Hello,
I'd like to take a look at how the taskPR package performs on our computational
cluster, and this morning I've spend some time trying to do a test install of
this package on one of our linux machines. Unfortunately I've been unsuccessful
in completing the install, and I wondered if someone could please advise me.
As I've noted I working on a linux machine, and it's running RHEL 4.0. I've
build the lam package (we're very familiar with all the mpi libraries and so
that is not an issue), and then I attempted to install taskPR...
A). I added the lam binaries to my command search PATH
B). Defined CC=mpicc
C). Started R, and tried the install using
install.packages(c("taskPR_0.2.7.tar.gz"), repos=NULL, configure.args=
c(taskPR="--with-mpi='/usr/local/lam-7.1.4'"))
The configure/install fails, and I've appended the output below. I can
understand why it's failing, however I don't understand how to fix the problem.
Could anyone please shead any light on this issue.
Thanks & Regards,
David Baker.
> install.packages(c("taskPR_0.2.7.tar.gz"), repos=NULL, configure.args=
> c(taskPR="--with-mpi='/usr/local/lam-7.1.4'"))
* Installing *source* package 'taskPR' ...
creating cache ./config.cache
checking for gcc... mpicc
checking whether the C compiler (mpicc ) works... yes
checking whether the C compiler (mpicc ) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether mpicc accepts -g... yes
checking how to run the C preprocessor... mpicc -E
checking for mpi.h... yes
checking for pthread_detach in -lpthread... yes
checking for MPI_Comm_spawn... yes
checking whether mpicc -Wall is understood... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
** arch -
gcc -std=gnu99 -I/usr/local/R-2.5.0/lib64/R/include
-I/usr/local/R-2.5.0/lib64/R/include -I/usr/local/include -g -O2 -Wall
-DPARALLEL_R_PACKAGE -fpic -g -O2 -c spawnhelper.c -o spawnhelper.o
spawnhelper.c:30:17: mpi.h: No such file or directory
spawnhelper.c: In function `main':
spawnhelper.c:41: warning: implicit declaration of function `MPI_Init'
spawnhelper.c:41: error: `MPI_SUCCESS' undeclared (first use in this function)
spawnhelper.c:41: error: (Each undeclared identifier is reported only once
spawnhelper.c:41: error: for each function it appears in.)
spawnhelper.c:46: warning: implicit declaration of function `MPI_Comm_rank'
spawnhelper.c:46: error: `MPI_COMM_WORLD' undeclared (first use in this
function)
spawnhelper.c:47: warning: implicit declaration of function `MPI_Comm_size'
spawnhelper.c:49: warning: implicit declaration of function `MPI_Bcast'
spawnhelper.c:49: error: `MPI_INT' undeclared (first use in this function)
spawnhelper.c:75: error: `MPI_CHAR' undeclared (first use in this function)
make: *** [spawnhelper.o] Error 1
ERROR: compilation failed for package 'taskPR'
** Removing '/usr/local/R-2.5.0/lib64/R/library/taskPR'
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
