Has anybody managed to create binary packages for os/x with openmp
enabled?
Is this the best place to ask?
Our working non-openmp enabled build is here,
https://travis-ci.org/github/OpenMx/OpenMx/jobs/706741686
Thank you.
--
Joshua N. Pritikin, Ph.D.
Virginia Institute for Psychiatric
Ah, brilliant. Thanks.
On Sun, Jun 14, 2020 at 11:28:17AM -0400, Duncan Murdoch wrote:
> On 14/06/2020 10:59 a.m., Joshua N Pritikin wrote:
> > On Sun, Jun 14, 2020 at 09:17:32AM -0400, Duncan Murdoch wrote:
> > > knitr::opts_chunk$set(eval = !is_CRAN)
> >
> > This
On Sun, Jun 14, 2020 at 09:17:32AM -0400, Duncan Murdoch wrote:
> Since you're using Rmarkdown, you can use a variable for the eval
> chunk option, e.g. put this in your setup chunk:
>
> knitr::opts_chunk$set(eval = !is_CRAN)
This works except for in-text `r 1+1` code fragments. Is there an
Ah, thank you!
Sorry for the duplicate posts.
On Sun, Jun 14, 2020 at 09:17:32AM -0400, Duncan Murdoch wrote:
> On 13/06/2020 1:29 p.m., Joshua N Pritikin wrote:
> >
> > I'm trying to include vignettes that take much too long for CRAN check.
> >
> > At the beginnin
lding 'TwoFactorModel.Rmd' using rmarkdown
> --- re-building 'UserSpecifiedGWASModels.Rmd' using rmarkdown
> --- re-building 'growth.Rmd' using rmarkdown
> Error: Vignette re-building failed.
> Execution halted
What's the correct way to avoid CRAN complaints?
--
Joshua N. Pritikin,
lding 'TwoFactorModel.Rmd' using rmarkdown
> --- re-building 'UserSpecifiedGWASModels.Rmd' using rmarkdown
> --- re-building 'growth.Rmd' using rmarkdown
> Error: Vignette re-building failed.
> Execution halted
What's the correct way to avoid CRAN complaints?
--
Joshua N. Pritikin,
lding 'TwoFactorModel.Rmd' using rmarkdown
> --- re-building 'UserSpecifiedGWASModels.Rmd' using rmarkdown
> --- re-building 'growth.Rmd' using rmarkdown
> Error: Vignette re-building failed.
> Execution halted
What's the correct way to avoid CRAN complaints?
--
Joshua N. Pritikin,
instance of 'std::runtime_error'
what(): MxComputeLoadData: out of data (record 250 requested but only 199
in file)
What solution is recommended?
Thank you.
--
Joshua N. Pritikin, Ph.D.
Virginia Institute for Psychiatric and Behavioral Genetics
Virginia Commonwealth University
PO Box 980126
800 E Leigh St, B
cond message had timestamp earlier than his first message?
As a new subscriber, I guess my messages got caught in moderation.
--
Joshua N. Pritikin, Ph.D.
Virginia Institute for Psychiatric and Behavioral Genetics
Virginia Commonwealth University
PO Box 980126
800 E Leigh St, Biotech One, Suite 1-
Incorrect code,
A <- matrix(1, 2, 2)
B <- matrix(2, 3, 2)
A %*% B
Produces
Error in A %*% B : non-conformable arguments
It would be helpful to show the matrix dimensions,
Error in A %*% B : non-conformable arguments of dimensions (2, 2) and (3, 2)
--
Joshua N. Pritikin, Ph.D.
Vi
With this patch,
> A <- matrix(1, 2, 2)
> B <- matrix(2, 3, 2)
> A %*% B
Error in A %*% B :
non-conformable arguments of dimension (2, 2) and (3, 2)
>From 205b591d4d14b5ff667325fb233a6deb08314726 Mon Sep 17 00:00:00 2001
From: Joshua Nathaniel Pritikin
Date: Fri, 5 Apr 2019 12:03:58 -0400
} catch (...) {
// clang gets here
which works on both compilers. I don't know why clang skips the first
catch clause.
--
Joshua N. Pritikin, Ph.D.
Virginia Institute for Psychiatric and Behavioral Genetics
Virginia Commonwealth University
PO Box 980126
800 E Leigh St, Bio
OS/X builds?
Thank you.
--
Joshua N. Pritikin, Ph.D.
Virginia Institute for Psychiatric and Behavioral Genetics
Virginia Commonwealth University
PO Box 980126
800 E Leigh St, Biotech One, Suite 1-133
Richmond, VA 23219
http://exuberant-island.surge.sh
We noticed,
https://cran.r-project.org/web/checks/check_issue_kinds.html
Are test results from alternative BLAS/LAPACK implementations available
somewhere?
--
Joshua N. Pritikin, Ph.D.
Virginia Institute for Psychiatric and Behavioral Genetics
Virginia Commonwealth University
PO Box 980126
wrapped <- strwrap("raw")
writeLines(wrapped)
q()
==8699== Conditional jump or move depends on uninitialised value(s)
==8699==at 0x40310A9: ???
==8699==by 0xB07F4EF: ???
==8699==by 0xB07F4EF: ???
==8699==by 0xB07F4F2: ???
==8699==by 0x1FFEFFA88F: ???
==8699==
For example, mvnfast CRAN binaries could take advantage of OpenMP.
The OpenMx team has been building Mac OS binaries with openmp enabled
for years. We compile with gcc and bundle the necessary openmp enabled
libraries with the binary. Why couldn't CRAN do this?
--
Joshua N. Pritikin
21 aug. 2015 22:50 schreef Joshua N Pritikin
[1]jpriti...@pobox.com:
Many CRAN packages offer improved performance when compiled with
OpenMP. However, the MacOS and Windows binaries built by CRAN are
built
without openmp enabled. Would it be possible to build openmp
On Mon, Aug 24, 2015 at 09:29:34AM -0500, Dirk Eddelbuettel wrote:
On 24 August 2015 at 09:14, Joshua N Pritikin wrote:
| So I take that answer as, No, CRAN cannot possibly enable openmp for
| binary builds. Is that correct?
The CRAN maintainers are not withholding OpenMP from you because
On Mon, Aug 24, 2015 at 10:14:10AM -0500, Dirk Eddelbuettel wrote:
On 24 August 2015 at 11:02, Joshua N Pritikin wrote:
| Currently, we have a configure script for package OpenMx that only
| enables openmp if gcc is the compiler (OS X only). Nice to hear that
| openmp is supported on Windows
to SHLIB_OPENMP_CXXFLAGS (when there is compiler
support) or not? It seems not.
--
Joshua N. Pritikin
Department of Psychology
University of Virginia
485 McCormick Rd, Gilmer Hall Room 102
Charlottesville, VA 22904
http://people.virginia.edu/~jnp3bc
---BeginMessage---
I tried. Although it is pretty
Many CRAN packages offer improved performance when compiled with
OpenMP. However, the MacOS and Windows binaries built by CRAN are built
without openmp enabled. Would it be possible to build openmp enabled
binaries for some CRAN packages?
--
Joshua N. Pritikin
Department of Psychology
check that always trips
because the thread's stack is different from what R is expecting.
+ Therefore, I need a C version of dmvnorm.
+ The mvtnorm package maintainer is not interested in
R_RegisterCCallable.
Can a C version of dmvnorm get added to the R core?
--
Joshua N. Pritikin
Department
22 matches
Mail list logo
