On Thu, Nov 20, 2014 at 12:17 PM, Thomas Girke wrote:
> Hi Valerie,
>
> Excellent. In addition to collecting log outputs, I have a few more
> suggestions that may be worth considering:
>
> - Collecting the results form parallel computing tasks directly in an R
> object is a great convenience, w
Hi Valerie,
Excellent. In addition to collecting log outputs, I have a few more
suggestions that may be worth considering:
- Collecting the results form parallel computing tasks directly in an R
object is a great convenience, which I like a lot. However, in the
context of slow computations t
Hi Valerie, Michel and others,
Finally, I freed up some time to revisit this problem. As it turns out,
it is related to the use of a module system on our cluster. If I add in
the template file for Torque (torque.tmpl) an explicit module load line
for the specific R version, I am using on the mas
Hi Michel,
In BiocParallel 0.99.24 .convertToSimpleError() now checks for NULL and
converts to NA_character_.
I'm testing with BatchJobs 1.4, BiocParallel 0.99.24 and SLURM. I'm
still not getting an informative error message:
xx <- bplapply(1:2, FUN)
SubmitJobs |++
This was a bug in BatchJobs::waitForJobs(). We now throw an error if
jobs "disappear" due to a faulty template file. I'd appreciate if you
could confirm that this is now correctly catched and handled on your
system. I furthermore suggest to replace NULL with NA_character_ in
.convertToSimpleError()
2014-09-23 23:41 GMT+02:00 Valerie Obenchain :
> Michel Lang (cc'd) implemented BatchJobs in BiocParallel. I'd like to get
> his opinion on how he wants to handle this type of error.
> Michel, let me know if you need more details, I can send another example
> off-line.
If the cluster is misconfigu
Hi Valerie,
Thanks for looking into this.
Yes, if I include the bogus 'MYR' in *.tmpl then I am getting the same
error in R-release as well.
To double-check whether it is related to some nodes on our cluster (ours
has different node architectures and the IB interconnect can be flaky at
times),
Hi,
Martin and I looked into this a bit. It looks like a problem with
handling an 'undefined error' returned from a worker (i.e., job did not
run). When there is a problem executing the tmpl script no error message
is sent back. The NULL is coerced to simpleError and becomes a problem
downstr
Hi Thomas,
Just wanted to let you know I saw this and am looking into it.
Valerie
On 09/20/2014 02:54 PM, Thomas Girke wrote:
Hi Martin, Micheal and Vincent,
If I run the following code, with the release version of BiocParallel then it
works (took me some time to actually realize that), but w
Hi Martin, Micheal and Vincent,
If I run the following code, with the release version of BiocParallel then it
works (took me some time to actually realize that), but with the development
version I am getting an error shown after the test code below. If I run the
same test with BatchJobs from the
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