Hardware specification on Borges

Borges is a SMP cluster of 4 nodes, each node has two dual-core 2.0GHZ Xeon "woodcrest" CPUs and 8GB of RAM. The nodes are interconnected with both Gigabit Ethernet and DDR Infiniband. The operating system is Red Hat Enterprise Linux 4.

CCA Chemistry Starter Section

If you are confused by all the processes required to create a chemistry component, this document may ease your frustration a little bit. It is a GAMESS CCA document, but may provide information for you to work on the other packages.

The souce of packages that we have installed on Borges are under /scratch/packages. It is not organized and contains many different version of a package. We will gradually put the organized packages under /scratch/cca-chem-pacakges. Currently there are only three packages under /scratch/cca-chem-packages: gamess-component, mpqc and nwchem-5.0.

Software installation and usage on Borges

Any software issue, installation or usage, contact mswu@scl.ameslab.gov.

If you are looking for a package, look under /opt/ifort-pkgs/ first.

  1. Some tips for installing software
  2. Fortran 90 compiler: Intel ifort
  3. Fortran 90 compiler: gfortran
  4. Compiling GAMESS
  5. Compiling GAMESS Component
  6. Compiling NWChem
  7. Compiling MPQC
  8. Building cca-chem-generic2, official cca-chem-generic2 document from Joe
  9. Building cca-chem-apps2
  10. MPICH-1.2.7p1
  11. MPICH2-1.0.5p4
  12. MVAPICH-0.9.8
  13. Compiling CCA-Tools
  14. How to install CCA with a Babel not of the default version
  15. Intel Math Kernel Library(MKL)
  16. Intel CPP Compiler
  17. Python issue with CCA after version 0.6.2_rc3
  18. JAVA
  19. GotoBLAS
  20. Instrumenting GAMESS, NWChem and MPQC with TAU
  21. Testing cca-chem-generic2 package
  22. Template


  1. Some tips for installing software

    1. CCA-tools needs Java, and it needs the right one. One Borges do NOT use the one under /usr/bin. Have "/opt/jdk1.6.0/include:/opt/jdk1.6.0/bin" included in your path before /usr/bin.

    2. There are several version of MPI under /opt/ifort-pkgs/. Pick the one you want to use, and have its "/bin/" and "/include/" in your path.

    3. I assume many people like to challenge themselves by trying to install cca-tools. Since there are different versions of cca-tools and babel, here is an important tip. Before you install a new version of cca-tools, REMOVE ANY ACCESS to previous installed cca-tools in your path. If you are installing a new version of cca-tools and in your path there is access to old cca-tools, it's very likely that the installation will fail and you will have a lot of fun looking for what went wrong.

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  2. Fortran 90 compiler: Intel ifort

    Intel FORTRAN compiler is located in /opt/intel/. The 32-bit version is under /fc sub-directory, and the 64-bit version is under /fce sub-directory. On Borges, I strongly suggest you use the 64-bit version to compile your FORTRAN 90 programs on Borges (The 32-bit version can not be used when compiling mpich2).

    To use Intel ifort, put the following line at the end of your login shell:

    source /opt/intel/fce/9.1.043/bin/ifortvars.sh

    When compiling some packages, you may need to set some environment variables to enable use of ifort. For example, when compiling mpich2, you will have to set F90=ifort (also, setting F77=ifort is strongly suggested).

    Intel ifort can produce binary code that is not compatible with binary codes generated by g77. If you have FORTRAN 77 codes compiled by g77, you may have to re-compile them with ifort to ensure the compatibility between your FORTRAN 77 and FORTRAN 90 codes.

    On Borges, packages compiled with Intel ifort (mpich, cca-tools etc.) are put undet the directory /opt/ifort-pkgs/.

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  3. Fortran 90 compiler: gfortran

    gfortran is the default FORTRAN 90 compiler on Borges. The version under /usr/bin/gfortran is 4.1.0. While it can be used to compile many FORTRAN 90 programs, we encountered some unexpected errors. For example, if mpich2 is compiled with gfortran and with option "--enable-sharedlib=gcc", and NWChem is also compiled with gfortran, running the testing data will encounter segmentation fault. We did not find this problem when all programs are compiled with Intel ifort.

    For some unknown reason, there are gfortran 4.1.1 or 4.1.2 rpm packages for different Linux, but none for RedHar Enterprise 4 (the one on Borges). gfortran-4.2.0 (pre-release) and gfortran-4.3.0 (experimental) are tested, they generated more problems then 4.1.0, and we don't encourage you use them on Borges. (If you insist to use them, they are under (/scratch/packages/gfortran/gcc-4.2/bin for gfortran 4.2.0 and /scratch/packages/gfortran/gcc-trunk/bin for gfortran 4.3.0).

    You can directly use gfortran on Borges without adding anything to your shell.

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  4. Which FORTRAN 90 compiler to use is totally up to you. Using Intel ifort you may encounter less troubles (on Borges); however, it is a commercial product and you don't know when Intel will drop their "Non-commercial download" again like they did in 2006. gfortran is free, but you may encountered some troubles that will take a while to figure out that they are caused by compiler. At this monent I suggest using Intel ifort for our short term projects.

  5. Compiling GAMESS

    The latest update for DDI is: March 2007

    The latest update for GAMESS is: March 2007

    1. copy the package "gamess.tgz" to the current directory

    cp /scratch/fangp/packages/gamess/gamess.tgz .

    2. uncompress the package

    tar zxvf gamess.tgz

    3. edit ddi/compddi
    set FC = ifort
    set TARGET = linux64
    set COMM = sockets (for "sockets" model), or set COMM = mpi (for "mpi" model)
    set MPI_INCLUDE_PATH = '-I/opt/ifort-pkgs/mpich2-1.0.5p4-sharedlib/include'

    4. compile ddi
    cd ddi; ./compddi
    mv ddikick.x ..
    cd ..

    5. modify activate tool
    cd tools
    cp actvte.code actvte.f
    vi actvte.f
    use the command ":%s/^*UNX/ /g" ------- four blanks
    use the command ":wq"
    ifort -o actvte.x actvte.f

    6. edit comp
    set TARGET = linux64
    set FC=ifort
    uncomment "chdir /u1/mike/gamess"

    7. edit compall
    set TARGET = linux64
    uncomment "chdir /u1/mike/gamess"

    8. compile GAMESS source code
    ./compall >& compall.log &
    tail -f compall.log

    9. edit lked
    set TARGET = linux64
    uncomment "chdir /u1/mike/gamess"
    set FC =ifort
    use the command ":%s/mkl\/\*\/lib/mkl\/9.0\/lib/g"

    10. link to executable

    11. edit rungms
    set SCR = /scratch/$USER
    setenv ERICFMT the-path-to-gamess-source-code
    setenv MCPPATH the-path-to-gamess-source-code
    make sure you have "~$USER/scr" directory for storing .irc and .dat files, otherwise, you need to modify the environment variables "IRCDATA", "PUNCH", "SIMEN" and "SIMCOR".
    under "$TARGET == sockets" section (search for "$TARGET == sockets"),
    if ($os == Linux) set GMSPATH=the-path-to-gamess-source-code

    12. edit runall
    uncomment "chdir /u1/mike/gamess"

    13. test gamess
    set LD_LIBRARY_PATH=/opt/intel/mkl/9.0/lib/em64t

    14. verify gamess
    cd tools/checktst
    vi checktst
    set GMSPATH=the-path-to-gamess-source-code

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  6. Compiling GAMESS Component


    Please always use the newest version of gamess-component

    Required Packages:

    cca-tools-0.6.1_rc2, babel-1.0.2, cca-chem-generic2

    Suggested Build Sequences:

    1. open the gamess-component package
    tar zxvf gamess-component-$VERSION.tgz

    2. configuring the package
    You can use "./configure --help" to check all of options. There are several options need to be specified carefully.
    "--with-cca-chem-config" specify the full path to cca-chem-config script.

    "--with-ccafe-config" specify the full path ccafe-config script.

    "--with-languages" specify the Babel-supported languages that also supported by CCA chemistry interfaces. The current supported languages are "cxx, f77".

    "--with-target" specify the machine used for compiling GAMESS. The legal values for TARGET are axp64,compaq-sc,cray-pvp,cray-t3e,cray-x1,cray-xd1,cray-xt3, fuji-pp32,fuji-pp64,hpux32,hpux64,ibm32,ibm64,ibm64-sp,ibm-bg, linux32,linux64,linux-ia64,mac32,macG5,necsx, sgi32,sgi64,sun32,sun64. The default value is "linux32".

    "--with-target-model" specify the prarallism model used by DDI. Use 'sockets' if a TCP/IP stack is available (every Unix has TCP/IP). Choosing 'sockets' will produce a process kickoff program 'ddikick.x' as well as the DDI library. Use 'mixed' or 'mpi' only for specialized hardware situations, for example if your network supports only MPI. The 'mpi' option runs using 100% MPI-1 calls. The 'mixed' option uses almost entirely MPI-1 calls, but uses TCP sockets to avoid some of MPI's polling, resulting in better wall clock times than 100% MPI. The current supported options are "sockets" and "mpi". The default value of this option is "sockets".

    "--with-scratch-dir" specify the directory where large temporary files can reside. This should be the fastest possible disk access, very spacious, and almost certainly a local disk. The default scratch directory is "/tmp".

    "--with-fc" specify the fortran 77 compiler used for compiling gamess component. The default compiler is g77.

    The following is an example of configuration:

    configure --prefix=/clusters/scl/fangp/prefix/gamess-component-0.1.2 --with-cca-chem-config=/clusters/scl/fangp/prefix/cca-chem-generic2/bin/cca-chem-config --with-target="linux64" --with-target-model="sockets" --with-languages="cxx f77" --with-fc=ifort

    3. compile gamess component
    use the command "make".
    goto the directory "gamess-component-$VERSION/shared", and "make clean;make".

    4. test gamess component
    goto the directory "gamess-component-$VERSION/components/example" and type "make test" to do a simple test.

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  7. Compiling NWChem

    (1). configuration:

    export NWCHEM_TOP=/clusters/scl/fangp/nwchem-5.0
    export ENABLE_COMPONENT=yes
    export LIB_DEFINES="-DDFLT_TOT_MEM=16777216"
    export TCGRSH=ssh
    export USE_MPI=y
    export MPI_INCLUDE=/opt/ifort-pkgs/mpich2-1.0.5p4-sharedlib/include
    export MPI_LIB=/opt/ifort-pkgs/mpich2-1.0.5p4-sharedlib/lib
    export LIBMPI="-lmpich -lpthread"
    export NWCHEM_MODULES=all
    cd $NWCHEM_TOP/src
    make nwchem_config

    I save the above as a file (for example, make_nwchem), then issue:
    source make_nwchem

    The available NWCHEM_MODULES are:
    NWints atomscf ddscf develop gradients moints nwdft rimp2 stepper driver dftgrad scfaux cphf ccsd vib mcscf prepar esp hessian plane_wave selci dplot mp2_grad oimp2 qhop property nwpw fft rimp2_grad python analyz nwmd cafe space drdy vscf uccsdt qmmm qmd etrans tddft tce geninterface bq cons perfm neb dntmc

    (2). build the package
    make FC = ifort (you can set it to FC = gfortran at your own risk)

    (3). test the package
    cd $NWCHEM_TOP/src
    export PATH=path-to-nwchem-binary:$PATH
    nwchem nwchem.nw

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  8. Compiling MPQC

    1. download the latest version of mpqc that work with babel-1.0 branch

    cvs -d:pserver:anonymous@mpqc.cvs.sourceforge.net:/cvsroot/mpqc login
    cvs -z3 -d:pserver:anonymous@mpqc.cvs.sourceforge.net:/cvsroot/mpqc co -P -r babel-1-0-branch mpqc

    2. create configure file

    goto the directory "mpqc"
    use the command: aclocal -I lib/autoconf; autoconf

    3. create a build directory for mpqc

    for example, we can create a "build" directory under mpqc:
    cd mpqc; mkdir build
    in the following steps, I will suppose we compile mpqc under the directory mpqc/build

    4. configuring mpqc

    There are several options that we need to specify to make mpqc work on borges wiith component enabled.

    "--with-default-parallel" option specify the default parallism model: none, mpi, armcimpi or mtmpi. The default value for this option is none.
    "--enable-components" option enable CCA components being built.
    "--with-cca-chem-config" option specify the path to the configure file "cca-chem-config".
    "--with-ccafe-config" option specify the path to the configure file "ccafe-config"
    "--enable-shared" option allow the shared library being generated.

    The path to some include or library directory should also be provided, such as the include and library path to mpi program and a math library. The compiler options can also be specified, such as "--with-f77", "--with-cc", "--with-cxx".

    An example of configuation is:

    ../configure --prefix=/clusters/scl/fangp/prefix/mpqc-babel-1.0 --with-default-parallel=mpi --enable-components --with-cca-chem-config=/clusters/scl/fangp/prefix/cca-chem-generic2/bin/cca-chem-config --with-ccafe-config=/opt/ifort-pkgs/cca-tools-0.6.1_rc2-babel-1.0.2/bin/ccafe-config --with-include="-I/opt/ifort-pkgs/mpich2-1.0.5p4-sharedlib/include" --with-libs="-lmpich -llapack -lpthread" --with-libdirs="-L/opt/ifort-pkgs/mpich2-1.0.5p4-sharedlib/lib -L/opt/intel/mkl/9.0/lib/em64t" --enable-shared --with-f77=ifort --with-cc=gcc --with-cxx=g++

    5. compiling mpqc

    use "make; make install" to compile and build mpqc.
    set environment variable PATH=path-to-mpqc-bin:$PATH

    6. test mpqc

    goto the directory "mpqc/build/src/bin/mpqc/validate"(if you can not get it work, try to run it under mpqc/build) and use "make check0" to do the simple check. You can choose to make more complicated tests by usin other test commands. The list of testing options is as follows:

    'make check0' to run and check the small test suite
    'make check0_run' to run the small test suite
    'make check0_chk' to check the small test suite
    'make check1' to run and check the intermediate test suite
    'make check1_run' to run the intermediate test suite
    'make check1_chk' to check the intermediate test suite
    'make check2' to inputs and check the full test suite
    'make check2_run' to run the full test suite
    'make check2_chk' to check the full test suite

    For each of the above, MPQCRUN_ARGS=... can be given to to control how the jobs are run. If MPQCRUN_ARGS is given to checkn_run, then the same MPQCRUN_ARGS must be given to the checkn_chk
    'make inputs' to make a run directory containing all inputs.
    This is not needed to run the checks since the inputs from the src directory are used. It is only for maintainer use.
    'make check_clean' removes output and scratch files from the run directory
    'make check_clean_scratch' removes scratch files from the run directory
    Deprecated make targets:
    'make checkrun' to check outputs of the run directory
    'make check' to compare the outputs in run with those in ref
    'make diff' to use the diff program to compare outputs

    7. test CCA component

    There is one mpqc test file - "mpqc.in" under this directory. You need to modify the path to mpqc libraries before the test file can be run. Use "mpqcrun mpqc.in" to do test. Or, you can find the description of commands by using "mpqcrun --help".

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  9. Building cca-chem-generic2

    Required Package


    cca-tools version >= 0.6.1

    babel version >= 1.0.0



    If you have an account for cca-forum.org, you can do the following steps:

    ssh username@cca-forum.org

    cvs co -r release-2-0-branch cca-chem-generic2

    If you don't have an account for cca-forum.org, you can copy the package from /scratch/fangp/packages/cca-chem-generic2



    You have to specify the path to "ccafe-config" script with the option "--with-ccafe-config". An example of configuration is:

    ../configure --with-ccafe-config=/opt/ifort-pkgs/cca-tools-0.6.1_rc2-babel-1.0.2/bin/ccafe-config --prefix=/clusters/scl/fangp/prefix/cca-chem-generic2



    make;make install

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  10. Building cca-chem-apps2

    Required Package


    cca-tools version >= 0.6.1

    babel version >= 1.0.0




    If you have an account for cca-forum.org, you can do the following steps:

    ssh username@cca-forum.org

    cvs co -r release-2-0-branch cca-chem-apps2

    If you don't have an account for cca-forum.org, you can copy the package from /scratch/fangp/packages/cca-chem-apps2



    You have to specify the path to "ccafe-config" script with the option "--with-ccafe-config" and the path to "cca-chem-config" script with the option "--with-ccafe-config". An example of configuration is:

    ./configure --prefix=/clusters/scl/fangp/prefix/cca-chem-apps2 --enable-mpqc --with-cca-chem-config=/clusters/scl/fangp/prefix/cca-chem-generic2/bin/cca-chem-config --with-ccafe-config=/clusters/scl/fangp/prefix/cca-tools-0.6.2_rc3/bin/ccafe-config --with-sc-config=/clusters/scl/fangp/babel-1.0-branch/mpqc/build/bin/sc-config --disable-nwchem --disable-tao



    make;make install

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  11. MPICH-1.2.7p1

    MPICH1 on Borges is compiled with the following settings:

    ./configure --prefix=/opt/ifort-pkgs/mpich-1.2.7p1-sharedlib --enable-sharedlib --enable-f90

    Which FORTRAN compile to used must be set through environment variables F77 or F90. Versions to support shared libraries (with extention -sharedlib in directory name) and without supporting shared libraries are built.

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  12. MPICH2-1.0.5p4

    MPICH2 on Borges is compiled with the following settings:

    ./configure --prefix=/opt/ifort-pkgs/mpich2-1.0.5p4-sharedlib --enable-sharedlibs=gcc --enable-f90 --disable-romio

    Which FORTRAN compile to used must be set through environment variables F77 or F90. Versions to support shared libraries (with extension -sharedlib in directory name) and without supporting shared libraries are built. ROMIO for parallel I/O is disabled as it causes linking error when building NWChem 5.0.

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  13. MVAPICH-0.9.8

    MVAPICH is compiled with the same option as MPICH-1.2.7 which it is built upon.

    ./configure --prefix=/opt/ifort-pkgs/mpich-1.2.7p1-sharedlib --enable-sharedlib --enable-f90

    MVAPICH utilizes Infiniband for message passing. It is installed under /opt/ifort-pkgs/ and currently is under testing.

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  14. Compiling CCA-Tools

    Before installing any version of cca-tools, make sure you remove any path to previously installed CCA tools in your $PATH. If you don't do this, you may not be able to install CCA tools properly.

    On Borges, CCA tools are installed with the following setting:

    ./configure --with-F77=/opt/intel/fce/9.1.043/bin/ifort --with-F90=/opt/intel/fce/9.1.043/bin/ifort --prefix=/opt/ifort-pkgs/cca-tools-0.6.1_rc2-babel-1.0.2 --with-F90-vendor=Intel --with-mpi=/opt/ifort-pkgs/mpich2-1.0.5p4-sharedlib/

    Versions of FORTRAN compilers, mpich2 and installed directory will have to be changed accordingly.

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  15. How to install CCA with a Babel not of the default version

    (1). modify cca-tools-version/ccaffeine-version/cxx/Makefile.Rules.in, under "bug babel stuff" section, edit the line:

    # support for regular babel releases and known-ok dev branches
    # should be inserted above.
    # Adjust the next line if you want to hackingly try another # babel version.
    YOUR_SPECIAL_BABEL=the babel version you want to test (for example: =1.0.2)

    (2). modify cca-tools-version/Makefile.in, at the first two lines, edit:

    # Put no spaces after the following variable.
    BABEL_NAME = the babel package you want to test (for example: =babel-1.0.2)

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  16. Intel Math Kernel Library(MKL)

    Intel MKL is installed under /opt/intel/mkl/. According to testing from Dr.Jonathan Bentz, it provides performance a lot better than using the other math libraries on Intel platforms.

    To use Intel KML, you need to include the path to Intel KML library into your LD_LIBRARY_PATH. There are several versions, make sure you include the libraries under em64t: /opt/intel/mkl/9.0/lib/em64t

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  17. Intel CPP Compiler

    Intel C++ compiler is installed under /opt/intel/mkl/cce. To use it, put the following line in your login script:

    source /opt/intel/cce/9.1.047/bin/iccvars.sh

    You can NOT use Intel CPP compiler to compiler cca-tools as cca-tools uses gcc, and there is no option in building cca-tools to let you specify c/c++ compiler you want.

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  18. Python issue with CCA after version 0.6.2_rc3

    For the CCA-Tools to support Python, you will need the python built with SHARED LIBRARY support, and the OLD numerical python installed. NOTE!!!! Not the new Numpy, the OLD numerical python. The original version of python built on borges does not support shared library, so I build a new version and have the library installed under /usr/local/lib and /usr/local/lib/python2.5. You will need to include either one of these two in your LD_LIBRARY_PATH.

    The old Numerical Python and the new Numpy are both installed on borges. You do not need to do anything w to use them except knowing the module names. If you want to install them on your own machine, the source code is under /scratch/packages. Just follow the instruction in the README file, it is very straightforward. You need root password if you want to install them under /usr/local/

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  19. JAVA

    To build cca-tools, you need java and javac. On borges, you need the version that support x86_64. There is only java under /usr/bin, no javac. The version that supports x86_64 is installed under /opt/jdk1.6.0/. Please include the following in your path before building cca-tools.


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  20. GotoBLAS

    GotoBLAS is another math library optimized for different platforms. I am still testing it. I hope I can find a time to do a comparison between GAMESS-GotoBLAS and GAMESS-IntelMKL and put the results here.

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  21. Instrumenting GAMESS, NWChem and MPQC with TAU

    The first thing you need to do is to include some path in your $PATH and $LD_LIBRARY_PATH.

    To use TAU, you need:

    Since TAU's automatic instrumentation use PDT, you also need:

    You may need Java to use ParaProf, a tool to view performance data generated with TAU:

    Now you need to set up a new environment variable:
    export TAU_MAKEFILE=/opt/perf/tau-2.17/x86_64/lib/Makefile.tau-mpi-pdt

    The above are the basic setup to use TAU's automatic instrumentation to acquire the most basic 'detailed' performance data provided through TAU's performance evaluation subroutines.
    For NWChem and most other programs that are developed with FORTRAN 77, use tau_90.sh instead of the FORTRAN 90 compiler you use in your makefile. For example, when compiling NWChem, instead of use 'make FC=ifort', you use 'make FC=tau_f90.sh' to build NWChem.
    TAU will generate output files from profining, called profile.0.0.0 if you are using only one single node for your computation and if you are using MPI for communication. You will need to set and output directory to store this output file. To do that set the environment variable: PROFILEDIR to the directory you want to store your performance data. If you are running your application in parallel and is using only MPI, you will have a set of files like profile.0.0.0, profile.1.0.0, profile.2.0.0... To view the results of performance evaluation, go to the directory where you store your performance data, type:

    to view data in the text mode, or:

    to view your data with the visualization tool.

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  22. Testing cca-chem-generic2 package

    Some people may want to build cca-chem-generic2 and test the compatiability by themselves. Here are the procedures for those with patience.

    First, all the packages required for the testing are under /scratch/cca-chem-packages/ directory on borges t1 node.

    Now, the interesting part, building and testing procedures.

    (1). Have a cup of good tea besides you. This is very important. Don't drink something with too much caffine; that makes you cranky and when things are not working well, you might smash your poor computer.

    (2). Start building the base packages; in this case, it's cca-tools-0.6.1_rc2.tar.gz, cca-chem-generic2-old.tgz, and gamess-component-0.1.4-v2.tgz. I have tested this combination on several platforms and they are happy with each other, no one complains. You can use the instructions in this page to build them. For gamess-component, there is a configuration example (plain text file) in it. Building sequence is (1) cca-tools-0.6.1_rc3, (2) cca-chem-generic2-old and (3) gamess-component.

    (3). If everything is built properly, you can type 'make test' under gamess-component directory and you should be able to see the result of a sample computation, followed by an error message. Ignore the error message, it will be solve in about another hundered years. If you are using mpich2 on your own machine, don't forget to type mpdboot before running the test.

    (4). Repeat the building procedures with cca-tools-0.6.2_rc3, and cca-tools-0.6.4_rc8. You will find that cca-tools-0.6.2_rc3 is workingwith the other two packages, but the combination of cca-tools-0.6.4_rc8, cca-chem-generic2-old and gamess-component-0.1.4-v2 is not.

    (5). Replace cca-chem-generic2-old with cca-chem-generic2-0925-2007.tgz, and gamess-component-0.1.4-v2 with gamess-component-0.1.4-v6.tgz. The two new packages are happy to see cca-tools-0.6.2_rc3 and 0.6.4_rc8, but not 0.6.1_rc2.

    (6). Remember the new base package combination: cca-tools-0.6.4_rc8, cca-chem-generic2-0925-2007 and gamess-component-0.1.4-v6. If some packages are updated, you have to build cca-tools first, then cca-chem-generic2, and then gamess-component and run the testing in GAMESS. If the newly built packages don't like each other, let me know. Or you can go through possible combinations to find out which package is the bully one and need some special attention.

    (7). I have those built on Borges (Redhat Enterprise), my own computer (Debian) and the virtual machine(Fedora Core 6) on my laptop (Mac-Intel). They are all behaving well so far. If you are using Debian and can not build cca-tools properly, you might want to check your python installation. CCA-tools need a configuration file in your python installation. It's not a problem on Redhat Enterprise or Fedora Core. On Debian, you need to install a python development package to get this, and it only works for python 2.3, not 2.4.

    (8). For those who are using Intel-base Mac, here is a tip to save money and be able to compile FORTRAN programs. NO FORTRAN77 COMPILER availabe on Intel-base Mac. If you want one, spend a couple hundred dollars to buy it from Intel. Well, thanks a lot.

    To walk around it, what you can do is to have the program 'Parallels Desktop' installed (less than a hundred bucks) and create a virtual machine, then run the cca-project on this virtual machine. Use Fedora Core 6, not 7. There is a bug in version 7 that prevents you from installind the OS properly on a virtual machine. Using version 6 is just fine for the cca-project.

    (9). To understand the inside of the cca-chem-generic2 package, you might want to build its documentation from scratch since there is no pdf or word file available. Here is the procedure I 'found' a while ago:

    According to Joe " As long as you have doxygen in your path, you should be able to build the html from your top object." This is, unfortunately, not the case on many platforms.

    In this version of cca-chem-generic2, you can not just build the document. You have to configure cca-chem-generic2 first then you can build the document (The Makefile to build the document will be generated from Makefile.in under /doc after you configure cca-chem-generic2).

    Once you have Makefile for /doc generated, and have doxygen in your path, you can type "make" to build the document, and you will FAIL. You will get the error message like:

    "sh: dot: command not found".

    If you type "man dot" under whatever linux system you are using, you will get a man page that is totally useless to you. This is because the "dot" command required to build cca-chem-generic2 is totally differernt from the "dot" command in linux.

    The dot command required to build cca-chem-generic2 document is part of a package called "graphviz". You have to manually build the package to be able to use this "dot" command. You can find a webpage with a lot of rpm packages for graphviz, but none for el4.x86_64 (Borges).

    With all those set, then the document can be built.

    (10) Now, have fun building these packages and drinking your tea.

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  23. Template

    I am not a HTML expert and I need this template to work on this webpage.
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