Sunday, December 29, 2013

Memory Consumption in Linux

This web article from http://emilics.com talks about memory consumption by a process in Linux. As Linux has a sophisticated  memory management system, measuring may not be that simple.

Inside the article, it mention VSZ (Virtual Memory Size) and Demand Paging, RSS (Resident Set Size) and Shared Libraries, PSS (Proportional Set Size) and more.

Do read the article from Memory Consumption in Linux

Thursday, December 26, 2013

Failed to build compat-rdma RPM when compiling OFED 3.5.1 on CentOS 5.8

I was compiling OFED 3.5.1 on CentOS 5.8. I have got this error.
make[3]: *** [/var/tmp/OFED_topdir/BUILD/compat-rdma-3.5/compat/main.o] Error 1
make[2]: *** [/var/tmp/OFED_topdir/BUILD/compat-rdma-3.5/compat] Error 2
make[1]: *** [_module_/var/tmp/OFED_topdir/BUILD/compat-rdma-3.5] Error 2
make[1]: Leaving directory `/usr/src/kernels/2.6.18-308.el5-x86_64'
make: *** [kernel] Error 2
error: Bad exit status from /var/tmp/rpm-tmp.99798 (%build)


RPM build errors:
    user rupertd does not exist - using root
    user rupertd does not exist - using root
    Bad exit status from /var/tmp/rpm-tmp.99798 (%build)

I tried to rebuild the SRPMS directly by using the commands, but it will fail the rpmbuild. For more information on rpmbuild command, you can take a look at Rebuild a Source RPM
# rpmbuild --rebuild ~OFED_HOME/SRPMS/compat-rdma-3.5-OFED.3.5.1.src.rpm

I finally fixed my OFED by installing 1.5.3.2

Monday, December 23, 2013

Compiling R-3.0.2 on CentOS 5

Do note that R-3.0.2 requires a higher version of gfortran 4.4.4 and above. To help ensure that the gfortran44 is installed, do check that the gnu44 are installed. For more information how to install, see Installing GNU 4.4 of C, C++ and gfortran for CentOS 5

Compiling R-3.0.2
# tar -zxvf 3.0.2.tar.gz 
# ./configure --prefix=/usr/local/R-3.0.2/ CC=gcc44 CXX=g++44 F77=gfortran44 FC=gfortran44
# make
# make install

Monday, December 16, 2013

GPFS NSD Nodes stuck in Arbitrating Mode

One of our GPFS NSD Nodes are forever stuck in arbitrating nodes. One of the symptoms that was noticeable was that the users was able to log-in but unable to do a "ls" of their own directories. You can get a quick deduction by looking at one of the NSD Nodes. For this kind of issues, do a mmdiag --waiters first. There are limited articles on this
# mmdiag --waiters 

.....
.....
0x7FB0C0013D10 waiting 27176.264845756 seconds, SharedHashTabFetchHandlerThread: 
on ThCond 0x1C0000F9B78 (0x1C0000F9B78) (TokenCondvar), reason 'wait for SubToken to become stable'
References:
  1. IZ17622: GPFS DEADLOCK WAITING FOR SUBTOKEN TO BECOME STABLE CAUSES HANG
  2. GPFS File System Deadlock

For more information on the resolution, see  GPFS NSD Nodes stuck in Arbitrating Mode (Linux Cluster)

Saturday, December 14, 2013

Convergence of Supercomputing and Extreme Big Data on the TSUBAME Supercomputer Exascale

I Saw this presentation by Satoshi Matsuoka, from the Tokyo Institute of Technology which shows how  Tokyo Institute of Technology converge HPC and Big Data. Do note that the presentation (pdf) is about 24MB.

Here is the links: http://www.opensfs.org/wp-content/uploads/2013/09/Matsuoka_TokyoTech_Tsubame.pdf

Thursday, December 5, 2013

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

Wednesday, December 4, 2013

Coprocessors Programming Codebook and Parallel Universe Magazine By Intel


Intel has put a 16-pages code book titled - Application Optimization for Intel® Processors and Coprocessors Programming CodeBook. Explore some of the tools, techniques, and models for creating highly parallelized code optimized for Intel® Core™, Intel® Xeon® processors, or the Intel® Xeon Phi™ coprocessor.


Download the latest issue of The Parallel Universe magazine and explore the implications of real-time everything as high-performance computing (HPC) moves out of the science lab and onto Main Street. Check out the features in OpenMP* 4.0, discover what’s new in Intel® Cluster Studio XE 2013 SP1, learn techniques for ID’ing and correcting HPC application bottlenecks, and more

Tuesday, December 3, 2013

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:

Saturday, November 30, 2013

SGI Receives Seven Top Honors in 2013 HPCwire Readers' and Editors' Choice Awards

SGI Receives Seven Top Honors in 2013 HPCwire Readers' and Editors' Choice Awards

Last week, SGI received seven awards for outstanding technology and implementation achievements as part of the 2013 HPCwire Readers' Choice Awards and HPCwire Editors' Choice Awards.


SGI was selected as a recipient of four HPCwire Readers’ Choice Awards, winning case studies that include:

  1. Top Supercomputing Achievement:  TOTAL S.A. and SGI “Pangea” the World’s Largest Commercial HPC Deployment for Oil and Gas Exploration
  2. Best use of HPC in Life Sciences:  Pittsburgh Supercomputing Center and SGI “Blacklight” for Next Generation Sequencing Assembly
  3. Best use of HPC in Financial Services:  PayPal and SGI, Mellanox, and DataDirect Networks technologies for fraud detection and prevention during PayPal transactions
  4. Best use of HPC in the Oil and Gas Industry:  TOTAL S.A. using SGI “Pangea” for oil and gas exploration

 HPCwire Editors’ Choice Awards selected SGI for two category wins based on customer implementation and standalone product offering, which include:

  1. Best use of HPC in Financial Services:  XSEDE PSC SGI “Blacklight” and SDSC Cray “Gordon” Research enables faster market analysis and imposes stricter regulations upon stock market trading
  2. Best HPC Storage Product or Technology:  SGI InfiniteStorage Gateway

For more information. See SGI Press release SGI Receives Seven Top Honors in 2013 HPCwire Readers' and Editors' Choice Awards

Wednesday, November 27, 2013

Intel Books24X7 Online Library

 
Key features of this unique online library configuration:
 
1. Choose two library options customized for your area of specialization:
  •  IT Pro™ (12,000 titles)
  • Engineering Pro™ (4,000 titles)
2. Search within any or all books by software source code (C, Java, C++ etc.)
3. Add notes and bookmarks (and share with your workgroup)
 
For more information, do look at the Intel Books24X7 Online Library 

Tuesday, November 26, 2013

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

Monday, November 25, 2013

Error: php53-common conflicts with php-common when installing php53-xml on CentOS 5

I was trying to install php53-xml on CentOS 5.5. But instead I encountered the error instead. I', assuming  you have activated the webtatic repo and install the rest of the php 5.3 components like the How to yum install PHP 5.3 for CentOS 5

php53-common-5.3.3-21.el5.i386 from base has depsolving problems
  --> php53-common conflicts with php-common
Error: php53-common conflicts with php-common
 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.

The issue of the problem is that the current PHP from webtatic is 5.3.27, but the one from yum php53-xml is 5.3.3 which is higher. To solve the issue, you have to use the php-xml from webtatic

# yum install  php-xml

Wednesday, November 20, 2013

How to yum install PHP 5.3 for CentOS 5

There is interesting article from Rackspace How to install/upgrade PHP 5.3 for CentOS 5.x

Step 1: Basically, you have to install a repository "webstatic" which is found at 
# wget http://repo.webtatic.com/yum/centos/5/latest.rpm
# rpm -Uvh latest.rpm
# yum check-update

Step 2: Enable WebStatic (enabled=1)
[webtatic]
name=Webtatic Repository $releasever - $basearch
#baseurl=http://repo.webtatic.com/yum/centos/5/$basearch/
mirrorlist=http://mirror.webtatic.com/yum/centos/5/$basearch/mirrorlist
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-webtatic-andy

Step 3a: Do a Yum Install
# yum install php php-cli php-gd php-mysql php-mbstring

Step 3b: If you are upgrading, do a yum upgrade
# yum upgrade php

Step 4: Restart the Web Server
# service httpd restart

Step 5: Check the PHP version
[root@web ~]# php -v
PHP 5.3.27 (cli) (built: Jul 13 2013 22:19:28)
Copyright (c) 1997-2013 The PHP Group
Zend Engine v2.3.0, Copyright (c) 1998-2013 Zend Technologies

Friday, November 15, 2013

Fixing Authentication is requried to set the network proxy used for download packages for CentOS 6

I encountered this pop-up error today when I was xrdp into my CentOS 6.3. The error was something like this

authentication is required to set the network proxy used for downloading packages.  
An application is attempting to perform an action that requires privileges.  
Authentication as the super user is required to perform this action" and asking  
for the root password

Non-root users

Step 1: Launch a Terminal Console and type
# gnome-session-properties

Step 2: Uncheck PackageKit Update Applet .

See pix below.

Root User

Step 1: Disabled /etc/yum/pluginconf.d
# vim /etc/yum/pluginconf.d/refresh-packagekit.conf

[main]
enabled=0

Tuesday, November 12, 2013

Conflict when yum install perl-XML-SAX-0.96-7.el6.noarch on CentOS 6

When yum install perl-XML-SAX, you may encounter an error something like this

Transaction Check Error:
  file /usr/share/man/man3/XML::SAX::Base.3pm.gz conflicts between attempted 
installs of perl-XML-SAX-0.96-7.el6.noarch and perl-XML-SAX-Base-1.04-1.el6.rf.noarch
  file /usr/share/man/man3/XML::SAX::Exception.3pm.gz conflicts between attempted 
installs of perl-XML-SAX-0.96-7.el6.noarch and perl-XML-SAX-Base-1.04-1.el6.rf.noarch

The reason for this is due to the conflict of packages between the CentOS base repo (perl-XML-SAX-0.96-7)  and those found at rpmforge (perl-XML-SAX-Base-1.04-1).

The resolution is to disable the perl-XML-SAX-Base-1.04-1 found at rpmforge. You can do it by putting this line at /etc/yum.repos.d/rpmforge.repo

.....
.....
exclude=perl-XML-SAX-Base
.....
.....

Monday, November 11, 2013

Announcing the Release of MVAPICH2 2.0b, MVAPICH2-X 2.0b and OSU Micro-Benchmarks (OMB) 4.2

The MVAPICH team is pleased to announce the release of MVAPICH2 2.0b,
MVAPICH2-X 2.0b (Hybrid MPI+PGAS (OpenSHMEM) with Unified
Communication Runtime) and OSU Micro-Benchmarks (OMB) 4.2.
Features, Enhancements, and Bug Fixes for MVAPICH2 2.0b (since
MVAPICH2 2.0a release) are listed here.
* Features and Enhancements (since 2.0a):
    - Based on MPICH-3.1b1
    - Multi-rail support for GPU communication
    - Non-blocking streams in asynchronous CUDA transfers for
      better overlap
    - Initialize GPU resources only when used by MPI transfer
    - Extended support for MPI-3 RMA in OFA-IB-CH3, OFA-IWARP-CH3, and
      OFA-RoCE-CH3
    - Additional MPIT counters and performance variables
    - Updated compiler wrappers to remove application dependency
      on network and other extra libraries
        - Thanks to Adam Moody from LLNL for the suggestion
    - Capability to checkpoint CH3 channel using the Hydra process manager
    - Optimized support for broadcast, reduce and other collectives
    - Tuning for IvyBridge architecture
    - Improved launch time for large-scale mpirun_rsh jobs
    - Introduced retry mechanism in mpirun_rsh for socket binding
    - Updated hwloc to version 1.7.2
* Bug-Fixes (since 2.0a):
    - Consider list provided by MV2_IBA_HCA when scanning device list
    - Fix issues in Nemesis interface with --with-ch3-rank-bits=32
    - Better cleanup of XRC files in corner cases
    - Initialize using better defaults for ibv_modify_qp (initial ring)
    - Add unconditional check and addition of pthread library
    - MPI_Get_library_version updated with proper MVAPICH2 branding
        - Thanks to Jerome Vienne from the TACC for the report
MVAPICH2-X 2.0b software package provides support for hybrid MPI+PGAS
(UPC and OpenSHMEM) programming models with unified communication
runtime for emerging exascale systems. This software package
provides flexibility for users to write applications using the
following programming models with a unified communication runtime:
MPI, MPI+OpenMP, pure UPC, and pure OpenSHMEM programs as well as
hybrid MPI(+OpenMP) + PGAS (UPC and OpenSHMEM) programs.
Features, enhancements and bug-fixes for MVAPICH2-X 2.0b
(since MVAPICH2-X 2.0a) are as follows:
* Features and Enhancements (since 2.0a)
    - OpenSHMEM Features
        - Based on OpenSHMEM reference implementation 1.0e
        - Enhanced optimization of OpenSHMEM collectives (shmem_collect,
          shmem_fcollect, shmem_barrier, shmem_reduce, and shmem_broadcast)
        - Optimized shmalloc routine
    - UPC Features
        - Based on Berkeley UPC 2.18.0
        - Support for GUPC translator
    - MPI Features
        - Based on MVAPICH2 2.0b (OFA-IB-CH3 interface)
    - Unified Runtime Features
        - Based on MVAPICH2 2.0b (OFA-IB-CH3 interface). All the runtime
          features enabled by default in OFA-IB-CH3 interface of
          MVAPICH2 2.0b are available in MVAPICH2-X 2.0b
* Bug Fixes (since 2.0a):
    - OpenSHMEM Bug Fixes
        - Fixed synchronization issue in shmem_fence
        - Fixed issue in shmem_collect which prevented variable length
          collect routine
New features and Enhancements of OSU Micro-Benchmarks (OMB) 4.2 (since
OMB 4.1 release) are listed here.
* New Features & Enhancements
    - New OpenSHMEM benchmarks
        * osu_oshm_fcollect
    - Enable handling of GPU device buffers in all MPI collective benchmarks
    - Add device binding for OpenACC benchmarks
* Bug Fixes
    - Add upc_fence after memput in osu_upc_memput benchmark
    - Removed incorrect reuse of pSync in OpenSHMEM benchmarks
        - Thanks Sayan Ghosh for the report
    - Correct CUDA configuration example in README
    - Fix several warnings
For downloading MVAPICH2 2.0b, MVAPICH2-X 2.0b, OMB 4.2, associated
user guides, quick start guide, and accessing the SVN, please visit
the following URL:
http://mvapich.cse.ohio-state.edu

RM Failure, rc: 15041, msg: 'Execution server rejected request MSG=cannot send job to mom, state=PRERUN'

I'm using Torque 4.2.5 and MAUI 3.3.1

When I was submitting a job, I always seem to get my job deferred and stuck. I used the MAUI "checkjob jobid" function and the detailed information will come up something like

RM Failure, rc: 15041, msg: 'Execution server rejected request 
MSG=cannot send job to mom, state=PRERUN'

The solution is quite simple. The compute nodes that the scheduler threw to have its iptables on and thus the job was blocked. To solve the issue, just turn off the iptables and it works.


Sunday, November 10, 2013

PBS Error: Unable to change the status of compute nodes from down state when using Torque 4.2.5

 I did my installation according to Torque Administration 4.0.2
PBS_Server;LOG_ERROR::get_node_from_str, Node node-c00 is reporting on 
node node-c00.cluster.spms.ntu.edu.sg, 
which pbs_server doesn't know about

The solution is simple. Use the full hostname used by the client nodes and update the $TORQUE_HOME/server_priv/nodes

Restart the pbs_server, pbs_sched, trqauthd services
# service pbs_server restart
# service pbs_sched restart
# service trqauthd restart

Thursday, November 7, 2013

Resolving mmremote: Unknown GPFS execution environment when issuing mmdelnode commands

I was issuing a mmdelnode from the NSD node to a client node which are having issues, but somehow I keep getting this error.

[root@nsd1]# mmdelnode -N node-c01

Verifying GPFS is stopped on all affected nodes ...
node-c01-nas:  mmremote: Unknown GPFS execution environment
mmdelnode: Command failed.  Examine previous error messages to determine cause.

If you do a mmgetstate -a on the NSD node, you will get something like this
# mmgetstate -a 
.....
.....
05      node-c01   unknown
.....
.....

The resolution is not too difficult. According to IBM GPFS Administration and Programming References mmdelnode

You have to power down the affected node and do the mmdelnode again. You can see it is successful.
# mmdelnode -N node-c01

Verifying GPFS is stopped on all affected nodes ...
mmdelnode: Command successfully completed
mmdelnode: Propagating the cluster configuration data to all
affected nodes.  This is an asynchronous process.

Do a mmgetstate -a and you will see that the node deletion is successful

Tuesday, November 5, 2013

Using Intel® C++ Compiler with the Eclipse* IDE on Linux*

There is a very good tutorial on how to use Eclipse IDE with Intel C++ Compilers. Do look at the article by Intel

Using Intel® C++ Compiler with the Eclipse* IDE on Linux*

Saturday, November 2, 2013

GPFS Error: Unable to delete Client Node from GPFS Cluster

Today when we were delete a Client GPFS Node, the error received was something like:

 Fri Nov  1 11:55:03 SGT 2013: mmaddnode: Processing node node01
mmaddnode: Node node01 was not added to the cluster.
   The node appears to already belong to a GPFS cluster.
mmaddnode: mmaddnode quitting.  None of the specified nodes are valid.

When we do the command mmlcluster, the node was not in the list. So in other words, we are not able to add or delete the node.

Solution: Just reinstall. But you may have to remove old information
# rm -fr /usr/lpp
# rm -fr /var/mmfs

Reinstall and add the GPFS Node again. For more information, do take a look at  Adding nodes to a GPFS cluster


Friday, November 1, 2013

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.

Step 1-3: For more information do see Compiling and Installing Meep-1.2.1 on CentOS 6 and OpenMPI (linuxcluster.wordpress.com)

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=-I/usr/local/libctl-3.2.1/lib \
CPPFLAGS=-I/usr/local/libctl-3.2.1/include \
--with-mpi=/usr/local/openmpi-1.6.5/

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

Thursday, October 31, 2013

crtbegin.o: No such file: No such file or directory Error when compiling Meep-1.2 on CentOS

When compiling Meep on CentOS, you may encounter the error
/usr/bin/ld: crtbegin.o: No such file: No such file or directory.
This error is quite misleading as it is likely could be due to the missing guile and guile-devel packages.

Do a yum install
# yum install guile guile-devel  
and recompile again

undefined reference to `dgetrf_' error when compiling Meep-1.2 on CentOS

When you are compiling meep-1.2 on CentOS, you may encounter this error

multilevel-atom.cpp:(.text+0x9a9): undefined reference to `dgetrf_'
multilevel-atom.cpp:(.text+0x9fb): undefined reference to `dgetri_'
multilevel-atom.cpp:(.text+0xa44): undefined reference to `dgetri_'
collect2: ld returned 1 exit status
make[3]: *** [meep_mpi] Error 1
make[3]: Leaving directory `/home/user1/meep-1.2/libctl'

The error is due to LAPACK linking problem

The solution is to use the pre-release Meep-1.2.1 found at http://jdj.mit.edu/~stevenj/meep-1.2.1.tar.gz

References:
  1. http://listarc.com/showthread.php?3713314-Meep+1.2+installation

Tuesday, October 29, 2013

Requirements to Support AVX

For more information, do take a look at  Wikipedia Advanced Vector Extensions for more information.

Centos OS / RH OS
Linux Kernel must be 2.6.30 and above. CentOS 6.2 and later will have full support for AVX. See PGI Forum discussion ). Do upgrade the OS 


Intel Compilers
From the Wikipedia, Intel Compiler version 11.1 onwards support AVXIt is recommended to use icc version 12.1.8 to make it work. You may want to take a look at StackOverflow Forum


GNU Compilers:
From the Wikipedia, GNU Compilers 4.6 and above.

Hardware
Sandy Bridge processor, Q1 2011[12]
Sandy Bridge E processor, Q4 2011[13]
Ivy Bridge processor, Q1 2012
Ivy Bridge E processor, Q3 2013
Haswell processor, Q2 2013.
Broadwell processor, 2014.



Sunday, October 27, 2013

Free online training on Fundamental of Hadoop from Cloudera



If you wish to understand the basics of Apache Hadoop and explore the basics of MapReduce, HDFS, ecosystem projects and the anatomy of a Hadoop Cluster. Do register in Cloudera University and watch online now.

Wednesday, October 23, 2013

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

Tuesday, October 22, 2013

Compiling Error "Could not run a simple Fortran 77 program. Aborting." when compiling OpenMPI 1.6.5 with GCC 4.8.1 on CentOS 6

I was compiling OpenMPI 1.6.5 with GCC 4.8.1 on CentOS 6.3, I encountered this error "Could not run a simple Fortran 77 program. Aborting."

For more information on compiling GCC, do take a look at  Compiling GNU 4.8.1 on CentOS 6


A quick look, shows that my .bashrc was incorrect written. My PATH and LD_LIBRARY_PATH should reflect the pathing of GCC

export PATH=$PATH:/usr/local/gcc-4.8.2/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/gcc-4.8.1/lib

Secondly, another possible issue could be due to incomplete or unlinked gfortran libraries. Do check with your /usr/local/gcc-4.8.1 that your libgfortran.so.3 is linked and present with the right libraries.


 Lastly, you can force the OpenMPI to compile F77 and FC with the following configuration
# ./configure --prefix=/usr/local/openmpi-1.6.5-gcc-4.8.1 \ 
F77=gfortran FC=gfortran --with-devel-headers --enable-binaries

Thursday, October 17, 2013

Mellanox Online Academy



The Mellanox Online Academy platform includes various courses, videos, best practices, and other free content to support learners of all levels and backgrounds in educating themselves on Mellanox products and related technologies (including general technologies). The flexibility and variety of the content enables students to acquire the knowledge to improve their personal and organizational performance.

Key Features:
  • Courses oriented toward both general and Mellanox-based technologies
  • Courses built and delivered by leading industry and product experts and certified instructors
  • Flexible learning options (content, time)
  • Flexible payment options (credit cards, PayPal, standard PO and purchase via phone)
  • Varied subscription plans, duration and additional services
  • Access to Mellanox's expert to support the learning process


Tuesday, October 15, 2013

Compiling and installing FFTW 3.3.3 with OpenMPI and OpenMP

To Compile FFTW 3.3.3 single precision with OpenMPI, make sure you compile and set your path for Intel and OpenMPI.  

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
....
....

Saturday, October 12, 2013

Encountering error -static-libstdc++ not implemented when compiling GNU 4.8.1 on CentOS 6

When compiling GNU 4.8.1 according to blog entry Compiling GNU 4.8.1 on CentOS 6, you may encounter an error in the config.log

.....
g++: unrecognized option '-static-libstdc++'
conftest.cpp:11:2: error: #error -static-libstdc++ not implemented
.....

The error indicate that you may missed packages such as glibc-static, glibc-devel, glibc-static, libstdc++ libstdc++-devel.

# yum install  glibc-static glibc-devel glibc-static libstdc++ libstdc++-devel

Another thing you may want to check is that the /etc/ld.so.conf.d has /usr/lib

Friday, October 11, 2013

On-Demand Training for SUSE

 
SUSE offers a convenient and affordable way to meet your training needs. Our video based training classes are available online, with 24x7 access to go through at your own pace.

Please visit our SUSE Shop and select the On-demand training that fits you best.  Select now! 

Courses include:
Certified Linux Administrator (CLA) Bundle - On-demand Training, 1-year subscription
Certified Linux Professional (CLP) Bundle - On-demand Training, 1-year subscription
Certified Linux Engineer (CLE) Bundle - On-demand Training, 1-year subscription
SUSE Library - On-demand Training, 1-year subscription
Full Library (NetIQ, Novell and SUSE) - On-demand Training, 1-year subscription

Wednesday, October 9, 2013

Error during installing Mellanox MLNX_OFED 1.5.3 for CentOS 6.3.

I downloaded the Mellanox MLNX_OFED Drivers for RH 6.3 and CentOS 6.3

[root@node-c01 iso]# ./mlnxofedinstall
This program will install the MLNX_OFED_LINUX package on your machine.
Note that all other Mellanox, OEM, OFED, or Distribution IB packages will be r                                                                                                                       ved.
Do you want to continue?[y/N]:y


rpm -e --allmatches --nodeps kernel-mft kernel-mft knem kernel-mft

Starting MLNX_OFED_LINUX-1.5.3-4.0.42 installation ...

Installing kernel-mft RPM
Preparing...                ##################################################
kernel-mft                  ##################################################
Installing knem RPM
Preparing...                ##################################################
knem                        ##################################################
libibumad was not created

This look like the libibumad packages are missing so I did a

# yum install  libibumad* 

But when I launched the ./mlnxofedinstall, the error appear again. Somehow the scripts remove the libibumad packages that I installed and the error occured again.

To resolve the issue, I used MLNX_OFED 2.0.3 and everything was ok.



Monday, October 7, 2013

Intel unveils Quark-based "maker board"



Intel has just launched the Intel Galileo board, the first product in a new family of Arduino-compatible development boards featuring Intel® architecture, and based on the recently announced Quark family of processors.

The Galileo development board is a great tool for quickly prototyping simple, interactive designs such as LED light displays that respond to social media, or for tackling more complex projects, from automating home appliances to building life-size robots controlled by a smartphone.

 This platform provides the ease of Intel architecture development through support for the Microsoft Windows*, Mac OS* and Linux* host operating systems. It also brings the simplicity of the Arduino software integrated development environment (IDE).........


Introducing the Gileo Development Board Video http://bcove.me/kxeu2dwz

Thursday, October 3, 2013

Availability of 3 new Chelsio High Performance Adapters

Chelsio announced the general availability of three new adapters powered by the fifth generation, highly integrated and hyper-virtualized 40/10/1GbE Chelsio Terminator 5 (T5) engine. T5 fully offloads a complete high performance Unified Wire suite of storage and cluster compute networking protocols.

 T580-CR
  1. High bandwidth and high IOPS, optimized for iSCSI & TOE
  2. Two 40/10/1Gb QSFP Ethernet ports, Half Size, PCIe Gen3 x8
  3. Concurrent offload of iSCSI, TCP/IP and UDP/IP, FCoE, iWARP 2.0 RDMA, NAT, vSwitch, Traffic Management, T10 DIX, PTP, classification, and all stateless and user-mode protocols

T540-CR


  1. Low latency and high IOPs
  2. Two 10Gb/1Gb Ethernet ports, Low Profile, PCIe Gen3 x8
  3. Concurrent offload of iSCSI, TCP/IP and UDP/IP, FCoE, iWARP 2.0 RDMA, NAT, vSwitch, Traffic Management, T10 DIX, PTP, classification, and all stateless and user-mode protocols

T522-CR
  1. Low latency and high IOPS
  2. Two 10/1GbE SFP+, Two 1GbE RJ-45, Low Profile, PCIe Gen3 x8
  3. Concurrent offload of iSCSI, TCP/IP and UDP/IP, FCoE, iWARP 2.0 RDMA, NAT, vSwitch, Traffic Management, T10 DIX, PTP, classification, and all stateless and user-mode protocols 
Other New Products
Chelsio released a beta TCP/IP offload driver for the Illumos kernel. Chelsio adapters can now deliver exceptional performance to TCP applications on Illumos, including kernel services such as NFS.

Chelsio has now released a software suite of L2 NIC, TOE, iWARP, iSCSI Target on the FreeBSD kernel for the T5 products. This will soon be joined by the FCoE Target in Q4 to complete the storage offering making T5 the most complete FreeBSD networking and storage solution.

Chelsio released Windows Server 2012 Network Direct drivers for T5. HPC applications can now leverage RDMA iWARP capabilities and performance in Microsoft Windows environments.

For More information, do look at Chelsio Website (http://www.chelsio.com)

Wednesday, October 2, 2013

Adaptive Computing Community Forum is available

From Adaptive Computing.....


Adaptive Computing would like to announce that our questions and answers community forums are now available. The forums are being launched in a beta format so we can fully test the functionality of the software. If you currently have a login to the Adaptive website, you should already have access to the forums. If you don't have access, please email us at customercare@adaptivecomputing.com to receive authorization. You can also register for the website here, then email us, and we'll grant you access just as soon as possible.

Please note that Adaptive employees will also be participating in the forums. The forums are in a Stackoverflow or Yahoo Answers style where answers to questions can be voted up and down, and the best answer can be selected by the user responsible for the question.

To access the forums, visit www.adaptivecomputing.com/questions, or go to our home page, then select "Support," then "Questions and Answers."

Tuesday, October 1, 2013

Friday, September 27, 2013

Cisco IOS Software Security Advisory Bundled Publication


Cisco IOS Software Security Advisories are released on the fourth Wednesday of the month in March and September of each calendar year. The publication includes eight Security Advisories that all address vulnerabilities in Cisco IOS Software. Exploits of the individual vulnerabilities could result in a denial of service (DoS) condition, interface queue wedge, or a device reload.

Release Date : 25Sept 2013

The 8 Security Advisories release are as follows:         
  1. Cisco IOS Software Multicast Network Time Protocol Denial of Service Vulnerability         
  2. Cisco IOS Software Internet Key Exchange Memory Leak Vulnerability          
  3. Cisco IOS Software IPv6 Virtual Fragmentation Reassembly Denial of Service Vulnerability   
  4. Cisco IOS Software DHCP Denial of Service Vulnerability           
  5. Cisco IOS SoftwareZone-Based Firewall and Content Filtering Vulnerability           
  6. Cisco IOS Software Queue Wedge Denial of Service Vulnerability          
  7. Cisco IOS Software Resource Reservation Protocol Interface Queue Wedge Vulnerability         
  8. Cisco IOS Software Network Address Translation Vulnerabilities
More information regarding the security advisory release and workarounds can be found on the link below: http://www.cisco.com/web/about/security/intelligence/Cisco_ERP_sep13.html

Compiling VASP 5.3.3 with OpenMPI 1.6.5 and Intel 12.1.5


Compiling VASP can be quite complex and tedious. Do look at Compiling VASP 5.3.3 with OpenMPI 1.6.5 and Intel 12.1.5 from linuxcluster.wordpress.com

References:
  1. How to Compile VASP on NSC’s Triolith
  2. Installing VASP
  3. How to build VASP-4.6.36 and VASP-5.2.8 on Intel Westmere with Infiniband network

Thursday, September 26, 2013

The World's First Hyperscale Server – Based On ARM® Processors


Server that only uses 5 watts of power!

The Boston Viridis uses the ARM® based Calxeda EnergyCore™ SoCs (Server on Chip) to create a
rack mountable 2U server cluster comprising 192 processing cores leading the way towards energy
efƒ cient hyperscale computing.
The Boston Viridis is a self contained, highly extensible, 48 node ultra-low power ARM® cluster with integral high-speed interconnect and storage within a standard single 2U rack mount enclosure.

Each 2U chassis contains a total of 12 Calxeda EnergyCards connected to a common mainboard
sharing power and fabric connectivity. The Calxeda EnergyCard is a single PCB module containing 4
Calxeda EnergyCore™ SoCs; each with 4GB DDR-3 Registered ECC Memory, 4 x SATA connectors and management interfaces.
.......

For more information, see  http://www.boston.co.uk/solutions/viridis/viridis-2u.aspx


Key Features

  • 192 cores per 2U enclosure
  • Ten times the performance at the same power in the same space
  • Cut energy and space by 90%
  • Industry leading low power consumption (<300w li="">
  • 5W Per Node
  • 48 Node Ultra-Low Power Arm Cluster
  • 192 Cores per 2U System

Sunday, September 22, 2013

Compiling GNU 4.7.2 on CentOS 5

Step 1: Download the following prerequistics applications libraries from ftp://gcc.gnu.org/pub/gcc/infrastructure/
  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 at your ~/.bashrc
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/mpc-0.8.1:/usr/local/mpfr-2.4.2/lib:/usr/local/gmp-4.3.2/lib

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 4.7.2
# tar -zxvf  gcc-4.7.2.tar.gz
# cd gcc-4.7.2
# mkdir build-gcc
# cd build-gcc
# ../configure --prefix=/usr/local/gcc-4.7.2 \ 
--with-mpfr=/usr/local/mpfr-2.4.2 \ 
--with-mpc=/usr/local/mpc-0.8.1 \
--with-gmp=/usr/local/gmp-4.3.2 \
--with-mpfr-include=/usr/local/mpfr-2.4.2/include \
--with-mpc-include=/usr/local/mpc-0.8.1/include
# make all-gcc
# make install-gcc
# make -j 8
# make -j 8 install

Saturday, September 21, 2013

Compiling OpenMPI 1.6.5 with Intel 12.1.5 on CentOS 6

Step 1: Download the OpenMPI Software from http://www.open-mpi.org/ . The current stable version at point of writing is OpenMPI 1.6.5

Step 2: Download and Install the Intel Compilers from Intel Website. More information can be taken from Free Non-Commercial Intel Compiler Download

 Step 3: Add the Intel Directory Binary Path to the Bash Startup
At my ~/.bash_profile directory, I've added
source /usr/local/intel/composerxe/bin/compilervars.sh intel64
export PATH=$PATH:/usr/local/intel/composerxe/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/RH6_apps/intel/composerxe/lib/intel64:/usr/local/intel/composerxe/mkl/lib/intel64
At command prompt
# source .bashrc

Step 4: Configuration Information
# gunzip -c openmpi-1.6.5.tar.gz tar xf -
# cd openmpi-1.6.5
# /configure --prefix=/usr/local/openmpi-1.6.5-intel-v12.1.5 CC=icc CXX=icpc F77=ifort FC=ifort --with-devel-headers --enable-binaries
# make all install
You will need to include --devel-headers --enable-binaries" or you will face the error Cannot open OpenMPI Configuration mpif90-wrapper-data.txt

Step 5: Test the configuration
$ mpicc -v
cc version 12.1.5 (gcc version 4.4.6 compatibility)

Friday, September 20, 2013

Compile and Build FFTW3 wrapper routines on MKL implementation of FFT

Software like VASP uses calling statements of the FFTW3 which differ to the implementation of FFT in MKL. You will need to compile the wrapper routines for MKL

# cd $MKLROOT/interfaces/fftw3xf
# make
After a successful compilation libfftw3xf_intel.a was created in this directory

The information is taken from Installing VASP

Wednesday, September 18, 2013

Cannot open OpenMPI Configuration mpif90-wrapper-data.txt

I was using Intel 12.1.5 to compile OpenMPI 1.6.5 and I have this error which I have not seen before.

If you encounter error
Cannot open configuration file: 
/usr/local/openmpi/openmpi-1.6.5/share/openmpi/mpif90-wrapper-data.txt
Error parsing data file mpif90: Not found 


Solution
# ./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort \
--with-devel-headers --enable-binaries
Somehow the development headers and binaries are excluded from the later version of OpenMPI.....

C compiler cannot create executables when compiling Openmpi 1.6.5 with Intel 12.1.5

When compiling OpenMPI 1.6.5 with Intel 12.1.5, I encountered this error

configure error: C compiler cannot create executable when compiling 
OpenMPI 1.6.5 with Intel 12.1.5

The solution is very simple. I have assumed that you have PATH and LD_LIBRARY_PATH the binaries and libraries for the intel compilers respectively. Just source the "compilervars.sh" intel64

# source /usr/local/intel/composerxe/bin/compilervars.sh intel64


Tuesday, September 17, 2013

Installing GNU 4.4 of C, C++ and gfortran for CentOS 5

Something I forget the package names of these essential compilers for  CentOS 5

# yum install gcc44 gcc44-c++ gcc44-gfortran

That's all..... One of the shortest blog entry

Friday, September 13, 2013

X Server -- no display in range is available. xrdp_mm_process_login_response: login failed

 I was having this error xrdp_mm_process_login_response: login failed. I tried the solution from this blog entry, but the error remain xrdp_mm_process_login_response: login failed

When I look into the /var/log/ xrdp-sesman.log, the error is followed:
[20130913-14:11:00] [INFO ] starting Xvnc session...
[20130913-14:11:00] [ERROR] X server -- no display in range is available

 I managed to solve the issue by changing /etc/xrdp/sesmain.ini - MaxSessions from 10 to 100
[Security]
AllowRootLogin=1
MaxLoginRetry=4
#TerminalServerUsers=tsusers
#TerminalServerAdmins=tsadmins

[Sessions]
X11DisplayOffset=10
MaxSessions=100
KillDisconnected=0
IdleTimeLimit=0
DisconnectedTimeLimit=0

Restart the Service
# service xrdp restart


Thursday, September 12, 2013

Settimg up a new network device in CentOS

If you added a new network device, but upon reboot, CentOS did not represent the card in the /etc/sysconfig/network-scripts/ifcfg-eth*, you may have to manually make aware the device to the OS.

Step 1: Make sure that the OS has detected the new card. From the example below, it detected my 2nd card. If you are unable to detect, you may want to reinstall or check the driver.
# lspci |grep -i ethernet
0b:00.0 Ethernet controller: VMware VMXNET3 Ethernet Controller (rev 01)
13:00.0 Ethernet controller: VMware VMXNET3 Ethernet Controller (rev 01)

Step 2: Launch the system-config-network and fill up the necessary information.
# system-config-network


You will see that the system-config-network create an entry at /etc/sysconfig/network-scripts/ifcfg-eth1.

Restart the network
# service network restart




Wednesday, September 11, 2013

Mellanox OFED 2.0-3.0.0 Linux Driver is now available.

Mellanox OFED 2.0-3.0.0 Linux Driver is now available.
MLNX_OFED 2.0-3.0.0 main features:
  1. SR-IOV for InfiniBand Ethernet         
  2. RoCE Over SR-IOV
  3. Port base QoS for both Ethernet and InfiniBand
  4. eIpoIB
  5. Connect-IB™
  6. Low Latency Socket
  7. 56GbE
  8. XRC
  9. Dynamically Connected Transport ( DCT)  - alpha level
  10. Flow Steering

MLNX_OFED 2.0-3.0.0 Download and Manual Page
MLNX_OFED 2.0-3.0.0 Release notes

 Differences between MLNX_OFED 1.5.3 and MLNX_OFED 2.0:
  1. MLNX_OFED 2.0 is based on Kernel 3.7 which is a huge leap forward from the 2.6.30 Kernel that the 1.5.x is based on.
  2. MLNX_OFED 2.0 supports the operating systems that are based on newer Kernels such as RHEL 6.x and SLES 11 SPx. MLNX_OFED 1.5.x will continue to support OS’s based on older kernels such as RHEL 5.x and SLES 10 SPx.
  3. MLNX_OFED 2.0 includes new functionality, 1.5.x does not.

Full Support Matrix for Both MLNX_OFED Branches 

For more information, do read
  1. Online version of Product and Support Updates Notification

Sunday, September 8, 2013

TORQUE Security Advisory - 6 September 2013


Vulnerability: A non-privileged user who can run jobs or login to a node running pbs_server or pbs_mom can submit an arbitrary job to the cluster; that job can run as root. The user can submit a command directly to a pbs_mom daemon to queue and run a job. A malicious user could use this vulnerability to remotely execute code as root on the cluster.

Versions Affected: All versions of TORQUE

Mitigating Factors:
- The user must be logged in on a node that is already legitimately able to contact pbs_mom daemons or submit jobs.
- If a user submits a job via this defect and pbs_server is running, pbs_server will kill the job unless job syncing is disabled. It may take up to 45 seconds for pbs_server to kill the job.
- There are no known instances of this vulnerability being exploited.

Remedy: All TORQUE users should patch their systems using the following instructions:

For 2.5.x versions of TORQUE:
----------------------------
1. Download the patch file:
     $ wget http://www.adaptivecomputing.com/torquepatch/fix_mom_priv_2.5.patch
2. Run the patch command in the root directory of the TORQUE source tree:
     $ patch -p1 < fix_mom_priv_2.5.patch
3. Recompile TORQUE:
     $ make
4. Install TORQUE:
     $ sudo make install
5. Restart pbs_mom (pbs_server is not affected)


For 4.x versions of TORQUE:
----------------------------
1. Download the patch file:
     $ wget http://www.adaptivecomputing.com/torquepatch/fix_mom_priv.patch
2. Run the patch command in the root directory of the TORQUE source tree:
     $ patch -p1 < fix_mom_priv.patch
3. Recompile TORQUE:
     $ make
4. Install TORQUE:
     $ sudo make install
5. Restart pbs_mom (pbs_server is not affected)

What the Patch Does: The patch checks that the connection to the pbs_mom daemon is coming from a privileged port. This follows the security model that only privileged users should be able to submit arbitrary jobs.

Attribution: This vulnerability was discovered by John Fitzpatrick of MWR InfoSecurity. Matt Ezell of Oak Ridge National Laboratory assisted in creating the patch. We thank these individuals for helping to improve TORQUE.

Thursday, September 5, 2013

Encountering __intel_sse2_strlen when compiling OpenMPI with Intel Compilers

I was compiling OpenMPI 1.6.x and Intel Compiler XE 2013, I used the following configuration found in

#./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort
Do specify CC=icc CXX=icpc F77=ifort FC=ifort as if you miss one of the parameters, it will take the default. For example, if you do not specify CXX=icpc, it will adopt CXX=g++
but when I run
# make -j8

I got this error:
..../openmpi-1.6.2/ompi/contrib/vt/vt/tools/opari/tool/../../../util/util.c:45: 
undefined reference to `__intel_sse2_strlen'
..../openmpi-1.6.2/ompi/contrib/vt/vt/tools/opari/tool/../../../util/util.c:61: 
undefined reference to `__intel_sse2_strlen'
..../openmpi-1.6.2/ompi/contrib/vt/vt/tools/opari/tool/../../../util/util.c:46: 
undefined reference to `__intel_sse2_strlen'
..../openmpi-1.6.2/ompi/contrib/vt/vt/tools/opari/tool/../../../util/util.c:46: 
undefined reference to `__intel_sse2_strlen' 
......
......

The solution is to do the following:

Firstly, make sure you compile with the following
# source /usr/local/intel/composerxe/bin/compilervars.sh
Do it again
#./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort
Run the make again
# make -j8
# make install

Wednesday, September 4, 2013

error while loading shared libraries: libcurand.so.5.5: cannot open shared object file: No such file or directory

If encountered this error:

....pmemd.cuda.MPI: Error while loading shared libraries:
 libcurand.so.5.5: cannot open shared object file: No such file or directory

It is due to the the LD_LIBRARY_PATH not referring to the CUDA Toolkits libraries. To solve the issue, just update your pathing in your .bashrc
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-5.5/lib64

You may also want to update /etc/ld.so.conf.d/ directories
# touch /etc/ld.so.conf.d/cuda.conf

/usr/local/cuda-5.5/lib64
/usr/local/cuda-5.5/lib


Tuesday, September 3, 2013

Error installing X11 libraries

If you have error installing X11 libraries for CentOS 5 or CentOS 6, you may want to check whether you have already installed the correct group. To do a grouplist,

 Do  yum grouplist
# yum grouplist 
Installed Groups:
   Administration Tools
   Authoring and Publishing
   Development Libraries
   Development Tools
   Editors
   GNOME Desktop Environment
   Graphics
   Legacy Network Server
   Legacy Software Development
   Legacy Software Support
   Mail Server
   MySQL Database
   Network Servers
   Office/Productivity
   OpenFabrics Enterprise Distribution
   Printing Support
   Server Configuration Tools
   System Tools
   X Software Development
   X Window System
Available Groups:
   Cluster Storage
   Clustering
   DNS Name Server
   Engineering and Scientific
   FTP Server
   GNOME Software Development
   Games and Entertainment
   Graphical Internet
   Java Development
   KDE (K Desktop Environment)
   KDE Software Development
   KVM
   News Server
   PostgreSQL Database
   Sound and Video
   Text-based Internet
   Web Server
   Windows File Server
   Xen

Do a yum groupinstall "X Software Development"
 # yum groupinstall "X Software Development"

Friday, August 30, 2013

Diagnostic Tools to diagnose Infiniband Fabric Information

There are a few diagnostic tools to diagnose Infiniband Fabric Information. Use man for the parameters for the
  1. ibnodes - (Show Infiniband nodes in topology)
  2. ibhosts - (Show InfiniBand host nodes in topology)
  3. ibswitches- (Show InfiniBand switch nodes in topology)
  4. ibnetdiscover - (Discover InfiniBand topology)
  5. ibchecknet - (Validate IB subnet and report errors)
  6. ibdiag (Scans the fabric using directed route packets and extracts all the available information regarding its connectivity and devices)
  7. perfquery (find errors on a particular or number of HCA's and switch ports)
For more information, do look at Diagnostic Tools to diagnose Infiniband Fabric Information

Thursday, August 29, 2013

New Intel® Enterprise Edition for Lustre* Software Designed to Simplify Big Data Management, Storage

NEWS HIGHLIGHTS from Intel
  1. Intel® Enterprise Edition for Lustre* software helps simplify configuration, monitoring, management and storage of high volumes of data.
  2. With Intel® Manager for Lustre* software, Intel is able to extend the reach of Lustre into new markets such as financial services, data analytics, pharmaceuticals, and oil and gas.
  3. When combined with the Intel® Distribution for Apache Hadoop* software, Hadoop users can access Lustre data files directly, saving time and resources.
  4. New software offering furthers Intel's commitment to drive new levels of performance and features through continuing contributions the open source community.
For more information, see Intel Expands Software Portfolio for Big Data Solutions

Wednesday, August 28, 2013

Issues when compiling OpenMPI 1.6 and Intel 2013 XE on CentOS 5

I encountered this same error when compiling on CentOS 5.3 and using OpenMPI 1.6 and Intel 2013 XE

.....
opal_wrapper.c:(............): undefined reference to `__intel_sse2_strdup'
opal_wrapper.c:(............): undefined reference to `__intel_sse2_strncmp'
......
opal_wrapper.o:opal_wrapper.c:(.......): more undefined references to 
`__intel_sse2_strncmp' follow
......

There is one interesting forum discussion from Intel (Problem with Openmpi+c++ compiler)
that helps to explain how someone solve it. Basically, it could be due to mixed mis-match libraries and binaries especially if you have multiple version of intel compilers. Do look at your $PATH and $LD_LIBRARY_PATH

Even with correct editing of the $PATH and $LD_LIBRARY_PATH, I was not able to get aaway from the error. But when I use CentOS 6 with OpenMPI 1.6 and Intel XE 2013, was I able spare from this errror.


Monday, August 26, 2013

Announcing the Release of MVAPICH2 2.0a, MVAPICH2-X 2.0a and OSU Micro-Benchmarks (OMB) 4.1



The MVAPICH team is pleased to announce the release of MVAPICH2 2.0a, MVAPICH2-X 2.0a (Hybrid MPI+PGAS (OpenSHMEM) with Unified Communication
Runtime) and OSU Micro-Benchmarks (OMB) 4.1.

Features, Enhancements, and Bug Fixes for MVAPICH2 2.0a (since MVAPICH2 1.9GA release) are listed here.

* Features and Enhancements (since 1.9GA):
     - Based on MPICH-3.0.4
     - Dynamic CUDA initialization. Support GPU device selection after MPI_Init
     - Support for running on heterogeneous clusters with GPU and non-GPU nodes
     - Supporting MPI-3 RMA atomic operations and flush operations
       with CH3-Gen2 interface
     - Exposing internal performance variables to MPI-3 Tools information
       interface (MPIT)
     - Enhanced MPI_Bcast performance
     - Enhanced performance for large message MPI_Scatter and MPI_Gather
     - Enhanced intra-node SMP performance
     - Tuned SMP eager threshold parameters
     - Reduced memory footprint
     - Improved job-startup performance
     - Warn and continue when ptmalloc fails to initialize
     - Enable hierarchical SSH-based startup with Checkpoint-Restart
     - Enable the use of Hydra launcher with Checkpoint-Restart

* Bug-Fixes (since 1.9GA):
     - Fix data validation issue with MPI_Bcast
         - Thanks to Claudio J. Margulis from University of Iowa for the report
     - Fix buffer alignment for large message shared memory transfers
     - Fix a bug in One-Sided shared memory backed windows
     - Fix a flow-control bug in UD transport
         - Thanks to Benjamin M. Auer from NASA for the report
     - Fix bugs with MPI-3 RMA in Nemesis IB interface
     - Fix issue with very large message (>2GB bytes) MPI_Bcast
         - Thanks to Lu Qiyue for the report
     - Handle case where $HOME is not set during search for MV2 user config file
         - Thanks to Adam Moody from LLNL for the patch
     - Fix a hang in connection setup with RDMA-CM


MVAPICH2-X 2.0a software package provides support for hybrid MPI+PGAS (UPC and OpenSHMEM) programming models with unified communication runtime for emerging exascale systems. This software package provides flexibility for users to write applications using the following programming models with a unified communication runtime: MPI, MPI+OpenMP, pure UPC, and pure OpenSHMEM programs as well as hybrid MPI(+OpenMP) + PGAS (UPC and
OpenSHMEM) programs.

Features and enhancements for MVAPICH2-X 2.0a (since MVAPICH2-X 1.9GA) are as follows:

* Features and Enhancements (since 1.9GA):
     - OpenSHMEM Features
         - Optimized OpenSHMEM Collectives (Improved performance for
           shmem_collect, shmem_barrier, shmem_reduce and shmem_broadcast)

     - MPI Features
         - Based on MVAPICH2 2.0a (OFA-IB-CH3 interface)

     - Unified Runtime Features
         - Based on MVAPICH2 2.0a (OFA-IB-CH3 interface). All the runtime
           features enabled by default in OFA-IB-CH3 interface of
           MVAPICH2 2.0a are available in MVAPICH2-X 2.0a

New features and Enhancements of OSU Micro-Benchmarks (OMB) 4.1 (since OMB
4.0.1 release) are listed here.

* New Features & Enhancements
     - New OpenSHMEM benchmarks
         * osu_oshm_barrier
         * osu_oshm_broadcast
         * osu_oshm_collect
         * osu_oshm_reduce
     - New MPI-3 RMA Atomics benchmarks
         * osu_cas_flush
         * osu_fop_flush

For downloading MVAPICH2 2.0a, MVAPICH2-X 2.0a, OMB 4.1, associated user guides, quick start guide, and accessing the SVN, please visit the following URL: