Installing on barre - 2013-12-23 - Experience


   
1) Absoft 11.5 needs an update patch:
wget http://www.absoft.com/electronicdelivery/linux-profortran-11.5.x86_64/absoft_profortran-11.5.3_x86_64_update.tar.gz
cd /opt/absoft11.5
sudo tar -xzvf ~/Downloads/absoft_profortran-11.5.3_x86_64_update.tar.gz
    This must be carried out after the installation of the compiler.
    This hint was given by atools
    The compiler procedure af90fe64 did not run ("file not found") until the update.
    The license data was no problem, neither when given for multiple nor single processors.

    Observe the advice from Absoft concerning required libraries under Ubuntu (red&fat: not installed when I took over):
Ubuntu 12.04
Ubuntu 13.04


A default installation of Ubuntu 12.04 or 13.04 requires the following additional software to fully support Absoft Fortran 2014:

Package                            Description
----------------------       ---------------------------------------
ia32-libs                    Support for running 32 bit programs
gcc                          Support for software development
g++                          Support for software development
gcc-multilib                 Support for building 32 bit programs
g++-multilib                 Support for building 32 bit programs


2) netcdf-4.3.1 with Absoft-11.5
This is the same ordeal we've had on holt.
setenv FC $ABSOFT/bin/af90
setenv F77 $ABSOFT/bin/af77
setenv FCFLAGS "-w -s -B108 -f"
setenv FFLAGS "-w -s -B108 -f"
cd ~/Downloads
wget http://downloads.absoft.com/electronicdelivery/library/cfortran.h
cp cfortran.h netcdf-4.1.3/fortran/cfortran.h
cd netcdf-4.3.1
sudo ./configure --prefix=/opt/netcdf64 --disable-shared --disable-netcdf-4
sudo make
# For some strange reason, on Holt f90/typesizes.mod and f90/netcdf.mod was not o.k.
sudo make install
cd /usr/local/lib
sudo ln -s /opt/netcdf64/lib/* .

3) Use synaptic to install ncurses, install the development package.
    The apt-get method resulted in broken packages and unresolved dependencies.

4) Web server and cgi-scripts
sudo apt-get install apache2
    Use synaptic to install mod-perl (with dependent packages, six such)
    How to configure apache? See http://stackoverflow.com/questions/560749/how-do-i-configure-apache2-to-run-perl-cgi-scripts
    On holt,
sudo scp -r /cgi-bin hgs@barre.oso.chalmers.se:./
   On barre:
cd /
sudo ln -s /usr/lib/cgi-bin .
sudo cp -r /home/hgs/cgi-bin/* /cgi-bin
# adjust user:group
cd /cgi-bin
# edit mailto.cgi and
# @referers = ('scriptarchive.com','barre.oso.chalmers.se');
# @recipients = ('loading@barre.oso.chalmers.se');

    further, on barre:
cd ~/www   # and the equiv. for user loading
html-chmachine -R -X # careful!
# there are a few files left where holt -> barre
locate '*.html' + holt
5) postfix. Use synaptic
    (I have ticked for installing packages uw-mailutils and mail-stack-delivery - needed?)
    The /etc/postfix/main.cf that worked has been copied to ~/postfix (on barre: main.cf  and on holt: barre-main.cf holt-main.cf)
    After editing main.cf, don't forget to
    sudo postfix reload

My corr with unidata.ucar.edu:
Subject: Re: [netCDF #QGB-866955]: make check: two tests failed
Date: 2012-02-25 13:24
Folder: Inbox/Upto_120630

Absoft's advice to build netcdf, http://absoft.absoft.com/newforums/index.php?topic=478.0
copy follows here in case they erase their blog:

Building NetCDF on 64 bit Linux

« on: March 02, 2011, 08:25:45 AM »
This post provides instructions on building NetCDF on 64 bit Linux with Absoft Fortran 95 11.0  and later.

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats
that support the creation, access, and sharing of array-oriented scientific data.

DOWNLOADING THE REQUIRED PACKAGE

The NetCDF package is available at this site http://www.unidata.ucar.edu/software/netcdf.
At the time this post was updated, the current stable release for NetCDF is 4.1.3. It was released on June  30, 2011.
The instructions below use the source code package named netcdf-4.1.3.tar.gz.

CREATING THE NetCDF SOURCE TREE

Extract the NetCDF source with the following command:

   tar -xzvf netcdf-4.1.3.tar.gz

This will create a directory named netcdf-4.1.3 in the current working directory.

UPDATING THE cfortran.h HEADER FILE

NetCDF uses the cfortran.h header file to define  the interface between C and Fortran. The version of
the cfortran.h file that is included in NetCDF does work correctly with recent versions of  Absoft Fortran 95
(10.2 and later.)  Before building NetCDF, you will will need to download an updated cfortran.h  file from this location:

http://downloads.absoft.com/electronicdelivery/library/cfortran.h

After obtaining the new version of cfortran.h, install it into the NetCDF source tree:

   cp cfortran.h netcdf-4.1.3/fortran/cfortran.h

MAKING A TARGET BUILD DIRECTORY

It is possible to configure and build NetCDF directly inside the source directory.
However, creating a separate build directory makes reconfiguring or maintaining more than one build (for example 32 and 64 bit builds) easier.
The instructions below assume that a separate build directory has been created in the directory containing  the NetCDF source directory using this command:

     mkdir  netcdf64-build

CONFIGURING, BUILDING AND INSTALLING 64 BIT NetCDF

Use following commands configure, build  and install 64 bit NetCDF with Absoft Fortran 95 11.0 and later.
These commands configure NetCDF to install into /opt/netcdf64.
If you want to install to a different location, replace /opt/netcdf64 in the --prefix= argument to the configure command.

   cd netcdf64-build
   export FC=$ABSOFT/bin/af90
   export F77=$ABSOFT/bin/af77
   export FCFLAGS="-w -s"
   export FFLAGS="-w -s"
   export CPPFLAGS=-DAbsoftProFortran11

   ../netcdf-4.1.3/configure --prefix=/opt/netcdf64 --disable-shared --disable-netcdf-4

   make
   make check
   make install

USING NetCDF

The following command  compiles a single Fortran 90 source file main.f90 that uses the NetCDF Fortran 90 module and links to the NetCDF library:

   af90 main.f90 -p/opt/netcdf64/include -L/opt/netcdf64/lib -lnetcdf

The following command compiles a single Fortran 77 source file main.f that uses the NetCDF FORTRAN 77 include file and links to the NetCDF library:

   af77 main.f -I/opt/netcdf64/include  -L/opt/netcdf64/lib -lnetcdf

FURTHER INFORMATION

Further information on NetCDF can be found in the files named  README, INSTALL, and RELEASE_NOTES  located in the netcdf-4.1.3 source directory.
« Last Edit: April 05, 2012, 09:29:42 AM by forumadmin »