Risks of Using the Intelligent Platform Management Interface (IPMI) - (TA13-207A)

Systems Affected
Any system connected to the internet running the Intelligent Platform Management Interface (IPMI) may be affected. IPMI is resident on many server platforms, and provides low-level access to a system that can override operating system controls.

Overview
Attackers can easily identify and access systems that run IPMI and are connected to the Internet. It is important to restrict IPMI access to specific management IP addresses within an organization and preferably separated into a separate LAN segment.

For more detail information, see Alert (TA13-207A) - Risks of Using the Intelligent Platform Management Interface (IPMI)

SINGAREN Network Configuration

Network Configuration of SINGAREN.

For more information, see SINGAREN Network Configuration

Installing cmake 2.8 on CentOS 5

If you are intending to compile and install cmake 2.8 on CentOS 5, you have to use a slightly older version of cmake 2.8.10.2 is compatible with CentOS 5. You can get it from this link

http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz

The most recent version of cmake-2.8.11 is only able to be compiled easily on CentOS 6 unless you wish to fix dependencies issues like GBLIC 2.7

Installation is quite easy to compile cmake-2.8.10.2

Step 1: You can use the bootstrap which will default the cmake to default location ie /usr/local/. If you are using bootstrap,

# tar -zxvf cmake-2.8.10.2
# cd cmake-2.8.10.2
# ./bootstrap
# make
# make install

Alternatively, I use the configure command which I’m more accustomed

# tar -zxvf cmake-2.8.10.2
# cd cmake-2.8.10.2
#./configure --prefix=/usr/local/cmake-2.8.10.2
# make
# make install

NetworkManager causing Device eth0 does not seem to be present, delaying initialization on CentOS

"Device eth0 does not seem to be present, delaying initialization on CentOS" error can be due to

1. Cannot get device settings No such device. 
2. "Device eth0 does not seem to be present" on cloned CentOS VM

Step 1. But it could be also due to the NetworkManager overridding your manual settings in the network configuration. You may want to disabled NetworkManager

# chkconfig --levels 2345 NetworkManager off

Step 2: At the /etc/sysconfig/network-scripts/ifcfg-eth0, do remember to put this line in

.....
..... 
NM_CONTROLLED="no"
.....
.....

Step 3: Reboot the machine and do a ifconfig

# ifconfig

You should be able to see the eth0

Compiling OpenMPI with CUDA and Intel Compilers

If you are intending to compile OpenMPI with CUDA Support, do note that you have to download the feature version of OpenMPI. The version I used for compiling OpenMPI with CUDA is version 1.7.2. The current stable version of OpenMPI 1.6.5 does not have CUDA-Support

1. Download and unpack OpenMPI 1.7.2 (features)

# wget http://www.open-mpi.org/software/ompi/v1.7/downloads/openmpi-1.7.2.tar.gz
# tar -zxvf openmpi-1.7.2.tar.gz
# cd openmpi-1.7.2

2. Configure the OpenMPI with CUDA Support

# ./configure --prefix=/usr/local/openmpi-1.7.2-intel-cuda CC=icc CXX=icpc 
F77=ifort FC=ifort --with-cuda=/opt/cuda --with-cuda-libdir=/usr/lib64
# make -j 8
# make install

References:

1. 34. How do I build Open MPI with support for sending CUDA device memory?

Compiling GNU 4.8.1 on CentOS 6

I encountered error when compiling GCC 4.8.1 on CentOS 6 I have the prequistics (via yum installed)

1. gmp 4.3.1-7.el6_2.2
2. mpfr 2.4.1-6.el6
3. mpc 0.19-1.el6.rf

But still I enountered the error

configure: error: Building GCC requires GMP 4.2+, MPFR 2.4.0+ and MPC 0.8.0+. 
Try the --with-gmp, --with-mpfr and/or --with-mpc options to specify their locations.  
Source code for these libraries can be found at their respective hosting sites as well as 
at ftp://gcc.gnu.org/pub/gcc/infrastructure/

To resolve the issue, download from the ftp://gcc.gnu.org/pub/gcc/infrastructure/ the following application and compile them.

1. gmp-4.3.2.tar.bz2
2. mpfr-2.4.2.tar.bz2
3. mpc-0.8.1.tar.gz

1. Install gmp-4.3.2

# bunzip2 gmp-4.3.2.tar.bz2
# tar -zxvf gmp-4.3.2.tar
# cd gmp-4.3.2
# ./configure --prefix=/usr/local/gmp-4.3.2
# make
# make install

2. Install mpfr-2.4.2 (requires gmp-4.3.2 as prerequisites)

# bunzip2 mpfr-2.4.2.tar.bz2
# tar -zxvf mpfr-2.4.2.tar
# cd mpfr-2.4.2
# ./configure --prefix=/usr/local/mpfr-2.4.2 --with-gmp=/usr/local/gmp-4.3.2/
# make
# make install

3. Install mpc-0.8.1 (requires gmp-4.3.2 and mpfr-2.4.2 as prerequisites )

# tar -zxvf mpc-0.8.1.tar.gz
# cd mpc-0.8.1
#./configure --prefix=/usr/local/mpc-0.8.1/ --with-gmp=/usr/local/gmp-4.3.2/ --with-mpfr=/usr/local/mpfr-2.4.2
# make
# make install

4. Update your LD_LIBRARY_PATH reflect /usr/local/mpc-0.8.1/lib In your .bash_profile include the following

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/mpc-0.8.1

5. Install the glibc-devel.i686. For more information, do look at Error when compiling GCC 4.8.1 (linuxtoolkit.blogspot.com)

6. Finally install GNU CC 4.8.1

# tar -zxvf  gcc-4.8.1.tar.gz
# cd gcc-4.8.1
# mkdir build-gcc
# cd build-gcc
# ../configure --prefix=/usr/local/gcc-4.8.1 --with-mpfr=/usr/local/mpfr-2.4.2 --with-mpc=/usr/local/mpc-0.8.1 --with-gmp=/usr/local/gmp-4.3.2
# make
# make install

Checking version of the Intel® IPP, Intel® MKL and Intel® TBB Libraries included in the Intel® Composer Bundles

Taken from Which version of the Intel® IPP, Intel® MKL and Intel® TBB Libraries are Included in the Intel® Composer Bundles?

Composer XE Edition	Intel C++ Compiler XE Version	Intel IPP Version	Intel MKL Version	Intel TBB Version
2013 update 4	13.1.2	7.1.1	11.0.4	4.1.3
2013 update 3 (not recommended)	13.1.1	7.1.1	11.0.3	4.1.3
2013 update 2	13.1.0	7.1.1	11.0.2	4.1.2
2013 update 1	13.0.1	7.1.1	11.0.1	4.1.1
2013	13.0.0	7.1	11.0	4.1
2011 update 13	12.1.7	7.0.7	10.3.12	4.0.5
2011 update 12	12.1.6	7.0.7	10.3.12	4.0.5
2011 update 11	12.1.5	7.0.7	10.3.11	4.0.5
2011 update 10	12.1.4	7.0.7	10.3.10	4.0.4
2011 update 9	12.1.3	7.0.6	10.3.9	4.0.3
2011 update 8	12.1.2	7.0.6	10.3.8	4.0.2
2011 update 7	12.1.1	7.0.5	10.3.7	4.0.1
2011 update 6 (or 2011 SP1)	12.1.0	7.0.5	10.3.6	4.0.0
2011 update 5	12.0.5	7.0.4	10.3.5	3.0.8
2011 update 4	12.0.4	7.0.4	10.3.4	3.0.7
2011 update 3	12.0.3	7.0.3	10.3.3	3.0.6
2011 update 2	12.0.2	7.0.2	10.3.2	3.0.5
2011 update 1	12.0.1	7.0.1a	10.3.1	3.0.4
2011	12.0.0	7.0.1	10.3.0	3.0.3

Compiling and Installing Gromacs 4.6.2 with OpenMPI and Intel on CentOS

Step 1: Compiling cmake To compile Gromacs 4.6.2, first you need to compile cmake 2.8 and above. At this point in writing, the current version is cmake 2.8.11.2

# tar -zxvf cmake-2.8.11.2.tar.gz
# cd cmake-2.8.11.2
# ./configure --prefix=/usr/local/cmake-2.8.11.2
# make
# make install

Step 2: Installing OpenMPI
See Blog Entry Building OpenMPI with Intel Compilers

Step 3: Installing FFTW (Single and Double Precision) 
See Blog Entry Compiling and installing FFTW 3.3.3.  

Step 4: Compiling Gromacs 4.6.2 (Single-Precision with Intel and OpenMPI)

# tar -zxvf gromacs-4.6.2.tar.gz
# cd gromacs-4.6.2
# mkdir build-cmake
# cd build-cmake
# CC=icc CMAKE_PREFIX_PATH=/usr/local/fftw-3.3.3-single/ /usr/local/cmake-2.8.11.2/bin/cmake .. 
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-4.6.2-single-intel -DGMX_X11=OFF -DGMX_MPI=ON 
-DGMX_PREFER_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF
# make
# make install

Step 5: Compiling Gromacs 4.6.2 (Double Precision with Intel and OpenMPI)

# tar -zxvf gromacs-4.6.2.tar.gz
# cd gromacs-4.6.2
# mkdir build-cmake
# cd build-cmake
# CC=icc CMAKE_PREFIX_PATH=/usr/local/fftw-3.3.3-single/ /usr/local/cmake-2.8.11.2/bin/cmake .. 
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-4.6.2-single-intel -DGMX_X11=OFF -DGMX_MPI=ON 
-DGMX_PREFER_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=OFF -DGMX_DOUBLE=ON# make
# make install

For more information,

1. Compiling Gromacs 4.6 and PLUMED from Source
2. Gromacs Installation instructions

Using Schrodinger Maestro provided graphics libraries for better and more stable performance

If you are using schrodinger, you might use Maestro via X windows forwarding to output Maestro to your workstation. You may find Maestro to be more stable if you launch the command below and substitute Mesa graphics libraries with Maestro bundled libraries

# $SCHRODINGER/maestro -SGL

Error when compiling GCC 4.8.1

For more information on installing GNU. See Blog Entry Compiling GNU 4.8.1 on CentOS 6.

During compilation, I encounter this error,

/usr/include/gnu/stubs.h:7:27: fatal error: gnu/stubs-32.h: 
No such file or directory compilation terminated. make: *** Error 1

This is due to a missing 32-bits libraries during GNU compilation. Do a yum install

# yum install glibc-devel.i686

Compiling and installing FFTW 3.3.3

1. FFTW 3.3.3 (Single Precision)

# ./configure --enable-float --enable-threads
# make
# make install

2. FFTW 3.3.3 (Double Precision)

# ./configure --enable threads
# make
# make install

3. Important Note. If you using FFTW with Gromacs, you may want to compile without threading as according to the document at Gromacs Installation Instructions .....On x86 hardware, compile only with --enable-sse2 (regardless of precision) even if your processors can take advantage of AVX extensions. Since GROMACS uses fairly short transform lengths we do not benefit from the FFTW AVX acceleration, and because of memory system performance limitations, it can even degrade GROMACS performance by around 20%...... 3a. FFTW 3.3.3 (Single Precision)

# ./configure --enable-float --enable-sse2 
# make 
# make install

3b. FFTW 3.3.3 (Double Precision)

# ./configure --enable-sse2 
# make 
# make install

References:

1. FFTW Home Page
2. Installation of FFTW (http://www.uvm.edu/~smanchu/fftw_installation.html)

Security Article from US-Cert on DNS Amplification Attacks.

A good article from US-Cert on DNS Amplification Attacks. Do read Alert (TA13-088A) DNS Amplification Attacks

Resolving cannot find -lm and -lz error on CentOS 6

While installing lblasr ( https://github.com/PacificBiosciences/blasr

I have this errors below.

g++ -O3 -Wno-div-by-zero -I ../common -I ../../seymour/dist/common/include bin/WordCounter.o -static -o bin/wordCounter
/usr/bin/ld: cannot find -lm
collect2: ld returned 1 exit status

g++ -static -O3 -Wno-div-by-zero -I ..//common -I ../../seymour/dist/common/include bin/SuffixArrayToBWT.o -o bin/sa2bwt -L../../seymour/dist/common/lib/ -lz -lpthread
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status

To solve the errors -lm on CentOS 6,  make sure you install 3 packages

# yum install glibc glibc-devel glibc-static

To solve the errors -lz on CentOS 6, make sure you install 3 packages from

 # yum install zlib zlib-devel zlib-static

Installing libm and libz for CentOS 5

To install libm libraries for CentOS 5, the package name is libm.so.6

# yum install libm.so.6 -y

To install libz libraries for CentOS 5, the package is libz.so.1

# yum install zlib-devel libz.so.1 -y

Cmake most commonly used variables

CMake is the cross-platform, open-source make system. CMake is used to control the software compilation process using simple platform and compiler independent configuration files. Do look at CMake Useful Variables.

Example of the most commonly used variables:

1. CMAKE_PREFIX_PATH (since CMake 2.6.0)
   This is used when searching for include files, binaries, or libraries using either the FIND_PACKAGE(), FIND_PATH(), FIND_PROGRAM(), or FIND_LIBRARY() commands. For each path in the CMAKE_PREFIX_PATH list, CMake will check "PATH/include" and "PATH" when FIND_PATH() is called, "PATH/bin" and "PATH" when FIND_PROGRAM() is called, and "PATH/lib" and "PATH" when FIND_LIBRARY() is called. See the documentation for FIND_PACKAGE(), FIND_LIBRARY(), FIND_PATH(), and FIND_PROGRAM() for more details.
2. CMAKE_LIBRARY_PATH
   This is used when searching for libraries e.g. using the FIND_LIBRARY() command. If you have libraries in non-standard locations, it may be useful to set this variable to this directory (e.g. /sw/lib on Mac OS X). If you need several directories, separate them by the platform specific separators (e.g. ":" on UNIX)
3. CMAKE_INCLUDE_PATH
   This is used when searching for include files e.g. using the FIND_PATH() command. If you have headers in non-standard locations, it may be useful to set this variable to this directory (e.g. /sw/include on Mac OS X). If you need several directories, separate them by the platform specific separators (e.g. ":" on UNIX)

References:

1.  CMake Useful Variables.

Using rpm to install cmake for CentOS 5

If you are using CentOS 5 and wish to install cmake without using yum, you basically need 2 packages which can be taken from http://www_karan_org/

 xmlrpc-c-1.06.18-1.el5.kb.x86_64.rpm
 cmake-2.6.4-5.el5.4.x86_64.rpm

Just run

# rpm -ivh xmlrpc-c-1.06.18-1.el5.kb.x86_64.rpm
# rpm -ivh cmake-2.6.4-5.el5.4.x86_64.rpm

Installing matplotlib using yum

matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms.

Make sure you have EPEL and RPMForge repositories installed. For more information, do look at
Useful Repositories for CentOS 5

To install matplotib using yum, do the following

# yum install python-matplotlib

Solving python-nose depsolving problems using yum

If you have this error below, it is because somehow yum is not able to download and install python-nose package. To resolve it, download manually python-nose package from a machine which is able to. The machine just name a internet connection and of course have the CentOS base repository enabled.

python-nose-0.11.3-2.el5.noarch from epel has depsolving problems
  --> Missing Dependency: python-setuptools is needed by package python-nose                  1.3-2.el5.noarch (epel)
Error: Missing Dependency: python-setuptools is needed by package python-nos                  11.3-2.el5.noarch (epel)
 You could try using --skip-broken to work around the problem
 You could try running: package-cleanup --problems
                        package-cleanup --dupes
                        rpm -Va --nofiles --nodigest
The program package-cleanup is found in the yum-utils package.

Do a yumloader python. For more information on  yumloader, do look at Using yum to download the rpm package that have already been installed

# yumdownloader python-setuptools

Next do a rpm install

# rpm -Uvh python-setuptools-0.6c5-2.el5.noarch.rpm
warning: python-setuptools-0.6c5-2.el5.noarch.rpm: Header V3 DSA signature: 
NOKEY, key ID e8562897
Preparing...                ########################################### [100%]
   1:python-setuptools      ########################################### [100%]

Now you can do a normal yum install