How Does Hyperthreading Affect an ALLPATHS-LG Run?

In running ALLPATHS-LG, a short read genome assembler, on a Dell PowerEdge R920 with four Xeon E7-4860v2 processors running at 2.60GHz, I did one run with hyperthreading on and one with hyperthreading off. This was mainly to see if the increased cache size on the physical CPU core with hyperthreading off had a positive effect on performance.

I'll take all the anticipation away: Nope. Hyperthreading wins.

No Hyperthreading Hyperthreading
available cpus 24 48
GB of total available memory 1511.6 1511.6
hours of total elapsed time 30.32 28.81
hours of total per-module elapsed 30.33 28.82
hours of total per-module user time 357.57 630.52
effective parallelization factor 11.79 21.88
GB memory usage peak 457.13 457.13

Installing rpy and rpy2 on RHEL6

I wanted to install rpy and rpy2 on Red Hat Enterprise Linux 6. Here's how I did it. There have been several fixes in the rpy SVN repository that have not shown up in the version downloadable from SourceForge. Hopefully that's been fixed by now, but here's how I installed it by retrieving rpy directly from the repository.

First I made sure that the python-devel package was installed to avoid the error src/RPy.h:63:20: error: Python.h: No such file or directory:

yum install python-devel

Then I installed R and R-devel from EPEL:

rpm -Uvh
yum install R R-devel

Then I downloaded rpy and extracted it:

curl > rpy.tar.gz
tar xvzf rpy.tar.gz
cd rpy
python install

Lo and behold, it imports without error:

python -c "import rpy"


Besides R and R-devel, rpy2 requires that the readline-devel package be installed, otherwise installation fails with ./rpy/rinterface/_rinterface.c:79:31: error: readline/readline.h: No such file or directory.

yum install readline-devel

After that, rpy2 installs easily:

curl > rpy2-2.2.0.tar.gz
tar xvzf rpy2-2.2.0.tar.gz
cd rpy2-2.2.0
python install

Adding threads support to perl built by MacPorts

I had installed perl5.12 from MacPorts. sudo port installed listed

perl5                          @5.12.3         lang/perl5
perl5.12                       @5.12.3         lang/perl5.12
perl5.8                        @5.8.9          lang/perl5.8

To enable threading support, I used

sudo port upgrade --enforce-variants perl5.12 +threads

Installing miRNAkey on Mac OS X 10.6 Snow Leopard

The following is a transcript of an installation of miRNAkey on Mac OS X 10.6. Actually it has more do with installation of the prerequisites. There is a handy script included with the miRNAkey distribution but I elected to do it by hand since some version numbers had changed and the Fastx-Toolkit binaries were for 10.5, not 10.6.

Step 1: Install bwa

The Burrows-Wheeler Aligner can be downloaded from Sourceforge.

tar xvfj bwa-0.5.9.tar.bz2
cd bwa-0.5.9
sudo cp bwa /usr/local/bin/bwa

Step 2: Install Required Perl Modules

I should note that my Perl is a MacPorts install.

sudo cpan
cpan[1]> install Math::CDF

Spreadsheet::WriteExcel and Getopt::Long were already fine on our machine:

cpan[2]> install Spreadsheet::WriteExcel
Spreadsheet::WriteExcel is up to date (2.37).

cpan[3]> install Getopt::Long
Getopt::Long is up to date (2.38).

Prior to installing GD::Graph::bars I needed to install libgd:

curl -O
tar xfjv gd-2.0.35.tar.bz2
cd gd-2.0.35
sudo make install

The GD perl module would not install because some tests would not pass:

Running make test
PERL_DL_NONLAZY=1 /opt/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/GD.t ........ 1/12 Testing using png support.
t/GD.t ........ Failed 1/12 subtests
(less 1 skipped subtest: 10 okay)
t/Polyline.t .. ok  

Test Summary Report
t/GD.t      (Wstat: 0 Tests: 12 Failed: 1)
  Failed test:  10
Files=2, Tests=13,  0 wallclock secs ( 0.02 usr  0.01 sys +  0.07 cusr  0.02 csys =  0.12 CPU)
Result: FAIL
Failed 1/2 test programs. 1/13 subtests failed.
make: *** [test_dynamic] Error 255
  /usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports LDS/GD-2.45.tar.gz
Running make install
  make test had returned bad status, won't install without force

So I decided to install it with force:

sudo perl -MCPAN -e "CPAN::Shell->force(qw(install GD));"

Then I could install GD::Graph::bars:

sudo cpan
cpan[1]> install GD::Graph::bars

Step 3: Install FASTX-Toolkit

First, libgtextutils:

curl -O
tar xvjf libgtextutils-0.6.tar.bz2
cd libgtextutils-0.6
sudo make install

Then the FASTX-Toolkit itself. Note the need to define PKG_CONFIG_PATH:

curl -O
tar xjvf fastx_toolkit-0.0.13.tar.bz2
cd fastx_toolkit-0.0.13
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH
sudo make install

Step 4: Install miRNAkey

For this, I simply put miRNAkey into the /Applications directory.

curl -O
tar xvzf miRNAkey.tar.gz
mv miRNAkey /Applications/miRNAkey


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