Full_Name: Peter Bosa Version: 2.6.2 OS: RHES 4.2 - 4.5 Submission from: (NULL) (67.138.101.226) I am experiencing a memory allocation error with R 2.6.2 which was not present in previous versions of R (2.4 and 2.2). I have several Linux machines with various Redhat OS versions loaded on them, ranging from 4.2 through 4.5. Each machine has 6 GB of RAM and 2 to 4 GB of virtual memory. The processes I am running include calculations on large matrices (1,015 x 2,029). While the programs are large users of memory, they were stable (i.e. no memory crashes with the earlier versions of R) on all machines. However, running the same programs using R 2.6.2, I consistently get the error message "Cannot allocate vector of size 15.7kb". I am calling the programs with the --max-vsize=3G command...no difference. Using a garbage collection command, I can see that the programs never use more heap than 2.5 GB. And, as stated before, this was not an issue when the same machines were loaded with R 2.4 or 2.2. I have verified that the OS settings are exactly the same as before (unlimited allocation of memory to programs). Also, when I re-install R 2.4, the programs run correctly. I have not been able to test R 2.5 or R 2.6.0, since I cannot find binary packages of these versions, and I have yet to compile the source code. Any thoughts?
Memory allocation error in 2.6.2 (PR#10903)
2 messages · bosap at metro.dst.or.us, Henrik Bengtsson
Before submitting a bug report, it is probably wise to bring it up on r-devel first. Remember, someone has to clean out all those false bug reports manually. There are so many potential reasons for your problem, which indicates fragmented memory allocations. One obvious one is that one of the packages you are using have been updated. In order for anyone to say anything about your problem, the minimum you can do is post your sessionInfo():s. Then maybe one of the authors of those packages reads this and know exactly what is going on. Also, some kind of script is also useful, because maybe it is obvious from your code. You might simply have "been lucky" in previously. My $0.02 /Henrik
On Thu, Mar 6, 2008 at 10:10 AM, <bosap at metro.dst.or.us> wrote:
Full_Name: Peter Bosa Version: 2.6.2 OS: RHES 4.2 - 4.5 Submission from: (NULL) (67.138.101.226) I am experiencing a memory allocation error with R 2.6.2 which was not present in previous versions of R (2.4 and 2.2). I have several Linux machines with various Redhat OS versions loaded on them, ranging from 4.2 through 4.5. Each machine has 6 GB of RAM and 2 to 4 GB of virtual memory. The processes I am running include calculations on large matrices (1,015 x 2,029). While the programs are large users of memory, they were stable (i.e. no memory crashes with the earlier versions of R) on all machines. However, running the same programs using R 2.6.2, I consistently get the error message "Cannot allocate vector of size 15.7kb". I am calling the programs with the --max-vsize=3G command...no difference. Using a garbage collection command, I can see that the programs never use more heap than 2.5 GB. And, as stated before, this was not an issue when the same machines were loaded with R 2.4 or 2.2. I have verified that the OS settings are exactly the same as before (unlimited allocation of memory to programs). Also, when I re-install R 2.4, the programs run correctly. I have not been able to test R 2.5 or R 2.6.0, since I cannot find binary packages of these versions, and I have yet to compile the source code. Any thoughts?
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