Dear R Devel Some of our R users are still insisting we run R-2.15.3 because of difficulties with a package called OpenMX. It can't cooperate with new R, oh well. Other users need to run R-3.0.1. I'm looking for the most direct route to install both, and allow users to choose at runtime. In the cluster, things run faster if I install RPMs to each node, rather than putting R itself on the NFS share (but I could do that if you think it's really better....) In the past, I've used the SRPM packaging from EPEL repository to make a few little path changes and build R RPM for our cluster nodes. Now I face the problem of building 2 RPMS, one for R-2.15.3 and one for R-newest, and somehow keeping them separate. If you were me, how would you approach this? Here's my guess First, The RPM packages need unique names, of course. Second, leave the RPM packaging for R-newest exactly the same as it always was. R is in the path, the R script and references among all the bits will be fine, no need to fight. It will find what it needs in /usr/lib64/R or whatnot. For the legacy R, I'm considering 2 ideas. I could install R with the same prefix, /usr, but very careful so the R bits are installed into separate places. I just made a fresh build of R and on RedHat 6, it appears to me R installs these directories: bin libdir share. So what if the configure line has the magic bindir=/usr/bin-R-2.15.3 libdir = /usr/lib64/R-2.15.3, and whatnot. If I were doing Debian packaging, I suppose I'd be obligated (by the file system standard) to do that kind of thing. But it looks like a headache. The easy road is to set the prefix at some out of the way place, like /opt/R-2.15.3, and then use a post-install script to link /opt/R-2/15.3/bin/R to /usr/bin/R-2.15.3. When I tried that, it surprised me because R did not complain about lack access to devel headers. It configures and builds fine. R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory: /tmp/R C compiler: gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler: gfortran -g -O2 Obj-C compiler: gcc -g -O2 -fobjc-exceptions Interfaces supported: X11, tcltk External libraries: readline, ICU, lzma Additional capabilities: PNG, JPEG, TIFF, NLS, cairo Options enabled: shared BLAS, R profiling, Java Recommended packages: yes Should I worry about any runtime complications of this older R finding its of the newer R in the PATH ahead of it? I worry I'm making lazy assumptions? After that, I need to do some dancing with the RPM packaging. I suppose there'd be some comfort if I could get the users to define R_HOME in their user environment before launching jobs, I think that would eliminate the danger of confusion between versions, wouldn't it? pj -- Paul E. Johnson Professor, Political Science Assoc. Director 1541 Lilac Lane, Room 504 Center for Research Methods University of Kansas University of Kansas http://pj.freefaculty.org http://quant.ku.edu [[alternative HTML version deleted]]
On Tue, Oct 15, 2013 at 1:15 PM, Paul Johnson <pauljohn32 at gmail.com> wrote:> Dear R Devel > > Some of our R users are still insisting we run R-2.15.3 because of > difficulties with a package called OpenMX. It can't cooperate with new R, > oh well. > > Other users need to run R-3.0.1. I'm looking for the most direct route to > install both, and allow users to choose at runtime.[...] Since no experts have replied, here's my non-expert opinion (take it as a disclaimer). R is happy to be installed in multiple versions. I have always had several versions of R installed (under Linux). I always compile from source and simply set the appropriate destination directories appropriately, then symlink the R and Rscript executables. In my case I put each version into a separate directory under /usr/local/lib64, for example /usr/local/lib64/R-3.0.2-patched . I put all executables into /usr/local/bin but change their names, e.g. R is called R-3.0.2-patched etc; then symlink the executable that I want to be my "default" version to /usr/local/bin/R and /usr/local/bin/Rscript. If I want to call another version of R, I invoke it explicitly as say R-2.15.3 (assuming such version exists). You could also create a separate directory for the executables for each version and symlink them under different names to /usr/bin or /usr/local/bin. I never had problems with versions of R clashing. The executable R that a user executes is a shell wrapper that sets up all necessary environment variables and then calls the actual executable (which sits in /usr/local/lib64/<R-directory>/bin/exec). Thus, other versions on $PATH do not cause any trouble. HTH, Peter
OpenMx does install on R 3.01. I haven't tested extensively, but after
installing with
install.packages('OpenMx',
dependencies = TRUE,
repos = c(getOption("repos"),
'http://openmx.psyc.virginia.edu/sequential/'))
the demos appear to run correctly.
Best,
Ista
On Tue, Oct 15, 2013 at 4:15 PM, Paul Johnson <pauljohn32 at gmail.com>
wrote:> Dear R Devel
>
> Some of our R users are still insisting we run R-2.15.3 because of
> difficulties with a package called OpenMX. It can't cooperate with new
R,
> oh well.
>
> Other users need to run R-3.0.1. I'm looking for the most direct route
to
> install both, and allow users to choose at runtime.
>
> In the cluster, things run faster if I install RPMs to each node, rather
> than putting R itself on the NFS share (but I could do that if you think
> it's really better....)
>
> In the past, I've used the SRPM packaging from EPEL repository to make
a
> few little path changes and build R RPM for our cluster nodes. Now I face
> the problem of building 2 RPMS, one for R-2.15.3 and one for R-newest, and
> somehow keeping them separate.
>
> If you were me, how would you approach this?
>
> Here's my guess
>
> First, The RPM packages need unique names, of course.
>
> Second, leave the RPM packaging for R-newest exactly the same as it always
> was. R is in the path, the R script and references among all the bits will
> be fine, no need to fight. It will find what it needs in /usr/lib64/R or
> whatnot.
>
> For the legacy R, I'm considering 2 ideas. I could install R with the
same
> prefix, /usr, but very careful so the R bits are installed into separate
> places. I just made a fresh build of R and on RedHat 6, it appears to me R
> installs these directories:
> bin
> libdir
> share.
>
> So what if the configure line has the magic bindir=/usr/bin-R-2.15.3
> libdir = /usr/lib64/R-2.15.3, and whatnot. If I were doing Debian
> packaging, I suppose I'd be obligated (by the file system standard) to
do
> that kind of thing. But it looks like a headache.
>
> The easy road is to set the prefix at some out of the way place, like
> /opt/R-2.15.3, and then use a post-install script to link
> /opt/R-2/15.3/bin/R to /usr/bin/R-2.15.3. When I tried that, it surprised
> me because R did not complain about lack access to devel headers. It
> configures and builds fine.
>
> R is now configured for x86_64-unknown-linux-gnu
>
> Source directory: .
> Installation directory: /tmp/R
>
> C compiler: gcc -std=gnu99 -g -O2
> Fortran 77 compiler: gfortran -g -O2
>
> C++ compiler: g++ -g -O2
> Fortran 90/95 compiler: gfortran -g -O2
> Obj-C compiler: gcc -g -O2 -fobjc-exceptions
>
> Interfaces supported: X11, tcltk
> External libraries: readline, ICU, lzma
> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo
> Options enabled: shared BLAS, R profiling, Java
>
> Recommended packages: yes
>
> Should I worry about any runtime complications of this older R finding its
> of the newer R in the PATH ahead of it? I worry I'm making lazy
> assumptions?
>
> After that, I need to do some dancing with the RPM packaging.
>
> I suppose there'd be some comfort if I could get the users to define
R_HOME
> in their user environment before launching jobs, I think that would
> eliminate the danger of confusion between versions, wouldn't it?
>
> pj
> --
> Paul E. Johnson
> Professor, Political Science Assoc. Director
> 1541 Lilac Lane, Room 504 Center for Research Methods
> University of Kansas University of Kansas
> http://pj.freefaculty.org http://quant.ku.edu
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> -----Original Message----- > From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] > On Behalf Of Paul Johnson > Sent: October-15-13 1:15 PM > To: R Devel List > Cc: Discussion of Rocks Clusters > Subject: [Rd] Two R editiosn in Unix cluster systems > > Dear R Devel > > Some of our R users are still insisting we run R-2.15.3 because of > difficulties with a package called OpenMX. It can't cooperate with new R, > oh well. > > Other users need to run R-3.0.1. I'm looking for the most direct route to > install both, and allow users to choose at runtime. > > In the cluster, things run faster if I install RPMs to each node, rather > than putting R itself on the NFS share (but I could do that if you think > it's really better....) > > In the past, I've used the SRPM packaging from EPEL repository to make a > few little path changes and build R RPM for our cluster nodes. Now I face > the problem of building 2 RPMS, one for R-2.15.3 and one for R-newest, and > somehow keeping them separate. > > If you were me, how would you approach this?Our bioinformatics group needs multiple versions of R and other software for a variety of compatibility issues. We thus gave up on trying to keep multiple versions of R and related pipeline software on all nodes of our cluster. We set up a mount point on each cluster node pointing to a directory structure on the head node (/share/apps). We compile and link all necessary materials in that directory structure, so that no executables or shared objects from /usr or other local drive locations need be accessed. All code is in e.g. /share/apps/R/R-x.yy.z so all the nodes can see all the versions. We have shared libraries in e.g. /share/apps/usr/lib All pipeline scripts use full paths to R and other executables, and since R is self-contained when appropriately compiled as you note below, there's no path clashing. (We also abandoned NFS for lustre so we don't have the speed issue you might face with such an arrangement. But generally code just needs to be read once and is then kept in memory by current OSs, so you might not notice much of a speed hit as far as getting the executable into memory.) Maintaining one set of code accessible to all nodes has made things much simpler than trying to set up all the rpms on the head node so that all compute nodes get it all installed locally. Some attention to detail is important at compile time, to ensure that all bits that go into the compilation really do come from /share/apps but that's about it. This has been easier to accomplish than maintaining a library of rpms on the head node and managing the distribution scripts to push out to the compute nodes. Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre> Here's my guess > > First, The RPM packages need unique names, of course. > > Second, leave the RPM packaging for R-newest exactly the same as it always > was. R is in the path, the R script and references among all the bits will > be fine, no need to fight. It will find what it needs in /usr/lib64/R or > whatnot. > > For the legacy R, I'm considering 2 ideas. I could install R with the same > prefix, /usr, but very careful so the R bits are installed into separate > places. I just made a fresh build of R and on RedHat 6, it appears to me R > installs these directories: > bin > libdir > share. > > So what if the configure line has the magic bindir=/usr/bin-R-2.15.3 > libdir = /usr/lib64/R-2.15.3, and whatnot. If I were doing Debian > packaging, I suppose I'd be obligated (by the file system standard) to do > that kind of thing. But it looks like a headache. > > The easy road is to set the prefix at some out of the way place, like > /opt/R-2.15.3, and then use a post-install script to link > /opt/R-2/15.3/bin/R to /usr/bin/R-2.15.3. When I tried that, it surprised > me because R did not complain about lack access to devel headers. It > configures and builds fine. > > R is now configured for x86_64-unknown-linux-gnu > > Source directory: . > Installation directory: /tmp/R > > C compiler: gcc -std=gnu99 -g -O2 > Fortran 77 compiler: gfortran -g -O2 > > C++ compiler: g++ -g -O2 > Fortran 90/95 compiler: gfortran -g -O2 > Obj-C compiler: gcc -g -O2 -fobjc-exceptions > > Interfaces supported: X11, tcltk > External libraries: readline, ICU, lzma > Additional capabilities: PNG, JPEG, TIFF, NLS, cairo > Options enabled: shared BLAS, R profiling, Java > > Recommended packages: yes > > Should I worry about any runtime complications of this older R finding its > of the newer R in the PATH ahead of it? I worry I'm making lazy > assumptions? > > After that, I need to do some dancing with the RPM packaging. > > I suppose there'd be some comfort if I could get the users to define R_HOME > in their user environment before launching jobs, I think that would > eliminate the danger of confusion between versions, wouldn't it? > > pj > -- > Paul E. Johnson > Professor, Political Science Assoc. Director > 1541 Lilac Lane, Room 504 Center for Research Methods > University of Kansas University of Kansas > http://pj.freefaculty.org http://quant.ku.edu > > [[alternative HTML version deleted]] > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel
Adam Brenner
2013-Oct-16 01:24 UTC
[Rd] [Rocks-Discuss] Two R editiosn in Unix cluster systems
Paul,
For our HPC cluster we have ran into this issue in the past. What we use is
modules[1]. We instructor our users to run a command, like
modules load R/2.15.2
This will load up the environment path in which R/2.15.2 lives. If they want
to switch or use R/3.0.1 they simply run
module unload R/2.15.2
module load R/3.0.1
For all our software install, we do *not* install software on each node. The
overhead for us to create a compilation script and fork that out to each node
within our cluster (100+) is not worth it. Instead we use modules, as I have
described above. We use a standard NFS server with lots of NFS processes that
gets mounted on each compute node. This has worked extremely well for us.
The primary reason, is due to the fact the linux kernel does a fairly good job
when caching libraries. In our setup, we have experienced most, if not all,
the R libraries stay in memory once loaded from our NFS server. The data/input
files R uses is on our Gluster or FraunhoferFS parallel file system. Of
course, keeping the data local to the compute node would be the fastest.
If you still want to install software locally on each compute node, you can
still take advantage of modules. I do suggest you install R (from source or
RPM, etc) in a non-standard location like /opt/ or make your own /apps, /data
and so on. Then create a module file similar to the following:
#%Module1.0
module load gcc/4.8.1
set ROOT /data/apps/R/3.0.1
prepend-path PATH $ROOT/bin
prepend-path MANPATH $ROOT/share
prepend-path R_LIBS $ROOT/lib64/R/library
prepend-path LD_LIBRARY_PATH $ROOT/lib64/R/lib
Replace the TCL variable ROOT with the path of where R lives and you are good
to go. This method of works with other software besides R :-)
[1]: http://modules.sourceforge.net
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebrenne at uci.edu
On Tue, Oct 15, 2013 at 1:15 PM, Paul Johnson <pauljohn32 at gmail.com>
wrote:> Dear R Devel
>
> Some of our R users are still insisting we run R-2.15.3 because of
> difficulties with a package called OpenMX. It can't cooperate with new
R,
> oh well.
>
> Other users need to run R-3.0.1. I'm looking for the most direct route
to
> install both, and allow users to choose at runtime.
>
> In the cluster, things run faster if I install RPMs to each node, rather
> than putting R itself on the NFS share (but I could do that if you think
> it's really better....)
>
> In the past, I've used the SRPM packaging from EPEL repository to make
a
> few little path changes and build R RPM for our cluster nodes. Now I face
> the problem of building 2 RPMS, one for R-2.15.3 and one for R-newest, and
> somehow keeping them separate.
>
> If you were me, how would you approach this?
>
> Here's my guess
>
> First, The RPM packages need unique names, of course.
>
> Second, leave the RPM packaging for R-newest exactly the same as it always
> was. R is in the path, the R script and references among all the bits will
> be fine, no need to fight. It will find what it needs in /usr/lib64/R or
> whatnot.
>
> For the legacy R, I'm considering 2 ideas. I could install R with the
same
> prefix, /usr, but very careful so the R bits are installed into separate
> places. I just made a fresh build of R and on RedHat 6, it appears to me R
> installs these directories:
> bin
> libdir
> share.
>
> So what if the configure line has the magic bindir=/usr/bin-R-2.15.3
> libdir = /usr/lib64/R-2.15.3, and whatnot. If I were doing Debian
> packaging, I suppose I'd be obligated (by the file system standard) to
do
> that kind of thing. But it looks like a headache.
>
> The easy road is to set the prefix at some out of the way place, like
> /opt/R-2.15.3, and then use a post-install script to link
> /opt/R-2/15.3/bin/R to /usr/bin/R-2.15.3. When I tried that, it surprised
> me because R did not complain about lack access to devel headers. It
> configures and builds fine.
>
> R is now configured for x86_64-unknown-linux-gnu
>
> Source directory: .
> Installation directory: /tmp/R
>
> C compiler: gcc -std=gnu99 -g -O2
> Fortran 77 compiler: gfortran -g -O2
>
> C++ compiler: g++ -g -O2
> Fortran 90/95 compiler: gfortran -g -O2
> Obj-C compiler: gcc -g -O2 -fobjc-exceptions
>
> Interfaces supported: X11, tcltk
> External libraries: readline, ICU, lzma
> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo
> Options enabled: shared BLAS, R profiling, Java
>
> Recommended packages: yes
>
> Should I worry about any runtime complications of this older R finding its
> of the newer R in the PATH ahead of it? I worry I'm making lazy
> assumptions?
>
> After that, I need to do some dancing with the RPM packaging.
>
> I suppose there'd be some comfort if I could get the users to define
R_HOME
> in their user environment before launching jobs, I think that would
> eliminate the danger of confusion between versions, wouldn't it?
>
> pj
> --
> Paul E. Johnson
> Professor, Political Science Assoc. Director
> 1541 Lilac Lane, Room 504 Center for Research Methods
> University of Kansas University of Kansas
> http://pj.freefaculty.org http://quant.ku.edu
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