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Advancing High Performance Computing Research Through International Cooperation  

Welcome to the Universidade de São Paulo-Rice University Blue Gene Collaboration

In 2012, Universidade de São Paulo (USP) and Rice University joined efforts to address some of the hardest scientific questions through the use of High Performance Computing. To initiate this collaboration, our universities co-invested in a 24,576 core Blue Gene/P supercomputer (pictured to the right). At the time, it was in the top500 list, making it one of the most powerful supercomputers in the world. After three years, the collaboration has upgraded to a 1-rack BG/Q.  With 2.5 times the computing power of the BG/P, this collaboration is helping USP and Rice build scientific and computational collaborations that will bring both universities to the forefront of research computing. Participants in this collaboration come from all areas of scientific training and currently include researchers in biophysics, materials science, atmospheric science, renewable energy, hard and soft condensed matter, bioinformatics, statistics, quantum chemistry, and more. The collaboration continues to grow, and we are optimistic that this momentum will continue to build. To facilitate the inclusion of both the USP and Rice communities, we provide information on what resources, opportunities and support are available, and how to gain access.

We would once again like to welcome you to our scientific community!

José Onuchic 
Harry C. and Olga K. Wiess Chair of Physics  
Professor of Physics and Astronomy, Chemistry, and Biochemistry and Cell Biology  
Co-Director of the Center for Theoretical Biological Physics (CTBP)

Paul Whitford 
Liaison to USP for Rice University 
Assistant Professor of Physics, Northeastern University

Uma mensagem do LCCA na USP

No contexto deste acordo de cooperação acadêmica, o LCCA-USP tem a tarefa de assessorar tecnicamente o comitê de professores responsáveis pelo acordo e zelar pela aplicação das políticas definidas pelo comitê.

Mantemos aberto um canal de comunicação com a Universidade de Rice para:

- Resolução ou encaminhamento de dúvidas dos pesquisadores da USP;

- Discussão de soluções técnicas;

- Inclusão de novos pesquisadores e grupos de pesquisa na lista de pessoas habilitadas a usar o BG;

- Organização de eventos que facilitem a troca de experiências e conhecimento sobre HPC para o desenvolvimento científico.

Desejamos que os recursos computacionais disponibilizados pelo acordo contribuam positivamente para o sucesso de seus artigos científicos e suas pesquisas. Consequentemente, esperamos que isto propicie avanços à produção científica da USP.

Sejam bem-vindos. Sucesso!


The Advanced Scientific Computing Laboratory (LCCA) at USP, is an virtual laboratory with HPC resources managed to optimize the availability of them to all USP researchers addressing their needs to scientific advance.

The LCCA is coordinated by a Director Council composed by five full professors chosen between the USP researchers. Each project, after an evaluation of scientific merit, receives computing hours on our HPC clusters.

The LCCA is operated by the associated USP computing centers, CCE and CISC.



Who can use the BG?

Since this is a joint resource, different policies apply to the Rice and USP communities.

If you are a member of the USP community: The policies that determine access for USP users are determined by the oversight committee at USP. Here, we will make every effort to post the most up-to-date information on those policies, but they are solely at the discretion of the committee, and may change at any time. At the moment, the committee has not restricted allocations. Accordingly, any member of the USP research community may be granted access on a temporary basis.  When the committee issues any future allocation policies, those policies will supersede any prior access. See below for details on obtaining an account. If you have questions about the status of operations at USP, please contact LCCA  at 

If you are a member of the Rice community: If you are interested in accessing this resource, please file an RT ticket with RCSG.  The form can be accessed here.

At 11/10/2015, the BGQ is updated for its XL compilers, and changed scheduling policies based on the needs from users. Generally speaking, the "compute" queue/class is no longer active. The new queues are: usp, rice, devel.

The devel queue allows 30 minutes for testing/debugging, and is accessible for all users. the other two queues (usp, rice) are the regular queues for running jobs. 

For the USP users, add these two lines into the job script:

#  @ class = usp

# @ group = usp

For the non-USP users, e.g. Rice users, add these two lines in the job script:

# @ class = rice
# @ group = rice

How to gain access to the BG?

For potential USP users: If you would like to access this resource, you must have a faculty sponsor at USP.  To request an account, follow these steps:

1) Send the following information from your USP email address to hpc@usp.brYour name, position (i.e. grad student, post-doc, professor), department, the name of the PI (make sure to cc the PI when making the request, since they will need to confirm the request), software you want to use on the BG, estimated number of cores per calculation, and a 1-2 paragraph description of the types of calculations you want to perform.

2) After you receive confirmation from LCCA, request a Rice Guest Account here. When requesting the Rice Account, indicate as your sponsor (DO NOT select "BlueGene USP Allocation" as the sponsor), and forward the LCCA approval email to that address. It is VERY important that you provide a valid email address when you request an account. If we can not contact you, then your accounts may be terminated without notice. Finally, if you do not obtain approval from LCCA first, the Rice Guest Account will not be approved. When your guest account is approved, you will be assigned a Rice NetID.  This will be your login information for all resources located at Rice, so don't lose it. Typically, the Rice ID will be activated within 24 hours.

3) Once the Rice ID is active, you need to request that an account is created on the BG/Q. To obtain the BG/Q account, request a regular user account, as described here. Again, indicate Paul Whitford as your sponsor. Assuming you have completed the first two steps, then your account will be approved and created. You will also be added to the USP BGQ listserve. If you don't receive confirmation within 3 business days about the listserve, or BG/Q account, please inquire with the sponsor (


Once your account is activated on the BG, you will need to connect via secure shell ( If you are not on the Rice network, this is accomplished by tunneling a connection through will use your Rice NetID account information.

For potential Rice users: The allocation policies are still being determined for Rice users.  If you are interested in accessing this resource, please file an RT ticket with RCSG.  The form can be accessed here.

More Information 

Getting Started on BG/Q
How to transfer data
Compiling and running specific applications
How to get help
Other available computational resources

Acknowledging use of the BG

Events and Updates

June 2nd, 2015: BG/P decommissioned and BG/Q activated

May 20th, 2015: Press release on USP-Rice collaboration

April 17th, 2015: 3rd HPC Workshop at USP

April 14, 2014: 2nd HPC Workshop at USP 

December 6-7, 2012: HPC Workshop at USP

August 1st, 2012: The BG/P USP-Rice agreement officially went into effect.

March 2012: Blue Gene Agreement Signed by USP and Rice

Early 2012: Installation of the BG/P at Rice

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