[Beowulf] Missing pvmd for Rpvm

Michael Muratet mmuratet at hudsonalpha.org
Tue Jul 14 15:07:00 EDT 2009


Greetings

I am trying to install the R rpvm package to run R on a scyld/beowulf  
cluster.

 > install.packages('rpvm',dependencies=TRUE)
also installing the dependency ‘rsprng’

trying URL 'http://mira.sunsite.utk.edu/CRAN/src/contrib/rsprng_0.4.tar.gz'
Content type 'application/x-gzip' length 36044 bytes (35 Kb)
opened URL
==================================================
downloaded 35 Kb

trying URL 'http://mira.sunsite.utk.edu/CRAN/src/contrib/rpvm_1.0.2.tar.gz'
Content type 'application/x-gzip' length 62737 bytes (61 Kb)
opened URL
==================================================
downloaded 61 Kb

* Installing *source* package ‘rsprng’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
Try to find sprng.h ...
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking sprng.h usability... no
checking sprng.h presence... no
checking for sprng.h... no
Cannot find sprng 2.0 header file.
ERROR: configuration failed for package ‘rsprng’
* Removing ‘/usr/local/lib64/R/library/rsprng’
* Installing *source* package ‘rpvm’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
Check if PVM_ROOT is defined... /usr/share/pvm3
Found pvm: /usr/share/pvm3
PVM_ROOT is /usr/share/pvm3
PVM_ARCH is BEOSCYLD
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking pvm3.h usability... no
checking pvm3.h presence... no
checking for pvm3.h... no
Try to find pvm3.h ...
Found in /usr/share/pvm3/include
checking for main in -lpvm3... no
Try to find libpvm3 ...
Found in /usr/share/pvm3/lib/BEOSCYLD
checking for pvmd... no
Cannot find pvmd executable
Include it in your path or check your pvm installation.
ERROR: configuration failed for package ‘rpvm’
* Removing ‘/usr/local/lib64/R/library/rpvm’

The downloaded packages are in
	‘/tmp/RtmpKJmN3z/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("rpvm", dependencies = TRUE) :
   installation of package 'rsprng' had non-zero exit status
2: In install.packages("rpvm", dependencies = TRUE) :
   installation of package 'rpvm' had non-zero exit status

I believe this to be a problem on the cluster and not with R.

There are messages in the archives going back a few years regarding  
problems starting pvm but nothing seems to apply to my case. I've been  
to the pvm webpage but I don't see anything that's beowulf specific.  
The pvm libraries are there but the daemon apparently doesn't run  
unless you start it. Before I start it, can anyone point me to any R-  
or pvm-specific documentation?

Thanks

Mike


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