Intel Software Network articles feed http://software.intel.com/en-us/articles/intel-mpi-library-for-linux-kb/installation/ en-us Building the GAMESS with Intel® Compilers, Intel® MKL and Intel® MPI on Linux Introduction :
This document explains how to build GAMESS using the Intel Software products:
Intel® C++ Compiler for Linux,
Intel® Fortran Compiler for LINUX,
Intel® MKL,
Intel® MPI for Linux.


Version :
GAMESS version January 12, 2009 R3 for 64 bit IA64/x86_64.

Obtaining Source Code :
The GAMESS sources can be downloaded here.

Prerequisites :
Should be installed Intel® Compilers with Intel® MKL and Intel® MPI for Linux.

Environment Set Up :
Environment variables for the Intel(R) C++ Compiler Professional Edition for Linux, Intel(R) Fortran Compiler Professional Edition for Linux and Intel(R) MPI should be set.
E.g.
$export INTEL_COMPILER_TOPDIR="/opt/intel/Compiler/11.1/046"
$. $INTEL_COMPILER_TOPDIR/bin/intel64/ifortvars_intel64.sh
$. $INTEL_COMPILER_TOPDIR/bin/intel64/iccvars_intel64.sh
$. /opt/intel/impi/3.2.1.009/bin64/mpivars.sh

Building the Application :
1)Copy/move tar file gamess-current.tar.gz to the directory /opt.

2)Decompress source files
$ tar -zxvf gamess-current.tar.gz
.
3)
$cd ./gamess
.
4) Creating actvte.x file:
$cd ./tools
$cp actvte.code actvte.f
Replace all "*UNX" by " "(4 spaces with out " ") in the file actvte.f. Can be used any text editor.
$ifort -o actvte.x actvte.f
$rm actvte.f
$cd ..
.
5)Building the Distributed Data Interface(DDI) with Intel(R) MPI:
$cd ./ddi
a) Editing file ./compddi.
Set machine type (approximately line 18):
set TARGET=linux-ia64
Set MPI communication layer (approximately line 48):
set COMM = mpi
Set include directory for Intel® MPI (approximately line 105):
set MPI_INCLUDE_PATH = '-I/net/spdr62/opt/spdtools/impi/intel64/3.2.011/include64'
b)Build DDI with Intel(R) MPI
$ ./compddi >&compddi.log
c) If building completed successfully then library libddi.a will appear. Otherwise check compddi.log for errors.
d) $cd ..
.
6) Compiling the GAMESS:
a) Editing file ./comp
Set machine type (approximately line 15):
set TARGET=linux-ia64
Set the GAMESS root directory (approximately line 16):
chdir /opt/gamess
Uncomment line 1461:
setenv MKL_SERIAL YES
.
b) Editing file ./compall:
Set machine type (approximately line 16):
set TARGET=linux-ia64
Set the GAMESS root directory (approximately line 17):
chdir /opt/gamess
Set to use Intel® C++ Compiler (approximately line 70):
if ($TARGET == linux-ia64) set CCOMP='icc'
c) Compiling the GAMESS:
$compall >&compall.log
Check file compall.log for errors.
d)
$cd ..
.
7)Liniking the GAMESS with Intel® Software products:
a) Editing file ./lked
Set machine type (approximately line 18):
set TARGET=linux-ia64
Set the GAMESS root directory (approximately line 19):
chdir /opt/games
Set MKL environment (approximately line 509):
setenv MKLPATH /net/spdr62/opt/spdtools/compiler/cpro/Compiler/11.1/046/mkl/lib/em64t
setenv MKL_SERIAL YES
set mklver=10
Set the message passing libraries in a single line (approximately line 714):
set MSG_LIBRARIES='../ddi/libddi.a -L/net/spdr62/opt/spdtools/impi/intel64/3.2.011/lib64 -lmpi -lmpigf -lmpigi -lrt -lpthread'
b) Link the GAMESS
$./lked >&lked.log
If linking completed successfully then executable file gamess.00.x will appear. Otherwise check lked.log for errors.

Running the Application :
This section below describes how to execute GAMESS with Intel® MPI. For further information check file ./ddi/readme.ddi.
For the testing GAMESS will be used script rungms as the base.
1)
Only few amends are needed.
Set the target for execution to mpi (line 59):
set TARGET=mpi
.
Set a directory SCR where large temporary files can reside(line 60):
E.g.
set SCR=/opt/gamess/tests
.
Correct the setting environment variables ERICFMT and MCPPATH (lines 127and 128):
E.g.
setenv ERICFMT /opt/gamess/ericfmt.dat
setenv MCPPATH /opt/gamess/mcpdata
.
Replace all “~$USER” by “/opt/gamess/tests”. Or by other directory.
NOTE: Directory /opt/gamess/tests/scr should exist. If no then create it.
Replace all “/home/mike/gamess” by “/opt/gamess”.
Correct the setting environment variables for Intel® MKL and MPI (lines 948 and 953):
E.g.
setenv LD_LIBRARY_PATH /opt/Compiler/11.1/046/mkl/lib/em64t
setenv LD_LIBRARY_PATH /opt/intel/impi/intel64/3.2.011/lib64:$LD_LIBRARY_PATH
.
Correct setting environment variables to execution Intel® MPI path (line 954):
E.g. set path=(/opt/intel/impi/intel64/3.2.011/bin64 $path)
.
Done.
2)
Now choose the testcase from directory ./tests and run GAMESS.
E.g.
$./rungms exam08
The output data will be stored in the directory /opt/gamess/scr.

3) To execute GAMESS on 2 or more processes on 1 node:
$ ./rungms exam08 00 2
]]> http://software.intel.com/en-us/articles/building-gamess-with-intel-compilers-intel-mkl-and-intel-mpi-on-linux Wed, 26 Aug 2009 07:02:09 -0700 http://software.intel.com/en-us/articles/building-gamess-with-intel-compilers-intel-mkl-and-intel-mpi-on-linux#comments http://software.intel.com/en-us/articles/building-gamess-with-intel-compilers-intel-mkl-and-intel-mpi-on-linux Intel Software Network communities Intel® MKL Intel® MPI Library Intel® C++ Compiler for Linux* Knowledge Base Intel® Fortran Compiler for Linux* Knowledge Base Intel® MPI Library for Linux* Knowledge Base Installing the Intel(R) Cluster Tools on Debian-based systems I have a Debian-based system and would like to use the Intel® Cluster Tools. Is there a way?

Officially, the Intel Cluster Tools support RPM-based installs only. For a full list of supported OSes, check out our compatibility matrix.

If you’d still like to use the tools on Debian and Ubuntu systems, the following steps can help you in, at least, installing the tools. Note that the process below still requires that a valid license for the desired Cluster Tool is present on the machine.

  1. Download the latest version of the Intel® MPI Library for Linux* from the Intel® Registration Center.

  2. Untar the package and go down into the newly created directory
    $ tar –xzf l_mpi_p_3.2.1.009.tgz
    $ cd l_mpi_p_3.2.1.009/

  3. Create a new directory and extract the RPM files using the provided install.sh script. Note that you’d need a valid license to do so.
    $ mkdir rpms

    $ ./install.sh --extract=./rpms
    Extracting components...
    Extracting files... ################################################ [100%]
    Product's rpm and EULA have been extracted in ./rpms
    Please carefully read EULA before using the product

    $ ls –l
    intel-mpi-em64t-3.2.1p-009.x86_64.rpm # SDK for the Intel MPI Library for Linux*
    intel-mpi-rt-em64t-3.2.1p-009.x86_64.rpm    
    		# Runtime component of the Intel MPI Library
    mpiEULA.txt # End-User License Agreement for the Intel MPI Library.
    # Read before using.
    redist.txt # List of Intel MPI Library files whose redistribution is allowed

  4. Convert the RPM files into DEB files, to be installed on your Debian-based system using the alien utility
    $ which alien
    /usr/bin/alien

    $ alien intel-mpi-em64t-3.2.1p-009.x86_64.rpm
    intel-mpi-em64t_3.2.1p-10_amd64.deb generated
    Here note that converting the SDK package for the Intel MPI Library is enough, as the runtime libraries are already contained within.

  5. Now that you have the .deb file generated, install using your preferred method. For example, this is how it’s done using the dpkg utility
    # This will use the default /opt/intel installation directory
    $ dpkg --install intel-mpi-em64t_3.2.1p-10_amd64.deb

  6. Done! You are now free to enjoy the Intel MPI Library at your leisure.

    7. Even though this example highlighted the Debian-based installation of the Intel MPI Library, the same technique can be applied to the Intel® Cluster Toolkit for Linux*, Intel® Cluster Toolkit Compiler Edition for Linux*, and the Intel® Trace Analyzer and Collector for Linux*.

]]> http://software.intel.com/en-us/articles/installing-cluster-tools-on-debian Wed, 19 Aug 2009 09:56:06 -0700 http://software.intel.com/en-us/articles/installing-cluster-tools-on-debian#comments http://software.intel.com/en-us/articles/installing-cluster-tools-on-debian Intel® Cluster Toolkit for Linux* Knowledge Base Intel® MPI Library for Linux* Knowledge Base Intel® Trace Analyzer and Collector for Linux* Knowledge Base Mutiple Installation Allowed for One User with Single User License  


Problem : 
I have a single user license. Can I install the product on different machines with mutiple times?

Resolution : 
Yes, you can. Single-user license allows the license owner to install the product on mutiple systems. however, only ONE copy of the software may be in use at any one time.
Please see End User License Agreement for your reference.
]]> http://software.intel.com/en-us/articles/mutiple-install-allowed-with-single-user-lic Mon, 18 May 2009 23:56:47 -0700 http://software.intel.com/en-us/articles/mutiple-install-allowed-with-single-user-lic#comments http://software.intel.com/en-us/articles/mutiple-install-allowed-with-single-user-lic Intel® C++ Compiler for Linux* Knowledge Base Intel® C++ Compiler for Mac OS X* Knowledge Base Intel® C++ Compiler for Windows* Knowledge Base Intel® Cluster Toolkit for Linux* Knowledge Base Intel® Cluster Toolkit for Windows* Knowledge Base Intel® Fortran Compiler for Linux* Knowledge Base Intel® Fortran Compiler for Mac OS X* Knowledge Base Intel® Math Kernel Library Knowledge Base Intel® MPI Library for Linux* Knowledge Base Intel® MPI Library for Windows* Knowledge Base Intel® Parallel Amplifier Knowledge Base Intel® Parallel Composer Knowledge Base Intel® Parallel Inspector Knowledge Base Intel® Software Development Products Registration Center Knowledge Base Intel® Thread Checker for Linux* Knowledge Base Intel® Thread Checker for Windows* Knowledge Base Intel® Thread Profiler for Windows* Knowledge Base Intel® Threading Building Blocks Knowledge Base Intel® Visual Fortran Compiler for Windows* Knowledge Base Intel® VTune™ Performance Analyzer for Linux* Knowledge Base Intel® VTune™ Performance Analyzer for Windows* Knowledge Base General installation information
  • Installation prerequisites
  • Installation tips
  • Possible installation problems

    • Installation prerequisites
    Before using the Intel® MPI Library, make sure that following packages are installed on your system:

    • Python* version 2.2 or higher, including the python-xml module. Python* distributions are available for download from your OS vendor or at http://www.python.org† .
    • An XML parser such as expat or pyxml
    • If using InfiniBand*, Myrinet*, or other RDMA-capable network fabrics, a DAPL* version 1.1 or DAPL* version 1.2 standard-compliant provider library/driver is required. DAPL* providers are typically provided with your network fabric hardware and software.

    Installation tips
    To install the Intel MPI Library for Linux*, do the following:

    1. Obtain a license key. Go to the Intel® Registration Center to obtain the license if you do not have a license key.
    2. The installer provides an ability to install the Intel MPI Library on every node of your cluster. To utilize this feature create a machines.LINUX file that lists the nodes in the cluster using one hostname per line before starting the installation process. Make sure that the cluster has ssh connectivity.
    3. Install the l_mpi[-rt]_p_<version>.<package#>.tar.gz package by using the following commands:
      # cp l_mpi[-rt]_p_<version>.<package#>.tar.gz /tmp
      # cd /tmp
      # tar -xzf l_mpi[-rt] ]_p_<version>.<package#>.tar.gz
      The last command will create subdirectory l_mpi[-rt]_p_<version>.<package#>
    4. Place the license file for the Intel MPI Library that is provided to you in /tmp/l_mpi_p_<version>.<package#> Do not change the file name as the ".lic" extension is critical. For instance, do the following:commands:
      <# cd cp l_mpi[-rt]_p_<version>.<package#>
      # cp <license key>.lic.
      Take into account the following notes:
      • This installation does not overwrite any pre-existing Intel MPI Library you may have installed.
        After installing the Intel® MPI Library you can continue to use the pervious versions of the Intel MPI Library by referring to the original installation directory.
      • The ./install script allows you to avoid modification of the /etc/ld.so.conf file during installation in root mode. Use the --update-ldsoconf option, for example:
        # ./install --update-ldsoconf no
      • You can install the Intel MPI Library as an ordinary user. Run the ./install script and follow the instructions, or add the --nonroot --nonrpm options to the ./install invocation string above to select the non-root, non-RPM installation mode.
      • You can install the Intel MPI Library on a system that does not use the RPM* package manager. Add the --nonrpm option to the ./install invocation string above to select the non-RPM installation mode.
        Alternatively, you can extract the Intel MPI Library RPM* package and mpiEULA.txt file. Use the --extract option and indicate the desired extraction directory, for example:
        # ./install --extract /tmp
      • The ./install script enables you to select the install location on most operating systems. Select the exact same install location when installing Intel MPI Library on each node of your cluster.
      • The default installation path for the Intel MPI Library is /opt/intel/impi/3.2
      • The ./install script has a silent installation mode that can help you to install Intel MPI Library on clusters with many nodes. In order to use this mode, edit the file SilentInstallConfigFile.ini contained in the unpacked package directory. In particular, change the line
        EULA=reject
        to read
        EULA=accept
        Other lines in the file enable you to define the INSTALLDIR, LICENSEPATH, INSTALLMODE, PROCEED_WITHOUT_PYTHON, UPDATE_LD_SO_CONF, INSTALLUSER, ARCH, AUTOMOUNTED_CLUSTER, MACHINES_CONFIG and SKIP_MOUNTED parameters.
        After editing the file use the following command instead of the usual # ./install command:
        # ./install --silent SilentInstallConfigFile.ini
    5. Add the following PATH and/or LD_LIBRARY_PATH settings in your .cshrc or .bashrc files so that the settings are visible on all nodes in your cluster:
    • Ensure that Python* is in your PATH
    • Source the appropriate mpivars.[c]sh script from the Intel MPI Library bin (or, if applicable, bin64) directory
    • If using Intel® compilers, source any required *vars.[c]sh scripts
    • Set up additional environment variables as needed. See the Intel MPI Library for Linux Getting Started Guide for more information.

    Possible installation problems

    • If installation of the Intel MPI Library package fails and shows the error message: "Intel® MPI Library already installed" when a package is not actually installed, try the following:
    • Determine the package number that the system believes is installed by typing:
      # rpm -qa | grep intel-mpi
      This command returns an Intel MPI Library <package name>.
    • Remove the package from the system by typing:
      # rpm -e <package name>
    • Re-run the Intel MPI Library installer to install the package.
      TIP: To avoid installation errors, always remove Intel MPI Library packages using the uninstall script provided with the package before trying to install a new package or reinstall an older one.
    • Due to an installer limitation, avoid installing earlier releases of the Intel MPI Library packages after having already installed the current release. It corrupts the installation of the current release and requires that you uninstall/reinstall it.

    † This link will take you off of the Intel Web site. Intel does not control the content of the destination Web Site.

    ]]>     http://software.intel.com/en-us/articles/intel-mpi-library-for-linux-general-installation-information Fri, 19 Sep 2008 00:00:00 -0700 http://software.intel.com/en-us/articles/intel-mpi-library-for-linux-general-installation-information#comments http://software.intel.com/en-us/articles/intel-mpi-library-for-linux-general-installation-information Intel® MPI Library for Linux* Knowledge Base