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Thread: Bowtie: Running out of memory with 2GB memory?!

  1. #1
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    Bowtie: Running out of memory with 2GB memory?!

    So I'm trying to run a program called bowtie 2 through terminal and I almost instantaneously get the error:

    Out of memory allocating the ebwt[] array for the Bowtie index. Please try
    again on a computer with more memory.

    I have a 32 bit processor and 2 GB of memory, which should be plenty.

  2. #2
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    Re: Program running out of memory with 2GB memory?!

    Please explain what Bowtie 2 is. What does it do? What resources does it use? Is it a GUI app or a CLI app?

    What flavour and version of 'buntu are you running? Are you using a swap? If you are running the Unity desktop, Unity is a resource hog and you might indeed reach the limit with only 2GB of memory. This depends on the memory requirements of the Bowtie 2 app and also on how many other services and apps you are running concurrently. But at this point,m this is just a general observation so lacking proper foundation that it is almost meaningless. Cannot advise you further without far more info.

  3. #3
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    Re: Program running out of memory with 2GB memory?!

    Bowtie 2 is alignment software for DNA analysis. It uses terminal (CLI). Basically, it takes a large 3.3 Gb data set and compares it to a large genome (~8 Gb). This software worked fine on my 64 bit laptop, which runs windows 7 for which I downloaded Wubi. Because it was so slow and it would freeze up, I installed the actual Ubuntu 12.04 LTS operating system on my older 32 bit laptop, complete replacing windows XP. I'm quite new to Ubuntu and Bowtie 2, so I don't know about what resources each takes up.

  4. #4
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    Re: Program running out of memory with 2GB memory?!

    Additional info clarifies many things...

    WUBI boots up a regular instance of Ubuntu. Difference is only in the way the OS is stored.

    Therefore, the obvious difference between your earlier experience and your current one is your hardware. Your 64-bit machine likely has enough memory and a powerful enough processor that it can handle Bowtie 2. Your current machine does not. Please post the specs for both machines, but this more than likely accounts for the difference in your experience.

    You mention that your current machine is 32-bit. Are you sure about this? Even quite old laptops are actually 64-bit. But if it is truly only 32-bit, then it is a very underpowered laptop and I am not surprised that you cannot get a huge data set (you mention 3.3 GB and ~8 GB) to process. And if you are running it on top of Unity rather than a plain command line interface, then so much of your resources are being used to support all of Unity's fancy effects that there is little left for apps. **NOTE** This is a generalization based on the fact that any laptop with a 32-bit processor is likely to be highly resource constrained for modern OSes.

  5. #5
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    Re: Program running out of memory with 2GB memory?!

    Memory requirements: Bowtie uses approximately as much memory as the size of the bowtie indices. For the human genome, this is about 3.4 GB. You should run this job on a node with at least 4 GB of RAM.
    Source: http://biowulf.nih.gov/apps/bowtie.html

    I don't know if this is relevant or not.

  6. #6
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    Re: Program running out of memory with 2GB memory?!

    Quote Originally Posted by rocketfish201 View Post
    ...I don't know if this is relevant or not...
    ...extremely, I would say. Clearly a laptop with 2GB is insufficient, even if Ubuntu wasn't hogging most of 1 GB for its OS overhead. Thanks for researching the reference, rocketfish.

  7. #7
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    Re: Program running out of memory with 2GB memory?!

    The newer laptop that the ware worked on is a 64 bit, Windows 7, 4 Gb RAM, i5 processor

    The old laptop that it's not working on is a 32 bit, Windows XP, 2 Gb RAM, Celeron processor.

    I am using a 64 bit version of Bowtie2 on my 64 bit system but a 32 bit version on the older system. I believe my processor only runs at 32 bit because when I click on "details" under "system settings" it says it's indeed 32 bits.

    I kind of follow with the whole unity thing, but is there a way around that on my older system? I'd hate to have to buy a new computer just to run this program

  8. #8
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    Re: Program running out of memory with 2GB memory?!

    Quote Originally Posted by rocketfish201 View Post
    Source: http://biowulf.nih.gov/apps/bowtie.html

    I don't know if this is relevant or not.
    This is definitely useful; however, I am using a 32 bit version of Bowtie 2 which is said to use less memory.

  9. #9
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    Re: Program running out of memory with 2GB memory?!

    Quote Originally Posted by adam20 View Post
    This is definitely useful; however, I am using a 32 bit version of Bowtie 2 which is said to use less memory.
    That doesn't change the fact that you have to load a 3.4GB file into RAM. You can't put 2 liters of water in a 1 liter bucket.

  10. #10
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    Re: Program running out of memory with 2GB memory?!

    The app may use less memory (and only marginally at that), but your resource hog/constraint is the size of your data-set.

    EDIT

    rocketfish and I gave the same response to two different ways.

    /EDIT
    Last edited by DuckHook; October 4th, 2013 at 02:32 AM. Reason: clarifying concurrent advice

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