Rmpi package

Dear All,

I tried to install the Rmpi for Mac OS X, by following this:
http://www.stats.uwo.ca/faculty/yu/Rmpi/


I successfully installed the Xcodeand verified thegcc.
When I installed the Homebrew, I got the message as below:

Rohmatuls-MacBook-Pro:~ rfajriyah$ ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"

-e:67: warning: Insecure world writable dir /usr/local/bin in PATH, mode 040777
-e:96: warning: Insecure world writable dir /usr/local/bin in PATH, mode 040777
==> This script will install:
/usr/local/bin/brew
/usr/local/Library/...
/usr/local/share/man/man1/brew.1
==> The following directories will be made group writable:
/usr/local/lib/pkgconfig
/usr/local/share/info
==> The following directories will have their group set to admin:
/usr/local/lib/pkgconfig
/usr/local/share/info

Press ENTER to continue or any other key to abort
-e:34: warning: Insecure world writable dir /usr/local/bin in PATH, mode 040777

then I quitted (aborted the process).

After read some sources, I guessed, I should change the PATH first. 
But there are things that I am not sure about:
a. Should I un-install the Xcode, change the PATH and re-install it again?
b. When I change the PATH to  /usr/local/bin, what will happen to my R at /usr/bin? Should I un-installed (delete) and re-install it at /usr/local/bin?

Dear Sir,

Thank you very much for your respond.

Dear Both,

OK.
Try 
install.packages("Rmpi") 

I have done it previously (but I did not tell here), it did not work since it has no binary just a source.
I have done sudo R CMD INSTALL Rmpi_0.6-4.tar at terminal too, and I got this message:
......
checking for mpi.h... no
configure: error: "Cannot find mpi.h header file"
ERROR: configuration failed for package 'Rmpi',

My mistake was I did not google it. Only search from r-sig-mac archives.

Now I am googling it and found some information (from R-sig-Debian and R-help archives ) that I need to give it a try.

MPI isn't the easiest build in the world so I'd imagine it will fail, but this will at least give us a sense of how your environment is configured. 

Needless to say: if you haven't got the compilers and command line tools available from XCode (the ones used to build R) do that first 

I think, I already installed the Xcode, following the instruction from here: (choose Rmpi for Mac OS X) 
http://www.stats.uwo.ca/faculty/yu/Rmpi/
Because the Mountain Lion?s default PATH is /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin, then --I think-- I need to change the path if I want to install Homebrew. On the other hand my current R is at /usr/bin. Which made me not sure what should I do.

 or you have no hope ;-)

Let me try the information that I found from google and get back here if I still have a trouble.

Prof. Winsemius: My apologise for that ... 

Thank you very much.

With kind regards,
Ema



From: Michael Weylandt <michael.weylandt at gmail.com>
To: Rohmatul Fajriyah <rfajriyah at yahoo.com> 
Cc: David Winsemius <dwinsemius at comcast.net>; "r-sig-mac at r-project.org" <r-sig-mac at r-project.org> 
Sent: Monday, August 19, 2013 2:19 AM
Subject: Re: [R-SIG-Mac] Rmpi package

As David noted, it's been de-CRAN'd for pushing some check times a bit far. 

This means you'll likely need to build it from source, which home brew won't help with (well, much beyond what 'regular' R does)

Try 

install.packages("Rmpi") 

to see what happens. MPI isn't the easiest build in the world so I'd imagine it will fail, but this will at least give us a sense of how your environment is configured. 

Needless to say: if you haven't got the compilers and command line tools available from XCode (the ones used to build R) do that first or you have no hope ;-)

Michael

On Aug 18, 2013, at 19:39, Rohmatul Fajriyah <rfajriyah at yahoo.com> wrote:

(Thank you Michael Weylandt, for notifying me about this. Here my previous email.)

Dear Sir,

Thank you very much for your respond.

 > What does this have to do with R? (Or for that matter, the directions referenced?) Generally Simon advises against using brew, fink, or other Mac/NIX package installers. 

Really? I don't know about it. Therefore, I should not continue to do this ...? 

Rmpi is not listed as available in CRAN at the moment, apparently because it took more than 30 minutes to unload:
http://www.r-project.org/nosvn/R.check/r-release-macosx-x86_64/Rmpi-00check.html

 I checked it and it's still there, Sir. (unless I am mistaken ...)

Certainly you need to do a better job of describing your OS, your system tools, which MPI you have installed or are intending to use, and what versions of R and Rmpi that you have.  
Also explain why you are not using the standard parallel package.

I tried to install the package to broaden my knowledge in doing parallel computing. 
 (Yes, I have used some R parallel packages).

My computer is Mac OS X 10.8.4 and R 3.0.1 (64 bit).
I downloaded the Rmpi_0.6-4.tar already, but I did not install it yet, due to as I have explained in my previous email.
 
Sincerely,
Ema

From: Michael Weylandt <michael.weylandt at gmail.com>
To: Rohmatul Fajriyah <rfajriyah at yahoo.com> 
Cc: David Winsemius <dwinsemius at comcast.net>; "r-sig-mac at r-project.org" <r-sig-mac at r-project.org> 
Sent: Monday, August 19, 2013 12:52 AM
Subject: Re: [R-SIG-Mac] Rmpi package

Hi Ema,

Can you try resenting this -- the quoting seems to have gotten messed up. 

MW