[Bioc-devel] BiocParallel-devel error

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 there should be an option to redirect to
  files instead and then assemble things in R in a second step that the
user can
  control. Perhaps this is possible already but it is not clear to me
  what the intended way is how to do this.

- A much higher level of fault tolerance by adding options to restart
failed
  jobs is another extremely important feature for parallel computations.
  This may only be possible if results are temporarily stored in files.
  For instance, if I farm out a computation to 10 compute nodes and one
  of them crashes, I want to be able to use the results form the 9
completed tasks
  but easily restart the computation assigned to the crashed node so that I
  get the final result quickly.

BatchJobs provides most of these facilities. Making it easier and/or
more obvious how to use these utilities from within BiocParallel may be
all what is needed.

Thomas


On Thu, Nov 20, 2014 at 04:43:54PM +0000, Valerie Obenchain wrote:

Interesting. I'm glad you figured that out. I'll add a line to the
vignette that mentions this as a possible configuration issue.

Using BatchJobs w/in BiocParallel should provide the same log files as
using BatchJobs alone. I haven't tested it but my understanding was that
the same options could be passed through '...' to name output files,
directories etc. The other backends do not have logging ability.

One of my current projects is to add logging to BiocParallel that works
for all backends. I've been trying out the futile.logger package which
looks promising for logging at both the system and user levels. We're
also exploring more interactive debugging when an error is thrown.


Valerie


On 11/19/14 19:48, Thomas Girke wrote:

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 master/head node, like

this

module load R/3.1.2-dev

then everything runs as expected without errors in any of the more
recent R release and development versions. Without this line the R
version on the compute nodes will be the one used by default, which may
result in an R version collision when submitting jobs from a different

R

version (e.g. R-dev). The reason that things worked in my specific case
with BatchJobs but not with BiocParallel may simply be related to a

less

stringent enforcement of R version matches. Sorry that I didn't try

this

simple solution earlier.

I guess what would help to isolate these kinds of problems in the

future

is a log file containing the STDOUTs of the processes submitted to the
nodes. BatchJobs captures this information in a jobs subdirectory which
is useful and pointed me to the source of the above error. Not sure

whether

this is available through BiocParallel?

Again sorry for the unnecessary noise.

Thomas


On Tue, Sep 23, 2014 at 06:59:11PM -0700, Thomas Girke wrote:

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), I restricted the computation to two specific nodes for all
comparisons using nodes="1:ppn=1+n02+n03". As you can see below, the

same

computation works in R-release with both BiocParallel and BatchJobs.

However,

if I run it in R-devel it only works with BatchJobs.

Certainly, there could still be another problem with our specfic
environment on the cluster, not sure?

For my specific application there is no rush to get things working in
BiocParallel right away. BatchJobs works fine for now.

Thomas

###############
## R-release ##
###############
library(BiocParallel); library(BatchJobs)
f <- function(i) system("hostname", intern=TRUE)
funs <- makeClusterFunctionsTorque("~/tmp/torque.tmpl")
param <- BatchJobsParam(4, resources=list(walltime="00:05:00",

nodes="1:ppn=1+n02+n03", memory="1gb"), cluster.functions=funs)

register(param)
xx <- bplapply(1:4, f)
xx

xx

[[1]]
[1] "n03"

[[2]]
[1] "n03"

[[3]]
[1] "n03"

[[4]]
[1] "n02"

library(BatchJobs)
loadConfig(conffile = "~/tmp/.BatchJobs.R")
reg <- makeRegistry(id="BatchJobTest", work.dir="results")
ids <- batchMap(reg, fun=f, 1:4)
done <- submitJobs(reg, resources=list(walltime="00:05:00",

nodes="1:ppn=1+n02+n03", memory="1gb"))

sapply(1:4, function(x) loadResult(reg, x))
[1] "n03" "n03" "n03" "n02"

sessionInfo()

R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  utils     datasets  grDevices methods   base

other attached packages:
[1] BatchJobs_1.2      BBmisc_1.7         BiocParallel_0.6.1

loaded via a namespace (and not attached):
  [1] BiocGenerics_0.10.0 DBI_0.2-7           RSQLite_0.11.4

Rcpp_0.11.2         brew_1.0-6          checkmate_1.0
 codetools_0.2-8     digest_0.6.4        fail_1.2            foreach_1.4.2

[11] iterators_1.0.7     parallel_3.1.0      plyr_1.8.1

sendmailR_1.1-2     stringr_0.6.2       tools_3.1.0

#############
## R-devel ##
#############

library(BiocParallel); library(BatchJobs)
f <- function(i) system("hostname", intern=TRUE)
funs <- makeClusterFunctionsTorque("~/tmp/torque.tmpl")
param <- BatchJobsParam(4, resources=list(walltime="00:05:00",

nodes="1:ppn=1+n02+n03", memory="1gb"), cluster.functions=funs)

register(param)
xx <- bplapply(1:4, f)

Error: 10 errors; first error:
For more information, use bplasterror(). To resume calculation,

re-call the

function and set the argument 'BPRESUME' to TRUE or wrap the previous

call in

bpresume().

bplasterror()
Error in vapply(head(which(is.error), n.print), f, character(1L)) :
values must be length 1, but FUN(X[[1]]) result is length 0

library(BatchJobs)
loadConfig(conffile = "~/tmp/.BatchJobs.R")
reg <- makeRegistry(id="BatchJobTest", work.dir="results")
ids <- batchMap(reg, fun=f, 1:4)
done <- submitJobs(reg, resources=list(walltime="00:05:00",

nodes="1:ppn=1+n02+n03", memory="1gb"))

sapply(1:4, function(x) loadResult(reg, x))
[1] "n03" "n03" "n03" "n02"

sessionInfo()

R Under development (unstable) (2014-05-05 r65530)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  utils     datasets  grDevices methods   base

other attached packages:
[1] BatchJobs_1.3        BBmisc_1.7           BiocParallel_0.99.19

loaded via a namespace (and not attached):
  [1] BiocGenerics_0.11.4 DBI_0.3.0           RSQLite_0.11.4

brew_1.0-6          checkmate_1.4       codetools_0.2-9     digest_0.6.4
    fail_1.2

       foreach_1.4.2       iterators_1.0.7
[11] parallel_3.2.0      sendmailR_1.1-2     stringr_0.6.2

 tools_3.2.0

On Tue, Sep 23, 2014 at 09:41:44PM +0000, Valerie Obenchain wrote:

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

downstream when the error processing is expecting messages of length

0.

You can reproduce the error by putting a typo in the script. For

example

replace R with something bogus such as MYR in this line:

MYR CMD --no-save --no-restore "<%= rscript %>" /dev/stdout

You said the script worked with release but not devel. Is it possible
there's a problem with how R devel is being called on the cluster?

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.

Valerie



On 09/22/2014 02:58 PM, Valerie Obenchain wrote:

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 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 devel branch alone then there is

no

problem.
Thus, it seems there is some change in the devel version of

BiocParallel

causing this error? The torque.tmpl file I am using on our cluster

is the

standard one from BatchJobs here:

https://github.com/tudo-r/BatchJobs/blob/master/examples/cfTorque/simple.tmpl

For my application, I could stick with BatchJobs, but it would be
nicer if I
could get things to work with BiocParallel.

Thanks,

Thomas

###############
## Test Code ##
###############
FUN <- function(i) system("hostname", intern=TRUE)
library(BiocParallel); library(BatchJobs)
funs <- makeClusterFunctionsTorque("torque.tmpl")
param <- BatchJobsParam(4, resources=list(walltime="48:00:00",
nodes="1:ppn=4", memory="4gb"), cluster.functions=funs)
register(param)
xx <- bplapply(1:4, FUN)

Error: 4 errors; first error:

For more information, use bplasterror(). To resume calculation,
re-call the function and
set the argument 'BPRESUME' to TRUE or wrap the previous call in
bpresume()

bplasterror()

Error in vapply(head(which(is.error), n.print), f, character(1L)) :
    values must be length 1,
   but FUN(X[[1]]) result is length 0

sessionInfo()

R Under development (unstable) (2014-05-05 r65530)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  utils     datasets  grDevices methods

 base

other attached packages:
[1] BatchJobs_1.3        BBmisc_1.7           BiocParallel_0.99.19

loaded via a namespace (and not attached):
   [1] BiocGenerics_0.11.4 DBI_0.3.0           RSQLite_0.11.4
brew_1.0-6          checkmate_1.4       codetools_0.2-9
digest_0.6.4        fail_1.2            foreach_1.4.2
iterators_1.0.7
[11] parallel_3.2.0      sendmailR_1.1-2     stringr_0.6.2
tools_3.2.0