Hi Lori, I don't know the answer to the specific question, but here is a general point: the best way to send us information so we can figure out how to solve a problem is to use the "report a bug" feature in Chimera. On the bottom of that error dialog in your image is a "Report Bug" button - clicking that will include the entire traceback (error message) but also relevant information about your system and the version of Chimera you are using. It will also let you enter additional text (such as your question) and your e-mail address for our response. From what I can see it might not even be an issue of the amount of memory you have, but a data type problem. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 23, 2009, at 7:27 AM, Lori Nyland wrote:
Ooops forgot attachment. Here it is.<Chimera error.jpg>
I have attached an image that shows the command line and the command where I am trying to save an image map of one volume relative to another. I received an error when the operation was executed. The error code is in the image. I noticed that there was an error in memory allocation (toward bottom of error script). So I think I need to allocate more memory. How do I do that?
Thanks so much!
Lori
Hi Lori, It looks like Chimera is trying to read the full map #0 into memory and it is running out of memory. How big is that map file? If it is several hundred megabytes that is probably the issue. It is difficult to avoid these problems if you work with large data sets. Chimera 32-bit versions can only handle about 1 Gbyte of data. If you have large maps of several hundred Mbytes you can easily exceed that. Or if you have models with a few hundred thousand atoms you will run into trouble (uses about 2 Kbytes per atom, 100,000 atom = 200 Mbytes). It doesn't matter how much memory your machine has -- the limitation is that Chimera uses 32-bit pointers that can only address at most 4 Gbytes of memory (and much of that space is used for things other than your data, eg libraries, stack, ...). The only answer is to close some of your data our use the 64-bit Linux Chimera. We plan to distribute a 64-bit Windows and 64-bit Mac Chimera but that is 6 months or a year away. Tom
Subject: creating more memory From: Lori Nyland Date: Fri, 23 Oct 2009 10:24:10 -0400 To: chimera-users
Hello,
I have attached an image that shows the command line and the command where I am trying to save an image map of one volume relative to another. I received an error when the operation was executed. The error code is in the image. I noticed that there was an error in memory allocation (toward bottom of error script). So I think I need to allocate more memory. How do I do that?
Thanks so much!
Lori
participants (3)
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Elaine Meng -
Lori Nyland -
Tom Goddard