Cipres Web Portal

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RAxML 7.2.7 on ABE

RAxML 7.2.7 is a hybrid code created by a collaboration between Alexandros Stamatakis and Wayne Pfeiffer. The Portal provides a familiar Black Box interface (at phylobench.vital-it.ch) and an advanced interface. The settings and semantics for RAxML 7.2.7 commands are different from RAxML 7.0.4, so if you use the advanced interface, please check RAxML (7.2.7). This interface submits to ABE, a large NSF Teragrid Resource. The ABE machine allows your job to run for up to 168 hours (7 days). The job is run using a hybrid mpi/pthreads RAxML, so run speed is 3 - 4.5 times faster than the old CIPRES cluster. RAxML on CIPRES Portal ONLY accepts matrices in relaxed Phylip format.

How to use it: Submission to the TeraGrid requires the user to provide parameters that determine job priority in the queue, help identify the number of processors required, and set a time for job termination (whether the run is finished or not). First time users should view the primer on using TeraGrid resources here. With either interface, most of decisions are made automatically, based on settings the user selects (advanced interface) or pre-set values (Black Box interface). However, both interfaces require the user to enter the number of characters in the the matrix. The value you enter can be approximate, just make sure it is pretty close.

Disadvantages:The queue times on Teragrid resources vary according to traffic and according to the size of your job (shorter jobs typically have shorter queue waits). Sometimes TeraGrid resources go down for preventative maintenance or due to unforeseen circumstances. At present, this will cause your job to fail, and you will have to restart it. There is no restart capability at present.

Click this icon to check the traffic on TeraGrid:
Click this icon to check the Teragrid maintenance schedule:

Known Issues:

• Interface configuration problems: The logic of the interface for RAxML-HPC2 on Abe can cause users to get into a dead end. This can happen if you uncheck "Specify an Explicit Number of Bootstraps" then check and uncheck "Let RAxML halt bootstrapping automatically". As a result, one of the "Select Bootstopping Strategy" boxes will remain checked, making it impossible to save the parameters. Should this happen, just click the Reset button at the bottom of the page, and the interface will reset to its default parameters.
• When specifying more than one outgroup, do not introduce blank spaces. Use outgroup1,outgroup2 not outgroup1, outgroup2. In the latter case you will see the following error message "Error, you must specify a model of substitution with the '-m' option"
  
• There is a fundamental difference in the management of jobs after RAXML 7.1.0, and the nomenclature can be confusing for users familiar with 7.0.4 and below.
  Please see the RAxML 7.2.7 page.

 

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