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
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
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$(SZIP_LIB) -lsz -lz
The above Makefile.inc can be modified. In line 2 the model is defined. There are several models available 199, 303, 401, 500, 501, 502, 600, 710, 711 and 712. The list of input parameters for each model can be found here. For the demonstration purposes model 303 is chosen.
Most of the necessary libraries are already available at the Gateway. There are two libraries Pastix (5.2.3) and Scotch (5.1.12) which are not available and have to be provided separately. The precompiled libraries can be found in ~g2iholod/public folder. The apropriate path is set in line 23 of Makefile.inc. Depending on the setting MUMPS library may also be needed but it is not used in the example run (see line19 of Makefile.inc).Compile JOREK with
Code Block make -j 8
This creates an executable file "jorek_model<model_number>" which is "jorek_model303" in our case.
Submitting jobs
Example of the batch job submission script
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#!/bin/bash #SBATCH --job-name=jorek #SBATCH --nodes=1 #SBATCH --ntasks=2 #SBATCH --cpus-per-task=24 #SBATCH --time=00:10:00 #SBATCH --partition=gw export OMP_NUM_THREADS=24 srun /pfs/work/$USER/jorek/jorek_model303 < ./inxflow > logfile.out |
The "inxflow" file with example input parameters can be found in ~g2iholod/public/jorek_dev/tmp directory. Since the example run is expected to finished within 30 minutes it is possible to change the standard partition "gw" to the debugging partition "gwdbg" by setting
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#SBATCH --partition=gwdbg |
in submit.sh script and omit the queue for jobs that take more time.
It is advised to run the script in a different folder than the repository. Output files are saved in a working directory and running jorek in the repository results in mixing source files with input and output files.
Submit the bash script with the command
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sbatch submit.sh |
Check your submission status with
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squeue -u $USER |