[Beowulf] Missing pvmd for Rpvm

Prentice Bisbal prentice at ias.edu
Thu Jul 16 10:42:10 EDT 2009


This is a problem for the rpvm mailing list (if one exists) or the rpvm
maintainer. You don't need to start pvmd. The configure script can't
find pvmd or libpvm. Try putting the path to pvmd in your PATH and
specifying the path to libpvm in LDFLAGS first.

--
prentice


Michael Muratet wrote:
> 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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