1. 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.

1.1. 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
```
ssh-keygen -t rsa -C "<key identifier>"
```
  Example:
```
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:
```
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

Your home directory is located on AFS file system (/afs/eufus.eu/user/g/<username>) which is protected by ACL and by default is not accessible by batch. If you intend to submit your jobs to batch system it is better to use GPFS file system. Save your repository for example in /pfs/work/<username>/jorek folder. You can read more about Gateway Storage Areas here.

Clone JOREK repository

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

1.2. Compiling JOREK

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

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

Makefile.inc

    # --- 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

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1. Installing JOREK on Eurofusion gateway.

1.1. How to obtain JOREK source code - ITER git platform

1.2. Compiling JOREK