Frequently Asked Questions

BioHPC Staff will add the answers to frequent questions from users here. Click a category name below to jump to questions and answers on that topic:

 

Accounts, Usage, Quotas

 

How can I create a BioHPC account, and access all of the services?

First, make sure your department or center has membership of BioHPC. If not, please contact us. Then, create an BioHPC account here  . Your account will not have full access to BioHPC services until you attend our "Introduction to BioHPC" training session. It is on first Wed of each month, from 10:30 - 12:00, usually at NL6.125. Remember to sign on the sheet when you attend the training. After 2 to 3 days, your account will be activated, you will have full access to BioHPC and will receive an email confirmation about your new account. 

Do I need to register the training session before I attend?

No, you don't need to register. Just come and join the training session.

The system says my account has expired, what can I do?

This is because your password has expired. According to UTSW policy, you need to change your password annually. Click here  to change your BioHPC password. 

I suddenly cannot get access to BioHPC system, why is that?
In most case, it is because your password has expired. Please refer to the above question for solution. 

The situations you have may be (but not limited to):

  • ssh: fail to login, saying "Your account has expired; please contact your system administrator"
  • lamella: access to your account on the server “lamella.biohpc.swmed.edu” has been denied
  • FileZilla: failed to connect
  • network drive: fail to connect
  • web visulization GUI session: connection refused
  • thin client: cannot login

How can I create a shared folder between two departments to share data?

Please provide us the information below: 

  • Which department will contribute the quota? We need assign a primary department to this folder.
  • Is the default 5TB quota enough for this shared folder? We need approval from the primary department chair to assign storage space.
  • Do you have a name for this folder? We will name it using the two PI's last names by default.

My /project storage space is over quota, what can I do?

  a) decrease disk usage

You may want to move files to your /archive directory. Usage on /archive will be calculated only 2/3 of the actual usage. The archive filesystem is laid out in the same structure as /project. The default quota is 5TB per lab, but can be increased.

  b) increase quota

Your PI can ask the department chair for approval to increase the lab quota on /project. We will increase the quota with the department chair's email approval.


GPU Nodes - CUDA and Visualization

How do I use the Dual Tesla P100 nodes?

There are 12 new Nvidia Tesla P100 GPU nodes available. Each node has two Tesla P100 GPU cards.

To run a job on the new GPU nodes, please specify ‘GPUv1’ as the partition in your SLURM script. You can also access the nodes through portal website - cloud services - web visualization, and choose ‘webGPUv1’.

# In your SLURM script, choose the new GPU partition

#SBATCH -p GPUv1

# In your script, request the use of 2 GPU cards

#SBATCH --gres=gpu:2

If your program does not seem to see both GPUs, you can try setting the CUDA_VISIBLE_DEVICES environment variable. Use the command:

export CUDA_VISIBLE_DEVICES=0,1  

... before you run your program. This should not be necessary as long as you use the 'gres' line in your batch scripts.


R & RStudio

I'm using a web service from R (e.g. biomaRt) and it complains about a 'redirection'. How can I make it work properly?

The UTSW web proxy can confuse some R packages that interact with web services. Before you use the web service, set download options in your R script:

options(RCurlOptions=list(followlocation=TRUE, postredir=2L))


Matlab

Why does my Matlab jobs being queued for a long time, while the cluster still have some idle nodes?

The reason is that your job is queueing for the matlab MDCS licence. Right now, we have 128 concurrent MDCS licences shared with all BIoHPC users. If there are other Matlab jobs running on the cluster now, and they consume all 128 licences of matlab MDCS, you have to wait till any of these jobs finish running and release the license.


Software Installation

How to install python module locally without conda environment? 
use pip install:
$pip install --user modulename
will install package automatically to your home directory: ~/.local/lib/python**/site-packages

Or use --prefix to install to a specific directory:
$pip install --prefix /directory/to/install modulename

This will install lib and bin to the path specified, if the software has executable, it will be put into the bin folder. 

How do I install R packages locally:
R packages will be installed automatically into your local R lib. You don't need to worry about permission issues.

Where to find all my local R packages:
Local R packages that user install stay in ~/R/x86_64-***-linux-gnu-library path/{version}.

Getting permission denied error while running a software or command.
The software or command is trying to access a file or a directory you don't have access to.

Possible causes: 

  • The destination does not exist due to misspelling or the command does not create the directories automatically.
  • The installed cluster software is trying to write into its own directory, but the user running the command does not have permission to write in that directory. Usually this happens during installation when a dependency needs upgrade. The software need to be installed in the personal directory. If still not working, please email us. 
  • Running code received from collegues and the code has hard coded paths. Change the hard coded paths to point to existing local directory.

Why do I have multiple version of same modules loaded?
When loading modules, all dependent modules are also added. So if two software depend on the same software but with different versions, multiple version will be loaded. This can cause imcompatibility problems when using the first loaded software. It's a good idea to load only the necessary modules when using certain software.

Where should I create link to locally installed software executable, since I dont have permission in any of the bin directory.
Simply create a bin directory under your home directory and link any executatbles to this directory. This directory is included in the PATH variable automatically. 

"lib***.so" files not found?
Library dependency is not resovled, most likely you are missing a path in LD_LIBRARY_PATH, can be resolved by adding apropriate module or add the path to variable.

"CXX****_1.x.x" not found?
wrong version of C c compiler is used, try adding newer version of gcc or intel.

".h" files not found?
The header file of the software is not found, this can be solved by adding the include directory of the software to CPATH when using c compilers. Or install .devel package of the software through package manager.