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Solar on Biowulf

SOLAR is a package of software to perform several kinds of statistical genetic analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. The name SOLAR stands for "Sequential Oligogenic Linkage Analysis Routines."

Solar was developed by researchers at the Southwest Foundation for Biomedical Research. Solar website.

New Solar users should send email to staff@helix.nih.gov asking to be registered as a Solar user. The Solar package requires each user to be registered.

Solar is not a parallel program. Single Solar jobs are most easily run interactively on Helix. It is useful to run on Biowulf only if you have multiple simultaneous Solar jobs to run.

The Solar binaries need to be added to your path before running Solar. This is most easily done by using the modules commands as in the example below:

biowulf% module avail solar

------------------- /usr/local/Modules/3.2.9/modulefiles ---------------
solar/4.2.7          solar/6.6.2(default)

biowulf% module load solar    (to load the default latest version)

biowulf% module load solar/4.2.7  (to load a specific version)

biowulf% module list      (to show what version is loaded)
Currently Loaded Modulefiles:
  1) solar/4.2.7

Submitting a swarm of Solar jobs

The swarm program is a convenient way to submit large numbers of jobs all at once instead of manually submitting them one by one.

1. First create different directories for each solar run. Put all the required input files under the created directories.

2. For each directory, create a script file which contains the solar commands as below:

-----------/data/user/solar/run1/script ----------
module load solar 
cd /data/user/solar/run1
solar << EOF
load pedigree ped.txt
load marker mrk.txt
verbosity min
freq mle
load map map.txt
.......
....
...
return ""
quit
EOF
-------------------------------------------------

3. Now prepare the swarm command file with one line for each Solar run, e.g.

#------- cmdfile -------------
/data/user/solar/run1/script
/data/user/solar/run2/script
/data/user/solar/run3/script
/data/user/solar/run4/script
.....
....
/data/user/solar/runX/script
#---- end of cmdfile ---------

Submit this swarm of Solar jobs with

swarm -f cmdfile

For more information regarding running swarm, see swarm.html

Running a single Solar batch job

1. Create a script file which contains the solar commands as below:

---------- /data/user/solar/run1/script --------------
#!/bin/bash 
#PBS -N solar1
#PBS -m be
#PBS -k oe

module load solar/6.6.2
cd /data/user/solar/run1

solar << EOF
load pedigree ped.txt
load marker mrk.txt
verbosity min
freq mle
load map map.txt
.......
....
analyzing commands
...
return ""
quit
EOF
----------------- end of script ----------------------

2. Now submit the script using the 'qsub' command, e.g.

qsub -l nodes=1 /data/user/solar/run1/script

Documentation
Solar 6.6.2 documentation

Solar website
Solar documentation