Recent changes to build-Guide

build-Guide modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 Nov 2024 09:10:31 -0000

--- v19
+++ v20
@@ -40,7 +40,7 @@

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

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

 #### When using MKL WITHOUT Intel Compiler

build-Guide modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 Nov 2024 03:13:57 -0000

--- v18
+++ v19
@@ -18,8 +18,8 @@

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

-    tar xzf ermod-0.x.xxx.tar.gz
-    cd ermod-0.x.xxx
+    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.

build-Guide modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Fri, 29 Nov 2024 02:30:06 -0000

--- v17
+++ v18
@@ -37,7 +37,11 @@
  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 CC=icc --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

build-Guide modified by Shun Sakuraba

Shun Sakuraba — Fri, 29 Nov 2024 02:04:36 -0000

--- v16
+++ v17
@@ -11,8 +11,8 @@
     * Intel(R) MKL
 +  LAPACK-compatible library

-Fortran compilers are currently supported actively only for GCC (gfortran) and intel fortran (ifort), however we have successfully compiled the program with IBM xlf90 and Fujitsu frt. For FFT library, we recommend FFTW3 because it is faster for 3D-FFT computation. For LAPACK library, we recommend [Intel(R) MKL](http://www.intel.com/software/products/mkl/), [AMD Core Math Library](http://www.amd.com/acml), or [ATLAS](http://math-atlas.sourceforge.net/).
-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 ver. 1.0, we do not recommend using OpenMP though.
+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](http://www.intel.com/software/products/mkl/), [OpenBLAS](http://www.openmathlib.org/OpenBLAS) or [ATLAS](http://math-atlas.sourceforge.net/).
+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

build-Guide modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 28 Nov 2024 10:02:00 -0000

--- v15
+++ v16
@@ -36,7 +36,7 @@

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

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

 #### When using MKL WITHOUT Intel Compiler

build-Guide modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 28 Nov 2024 05:41:58 -0000

--- v14
+++ v15
@@ -36,7 +36,7 @@

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

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

 #### When using MKL WITHOUT Intel Compiler

@@ -53,7 +53,7 @@

 After sourcing var.sh configure should find MKL libraries.

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

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

@@ -83,13 +83,13 @@

 After sourcing the environmental variables related to MKL,

-    ./configure --with-mkl --prefix=$HOME/(directory to install ERmod program)
+    ./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=$HOME/(directory to which FFTW is installed) --prefix=$HOME/(directory to install ERmod program)
+    ./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)

build-Guide modified by Shun Sakuraba

Shun Sakuraba — Fri, 08 Nov 2024 07:37:51 -0000

--- v13
+++ v14
@@ -36,6 +36,8 @@

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

+    ./configure
+
 #### When using MKL WITHOUT Intel Compiler

 Before executing the configure script, it is necessary to re-load environmental variables related to MKL
@@ -48,6 +50,10 @@
  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 older MKL (Intel Compiler 12.0+) (in X86_64 environment)

build-Guide modified by Shun Sakuraba

Shun Sakuraba — Fri, 08 Nov 2024 07:35:49 -0000

--- v12
+++ v13
@@ -1,10 +1,10 @@
-# Build Guide (for ver. 0.2.x and ver. 0.3.x)
+# Build Guide

 ## Prerequisites

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

-1. Fortran 90 compiler
+1. Fortran 2003 compiler
 +  C compiler
 +  FFT library, one of:
     * FFTW
@@ -12,7 +12,7 @@
 +  LAPACK-compatible library

 Fortran compilers are currently supported actively only for GCC (gfortran) and intel fortran (ifort), however we have successfully compiled the program with IBM xlf90 and Fujitsu frt. For FFT library, we recommend FFTW3 because it is faster for 3D-FFT computation. For LAPACK library, we recommend [Intel(R) MKL](http://www.intel.com/software/products/mkl/), [AMD Core Math Library](http://www.amd.com/acml), or [ATLAS](http://math-atlas.sourceforge.net/).
-Optionally, ERmod can also be run in parallel environment with the MPI (MPI-1.3 or later) and/or OpenMP (3.0 or later). 
+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 ver. 1.0, we do not recommend using OpenMP though.

 ## Configuration

@@ -25,11 +25,31 @@
 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
+#### 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. 
+
+#### 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 (Intel Compiler 12.0+) (in X86_64 environment)
+###### 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
+
+###### with older MKL (Intel Compiler 12.0+) (in X86_64 environment)

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

@@ -43,7 +63,7 @@

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

-###### with older MKL (in X86_64 environment)
+###### with very old MKL (in X86_64 environment)

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

build-Guide modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Wed, 04 Mar 2015 06:38:02 -0000

--- v11
+++ v12
@@ -61,9 +61,9 @@

 The option of --prefix will be described below.

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

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

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

build-Guide modified by Nobuyuki MATUBAYASI

Nobuyuki MATUBAYASI — Thu, 22 Jan 2015 09:33:39 -0000

--- v10
+++ v11
@@ -21,24 +21,32 @@
     tar xzf ermod-0.x.xxx.tar.gz
     cd ermod-0.x.xxx

-The “configuration part” can be performed by executing the configure script. This script checks whether the library is accessible, and absorbs the system difference. Here are typical use cases and corresponding commands:
+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 the latest MKL (Intel Compiler 12.0+) (in X86_64 environment)
+#### When using MKL

-    source /opt/intel/Compiler/12.0/084/mkl/bin/intel64/mklvars_intel64.sh
-    ./configure --with-mkl --prefix=$HOME/(directory to install ERmod program)
+Before executing the configure script, it is necessary to re-load environmental variables related to MKL

-The option of --prefix will be described below.
+###### with the latest 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/Compiler/12.0/084/mkl/bin/intel64/mklvars_intel64.csh
+    source /opt/intel/(directory name)/mkl/bin/mklvars.csh intel64

-#### When using older MKL (in X86_64 environment)
+###### with older MKL (in X86_64 environment)

     source /opt/intel/mkl/xx.x.x.xxx/tools/environment/mklvarsem64t.sh
-    ./configure --with-mkl --prefix=$HOME/(directory to install ERmod program)
-
-The option of --prefix will be described below.
+    
 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
@@ -46,6 +54,12 @@
 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=$HOME/(directory to install ERmod program)
+
+The option of --prefix will be described below.

 #### When using FFTW installed under $HOME, and system-wide LAPACK