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Error when installing xCAT 2.8.2

If you have error such as those below,

Error: Package: xCAT-2.8.2-snap201307222333.x86_64 (xcat-2-core)
Requires: conserver-xcat
Error: Package: xCAT-2.8.2-snap201307222333.x86_64 (xcat-2-core)
Requires: syslinux-xcat
Error: Package: xCAT-2.8.2-snap201307222333.x86_64 (xcat-2-core)
Requires: elilo-xcat
Error: Package: xCAT-2.8.2-snap201307222333.x86_64 (xcat-2-core)
Requires: ipmitool-xcat >= 1.8.9
Error: Package: 1:xCAT-genesis-scripts-x86_64-2.8.2-snap201307222333.noarch (xcat-2-core)
Requires: xCAT-genesis-base-x86_64
Error: Package: xCAT-2.8.2-snap201307222333.x86_64 (xcat-2-core)
Requires: xnba-undi

Go to http://sourceforge.net/projects/xcat/files/yum/xcat-dep/rh6/x86_64/ and find the respective rpms that fit the package name

 

 

 

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Compiling SQLite 3.8.1 on CentOS 5

Taken from Beyond Linux® From Scratch – Version 2013-11-30

SQLite 3.8.1

  1. Download (HTTP): http://sqlite.org/2013/sqlite-autoconf-3080100.tar.gz
  2. Download size: 1.9 MB

SQLite 3.8.1 Documents

  1. Download (HTTP): http://sqlite.org/2013/sqlite-doc-3080100.zip
  2. Download size: 4.1 MB

Compiling SQLite 3.8.1

# ./configure --prefix=/usr/local/sqlite-3.8.1 --disable-static        \
CFLAGS="-g -O2 -DSQLITE_ENABLE_FTS3=1 \
-DSQLITE_ENABLE_COLUMN_METADATA=1     \
-DSQLITE_ENABLE_UNLOCK_NOTIFY=1       \
-DSQLITE_SECURE_DELETE=1" &&
# make
# make install

Compiling SQLite Documents

# install -v -m755 -d /usr/local/sqlite-3.8.1/share/doc/sqlite-3.8.1 &&
# cp -v -R sqlite-doc-3080100/* /usr/local/sqlite-3.8.1/share/doc/sqlite-3.8.1

For more information,

Command Explanations (taken from Beyond Linux® From Scratch – Version 2013-11-30)

–disable-static: This switch prevents installation of static versions of the libraries.

CFLAGS=”-g -O2 -DSQLITE_ENABLE_FTS3=1 -DSQLITE_ENABLE_COLUMN_METADATA=1 -DSQLITE_SECURE_DELETE -DSQLITE_ENABLE_UNLOCK_NOTIFY=1“: Applications such as Firefox require secure delete and enable unlock notify to be turned on. The only way to do this is to include them in the CFLAGS. By default, these are set to “-g -O2” so we specify that to preserve those settings. You may, of course, wish to omit the ‘-g’ if you do not wish to create debugging information. For further information on what can be specified see http://www.sqlite.org/compile.html.

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Installing HTseq for python 26 for CentOS 6

Installing HTseq is very straightforward for CentOS 6. You will need to do just follow the installation manual

# yum install python-devel numpy python-matplotlib

Download and untar the HTSeq source files.

# tar -zxvf HTSeq-0.5.4p5.tar.gz
# cd HTSeq-0.5.4p5

Inside the expanded HTSeq home directories, to make HTSeq available for all users

# python setup.py build
# python setup.py install

For more information, do look at

  1. HTSeq Prerequisites and Installation
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Installing Torque 4.2.5 on CentOS 6

References:

Do take a look at the Torque Admin Manual

Step 1: Download the Torque Software from Adaptive Computing

Download the Torque tarball from Torque Resource Manager Site

Step 2: Ensure you have the gcc, libssl-devel, and libxml2-devel packages

# yum install libxml2-devel openssl-devel gcc gcc-c++

Step 3: Configure the Torque Server

./configure \
--prefix=/opt/torque \
--exec-prefix=/opt/torque/x86_64 \
--enable-docs \
--disable-gui \
--with-server-home=/var/spool/torque \
--enable-syslog \
--with-scp \
--disable-rpp \
--disable-spool \
--enable-gcc-warnings \
--with-pam

Step 4: Compile the Torque

# make -j8
# make install

Step 5: Configure the trqauthd daemon to start automatically at system boot for the PBS Server

# cp contrib/init.d/trqauthd /etc/init.d/
# chkconfig --add trqauthd
# echo /usr/local/lib > /etc/ld.so.conf.d/torque.conf
# ldconfig
# service trqauthd start

Step 6: Copy the pbs_server and pbs_sched daemon for the PBS Server

# cp contrib/init.d/pbs_server /etc/init.d/pbs_server
# cp contrib/init.d/pb_sched /etc/init.d/pbs_sched

Step 6: Initialize serverdb by executing the torque.setup script for the PBS Server

# ./torque.setup root

Step 7: Make self-extracting tarballs packages for Client Nodes

# make packages
Building ./torque-package-clients-linux-i686.sh ...
Building ./torque-package-mom-linux-i686.sh ...
Building ./torque-package-server-linux-i686.sh ...
Building ./torque-package-gui-linux-i686.sh ...
Building ./torque-package-devel-linux-i686.sh ...
Done

Step 7b. Run libtool –finish /opt/torque/x86_64/lib

libtool: finish: PATH="/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/share/xcat/tools:/usr/lib64/qt-3.3/bin:/usr/local/intel/composer_xe_2011_sp1.11.339/bin/intel64:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/ibutils/bin:/usr/local/intel/composer_xe_2011_sp1.11.339/mpirt/bin/intel64:/opt/maui/bin:/opt/torque/x86_64/bin:/root/bin:/sbin" ldconfig -n /opt/torque/x86_64/lib
----------------------------------------------------------------------
Libraries have been installed in:
/opt/torque/x86_64/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------

 

Step 8a: Copy and install on the Client Nodes

for i in node01 node02 node03 node04 ; do scp torque-package-mom-linux-i686.sh ${i}:/tmp/. ; done
for i in node01 node02 node03 node04 ; do scp torque-package-clients-linux-i686.sh ${i}:/tmp/. ; done
for i in node01 node02 node03 node04 ; do ssh ${i} /tmp/torque-package-mom-linux-i686.sh --install ; done
for i in node01 node02 node03 node04 ; do ssh ${i} /tmp/torque-package-clients-linux-i686.sh --install ; done

Step 8b: Alternatively, you can use xCAT to push and run the packages from the PBS Server to the Client Node (auuming you install XCAT on the PBS Server)

# pscp  torque-package-mom-linux-i686.sh compute_noderange:/tmp
# pscp torque-package-clients-linux-i686.sh compute_noderange:/tmp
# psh compute_noderange:/tmp/torque-package-mom-linux-i686.sh
# psh compute_noderange:/tmp/torque-package-clients-linux-i686.sh

Step 9: Enabling Torque as a service for the Client Node

# cp contrib/init.d/pbs_mom /etc/init.d/pbs_mom
# chkconfig --add pbs_mom

Step 10a: Start the Services for each of the client nodes

# service pbs_mom start

Step 10b: Alternatively, Use XCAT to start the service for all the Client Node

# psh compute_noderange "/sbin/service/pbs_mom start"
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Adding and Specifying Compute Resources at Torque

This blog entry is the follow-up of Installing Torque 2.5 on CentOS 6 with xCAT tool.

After installing of Torque on the Head Node and Compute Node, the next things to do is to configure the Torque Server. In this blog entry, I will focus on the Configuring the Compute Resources at Torque Server

 Step 1: Adding Nodes to the Torque Server

# qmgr -c "create node node01"

Step 2: Configure Auto-Detect Nodes CPU Detection. Setting auto_node_np to TRUE overwrites the value of np set in $TORQUEHOME/server_priv/nodes

# qmgr -c "set server auto_node_np = True"

Step 3: Start the pbs_mom of the compute nodes, the torque server will detect the nodes automatically

# service pbs_mom start
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Using Eclipse IDE with Intel C++ Compilers on CentOS

This article is taken from Intel C++ Compiler with the Eclipse IDE on Linux

Introduction
Intel C++ Compilers for Linux can be used together with the Eclipse IDE to create C/C++ applications. Via an Intel C++ Eclipse extension the compiler is integrated using the well-known Eclipse C/C++ Development Tooling (CDT) plug-in. Hence all existing features of CDT, like different views, wizards, a powerful editor, and debugging, can be easily used with the Intel compiler as well. In the following a “How-to” guide is provided which explains configuration and usage.


Requirements

  1. Eclipse 3.7, 3.8 or 4.2 ans above
    [http://www.eclipse.org/downloads/]
  2. CDT 8.0 or later
    [http://www.eclipse.org/cdt/]
  3. Java Runtime Environment (JRE) version 6.0 (also called 1.6) update 11 or later
    [http://www.oracle.com/technetwork/java/javase/downloads/index.html]
  4. Intel® Composer XE 2013 and above (separate or any suite that provides it, like Intel® Parallel Studio XE 2013)
    [http://software.intel.com/en-us/intel-composer-xe]

Note:
In case Eclipse has to be installed first, use the package Eclipse IDE for C/C++ Developers. It already comes with everything needed for C/C++ development. We will use it as reference in the following.

Installing the Integration
The following is a brief overview about how to install the Intel C++ Eclipse extension. More information see Learn More below.

  1. Open the Install dialog for plug-ins via menu Help->Install New Software…:
  2. Click on the Add… button and the Add Repository dialog opens:
  3. Click on the Local… button, specify the directory containing the Intel C++ Eclipse extension and confirm. The Intel C++ Eclipse extension can be found in the installation directory of Intel Composer XE, subdirectory eclipse_support/cdt8.0/eclipse.
  4. Back in the Install dialog select the item Intel(R) C++ Compiler XE 13.0 for Linux* OS and continue by pressing the button Next >.
    Optionally you can also install compiler documentation (recommended) and Intel® Debugger support for native & Intel® MIC architecture (provided they are already installed with Intel Composer XE).
  5. In case there are no items listed, ensure that Group items by category is not selected.
  6. The next dialog summarizes all plug-ins to install. Continue via button Next >:
  7. Finally, the license files are displayed. Make sure to read them. Accept and start installation by clicking on button Finish:
  8. Eventually you will be faced with a warning about unsigned content. Confirm by clicking on button OK:
  9. After installation is complete, restart Eclipse

Using Intel C++ Eclipse Extension

  1. Once the Intel C++ Eclipse extension is installed it can be used for all C/C++ projects – new ones as well as existing ones.
  2. When using the extension, make sure to source the compiler scripts before starting Eclipse:
    $ source <composer_xe_path>/bin/compilervars.[sh|csh] [ia32|intel64]
    $ eclipse
  3. This is crucial to locate the compiler installation. See the compiler documentation for more information about the compiler scripts.
  4. If you experience issues with the integration try to set the locale to en_US when starting Eclipse, e.g.:
    $ LANG=en_US eclipse

 

Create New Project

  1. To create a new C/C++ project, use the Eclipse/CDT wizard via File->New->C Project or C++ Project;
  2. By default the flag Show project types and toolchains only if they are supported on the platform is selected. Thus, all toolchains are shown for which there is an existing compiler installation. Select the toolchains for your project – multiple can be selected at once. To use the latest compiler from Intel Composer XE 2013, select version v13.0.0. It is also possible to use older versions in addition as long as there are existing compiler installations.
    When unchecking the flag Show project types and toolchains only if they are supported on the platform, all toolchains are shown, even if no appropriate compiler is installed on the local system. This can be used for environments with distributed build systems where not all nodes have all compilers installed, but only subsets each. Those toolchains can’t be used unless the proper compiler is installed but they will be present and can be configured.

Once a new project is created like this building, linking, executing and debugging is no different than used from CDT with the default toolchain.

For more information, do see Intel C++ Compiler with the Eclipse IDE on Linux

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Compiling and Installing Meep-1.2.1 on CentOS 6 and OpenMPI

Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with our MPB eigenmode package. The latest official version is 1.2 and can be found at  Download Page for Meep

But there is a Lapack linking problem for 1.2 which is explained in Error when compiling Meep-1.2 on CentOS. It is strongly recommended to use the pre-release Meep 1.2.1 found at http://jdj.mit.edu/~stevenj/meep-1.2.1.tar.gz

Before you compile Meep 1.2.1, you need to first compile the libctl library. Compiling the libctl library is quite straightforward. After downloading,

Step 1: Compiling libctl-3.2.1

# tar -zxvf libctl-3.2.1.tar.gz
# cd libctl-3.2.1
# ./configure --prefix=/usr/local/libctl-3.2.1
# make -j8
# make install

Step 2: Other Prerequisites include guile and guile-devel. Do make sure you install these 2 packages which can be done

# yum install guile guile-devel

Step 3: Compiling OpenMPI,
Do look at Compiling OpenMPI 1.6.5 with Intel 12.1.5 on CentOS 6

Step 4: Compiling meep-1.2.1

# tar -zxvf meep-1.2.1.tar.gz
# cd meep-1.2.1
#  ./configure --prefix=/usr/local/meep-1.2.1 \
--with-libctl=/usr/local/libctl-3.2.1/share/libctl/ \
LDFLAGS=-L/usr/local/libctl-3.2.1/lib \
CPPFLAGS=-I/usr/local/libctl-3.2.1/include \
--with-mpi

References:

  1. Undefined reference to `dgetrf_’ error when compiling Meep-1.2 on CentOS
  2. crtbegin.o: No such file: No such file or directory Error when compiling Meep-1.2 on CentOS
  3. My opinion: Compiling Meep
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Compiling GNU Scientific Library (GSL) gsl-1.16 on CentOS 6

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.

The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

Step 1: The current version of GSL is gsl-1.16.tar.gz

Step 2: You may want to use the latest GCC 4.8.1 to compile. For more information on how to compile GCC 4.8.1, see Compiling GNU 4.8.1 on CentOS 6. This compilation will help to fix all the components required for gsl-1.16

Step 3: After packing gsl, To compile

# cd /root/gsl-1.15/
# mkdir build-gsl
# cd build-gsl
# ../configure --prefix=/usr/local/gsl-1.16/
# make 
# make install
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Compiling and installing FFTW 3.3.3 with OpenMPI and OpenMP

This Blog entry is an extension of the Compiling and installing FFTW 3.3.3

To Compile FFTW 3.3.3 single precision with OpenMPI, make sure you compile and set your path for Intel and OpenMPI. You may want to get more information from Compiling OpenMPI 1.6.5 with Intel 12.1.5 on CentOS 6

Step 1: Compiling FFTW 3.3.3 (Single Precision) with OpenMPI and OpenMP

After unpacking FFTW 3.3.3, you may want to use the flags

# ./configure CC=icc 
--enable-float --enable-threads --enable-openmp \
--enable-mpi MPICC=mpicc \
LDFLAGS=-L/usr/local/openmpi/intel/lib CPPFLAGS=-I/usr/local/openmpi/intel/include \ 
--prefix=/usr/local/fftw-3.3.3-single
# make -j8
# make install

Inside /usr/local/fftw-3.3.3-single/lib, you should see at least the files below

libfftw3f.a
libfftw3f_mpi.a
libfftw3f_omp.a
libfftw3f_threads.a
....
....

Step 2: Compiling FFTW 3.3.3 (Double Precision) with OpenMPI and OpenMP

# ./configure CC=icc 
--enable-threads --enable-openmp \
--enable-mpi MPICC=mpicc \
LDFLAGS=-L/usr/local/openmpi/intel/lib CPPFLAGS=-I/usr/local/openmpi/intel/include \ 
--prefix=/usr/local/fftw-3.3.3-single
# make -j8
# make install

Inside /usr/local/fftw-3.3.3-double/lib, you should see at least the files below

libfftw3.a
libfftw3_mpi.a
libfftw3_omp.a
libfftw3_threads.a
....
....
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Compiling Open Tool for Parameter Optimization (otpo)

Taken from Open Tool for Parameter Optimization (otpo) Documentation

OTPO (Open Tool for Parameter Optimizations) is an Open MPI specific tool that is meant to explore the MCA parameter space. In Open MPI, the user can specify at runtime many values for MCA parameters, try e.g. (ompi_info –param all all). Alternatively, to focus on a single aspect of parameters, e.g. the parameters of the OpenIB BTL (ompi_info –param btl openib).

OTPO is a tool that takes in a list of any MCA parameters, with a user specified range of values for those parameters, and for every combination of the MCA parameter values, OTPO executes an MPI job, measuring execution time (the only measurement available right now), bandwidth, etc.. The tests used for the measurements are modular. Right now, OTPO supports

Netpipe
Skampi
NAS Parallel Benchmarks

OTPO outputs a list of the best parameter combinations for a certain test.

The main purpose of OTPO is to explore the effect of the MCA parameters on different machines with different architectures and configurations, and explore the dependencies between the MCA parameters themselves. OTPO is meant to run on the head node of a cluster, and it forks MPI jobs after exporting the current combination of MCA parameters on the nodes.

OTPO is built on top of ADCL (Abstract Data and Communication Library). ADCL is an application level communication library aiming at providing the highest possible performance for application level communication operations in a given execution environment. OTPO uses ADCL to provide the runtime selection logic and choosing the best combination of parameters.

A. Compiling OTPO

Step 1: Make sure your PATH and LD_LIBRARY_PATH has the necessary pathing for the OpenMPI and Compilers

In your .bashrc, it should look something like

export PATH=$PATH:/usr/local/intel/composerxe/bin:/usr/local/openmpi-1.6.5-intel-v12.1.5/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/mpc-0.8.1/lib:/usr/local/intel/composerxe/lib/intel64:/usr/local/intel/composerxe/mkl/lib/intel64:/usr/local/openmpi-1.6.5-intel-v12.1.5/lib

Step 2: Download and compile ADCL within OTPO

# wget http://www.open-mpi.org/software/otpo/v1.0/downloads/otpo-1.0.tar.gz
# tar -zxvf otpo-1.0.tar.gz
# cd otpo
# cd ADCL
# ./configure --prefix=/usr/local/ADCL
# make
# make install
# cp /root/otpo/ADCL/include/*.h /usr/local/ADCL

After the compilation, you should see libadcl.a inside the lib folder of ADCL. Remember to copy the ADCL headers to the /usr/local/ADCL/include

Step 3: Compile OTPO

# ./autogen.sh
# ./configure --prefix=/usr/local/otpo-1.0 --with-adcl-dir=/usr/local/ADCL
# make
# make install