build-Guide

Build Guide

Prerequisites

The installation of “solvation free energy calculator based on the method of energy representation” (called ERmod hereafter) requires:

1. Fortran 2003 compiler
2. C compiler
3. FFT library, one of:
   • FFTW
   • Intel(R) MKL
4. LAPACK-compatible library

Fortran compilers are currently supported actively only for GCC (gfortran) and intel fortran (ifort/ifx), however we have successfully compiled the program with other Fortran compilers such as Fujitsu frt. For FFT library, we recommend FFTW3 because it is readily available for many Linux distributions. For LAPACK library, we recommend Intel(R) MKL, OpenBLAS or ATLAS.
Optionally, ERmod can also be run in parallel environment with the MPI (MPI-1.3 or later) and/or OpenMP (3.0 or later). At the momoent of ERmod ver. 1.0, we do not recommend using OpenMP, because OpenMP version does not provide good scaling compared to flat MPI.

Configuration

The ERmod can be built like standard UNIX packages. First of all, unpack the distribution package in a working directory:

tar xzf ermod-x.x.xx.tar.gz
cd ermod-x.x.xx

The “configuration part” can be performed by executing the configure script.
This script checks whether the library is accessible, and absorbs the system difference.
The followings are typical use cases and corresponding commands:

When using MKL with Intel Compiler

source /opt/intel/(version)/compiler/(version+)/env/vars.sh

where (version) can be e.g. 2023.2 and (version+) can be e.g. 2023.2.0.
The script may be found with the following command:

 find /opt/intel -name vars.sh

After sourcing vars.sh, MKL will be automatically found and linked.

./configure --with-mkl --prefix=(directory to install ERmod program)

If the above configure fails with errors, use the following command.

./configure FC=ifort --with-mkl --prefix=(directory to install ERmod program)

When using MKL WITHOUT Intel Compiler

Before executing the configure script, it is necessary to re-load environmental variables related to MKL

with the latest MKL

source /opt/intel/(version)/mkl/(version+)/env/vars.sh

where (version) can be e.g. 2023.2 and (version+) can be e.g. 2023.2.0.
The script may be found with the following command:

 find /opt/intel -name vars.sh

After sourcing var.sh configure should find MKL libraries.

./configure --with-mkl --prefix=(directory to install ERmod program)

with older MKL (Intel Compiler 12.0+) (in X86_64 environment)

source /opt/intel/(directory name)/mkl/bin/mklvars.sh intel64

where (directory name) can be composer_xe_20xx.x.xxx, compilerpro-12.x.x.xxx or Compiler/12.0/xxx, depending on the edition and/or version.
In future versions of Intel compiler, it may not be apparent where the script is.
The script may be found with the following command:

 find /opt/intel -name mklvars.sh

When the shell is csh or tcsh, the above source command reads as

source /opt/intel/(directory name)/mkl/bin/mklvars.csh intel64

with very old MKL (in X86_64 environment)

source /opt/intel/mkl/xx.x.x.xxx/tools/environment/mklvarsem64t.sh

When the shell is csh or tcsh, the above source command reads as

source /opt/intel/mkl/xx.x.x.xxx/tools/environment/mklvarsem64t.csh

In the above, xx.x.x.xxx denotes the version of the MKL. To see it, type

ls /opt/intel/mkl

After sourcing the environmental variables related to MKL,

./configure --with-mkl --prefix=(directory to install ERmod program)

The option of --prefix will be described below.

When using FFTW installed under user's own directory, and system-wide LAPACK

./configure --with-fftw=(directory to which FFTW is installed) --prefix=(directory to install ERmod program)

When using system-wide FFTW and system-wide LAPACK, and installs system-wide (you must be root)

./configure

---

If configuration finished successfully, the final line in the configuration should be:

Configuration complete; type "make" to start compiling

If you see this message, proceed to the next ("Building core").

Otherwise, you should see an error message about which library is missing. Check your environment and contact system administrator of the computer. config.log file may help finding the problem.

Several other compilation options can be specified through command line and environment variables. Try ./configure --help to see the list of switches. Notable options are:

--prefix=/foo/bar

Installs program at /foo/bar.

--with-fft=fftw

Uses fftw even if mkl is found

Building core

If configuration completed successfully, type

make

to start compiling. After successful compilation, two executable binaries will be created, namely ermod and slvfe. If something went wrong, check errors and try reconfiguring with additional options.

Building plugins

In order to use the ermod program, VMD plugins to access trajectories needs to be compiled. Considering the current trends on cluster computing, ERmod is shipped with plugin compiled with x86_64/Linux environment. Check your environment with:

uname –mo

If the result is “x86_64 GNU/Linux”, precompiled plugins works without any special procedure. Otherwise, follow the instructions in [build-VMDPlugin].

Installation

Install programs, plugins, and tools to appropriate directories with

make install