLAGS = 
+FCFLAGS  = $(DFLAGS) -O3 -msse2 -funroll-loops -finline -ffree-form
+FCFLAGS2 = $(DFLAGS) -O3 -msse2 -funroll-loops -finline -ffree-form
+LDFLAGS  = $(FCFLAGS) 
+LIBS     = /usr/local/Scalapack/lib/libscalapack.a \
+           /usr/local/Atlas/lib/liblapack.a \
+           /usr/local/Atlas/lib/libf77blas.a \
+           /usr/local/Atlas/lib/libcblas.a \
+           /usr/local/Atlas/lib/libatlas.a \
+           /usr/local/fftw3/lib/libfftw3_threads.a \
+           /usr/local/fftw3/lib/libfftw3.a \
+           /usr/local/libint-1.1.4/lib/libderiv.a \
+           /usr/local/libint-1.1.4/lib/libint.a \
+           -lstdc++ -lpthread
+
+OBJECTS_ARCHITECTURE = machine_gfortran.o
+#=======================================================================================================

cp2k/CP2K_Download_README.txt

+CP2K can be downloaded from : http://www.cp2k.org/download
+It is free for all users under GPL license, 
+see Obtaining CP2K section in the download page.
+In UEABS(2IP) the 2.3 branch was used that can be downloaded from : 
+http://sourceforge.net/projects/cp2k/files/cp2k-2.3.tar.bz2
+Data files are compatible with at least 2.4 branch.
+
+Tier-0 data set requires the libint-1.1.4 library. If libint version 1 
+is not available on your machine, libint can be downloaded from : 
+http://sourceforge.net/projects/libint/files/v1-releases/libint-1.1.4.tar.gz

cp2k/CP2K_Run_README.txt

+Run instructions for CP2K.
+2013-08-13 : ntell@iasa.gr
+
+After build of hybrid MPI/OMP CP2K you have an executable called cp2k.psmp.
+You can try any combination of TASKSPERNODE/THREADSPERTASK.
+The input file is H2O-1024.inp for tier-1 and input_bulk_HFX_3.inp for tier-0 systems.
+For tier-1 systems the best performance is usually obtained with pure MPI,
+while for tier-0 systems the best performance is obtained using 1 MPI task per
+node with the number of threads/MPI_Task being equal to the number of 
+cores/node.
+Tier-0  case requires a converged wavefunction file, that can be obtained
+running with any number of cores, 1024-2048 cores are suggested : 
+WRAPPER WRAPPER_OPTIONS PATH_TO_cp2k.psmp -i  input_bulk_B88_3.inp  -o input_bulk_B88_3.log
+When this run finish, mv the saved restart file LiH_bulk_3-RESTART.wfn to
+B88.wfn
+
+The general way to run is :
+WRAPPER WRAPPER_OPTIONS PATH_TO_cp2k.psmp -i inputfile -o logile
+
+WRAPPER and WRAPPER_OPTIONS  depend on system, batch system etc.
+Few common pairs are :
+
+CRAY     : aprun -n TASKS -N NODES -d THREADSPERTASK
+Curie    : ccc_mrun with no options - obtained from batch system
+Juqueen  : runjob --np TASKS --ranks-per-node TASKSPERNOD --exp-env OMP_NUM_THREADS
+Slurm    : srun  with no options, obtained from slurm if the variables below are set.
+#SBATCH --nodes=NODES
+#SBATCH --ntasks-per-node=TASKSPERNODE
+#SBATCH --cpus-per-task=THREADSPERTASK
+
+
+The run walltime is reported near the end of logfile : grep ^\ CP2K\^  logile | tail -1 | awk -F ' ' '{print $7}'
+
+
+

gadget/gadget3_Build_README.txt

+1. Install FFTW-2,  available at http://www.fftw.org
+2. Install GSL,  availavle at http://www.gnu.org/software/gsl
+3. Install HDF5,  availavle at http://www.hdfgroup.org/HDF5/
+4. Go to Gadget3/
+5. Edit Makefile, set:
+   CC
+   CXX
+   GSL_INCL
+   GSL_LIBS
+   FFTW_INCL
+   FFTW_LIBS
+   HDF5INCL
+   HDF5LIB
+6. make CONFIG=Config-Medium.sh
+	
\ No newline at end of file

gadget/gadget3_Run_README.txt

+1. Creation of input 
+     mpirun -np 128  ./N-GenIC  ics_medium.param  
+   ics_medium.param is in N-GenIC directory
+2. Run calculation
+     mpirun -np 128  ./Gadget3  param-medium.txt
+   param-medium.txt is in Gadget3 directory

gene/GENE_Run_README.txt

+This is the README file for the GENE application benchmark,
+distributed with the Unified European Application Benchmark Suite.
+
+-----------
+GENE readme
+-----------
+
+Contents
+--------
+
+1. General description
+2. Code structure
+3. Parallelization
+4. Building
+5. Execution
+6. Data
+
+1. General description
+======================
+
+The gyrokinetic plasma turbulence code GENE (this acronym stands for
+Gyrokinetic Electromagnetic Numerical Experiment) is a software package
+dedicated to solving the nonlinear gyrokinetic Integro-Differential system 
+of equations in either flux-tube domain or in a radially nonlocal domain.
+GENE has been developed by a team of people (the Gene Development Team,
+led by F. Jenko, Max-Planck-Institut for Plasma Physics) over the last
+several years. 
+
+For further documentation of the code see: http://www.ipp.mpg.de/~fsj/gene/
+
+2.  Code structure
+==================
+
+Each particle species is described by a time-dependent distribution function
+in a five-dimensional phase space.
+This results in 6 dimensional arrays, which have the following coordinates:
+x y z	three space coordinates
+v	parallel velocity
+w	perpendicular velocity
+spec	species of particles
+
+GENE is written completely in FORTRAN90, with some language structures
+from Fortran 2003 standard. It also contains preprocessing directives.
+
+3. Parallelization
+==================
+
+Parallelization is done by domain decomposition of all 6 coordinates using MPI.
+x, y, z	3 space coordinates
+v	parallel velocity
+w	perpendicular velocity
+spec	species of particles
+
+
+4. Building
+===========
+
+The source code (fortran-90) resides in directory src.
+The compilation of GENE will be done by JuBE.
+Compilation will be done automatically if a new executable for the
+benchmark runs is needed.
+
+
+5.  Running the code
+====================
+A very brief description of the datasets:
+
+parameters_small
+	A small data set for test purposes. Needs only 8 cores to run.
+parameters_tier1
+	Global simulation of ion-scale turbulence in Asdex-Upgrade, 
+	needs 200-500GB total memory, runs from 256 to 4096 cores
+parameters_tier0
+	Global simulation of ion-scale turbulence in JET, 
+	needs 3.5-7TB total memory, runs from 4096 to 16384 cores
+
+For running the benchmark for GENE, please follow the instructions for
+using JuBE.
+JuBE generates for each benchmark run a run directory and generates from
+a template input file the input file 'parameters' and stores it in the
+run directory.
+A job submit script is created as well and is submitted.
+
+
+6. Data
+=======
+
+The only input file is 'parameters'. It has the format of a f90 namelist.
+
+The following output files are stored in the run directory.
+
+nrg.dat		The content of this file is used to verify the correctness
+		of the benchmark run.
+
+stdout		is redirected by JuBE.
+		It contains logging information,
+		especially the result of the time measurement.
+ 
+--------------------------------------------------------------------------

gpaw/GPAW_Build_README.txt

+Instructions for obtaining GPAW and its test set for PRACE benchmarking
+
+GPAW is licensed under GPL, so there are no license issues
+
+Software requirements
+=====================
+* MPI
+* BLAS, LAPACK, Scalapack
+* HDF5
+* Python (2.x series from 2.4 upwards)
+  * For very large calculations ( > 4000 CPU cores) it is recommended to
+    to use the special Python interpreter which reduces the 
+    initialization time related to Python's import mechanism:
+    https://gitorious.org/scalable-python
+* NumPy ( > 1.3)
+
+Obtaining the source code
+=========================
+
+* This benchmark uses the 3.6.1.3356 version of Atomic Simulation Environment 
+  (ASE), which can be obtained as follows:
+
+  svn co -r 3356 https://svn.fysik.dtu.dk/projects/ase/trunk ase
+
+* This benchmark uses the 0.9.10710 version of GPAW, which can be 
+  obtained as follows:
+
+  svn co -r 10710 https://svn.fysik.dtu.dk/projects/gpaw/trunk gpaw
+
+* Installation instructions for various architectures are given in
+  https://wiki.fysik.dtu.dk/gpaw/install/platforms_and_architectures.html
+
+Support
+=======
+* Help regarding the benchmark can be requested from jussi.enkovaara@csc.fi
+

gpaw/GPAW_Run_README.txt

+This benchmark set contains a short functional test as well as scaling
+tests for electronic structure simulation software GPAW. More information on 
+GPAW can be found at wiki.fysik.dtu.dk/gpaw
+
+Functional test: functional.py
+==============================
+A calculation for the ground state electronic structure of small Si cluster 
+followed by linear response time-dependent density-functional theory 
+calculation. This test works with 8-64 CPU cores.
+
+Medium scaling test: Si_gs.py
+=============================
+A ground state calculation (few iterations) for spherical Si 
+This test should scale to ~2000 processor cores in x86 architecture. 
+Total running time with ~2000 cores is ~7 min. In principle, arbitrary
+number of CPU cores can be used, but recommended values are powers of 2.
+This test produces a 47 GB output file Si_gs.hdf5 to be used for the 
+large scaling test Si_lr1.py.
+
+For scalability testing the relevant timer in the text output 
+'out_Si_gs_pXXXX.txt' (where XXXX is the CPU core count) is 'SCF-cycle'.
+The parallel I/O performance (with HDF5) can be benchmarked with the
+'IO' timer.
+
+Large scaling test: Si_lr1.py
+=============================
+Linear response TDDFT calculation for spherical Si cluster
+This benchmark should be scalable to ~20 000 CPU cores
+in x86 architecture. Number of CPU cores has to be a multiple of 256.
+Estimated total running time with 20 000 CPU cores is 5 min. 
+The benchmark requires as input the ground state wave functions in
+the file Si_gs.hdf5 which can be produced by the ground state benchmark
+Si_gs.py
+
+The relevant timer for this benchmark is 'Calculate K matrix',
+timing information is written to a text output file Si_lr1_pxxxx.txt where 
+xxxx is the number of CPU cores.
+
+Optional large scaling test: Au38_lr.py
+=======================================
+Linear response TDDFT calculation for Au38 cluster surrounded by CH3 
+ligands. This benchmark should be scalable to ~20 000 CPU cores
+in x86 architecture. Number of CPU cores has to be a multiple of 256. 
+Estimated running with 20 000 CPU cores is 5 min. 
+The benchmark requires as input the ground state wave functions
+which can be produced by input Au38_gs.py (about 5 min calculation with 
+64 cores).
+
+The relevant timer for this benchmark is 'Calculate K matrix',
+timing information is written to a text output file Au38_lr_pxxxx.txt where 
+xxxx is the number of CPU cores.
+
+How to run
+==========
+* Download and build the source code along the instructions in GPAW_Build_README.txt
+
+* Benchmarks do not need any special command line options and can be run
+  just as e.g. :
+
+  mpirun -np 64 gpaw-python functional.py
+  mpirun -np 1024 gpaw-python Si_gs.py
+  mpirun -np 16384 gpaw-python Si_lr1.py
+

gromacs/GROMACS_Download_README.txt

+Gromacs can be downloaded from : http://www.gromacs.org/Downloads
+The UEABS benchmark cases require the use of 4.6 or newer branch,
+the latest 4.6.x version is suggested.
+

gromacs/GROMACS_Run_README.txt

+There are two data sets in UEABS for Gromacs.
+1. ion_channel that use PME for electrostatics, for Tier-1 systems
+2. lignocellulose-rf that use Reaction field for electrostatics, for Tier-0 systems. Reference :  http://pubs.acs.org/doi/abs/10.1021/bm400442n
+
+The input data file for each benchmark is the corresponding .tpr file produced using
+tools from a complete gromacs installation and a series of ascii data files 
+(atom coords/velocities, forcefield, run control).
+If it happens to run the tier-0 case on BG/Q use lignucellulose-rf.BGQ.tpr
+instead lignocellulose-rf.tpr. It is the same as lignocellulose-rf.tpr 
+created on a BG/Q system.
+
+The general way to run gromacs benchmarks is :
+WRAPPER WRAPPER_OPTIONS PATH_TO_MDRUN -s CASENAME.tpr -maxh 0.50 -resethway -noconfout -nsteps 10000 -g logile
+
+CASENAME is one of ion_channel or lignocellulose-rf
+maxh        : Terminate after 0.99 times this time (hours) i.e. gracefully terminate after ~30 min
+resethwat   : Reset Timer counters at half steps. This means that the reported
+	      walltime and performance referes to the last 
+              half steps of sumulation.
+noconfout   : Do not save output coordinates/velocities at the end.
+nsteps      : Run this number of steps, no matter what is requested in the input file
+logfile     : The output filename. If extension .log is ommited 
+	      it is automatically appended. Obviously, it should be different
+	      for different runs.
+
+WRAPPER and WRAPPER_OPTIONS  depend on system, batch system etc.
+Few common pairs are :
+
+CRAY     : aprun -n TASKS -N NODES -d THREADSPERTASK
+Curie    : ccc_mrun with no options - obtained from batch system
+Juqueen  : runjob --np TASKS --ranks-per-node TASKSPERNOD --exp-env OMP_NUM_THREADS
+Slurm    : srun  with no options, obtained from slurm if the variables below are set.
+#SBATCH --nodes=NODES
+#SBATCH --ntasks-per-node=TASKSPERNODE
+#SBATCH --cpus-per-task=THREADSPERTASK
+
+The best performance is usually obtained using pure MPI i.e. THREADSPERTASK=1.
+You can check other hybrid MPI/OMP combinations.
+
+The execution time  is reported at the end of logfile : grep Time: logfile | awk -F ' ' '{print $3}'
+
+NOTE : This is the wall time for the last half number of steps. 
+       For sufficiently large nsteps, this is half of the total wall time.
+

namd/NAMD_Build_README.txt

+Build instructions for namd.
+In benchmarks the memopt version is used with SMP support. 
+In order to build this version, your MPI need to have level of thread support: MPI_THREAD_FUNNELED
+You need a NAMD CVS 2.9 version 2013-02-06 or later.
+
+1. 	Uncompress/tar the source. 
+2. 	cd NAMD_Source_BASE (the directory name depends on how the source obtained,
+	typically : namd2 or NAMD_CVS_2013-02-06_Source )
+3.	untar the charm-VERSION.tar that exists. If you obtained the namd source via
+	cvs, you need to download separately charm.
+4.      cd to charm-VERSION directory
+5.      configure and compile charm :
+        This step is system dependent. Some examples are :
+
+CRAY XE6  : ./build charm++ mpi-crayxe        smp                         --with-production -O -DCMK_OPTIMIZE
+CURIE     : ./build charm++ mpi-linux-x86_64  smp  mpicxx  ifort          --with-production -O -DCMK_OPTIMIZE
+JUQUEEN   : ./build charm++ mpi-bluegeneq     smp  xlc                    --with-production -O -DCMK_OPTIMIZE
+The syntax is : ./build charm++ ARCHITECTURE  smp (compilers, optional)   --with-production -O -DCMK_OPTIMIZE
+You can find a list of supported architectures/compilers in charm-VERSION/src/arch
+The smp option is mandatory to build the Hybrid version of namd.
+This builds charm++.
+
+6.	cd ..
+7.	Configure NAMD.
+        This step is system dependent. Some examples are :
+CRAY-XE6    	./config CRAY-XT-g++ --charm-base ./charm-6.5.0 --charm-arch mpi-crayxe-smp --with-fftw3 --fftw-prefix $CRAY_FFTW_DIR --without-tcl --with-memopt --charm-opts -verbose
+
+CURIE		./config Linux-x86_64-icc --charm-base ./charm-6.5.0  --charm-arch mpi-linux-x86_64-ifort-smp-mpicxx --with-fftw3 --fftw-prefix PATH_TO_FFTW3_INSTALLATION --without-tcl --with-memopt --charm-opts -verbose --cxx-opts "-O3 -xAVX "  --cc-opts "-O3 -xAVX" --cxx icpc --cc icc --cxx-noalias-opts "-fno-alias -ip -fno-rtti -no-vec  "
+
+Juqueen: 	./config BlueGeneQ-MPI-xlC --charm-base ./charm-6.5.0 --charm-arch mpi-bluegeneq-smp-xlc --with-fftw3 --with-fftw-prefix PATH_TO_FFTW3_INSTALLATION  --without-tcl --charm-opts -verbose --with-memopt
+
+	You need to specify the fftw3 installation directory. On systems that
+	use environment modules you need to load the existing fftw3 module
+	and probably use the provided environment variables - like in CRAY-XE6
+	example above. 
+	If fftw3 libraries are not installed on your system,
+	download and install fftw-3.3.3.tar.gz from http://www.fftw.org/.
+
+	You may adjust the compilers and compiler flags as the CURIE example.
+
+	When config ends prompts to change to a directory and run make. 
+
+8.	cd to the reported directory and run make 
+	If everything is ok you'll find the executable with name namd2 in this
+	directory.
+
+
+
+
+

namd/NAMD_Download_README.txt

+The official site to download namd is :
+http://www.ks.uiuc.edu/Research/namd/
+
+You need to register for free here to get a namd copy from here :
+http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD
+
+In order to get a specific CVS snapshot, you need first to ask for
+username/password :  http://www.ks.uiuc.edu/Research/namd/cvsrequest.html
+When your cvs access application is approved, you can use your username/password
+to download a specific cvs snapshot :
+cvs  -d :pserver:username@cvs.ks.uiuc.edu:/namd/cvsroot co -D "2013-02-06 23:59:00 GMT" namd2
+
+In this case, the charm++ is not included. 
+You have to download separately and put it in the namd2 source tree :
+http://charm.cs.illinois.edu/distrib/charm-6.5.0.tar.gz
+
+

namd/NAMD_Run_README.txt

+Run instructions for NAMD.
+ntell@iasa.gr
+
+After build of NAMD you have an executable called namd2.
+
+The best performance and scaling of namd is achieved using
+hybrid MPI/MT version. On a system with nodes of NC cores per node
+use 1 MPI task per node and NC threads per task,
+for example on a 32 cores/node system use 1 MPI process,
+set OMP_NUM_THREADS or any batch system related variable to 32. 
+
+Set a  variable, for example MYPPN to NC-1, 
+for example to 31 for a 32 cores/node system.
+
+You can also try other combinations of TASKSPERNODE/THREADSPERTASK to check.
+
+The control file is stmv.8M.memopt.namd for tier-1 and stmv.28M.memopt.namd
+for tier-0 systems.
+
+The general way to run is :
+WRAPPER WRAPPER_OPTIONS PATH_TO_namd2 +ppn $MYPPN stmv.8M.memopt.namd > logfile
+
+WRAPPER and WRAPPER_OPTIONS  depend on system, batch system etc.
+Few common pairs are :
+
+CRAY     : aprun -n TASKS -N NODES -d THREADSPERTASK
+Curie    : ccc_mrun with no options - obtained from batch system
+Juqueen  : runjob --np TASKS --ranks-per-node TASKSPERNOD --exp-env OMP_NUM_THREADS
+Slurm    : srun  with no options, obtained from slurm if the variables below are set.
+#SBATCH --nodes=NODES
+#SBATCH --ntasks-per-node=TASKSPERNODE
+#SBATCH --cpus-per-task=THREADSPERTASK
+
+
+The run walltime is reported at the end of logfile : grep WallClock: logfile  | awk -F ' ' '{print $2}'
+
+

nemo/NEMO_Build_README.txt

+NEMO_Build_README
+
+Written in 2013-09-12, as a product of NEMO benchmark in PRACE 2IP-WP7.4.
+Written by Soon-Heum "Jeff" Ko at Linkoping University, Sweden (sko@nsc.liu.se).
+
+0. Before start
+- Download two tarball files (src and input) from PRACE benchmark site.
+- Create a directory, 'ORCA12_PRACE' and untar above-mentioned files under that directory. Then the directory structure would be as
+----- ORCA12_PRACE
+                  |
+                  |------ DATA_CONFIG_ORCA12/
+                  |
+                  |------ FORCING/
+                  |
+                  |------ NEMOGCM/
+                  |
+                  |------ README
+                  |
+                  |------ Instruction_for_JuBE.tar.gz
+
+1. Build-up of standalone version
+- You can find the easy how-to from ORCA12_PRACE/README file, which is an instruction document written after PRACE 1IP contribution. To repeat the instruction,
+1) cd NEMOGCM/ARCH
+2) create a arch-COMPUTER.fcm file in NEMOGCM/ARCH corresponding to your needs. You can refer to 'arch-ifort_linux_curie.fcm' which is tuned for CURIE x86_64 system.
+3) cd NEMOGCM/CONFIG
+4) ./makenemo -n ORCA12.L75-PRACE -m COMPUTER
+Then you will have a subdirectory 'ORCA12.L75-PRACE' is created.
+
+2. Build-up under JuBE benchmark framework
+- You shall first download JuBE benchmark suite and PRACE benchmark applications from PRACE SVN. Then you will find 'nemo' benchmark under PABS/applications. Because the old nemo benchmark set has been ill-written and there have been changes on NEMO source, we provide the benchmark setup for the current NEMO version in a separate tarball file (Instruction_for_JuBE.tar.gz). You can follow the instruction specified there for installing and running NEMO v3.4. in the JuBE benchmark suite.
\ No newline at end of file

nemo/NEMO_Run_README.txt

+NEMO_Run_README
+
+Written in 2013-09-12, as a product of NEMO benchmark in PRACE 2IP-WP7.4.
+Written by Soon-Heum "Jeff" Ko at Linkoping University, Sweden (sko@nsc.liu.se).
+
+0. Before start
+- Follow the instriction in 'NEMO_Build_README.txt' so that you have the directory structure as specified, along with compiled binary:
+----- ORCA12_PRACE
+                  |
+                  |------ DATA_CONFIG_ORCA12/
+                  |
+                  |------ FORCING/
+                  |
+                  |------ NEMOGCM/
+                  |
+                  |------ README
+                  |
+                  |------ Instruction_for_JuBE.tar.gz
+
+1. Running standalone version
+- After compilation, you will have 'ORCA12.L75-PRACE' directory created under NEMOGCM/CONFIG.
+1) cd ORCA12.L75-PRACE/EXP00
+2) Link to datasets. Perform follows:
+$ ln -s ../../../../DATA_CONFIG_ORCA12/* .
+$ ln -s ../../../../FORCING/* .
+3) Locate 'namelist' and 'namelist_ice' files in this directory and edit them
+4) Run it. It does not have any special command line arguments, thus you can simply type 'mpirun opa'.
+
+2. Running under JuBE benchmark framework
+- You can prepare your own XML file to complete from compiling to running at the same time. A file 'ORCA_PRACE_CURIE.xml' under Instruction_for_JuBE.tar.gz could be used as an example. One remark for CURIE user: you shall specify your project ID and which type of queues (standard; large; ...) you are to use. That information is found from 'ccc_myproject' command.
\ No newline at end of file

qcd/QCD_Build_README.txt

+Description and Building of the QCD Benchmark
+=============================================
+
+Description
+===========
+The QCD benchmark is, unlike the other benchmarks in the PRACE
+application benchmark suite, not a full application but a set of 5
+kernels which are representative of some of the most compute-intensive
+parts of QCD calculations.  
+
+Test Cases
+----------
+Each of the 5 kernels has one test case to be used for Tier-0 and
+Tier-1: 
+
+Kernel A is derived from BQCD (Berlin Quantum ChromoDynamics program),
+a hybrid Monte-Carlo code that simulates Quantum Chromodynamics with
+dynamical standard Wilson fermions. The computations take place on a
+four-dimensional regular grid with periodic boundary conditions. The
+kernel is a standard conjugate gradient solver with even/odd
+pre-conditioning. Lattice size is 322 x 642. 
+
+Kernel B is derived from SU3_AHiggs, a lattice quantum chromodynamics
+(QCD) code intended for computing the conditions of the Early
+Universe. Instead of "full QCD", the code applies an effective field
+theory, which is valid at high temperatures. In the effective theory,
+the lattice is 3D. Lattice size is 2563. 
+
+Kernel C Lattice size is 84. Note that Kernel C can only be run in a