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For more information, see
1. You have to compile OpenMPI 1.4.x with g77 and gfortran. I’m compiling with OpenIB and Torque as well
./configure --prefix=/usr/local/mpi/gnu-g77/ \ F77=g77 FC=gfortran \ --with-openib \ --with-openib-libdir=/usr/lib64 \ --with-tm=/opt/torque
2. Download BLACS from www.netlib.org/blacs. Remember to download both mpiblacs.tgz and the mpiblacs-patch03.tgz
# cd /root # tar -xzvf mpiblacs.tgz # tar -xzvf mpiblacs-patch03.tgz # cd BLACS # cp ./BMAKES/BMake.MPI-LINUX Bmake.inc
3. Edit Bmake.inc according to the recommendation from OpenMPI FAQ
# Section 1: # Ensure to use MPI for the communication layer COMMLIB = MPI # The MPIINCdir macro is used to link in mpif.h and # must contain the location of Open MPI's mpif.h. # The MPILIBdir and MPILIB macros are irrelevant # and should be left empty. MPIdir = /path/to/openmpi-1.4.3 MPILIBdir = MPIINCdir = $(MPIdir)/include MPILIB = # Section 2: # Set these values: SYSINC = INTFACE = -Df77IsF2C SENDIS = BUFF = TRANSCOMM = -DUseMpi2 WHATMPI = SYSERRORS = # Section 3: # You may need to specify the full path to # mpif77 / mpicc if they aren't already in # your path. IF not type the whole path out. F77 = /usr/local/mpi/gnu-g77/bin/mpif77 F77LOADFLAGS = CC = /usr/local/mpi/gnu-g77/bin/mpicc CCLOADFLAGS =
4. Following the recommendation from BlACS Errata (Necessary flags for compiling the BLACS tester with g77)
blacstest.o : blacstest.f $(F77) $(F77NO_OPTFLAGS) -c $*.f to: blacstest.o : blacstest.f $(F77) $(F77NO_OPTFLAGS) -fno-globals -fno-f90 -fugly-complex -w -c $*.f
5. Compile the Blacs tests. You should see
# cd /root/BLACS/TESTING # make clean # make
You should see xCbtest_MPI-LINUX-1 and xFbtest_MPI-LINUX-1
6. Tun the Tests
# mpirun -np 5 xCbtest_MPI-LINUX-0 # mpirun -np 5 xFbtest_MPI-LINUX-0
7. If the test is successful, you may wish to copy the BLACS library to /usr/local/lib. But I like to separate my compiled libraries separately to /usr/local/blacs/lib
# cp /root/BLACS/LIB*.a /usr/local/blacs/lib # chmod 555 /usr/local/blacs/lib/*.a
Download the lapack latest stable version (lapack-3.3.0.tgz) from http://www.netlib.org/lapack
# cd /root # tar -xzvf lapack-3.3.0.tgz # cd /root/lapack-3.3.0 # cp make.inc.example make.inc
Assuming Edit make.inc. Assuming the Compiling ATLAS on CentOS 5
#BLASLIB = ../../blas$(PLAT).a BLASLIB = /usr/local/atlas/lib/libf77blas.a /usr/local/atlas/lib/libatlas.a
Compile lapack package
# make
Copy the libraries to
# mkdir /usr/local/lapack/lib # cp /root/lapack-3.3.0/*.a /usr/local/lapack/lib # cd /usr/local/lapack/lib/ # chmod 555 *.a
Other related Information
This tutorial is to help you compile ATLAS (Automatically Tuned Linear Algebra Software) with gFortran. For those who are using Intel Compiler, you have the reliable Intel MKL (Math Kernel Library)
First thing first, some comparison between ATLAS and MKL.
ATLAS
ATLAS The Automatically Tuned Linear Algebra Software (ATLAS) provides a complete implementation of the BLAS API 3 and a subset of LAPACK 3. A big number of instructions-set specific optimizations are used throughout the library to achieve peak-performance on a wide variety of HW-platforms.
ATLAS provides both C and Fortran interfaces.
ATLAS is available for all HW-platforms capable of running UNIX or UNIX-like operating systems as well as Windows ™.
MKL
Intel’s Math Kernel Library (MKL) implements a set of linear algebra, fast Fourier transforms and vector math functions. It includes LAPACK 3, BLAS 3 and extended BLAS and provides both C and Fortran interfaces.
MKL is available for Windows ™ and Linux (x86/i686 and above) only.
Download the latest stable package from ATLAS (http://sourceforge.net/projects/math-atlas/files/Stable/). The current stable version is atlas3.8.0.tar.gz. Do note that ATLAS don’t like configuration on its original location, hence the need to create ATLAS_BUILD directory.
# cd /root # tar -xzvf atlas3.8.3.tar.gz # mkdir /root/ATLAS_BUILD # cd /root/ATLAS_BUILD # /root/ATLAS/configure
You will need to turn off CPU Throttling. For CentOS and Fedora, you will use
# /usr/bin/cpufreq-selector -g performance
For more information, you can see my blog entry Switching off CPU Throttling on CentOS or Fedora
Compile ATLAS
make make check make ptcheck make time make install
By default, ATLAS installed to /usr/local/atlas
Finally remember to add /usr/local/atlas/lib to your LD_LIBRARY_PATH
Notes:
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers
Do note that this Gromacs Installation Guide is for Gromacs 4.0.x. For detailed instruction, see GROMACS Installation Instructions. For installation of FFTW, you may want to take a look at Blogh Entry Installing FFTW
Since I’m using FFTW, MPI (OpenMPI to be exact) and configure FFTW with –prefix=/usr/local/fftw,
I’ve configured the following
# ./configure CPPFLAGS="-I/usr/local/fftw/include" LDFLAGS="-L/usr/local/fftw/lib" \ --with-fft=fftw3 --enable-mpi --disable-float
Some notes…… (Assuming you are using bash)
# make -j 8
where 8 is the number of cores.
# make mdrun
* if you have configure with “–enable-mpi”
# make install
* Install all the binaries, libraries and shared data files with:
# make install-mdrun
* If you only want to build the mdrun executable (in the case of an MPI build),
# make links
* If you want to create links in /usr/local/bin to the installed GROMACS executables
Vmware View Client for iPAD is finally here…….
VMware View Client for iPad makes it easy to access your Windows virtual desktop from your iPad with the best possible user experience on the Local Area Network (LAN) or across a Wide Area Network (WAN).
The Article from F5 deals with the following issues
Deploying the Big-IP Edge Gateway and Local Traffic Manager with Vmware View 4.0 and 4.5 (pdf)
This article taken from F5 deals with the following
check_mk is a wonderful “a new general purpose Nagios-plugin for retrieving data”. But this wonder plugins is a good replacement for NRPE, NSClients++ etc. I’ve tried using check_mk in place of NSClient++ to monitor my Windows Machines successfully
Installing Nagios is straightforward. You may want to see Blog Entry Using Nagios 2.x/3.x on CentOS. In a nutshell, do this in sequence to avoid dependency issues
# yum install nagios nagios-devel
# yum install nagios-plugins-all
Downloading and unpacking check_mk
# wget http://mathias-kettner.de/download/check_mk-1.1.8.tar.gz
# tar -zxvf check_mk-1.1.8.tar.gz
# cd check_mk-1.1.8
# ./setup.sh --yes
Restart the Service
# service nagios restart # service apache restart
Making the agent accessible through xinetd
# cp -p /usr/share/check_mk/agents/check_mk_agent.linux /usr/bin/check_mk_agent # cp -p /usr/share/check_mk/agents/xinetd.conf /etc/xinetd.d/check_mk
Restart xinetd service.
# service xinetd restart
For more information on check_mk on Debian Derivative, do look at the excellent writup “HOWTO: How to install Nagios with check_mk, PNP and NagVis“
This is a continuation of the article Testing the Infiniband Interconnect Performance with Intel MPI Benchmark (Part I)
B. Running IMB
After “make” the executable has been located. Run IMB_MPI1 pingpong from management node or head node. Ensure the IMB-MPT1 is on the directory.
# cd /home/hpc/imb/src
# mpirun -np 16 -host node1,node2 /home/hpc/imb/src/IMB-MPI1 pingpong
# mpirun -np 16 -host node1,node2 /home/hpc/imb/src/IMB-MPI1 sendrecv
# mpirun -np 16 -host node1,node2 /home/hpc/imb/src/IMB-MPI1 exchange
Example of output from “pingpong”
benchmarks to run pingpong #--------------------------------------------------- # Intel (R) MPI Benchmark Suite V3.2.2, MPI-1 part #--------------------------------------------------- # Date : Mon Feb 7 10:42:48 2011 # Machine : x86_64 # System : Linux # Release : 2.6.18-164.el5 # Version : #1 SMP Thu Sep 3 03:28:30 EDT 2009 # MPI Version : 2.1 # MPI Thread Environment: MPI_THREAD_SINGLE # New default behavior from Version 3.2 on: # the number of iterations per message size is cut down # dynamically when a certain run time (per message size sample) # is expected to be exceeded. Time limit is defined by variable # "SECS_PER_SAMPLE" (=> IMB_settings.h) # or through the flag => -time # Calling sequence was: # /home/shared-rpm/imb/src/IMB-MPI1 pingpong # Minimum message length in bytes: 0 # Maximum message length in bytes: 4194304 # # MPI_Datatype : MPI_BYTE # MPI_Datatype for reductions : MPI_FLOAT # MPI_Op : MPI_SUM # # # List of Benchmarks to run: # PingPong #--------------------------------------------------- # Benchmarking PingPong # #processes = 2 # ( 46 additional processes waiting in MPI_Barrier) #--------------------------------------------------- #bytes #repetitions t[usec] Mbytes/sec 0 1000 8.74 0.00 1 1000 8.82 0.11 2 1000 8.83 0.22 4 1000 8.89 0.43 8 1000 8.90 0.86 16 1000 8.99 1.70 32 1000 9.00 3.39 64 1000 10.32 5.91 128 1000 10.52 11.60 256 1000 11.24 21.72 512 1000 12.12 40.30 1024 1000 13.76 70.98 2048 1000 15.55 125.59 4096 1000 17.81 219.35 8192 1000 22.47 347.67 16384 1000 45.24 345.41 32768 1000 59.83 522.29 65536 640 87.68 712.85 131072 320 154.80 807.47 262144 160 312.87 799.05 524288 80 556.20 898.96 1048576 40 1078.94 926.84 2097152 20 2151.90 929.41 4194304 10 4256.70 939.69 # All processes entering MPI_Finalize
If you wish to use the torque to run the IMB, do read the IBM “Setting up an HPC cluster with Red Hat Enterprise Linux“
The Linux Cluster 
