Installation

Requirements

The recommended compilers, preprocessors, and libraries for GENESIS ver. 1.4.0 or later are listed below. Please make sure that at least one of them in each section is installed on your system. If the users do not use the Intel or Fujitsu compilers, the combination of GCC compiler, GCC preprocessor, and OpenMPI is recommended. Detailed information about the requirements for each version is described in the user manual (see Chapter “Getting started”).

  • Operating systems
    • Linux
    • Mac OSX
  • Fortran and C compilers
    • GCC compiler gfortran, gcc (version 4.4.7 or higher is required)
    • Intel compiler ifort, icc
    • Fujitsu compiler frtpx, fccpx
  • Preprocessors
    • GCC preprocessor cpp
    • Intel preprocessor fpp
    • Fujitsu compiler frtpx
  • MPI libraries for parallel computing
    • OpenMPI mpirun, mpif90, mpicc
    • Intel MPI
    • Fujitsu MPI
  • Numerical libraries for mathematical algorithms
    • LAPACK/BLAS
    • Intel Math Kernel Library (MKL)
    • Fujitsu Scientific Subroutine Library (SSL II)
  • GPU (Optional)
    • NVIDIA GPU cards which support Compute Capability (CC) 3.5 or higher
    • The following GPU cards and CUDA versions have been tested by the GENESIS developers
      • NVIDIA K20, K40, P100, TITAN V, GTX 1080, GTX 1080Ti, RTX 2080, RTX 2080Ti
      • CUDA ver. 8.0, 9.0, 9.1, 9.2, 10.0


General scheme for installation

The source code of GENESIS is available in the Download page. The users have to first uncompress the download file in an appropriate directory. In order to compile the source code, the users execute a “configure” script in the directory. This script automatically detects appropriate compilers, preprocessors, and libraries in the users’ computer, and create “Makefile“. The users may have to add some options in the command according to the user’s computer environment. For example, “--enable-gpu” should be appended to turn on the GPGPU calculation (see Chapter “Getting started” in the user manual). After the “configure” command is successfully finished, type the following command to compile and install GENESIS. All programs of GENESIS are compiled and installed into the “./bin” directory by default. The followings are example commands to install GENESIS for typical Linux workstations.

$ mv ~/Downloads/genesis-X.Y.Z.tar.bz2 ./
$ tar xvfj genesis-X.Y.Z.tar.bz2
$ cd genesis-X.Y.Z
$ ./configure
$ make install

If the users encountered a failure during the installation, check the error message carefully. In most cases, errors are caused by invalid path of compilers and libraries. The followings are possible suggestions to solve frequent problems.

Trouble shooting (Last update: Oct. 31, 2019)

Configure
  • If the error message is like “configure: error: Fortran compiler cannot create executables”, any Fortran compilers might not be detected. Basically, the configure script looks for “mpif90”, “mpifrtpx”, or “mpifrt” for Fortran compiler, and “mpicc”, “mpifccpx”, or “mpifrt” for C compiler. If one of them was not detected in your computer, the configure will be failed with such error. To solve such problems, you may have to set the path to the executables and libraries about MPI in “~/.bashrc” or specify the compilers explicitly in the configure command. You should also check the typing mistakes in the path.
  • If recommended software is not used for compilation, warning messages might be displayed in the terminal when the configure command is executed. That message is just a warning (not an error), and you can continue the compilation. However, we strongly recommend you perform installation check in such cases
  • In some supercomputer systems, “module load [module]” command might be required before the configure command. See the user guide of the supercomputer system.
  • Make an attempt to execute “autoreconf” or “./bootstrap” before the configure. If your computer environment is significantly different from the developer’s one, or if you modified “configure.ac” or “Makefile.am” by yourself, this attempt may work well.
Make install
  • If the error message is like “/usr/bin/ld: cannot find -lblas” or “/usr/bin/ld: cannot find -llapack”, make sure that the BLAS or LAPACK libraries are installed in the computer. The users may also have to set the path to the libraries in the “configure” command with the “LAPACK_LIBS” or “LAPACK_PATH” option.
  • If the error message is like “Fatal Error: Can’t delete temporary module file ‘…’: No such file or directory”, please try to run “make install” without the “-j” option.
Other minor errors
  • If compilation stops at math_libs.f90 with a lot of error messages saying “no such instruction”, please change all “-march=native” to “-march=corei7” in ./src/configure. This kind of error was found when Haswell CPU and gcc4.6 (or older?) are used.
  • ifort version 12.1.0 (20110811) and ifort version 15.0.1 (20141023) have a serious problem in GENESIS. Do not use these compiler versions. Later versions of 12.1.x or 15.0.x series work fine.
  • If the error message is like “aclocal-xxx: command not found or configure.ac:xxxx: error: possibly undefined macro AM_COND_IF”, your environment is very much different from the developer’s one. In this case, you need to run ./bootstrap and ./configure again. This problem may not happen in GENESIS 1.2.0 or later.
  • If Makefile.depends is lost or broken, parallel compilation using -j option will fail. If you encounter this situation, please go to the directory where the error occurred and check the existence of Makefile.depends. If Makefile.depends does not exist, you can create the file by executing make depend.


Verify the installation

The users can verify the installation of GENESIS by using “test sets” prepared by the developers, which are available in the Download page. The following commands verify the installed spdyn. For detailed usage of the test sets, see Chapter “Getting started” in the user manual.

$ mv ~/Downloads/tests-X.Y.Z.tar.bz2 ./
$ tar xvfj tests-X.Y.Z.tar.bz2
$ cd tests-X.Y.Z/regression_test
$ export OMP_NUM_THREADS=1
$ ./test.py "mpirun -np 8 /home/user/genesis-X.Y.Z/bin/spdyn"


Installation for various computer systems