Upgrading Mellanox ConnectX® EN 10GbE Drivers for VMware® ESX 5.x Server

Do read the Blog Entry Installing Mellanox ConnectX® EN 10GbE Drivers for VMware® ESX 5.x Server

Step 1: At VMware ESX 5.x Hypervisor,

  • Click the F2 button
  • Select “Troubleshoot Options”
  • “Enable ESXi Shell” and “Enable SSH”

Step 2: Download the VMware ESXi 5.0 Driver for Mellanox ConnectX Ethernet Adapters

Step 3: Unzip the mlx4_en-mlnx-1.6.1.2-offline_bundle-471530.zipEdit

Step 4: The upgrade process is similar to a new install, except the command that should be issued is the following:

#   esxcli software vib upgrade -v {VIBFILE}

In the example above, this would be:

#  esxcli software vib update -v 
/tmp/net-mlx4-en-1.6.1.2-1OEM.500.0.0.406165.x86_64.vib

Installing Mellanox ConnectX® EN 10GbE Drivers for VMware® ESX 5.x Server

If you have Mellanox Technologies MT27500 Family [ConnectX-3] 10G Ethernet Card, it may not be automatically detected by VMware ESX 5.x Hypervisor. You have to install the driver manually into Vmware 5.x

Step 1: At VMware ESX 5.x Hypervisor,

  • Click the F2 button
  • Select “Troubleshoot Options”
  • “Enable ESXi Shell” and “Enable SSH”

Step 2: Download the VMware ESXi 5.0 Driver for Mellanox ConnectX Ethernet Adapters

Step 3: Unzip the mlx4_en-mlnx-1.6.1.2-offline_bundle-471530.zip

Step 4: Read the README file

VMware uses a file package called a VIB (VMware Installation Bundle) as the  mechanism for installing or upgrading software packages on an ESX server.

The file may be installed directly on an ESX server from the command line, or through the VMware Update Manager (VUM).

Step 5:  For New Installation (From README and modified)

For new installs, you should perform the following steps:

Step 5a: Copy the VIB to the ESX server.  Technically, you can place the file anywhere that is accessible to the ESX console shell, but for these instructions, we’ll assume the location is in ‘/tmp’.

Here’s an example of using the Linux ‘scp’ utility to copy the file from a local system to an ESX server located at 10.10.10.10:

# scp net-mlx4-en-1.6.1.2-1OEM.500.0.0.406165.x86_64.vib root@10.10.10.10:/tmp

Step 5b: Issue the following command (full path to the VIB must be specified):

# esxcli software vib install -v {VIBFILE}

In the example above, this would be:

# esxcli software vib install -v 
/tmp/net-mlx4-en-1.6.1.2-1OEM.500.0.0.406165.x86_64.vib

Platform LSF – Administration and Accounting Commands

I thought I list out some useful commands that can be used for for viewing a cluster using an LSF Cluster. Please read the manual for more in-depth information. Taken from Platform LSF 8.3 Quick References.

Administration and Accounting commands
lsadmin LSF administrative tool to control the operation of the LIM and RES daemons in an LSF cluster, lsadmin help shows all subcommands
lsfinstall Install LSF using install.config input file
lsfrefresh Restart the LSF daemons on all hosts in the local cluster
lsfshutdown Shut down the LSF daemons on all hosts in the local cluster
lsfstartup Start the LSF daemons on all hosts in the local cluster
badmin LSF administrative tool to control the operation of the LSF Batch
system including sbatchd, mbatchd, hosts and queues, badmin help
shows all subcommands
bconf Changes LSF configuration in active memory
bladmin Displays the current LSF version number, cluster name and master host name

References

  1. Platform LSF – Monitoring jobs and tasks
  2. Platform LSF – Administration and Accounting Commands
  3. Platform LSF – View Information about Cluster
  4. Platform LSF – Submitting and Controlling jobs

Platform LSF – View Information about Cluster

I thought I list out some useful commands that can be used for for viewing a cluster using an LSF Cluster. Please read the manual for more in-depth information. Taken from Platform LSF 8.3 Quick References.

View Information about Cluster
bhosts Display hosts and static and dynamic resources
bmgroup Displays Information about host groups and compute units
blimits Displays Information about resource allocation limits of running jobs
bparams Displays Information about tunable batch system parameter
bqueues Displays Information about batch queue
busers Displays Information about users and user groups
lshosts Displays hosts and their static resource Information
lsid Displays the current LSF version number, cluster name and master host name
lsinfo Displays load sharing configuration information
lsload Displays dynamic load indices for hosts

References

  1. Platform LSF – Monitoring jobs and tasks
  2. Platform LSF – Administration and Accounting Commands
  3. Platform LSF – View Information about Cluster
  4. Platform LSF – Submitting and Controlling jobs

Compiling Cufflinks

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

Preliminary Compilation

  1. Compiling and Installing Boost 1.53
  2. Compiling SamTools
  3. Compiling Eigen

Step 1: Download Cufflinks

Download Cufflinks

Step 2: Compile Cufflinks

# tar -zxvf cufflinks-2.1.1.tar.gz
# cd cufflinks-2.1.1
#  ./configure --prefix=/usr/local/cufflinks/ \
--with-boost=/usr/local/boost \ 
--with-eigen=/usr/local/include
# make
# make install

Step 3: Testing the installation

Download the test data

# /usr/local/cufflinks/bin/cufflinks ./test_data.sam

You should see the following output:

[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./test_data.sam doesn't appear to be a valid BAM file, trying SAM...
[13:23:15] Inspecting reads and determining fragment length distribution.
> Processed 1 loci.                            [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges.  
It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
>       Total Map Mass: 102.50
>       Read Type: 75bp x 75bp
>       Fragment Length Distribution: Truncated Gaussian (default)
>                     Estimated Mean: 200
>                  Estimated Std Dev: 80
[13:23:15] Assembling transcripts and estimating abundances.
> Processed 1 loci.                            [*************************] 100%

Verify that the file transcripts.gtf   is in the current directory and looks like this  (your file will have GTF attributes, omitted here for clarity)

test_chromosome Cufflinks       exon    53      250     1000    +       . 
test_chromosome Cufflinks       exon    351     400     1000    +       . 
test_chromosome Cufflinks       exon    501     550     1000    +       .

Compiling Eigen

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.. The current version is 3.1.3

To use the Eigen libraries, just untar and enter the source the directory

# tar -xvf eigen-3.1.3.tar

Copy the whole Eigen directory found in “eigen-eigen-2249f9c22fe8” folder to the /usr/local/include directory

# cd eigen-eigen-2249f9c22fe8/
# cp -Rv Eigen /usr/local/include

Compiling SamTools

Taken from Cufflinks – Getting Started

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

SAMTools (0.1.19)

Step 1: – Download SAMTools

Step 2: – Unpack and compile the SAMTools

# tar -zxvf samtools-0.1.19
# make

Step 3: – Copy the compiled libraries to /usr/local/lib

# cp $SAMTOOLS_HOME/libbam.a /usr/local/lib

Step 4: Copy headers to /usr/local/include

# mkdir /usr/local/include/bam
# cp $SAMTOOLS_HOME/*.h /usr/local/include/bam

Compiling and Installing Boost 1.53

Referenced from Cufflinks – Get started

Step 1 – Download Boost from Boost Website

Step 2 – Unpack the boost

# tar -zxvf boost_1_53_0.tar.gz

Step 3 – Run Bootstrap.sh

# ./bootstrap.sh
Building Boost.Build engine with toolset gcc...
.....

Step 4 – Run the binary b2

# ./b2 install --prefix=/usr/local/boost

It will take a while……

Step 5: Test that the compilation is working.

Compile the test case.

# cd $BOOST_ROOT/boost_1_53_0/tools/build/v2/example/hello
# $BOOST_ROOT/b2

You should see a binary file “hello” at

# $BOOST_ROOT/boost_1_53_0/tools/build/v2/example/hello/bin/gcc-4.4.6/debug