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

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.

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.

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

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

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

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
....
....

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

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

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.

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

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)

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."

Linux Commands Line Resources

Recommended Sites for Linux Command Lines. Good and easy to start

1. LinuxCommand.Org
2. LinuxCommand.org: Tips, News And Rants