Hi Stephen,
Thanks, I’m now trying to use R 3.6.3 on the HPC, I was able to run a few
tests remote and get reproducible results. The batches have not yet run,
but I’m hoping will give reproducible results when they do.
Thanks,
Kevin
On Sun, Aug 9, 2020 at 08:42 stephen sefick wrote:
> Hi Kevi
On 09/08/2020 8:33 a.m., Kevin Egan wrote:
Hi Abby,
After running a few tests on my local and remote versions of R, this seems
to be the most plausible answer to the problem. I put set.seed(123)
several times within my code and produced the same results but would rather
not have to do that if po
Hi Kevin,
I think Abby has suggested something similar to what I think the problem is
related to - environment setup.
Some possible solutions:
The renv and packrat packages are a way to version your packages to help
with reproducability. Anaconda might be a solution for the R version and
package
Hi Abby,
After running a few tests on my local and remote versions of R, this seems
to be the most plausible answer to the problem. I put set.seed(123)
several times within my code and produced the same results but would rather
not have to do that if possible.
On Sat, Aug 8, 2020 at 6:05 PM Abby
Local:
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6
Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.fram
Caveat, I have only skimmed this email thread, so please forgive me if I
have missed something.
Are you able to use Renv, packrat, docker, or anaconda? Your compute
environments are very different.
Kindest regards,
Stephen Sefick
On Sat, Aug 8, 2020, 19:05 Abby Spurdle wrote:
> Hi Kevin,
>
> I
On 08/08/2020 9:34 a.m., Marc Schwartz via R-help wrote:
Hi,
I was initially going to think that the change in the RNG might be the source,
however, that change was made in 3.6.0 and would have applied to runif() and
sample():
"sample.kind can be "Rounding" or "Rejection", or partial matches
Hi Kevin,
Intuitively, the first step would be to ensure that all versions of R,
and all the R packages, are the same.
However, you mention HPC.
And the glmnet package imports the foreach package, which appears
(after a quick glance) to support multi-core and parallel computing.
If your code use
You did not load the corresponding packages in both environments.
Also.. please post plain text format per the Posting Guide mentioned in the
footer of every post.
On August 8, 2020 7:15:16 AM PDT, Kevin Egan wrote:
>Local:
>R version 4.0.2 (2020-06-22)
>Platform: x86_64-apple-darwin17.0 (64-bi
Hi,
I was initially going to think that the change in the RNG might be the source,
however, that change was made in 3.6.0 and would have applied to runif() and
sample():
"sample.kind can be "Rounding" or "Rejection", or partial matches to these. The
former was the default in versions prior to
Compare the sessionInfo outputs for the different environments.
On August 7, 2020 1:24:55 PM PDT, Kevin Egan wrote:
>I posted this question:
>
>I am currently using R , RStudio , and a remote computer (using an R
>script) to run the same code. I start by using set.seed(123) in all
>three versions
I posted this question:
I am currently using R , RStudio , and a remote computer (using an R script) to
run the same code. I start by using set.seed(123) in all three versions of the
code, then using glmnet to assess a matrix. Ultimately, I am having trouble
reproducing the results between my l
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