Rhon Calderon, Eric
2022-Oct-04 13:36 UTC
[R] Help executing R on High Performance Cluster
Hi,
I need some help executing recently downloaded R on my HPC.
Here is the script I used to install R on my HPC module:
wget https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz
tar -xvf R-devel.tar.gz
cd /home/ericrhon/labsoftware/R-devel/
./configure --prefix=/home/ericrhon/labsoftware/R-devel
-with-recommended-packages=no --without-x --with-cairo --with-libpng
--with-libtiff --with-jpeglib --enable-R-shlib --with-pcre1
make
make install
After I installed, I tried to run /home/ericrhon/labsoftware/R-devel/R. But I
get the next error:
/home/ericrhon/labsoftware/R-devel/bin/exec/R: line 272:
/home/ericrhon/labsoftware/R-devel/bin/exec/R: Argument list too long
/home/ericrhon/labsoftware/R-devel/bin/exec/R: line 272:
/home/ericrhon/labsoftware/R-devel/bin/exec/R: Success
Here is the exec script of R, line 272 is highlighted:
#!/bin/sh
# Shell wrapper for R executable.
R_HOME_DIR="/home/ericrhon/labsoftware/R-devel"
if test "${R_HOME_DIR}" =
"/home/ericrhon/labsoftware/shared_Renv/versions/R-devel/lib64/R";
then
case "linux-gnu" in
linux*)
run_arch=`uname -m`
case "$run_arch" in
x86_64|mips64|ppc64|powerpc64|sparc64|s390x)
libnn=lib64
libnn_fallback=lib
;;
*)
libnn=lib
libnn_fallback=lib64
;;
esac
if [ -x
"/home/ericrhon/labsoftware/shared_Renv/versions/R-devel/${libnn}/R/bin/exec/R"
]; then
R_HOME_DIR="/home/ericrhon/labsoftware/shared_Renv/versions/R-devel/${libnn}/R"
elif [ -x
"/home/ericrhon/labsoftware/shared_Renv/versions/R-devel/${libnn_fallback}/R/bin/exec/R"
]; then
R_HOME_DIR="/home/ericrhon/labsoftware/shared_Renv/versions/R-devel/${libnn_fallback}/R"
## else -- leave alone (might be a sub-arch)
fi
;;
esac
fi
if test -n "${R_HOME}" && \
test "${R_HOME}" != "${R_HOME_DIR}"; then
echo "WARNING: ignoring environment value of R_HOME"
fi
R_HOME="${R_HOME_DIR}"
export R_HOME
R_SHARE_DIR="${R_HOME_DIR}/share"
export R_SHARE_DIR
R_INCLUDE_DIR="${R_HOME_DIR}/include"
export R_INCLUDE_DIR
R_DOC_DIR="${R_HOME_DIR}/doc"
export R_DOC_DIR
# Since this script can be called recursively, we allow R_ARCH to
# be overridden from the environment.
# This script is shared by parallel installs, so nothing in it should
# depend on the sub-architecture except the default here.
: ${R_ARCH=}
usage="
Usage: R [options] [< infile] [> outfile]
or: R CMD command [arguments]
Start R, a system for statistical computation and graphics, with the
specified options, or invoke an R tool via the 'R CMD' interface.
Options:
-h, --help Print short help message and exit
--version Print version info and exit
--encoding=ENC Specify encoding to be used for stdin
--encoding ENC
RHOME Print path to R home directory and exit
--save Do save workspace at the end of the session
--no-save Don't save it
--no-environ Don't read the site and user environment files
--no-site-file Don't read the site-wide Rprofile
--no-init-file Don't read the user R profile
--restore Do restore previously saved objects at startup
--no-restore-data Don't restore previously saved objects
--no-restore-history Don't restore the R history file
--no-restore Don't restore anything
--vanilla Combine --no-save, --no-restore, --no-site-file,
--no-init-file and --no-environ
--no-readline Don't use readline for command-line editing
--max-ppsize=N Set max size of protect stack to N
--min-nsize=N Set min number of fixed size obj's (\"cons
cells\") to N
--min-vsize=N Set vector heap minimum to N bytes; '4M' = 4
MegaB
-q, --quiet Don't print startup message
--silent Same as --quiet
-s, --no-echo Make R run as quietly as possible
--interactive Force an interactive session
--verbose Print more information about progress
-d, --debugger=NAME Run R through debugger NAME
--debugger-args=ARGS Pass ARGS as arguments to the debugger
-g TYPE, --gui=TYPE Use TYPE as GUI; possible values are 'X11'
(default)
and 'Tk'.
--arch=NAME Specify a sub-architecture
--args Skip the rest of the command line
-f FILE, --file=FILE Take input from 'FILE'
-e EXPR Execute 'EXPR' and exit
FILE may contain spaces but not shell metacharacters.
Commands:
BATCH Run R in batch mode
COMPILE Compile files for use with R
SHLIB Build shared library for dynamic loading
INSTALL Install add-on packages
REMOVE Remove add-on packages
build Build add-on packages
check Check add-on packages
LINK Front-end for creating executable programs
Rprof Post-process R profiling files
Rdconv Convert Rd format to various other formats
Rd2pdf Convert Rd format to PDF
Rd2txt Convert Rd format to pretty text
Stangle Extract S/R code from Sweave documentation
Sweave Process Sweave documentation
Rdiff Diff R output ignoring headers etc
config Obtain configuration information about R
javareconf Update the Java configuration variables
rtags Create Emacs-style tag files from C, R, and Rd files
Please use 'R CMD command --help' to obtain further information about
the usage of 'command'.
Options --arch, --no-environ, --no-init-file, --no-site-file and --vanilla
can be placed between R and CMD, to apply to R processes run by
'command'
Report bugs at <https://bugs.R-project.org>."
## some systems have a more portable sed, e.g. /usr/xpg4/bin/sed on Solaris,
## so make sure that is used.
SED=/usr/bin/sed
export SED
error () {
echo "ERROR: $*" >&2
exit 1
}
### Argument loop
args
debugger
debugger_args
gui
while test -n "${1}"; do
case ${1} in
RHOME|--print-home)
echo "${R_HOME}"; exit 0 ;;
CMD)
shift;
export R_ARCH
. "${R_HOME}/etc${R_ARCH}/ldpaths"
exec sh "${R_HOME}/bin/Rcmd" "${@}" ;;
-g|--gui)
if test -n "`echo ${2} | ${SED} 's/^-.*//'`"; then
gui="${2}"
args="${args} ${1} ${2}"
shift
else
error "option '${1}' requires an argument"
fi
;;
--gui=*)
gui=`echo "${1}" | ${SED} -e 's/[^=]*=//'`
args="${args} ${1}"
;;
-d|--debugger)
if test -n "`echo ${2} | ${SED} 's/^-.*//'`"; then
debugger="${2}"; shift
else
error "option '${1}' requires an argument"
fi
;;
--debugger=*)
debugger=`echo "${1}" | ${SED} -e 's/[^=]*=//'` ;;
--debugger-args=*)
debugger_args=`echo "${1}" | ${SED} -e 's/[^=]*=//'` ;;
-h|--help)
echo "${usage}"; exit 0 ;;
--args)
break ;;
--arch)
if test -n "`echo ${2} | ${SED} 's/^-.*//'`"; then
R_ARCH="/${2}"
shift
else
error "option '${1}' requires an argument"
fi
## check sub-architecture here for a better error message
if ! test -d ${R_HOME}/etc${R_ARCH}; then
error "sub-architecture '${1}' is not installed"
fi
;;
--arch=*)
r_arch=`echo "${1}" | ${SED} -e 's/[^=]*=//'`
R_ARCH="/${r_arch}"
## check sub-architecture here for a better error message
if ! test -d ${R_HOME}/etc${R_ARCH}; then
error "sub-architecture '${r_arch}' is not installed"
fi
;;
-e)
TAB=`printf "\t"`
if test -n "`echo ${2} | ${SED} 's/^-.*//'`"; then
a=`(echo "${2}" && echo) | ${SED} -e 's/
/~+~/g' | \
${SED} -e :a -e N -e '$!ba' -e 's/\n/~n~/g' -e
's/~n~$//g' -e "s/$TAB/~t~/g"`
shift
else
error "option '${1}' requires a non-empty
argument"
fi
args="${args} -e $a"
;;
-f)
if test -n "`echo ${2} | ${SED} 's/^-.*//'`"; then
a=`echo "${2}" | ${SED} -e 's/ /~+~/g'`; shift
else
error "option '${1}' requires a filename argument"
fi
args="${args} -f $a"
;;
--file=*)
a=`echo "${1}" | ${SED} -e 's/[^=]*=//' | ${SED} -e
's/ /~+~/g'`
args="${args} --file=$a"
;;
--no-environ)
R_ENVIRON=''
export R_ENVIRON
R_ENVIRON_USER=''
export R_ENVIRON_USER
args="${args} ${1}"
;;
--no-site-file)
R_PROFILE=''
export R_PROFILE
args="${args} ${1}"
;;
--no-init-file)
R_PROFILE_USER=''
export R_PROFILE_USER
args="${args} ${1}"
;;
--vanilla)
R_ENVIRON=''
export R_ENVIRON
R_ENVIRON_USER=''
export R_ENVIRON_USER
R_PROFILE=''
export R_PROFILE
R_PROFILE_USER=''
export R_PROFILE_USER
args="${args} ${1}"
;;
*)
args="${args} ${1}" ;;
esac
shift
done
. "${R_HOME}/etc${R_ARCH}/ldpaths"
R_binary="${R_HOME}/bin/exec${R_ARCH}/R"
export R_ARCH
case "${gui}" in
Tk|tk|X11|x11)
;;
"")
;;
*)
error "unknown GUI ${gui}"
esac
## R_HOME may have moved, so check
if test -x "${R_HOME}"; then
:
else
error "R_HOME ('${R_HOME}') not found"
fi
## Startup
if test -z "${debugger}"; then
exec "${R_binary}" ${args} "${@}"
else
## Ideally, we would like the debugger to start R with additional
## ('inferior') arguments, but not all debuggers can do this. We know
## about valgrind and some versions of GDB , and deal with these.
## Otherwise, to be on the safe side, we disregard non-debugger
## command line args.
args_ok=no
case "`${debugger} --version 2>/dev/null`" in
"GNU gdb"*)
if ${debugger} --help 2>/dev/null | \
grep ' *--args' >/dev/null; then
args_ok=yes
debugger_args="${debugger_args} --args"
fi
;;
valgrind*)
args_ok=yes
;;
esac
if test -n "${args}${*}" && test "${args_ok}" =
no; then
args=`expr "${args} ${*}" : " *\(.*\)"`
echo "*** Further command line arguments ('${args}')
disregarded"
echo "*** (maybe use 'run ${args}' from *inside*
${debugger})"
echo ""
exec ${debugger} ${debugger_args} "${R_binary}"
else
exec ${debugger} ${debugger_args} "${R_binary}" ${args}
"${@}"
fi
fi
### Local Variables: ***
### mode: sh ***
### sh-indentation: 2 ***
### End: ***
Could you please help me? I have been trying to load it unsuccessfully.
Thanks.
Eric
[[alternative HTML version deleted]]
Hi Eric! ? Tue, 4 Oct 2022 13:36:59 +0000 "Rhon Calderon, Eric" <Eric.RhonCalderon at pennmedicine.upenn.edu> ?????:> cd /home/ericrhon/labsoftware/R-devel/> ./configure --prefix=/home/ericrhon/labsoftware/R-develI'm not sure, but the reason for the confusing behaviour could be that the installation prefix is set to be the same as the directory where you had unpacked the source code. This may have caused file path conflicts and maybe some kind of recursion when building the final executable path. R can run straight from the build directory, without installation. If you start from scratch, does bin/R work without `make install`? If not, do you get any useful output if you run bin/R under sh -x? (Additionally, R supports building away from the source code directory. For example, if you navigate to the source code directory, then run mkdir build && cd build && ../configure $CONFIGURE_ARGUMENTS, the build will be mostly self-contained to that directory, which may be useful when experimenting.) Why are you building R with --with-recommended-packages=no? R is supposed to be easy to build and start working with, but there may be important details to consider, especially on an HPC, in the "R installation and administration" guide: https://cran.r-project.org/doc/manuals/r-release/R-admin.html> Here is the exec script of R, line 272 is highlighted:<...>> [[alternative HTML version deleted]]This mailing list strips the HTML version of the e-mails; here's what we see: https://stat.ethz.ch/pipermail/r-help/2022-October/475956.html One way to link to R source code is to use the GitHub mirror: https://github.com/r-devel/r-svn -- Best regards, Ivan