GTC is used for Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasmas. It is a fully self-consistent, 3D Particle-in-cell code (PIC) with a non-spectral Poisson solver and a grid that follows the magnetic field lines (twisting around the torus). It solves the gyro-averaged Vlasov equation in real space; the Vlasov equation describes the evolution of a system of particles under the effects of self-consistent electromagnetic fields. The unknown is the flux, f(t,x,v), which is a function of time t , position x, and velocity v, and represents the distribution function of particles (electrons, ions,...) in phase space.
TrN8GTCApr25.tar (Updated April 25, 2013)
How to Build
1. You need GNUmake to compile GTC. The Makefile contains some gmake syntax, such as VARIABLE:=
2. The Makefile runs the command "uname -s" to determine the OS of the current computer. There are different sections of the Makefile for various systems, such as IRIX64, AIX, Linux, SUPER-UX, and UNICOS/mp. You will have to edit compiler name (CMP and F90C), compiler options (OPT), and other symbols.
3. There are a variety of build options listed at the top of the Makefile. Most important of these are OPENMP, DOUBLE_PRECISION, and 64BITS.
You should use DOUBLE_PRECISION=n and 64BITS=y. Just below the comments explaining the list of options you will see the settings. The code contains separate code paths for OpenMP which are defined with the _OPENMP macro, which should be set by the compiler.
4. Note that currently the max number of OpenMP threads is set to 32. To increase beyond that change: line 15 shifti.f90 2nd index of msleft & msright is max_no_OpenMP threads.
5. The MPI-only executable is called "gtcmpi". The mixed MPI/OpenMP executable is called "gtcomp." The code contains OpenMP compiler annotations for DO-loops in several subroutines and files.
6. After editing the makefile just type 'gmake' to build the code.
How to Run
GTC reads an input file called "gtc.input". The distribution contains two input files. To run one of the cases, copy the chosen input file into "gtc.input". All input files use 100 particles par cell (micell=100).
The series of input files provided all keep the grid-based 1-D toroidal domain decomposition constant (mzetamax=64) and increase the particle
decomposition within a domain (from npartdom = 1 for 64 cores to npartdom = 300 for 19,200 cores). For example, for npartdom=300 (the 19200p input file), the particles within each toroidal domain are split equally between two cores. The number of particles per cell is also increased concomitantly (from 100 per cell for 64 cores to 30000 per cell for 16,384 cores).
Memory requirements for the code are approx 32 GB total for the 64p case and approx 10TB for the 19200p case.
To run the code do something like:
cp gtc.input.64p gtc.input
mpirun -np 64 ../gtcmpi
The NERSC-8 "base case" runs are for 64- and 19200-MPI process configurations. Use the gtc.input.64p and gtc.input.19200p input files for these runs, respectively.
Note that these values, 64 and 19200, represent the MAXIMUM mpi concurrency that these problem size can be run with. Runs with greater MPI concurrencies will produce incorrect results and are invalid.
Capability Improvement Runs
Capability improvement runs are enabled by increasing three parameters in the input file. For the 19,200-MPI rank large case these have the values
To increase the size of the problem:
1) Increase npartdom. The total number of MPI ranks = 64*npartdom.
2) Increase micell & mecell simultaneously. They should be equal to 100*mpartdom.
For example, to increase the max MPI concurrency by a factor of 3 over the large problem nicell=mecell=90000 & npartdom=900. In this case the increase in problem size will be 3 and the capability increase will be 3 times the runtime change.
The value of "NERSC_TIME" should be reported.
Verfication is challenging. The initial configuration is a function of the number of MPI ranks and thus runs using the same input at different MPI concurrencies cannot be compared. (After the system has been run for enough timesteps the simulations will produce the same statistical averages, but the benchmark as currently configured does not run long enough to reach this point.)
Thus, although offerors may report their best runtimes at any MPI concurrency below the max, verification must be performed at the 'selected' concurrencies of 64 and 19,200 MPI tasks and any code modifications made should pass these checks.
The code checks itself after the last time step and compares a computed value with the corresponding value calculated on the Cray XE6 system at NERSC using the PGI compiler. The difference reported should be less than .01. The internal error will only report with the # of MPI tasks equal 64, or 19200.
The code comes from the SciDAC GPSC Center based at the Princeton Plasma Physics Laboratory (lead P.I. W.W. Lee), with collaborators Stephane Ethier (PPPL) and Prof. Zhihong Lin (now at UC Irvine).