Installing JOREK on Eurofusion gateway.

Part of the instructions is copied from JOREK wiki pages, eventually instructions found here should overlap with those from JOREK wiki.

How to obtain JOREK source code - ITER git platform

• Request an account for the ITER platform via email.
• Request access to JOREK code
• Create an ssh keypair (help)

  • Run the command

    Code Block
    language actionscript3
    ssh-keygen -t rsa -C "<key identifier>"

    Example:

    Code Block
    language actionscript3
    ssh-keygen -t rsa -C "git.iter.org"

    
    

  • You will be prompted for a location to save your key. Be careful not to overwrite any existing keys that you still need!

  • You can add a password for an additional layer of security (encrypting your private key file) or proceed without a password. Push Enter when prompted for a password if you don't want to add a password.

  • Upload your public ssh key: https://git.iter.org/plugins/servlet/ssh/account/keys

    • The public key is stored in the .pub file.

    • The .pub file is a regular text file. You will need to copy its contents into the web form that you get after clicking “Add key”.

  • If you are using other keys, configure a .ssh/config file by adding:

    Code Block
    Host git.iter.org HostName git.iter.org IdentityFile ~/.ssh/id_rsa_iter

    if you named your file id_rsa_iter,

• Get the code from ITER platform

...

• • Clone JOREK repository

    Code Block
    git clone ssh://git@git.iter.org/stab/jorek.git

    
    

Compiling JOREK

• The following modules need to be loaded e.g. by including in the ~/.bashrc 

  Code Block
  module purge module load cineca module load intel/pe-xe-2017--binary module load intelmpi/2017--binary module load mkl/2017--binary module load fftw/3.3.4--intelmpi--2017--binary module load szip/2.1--gnu--6.1.0 module load zlib/1.2.8--gnu--6.1.0 module load hdf5/1.8.17--intelmpi--2017--binary

  
  

• Before compilation one has to specify which compiler and libraries will be used. This depends on the machine. For the Eurofusion Gateway the following Makefile.inc for compiling JOREK needs to be copied to JOREK repository directory 

  Code Block
  title Makefile.inc linenumbers true collapse true
  --- Select physics model MODEL = model303 # --- Compiler and options FC = mpiifort CC = mpiicc CXX = mpiicpc FFLAGS += -O3 FFLAGS += -vecabi=compat -mcmodel=medium # --- Various switches USE_PASTIX = 1 USE_PASTIX_MURGE = 0 USE_COMPLEX_PRECOND = 0 USE_STRUMPACK = 0 USE_HDF5 = 1 USE_FFTW = 1 USE_MUMPS = 0 USE_DIRECT_CONSTRUCTION = 0 USE_BLOCK = 1 LIBDIR = /afs/eufus.eu/user/g/g2iholod/public LIBS += -liomp5 -pthread -ldl -lm ifeq (1, $(USE_MUMPS)) # --- MUMPS MKLLIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 \ -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 MKLINC = -I${MKL_HOME}/include MUMPSDIR = $(LIBDIR)/MUMPS_5.2.1 LIB_MUMPS = -L$(MUMPSDIR)/lib -ldmumps -ldmumps -lmumps_common -lpord INC_MUMPS = $(MUMPSDIR)/include LIB_MUMPS += $(MKLLIB) INC_MUMPS += $(MKLINC) endif ################## ifeq (1, $(USE_PASTIX)) MKLLIB = -L${MKL_HOME}/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core MKLINC = -I${MKL_HOME}/include INC_PASTIX += $(MKLINC) LIB_PASTIX += $(MKLLIB) PASTIX_DIR=$(LIBDIR)/pastix_5.2.3/install SCOTCH_DIR=$(LIBDIR)/scotch_5.1.12 LIB_PASTIX += $(PASTIX_DIR)/libpastix.a $(SCOTCH_DIR)/lib/libscotch.a $(SCOTCH_DIR)/lib/libscotcherr.a INC_PASTIX += -I$(PASTIX_DIR) endif ################## ifeq (1, $(USE_STRUMPACK)) MKLLIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 \ -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 MKLINC = -I${MKL_HOME}/include PARMETIS_HOME=$(LIBDIR)/parmetis-4.0.3/build STRUMPACK_HOME=$(LIBDIR)/STRUMPACK_MKL/install STRUMPACKINC = -I$(STRUMPACK_HOME)/include STRUMPACKLIB = $(STRUMPACK_HOME)/lib/libstrumpack.a STRUMPACKINC += -I$(PARMETIS_HOME)/include STRUMPACKLIB += $(PARMETIS_HOME)/libparmetis/libparmetis.a STRUMPACKINC += -I$(PARMETIS_HOME)/metis/include STRUMPACKLIB += $(PARMETIS_HOME)/libmetis/libmetis.a STRUMPACKINC += $(MKLINC) STRUMPACKLIB += $(MKLLIB) DEFINES += -DNEWSPK endif ################## LIBFFTW = $(FFTW_LIB)/libfftw3f.a INC_FFTW = -I$(FFTW_INC) HDF5INCLUDE = $(HDF5_HOME)/include HDF5LIB =-L$(HDF5_HOME)/lib -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -L$(SZIP_LIB) -lsz -lz

  The above Makefile.inc can be modified. In line 2 the model is defined. There are several models available 199, 303, 401, 500, 501, 502, 600, 710, 711 and 712. The list of input parameters for each model can be found here. For the demonstration purposes model 303 is chosen.

  Most of the necessary libraries are already available at the Gateway. There are two libraries Pastix (5.2.3) and Scotch (5.1.12) which are not available and have to be provided separately. The precompiled libraries can be found in ~g2iholod/public folder. The apropriate path is set in line 23 of Makefile.inc. Depending on the setting MUMPS library may also be needed but it is not used in the example run (see line19 of Makefile.inc).

• Compile JOREK with 

  Code Block
  make -j 8

  This creates an executable file "jorek_model<model_number>" which is "jorek_model303" in our case.

Submitting jobs

Example of the batch job submission script

...

squeue -u $USER

Creating namelist

Procedure of creating a JOREK namelist for a given model number is a variation of running a "JOREK for the first time case" instruction described in jorek wiki. We describe the procedure step by step here.

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