[Rd] Installing Rmpi on 64-bit Linux Athlon
c.farrow at compserv.gla.ac.uk
c.farrow at compserv.gla.ac.uk
Tue Oct 10 10:22:25 CEST 2006
Hi,
I think you need to reverse the order of the first two lines as
currently you are using $prefix before it is defined.
setenv prefix "/home/a347549/local64"
setenv LD_LIBRARY_PATH "-L$prefix/lib -L$prefix/lib64"
colin.
On 9 Oct, McGehee, Robert wrote:
> Hello,
> We have recently added a 64-bit 2 x Dual-Core Athlon server running Red
> Hat Enterprise Linux AS release 3 to allow for processing of large data
> sets (>4GB) in R. To integrate this server into our Linux cluster, I
> have been trying (unsuccessfully) to use Rmpi/lam-mpi to parallel
> process some of our scripts. While I have successfully compiled R 2.4.0
> and lam-mpi 7.1.2 on this server using a 64-bit architecture, I have not
> been able to install Rmpi to interface with lam-mpi, despite success on
> nearly identical servers in a 32-bit architecture. When trying on the
> 64-bit server, I receive the error "cannot find -lmpi" during
> compilation (see below).
>
> If anyone has had success in this regards and notice an installation
> problem that I may have overlooked, I would greatly appreciate any
> advice. Note that because I do not have root access, all of the lam-mpi
> and R files were installed locally.
>
> Thanks in advance,
> Robert
>
> ### Below is configuration scripts for R, Lam-MPI and Rmpi:
>
> setenv LD_LIBRARY_PATH "-L$prefix/lib -L$prefix/lib64"
> setenv prefix "/home/a347549/local64"
>
> ### R 2.4.0 Configure
> ./configure --prefix=$prefix --with-x
> --with-tcl-config="$prefix/lib/tclConfig.sh"
> --with-tk-config="$prefix/lib/tkConfig.sh"
> --with-blas="-L$builddir/ATLAS/lib/Linux_HAMMER64SSE2_4 -lptf77blas
> -lpthread -latlas"
>
> ### Lam-MPI 7.1.2 Configure:
> ./configure --prefix=$prefix --enable-shared --disable-static
> --without-romio --with-rsh="ssh -xq"
>
> ### Rmpi INSTALL
> R CMD INSTALL Rmpi --configure-args="--with-mpi=$prefix --prefix=$prefix
> CC=mpicc" -l $R_LIBS
>
> * Installing *source* package 'Rmpi' ...
> Try to find mpi.h ...
> Found in /gcm/home/a347549/local64/include
> Try to find libmpi or libmpich ...
> checking for main in -lmpi... yes
> Try to find liblam ...
> checking for main in -llam... yes
> checking for openpty in -lutil... yes
> checking for main in -lpthread... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -I/gcm/home/a347549/local64/lib64/R/include
> -I/gcm/home/a347549/local64/lib64/R/include -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/gcm/home/a347549/local64/include -DMPI2
> -I/usr/local/include -fpic -g -O2 -std=gnu99 -c RegQuery.c -o
> RegQuery.o
> gcc -I/gcm/home/a347549/local64/lib64/R/include
> -I/gcm/home/a347549/local64/lib64/R/include -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/gcm/home/a347549/local64/include -DMPI2
> -I/usr/local/include -fpic -g -O2 -std=gnu99 -c Rmpi.c -o Rmpi.o
> gcc -I/gcm/home/a347549/local64/lib64/R/include
> -I/gcm/home/a347549/local64/lib64/R/include -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/gcm/home/a347549/local64/include -DMPI2
> -I/usr/local/include -fpic -g -O2 -std=gnu99 -c conversion.c -o
> conversion.o
> gcc -I/gcm/home/a347549/local64/lib64/R/include
> -I/gcm/home/a347549/local64/lib64/R/include -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/gcm/home/a347549/local64/include -DMPI2
> -I/usr/local/include -fpic -g -O2 -std=gnu99 -c internal.c -o
> internal.o
> gcc -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o conversion.o
> internal.o -lmpi -llam -lutil -lpthread
> /usr/bin/ld: cannot find -lmpi
> collect2: ld returned 1 exit status
> make: *** [Rmpi.so] Error 1
> chmod: cannot access `/home/a347549/code/rlib64/Rmpi/libs/*': No such
> file or directory
> ERROR: compilation failed for package 'Rmpi'
> ** Removing '/home/a347549/code/rlib64/Rmpi'
> [lwtc5.fmr.com/A347549] /home/a347549/code
>
>
> ############################################################
> In addition, here is the output of Rmpi's config.log
> ############################################################
>
>> cat config.log
> This file contains any messages produced by compilers while
> running configure, to aid debugging if configure makes a mistake.
>
> It was created by configure, which was
> generated by GNU Autoconf 2.59. Invocation command line was
>
> $ ./configure --with-mpi=/gcm/home/a347549/local64
> --prefix=/gcm/home/a347549/local64 CC=mpicc
>
> ## --------- ##
> ## Platform. ##
> ## --------- ##
>
> hostname = lwtc5.fmr.com
> uname -m = x86_64
> uname -r = 2.6.9-34.0.1.ELsmp
> uname -s = Linux
> uname -v = #1 SMP Wed May 17 16:59:36 EDT 2006
>
> /usr/bin/uname -p = unknown
> /bin/uname -X = unknown
>
> /bin/arch = x86_64
> /usr/bin/arch -k = unknown
> /usr/convex/getsysinfo = unknown
> hostinfo = unknown
> /bin/machine = unknown
> /usr/bin/oslevel = unknown
> /bin/universe = unknown
>
> PATH: /home/a347549/local64/java/bin
> PATH: /home/a347549/local64/tibrv/bin
> PATH: /home/a347549/local64/ant/bin
> PATH: /home/a347549/local64/bin
> PATH: /usr/bin/X11
> PATH: /home/a347549/bin
> PATH: /home/a347549/local64/java/bin
> PATH: /home/a347549/local64/tibrv/bin
> PATH: /home/a347549/local64/ant/bin
> PATH: /home/a347549/local64/bin
> PATH: /usr/bin/X11
> PATH: /home/a347549/bin
> PATH: /usr/kerberos/bin
> PATH: /usr/local/bin
> PATH: /bin
> PATH: /usr/bin
> PATH: /usr/X11R6/bin
> PATH: .
> PATH: .
>
>
> ## ----------- ##
> ## Core tests. ##
> ## ----------- ##
>
> configure:2944: checking for main in -lmpi
> configure:2968: mpicc -o conftest conftest.c -lmpi >&5
> configure:2974: $? = 0
> configure:2978: test -z
> || test ! -s conftest.err
> configure:2981: $? = 0
> configure:2984: test -s conftest
> configure:2987: $? = 0
> configure:3000: result: yes
> configure:3018: checking for main in -llam
> configure:3042: mpicc -o conftest conftest.c -llam >&5
> configure:3048: $? = 0
> configure:3052: test -z
> || test ! -s conftest.err
> configure:3055: $? = 0
> configure:3058: test -s conftest
> configure:3061: $? = 0
> configure:3074: result: yes
> configure:3086: checking for openpty in -lutil
> configure:3116: mpicc -o conftest conftest.c -lutil >&5
> configure:3122: $? = 0
> configure:3126: test -z
> || test ! -s conftest.err
> configure:3129: $? = 0
> configure:3132: test -s conftest
> configure:3135: $? = 0
> configure:3148: result: yes
> configure:3154: checking for main in -lpthread
> configure:3178: mpicc -o conftest conftest.c -lpthread >&5
> configure:3184: $? = 0
> configure:3188: test -z
> || test ! -s conftest.err
> configure:3191: $? = 0
> configure:3194: test -s conftest
> configure:3197: $? = 0
> configure:3210: result: yes
> configure:3352: creating ./config.status
>
> ## ---------------------- ##
> ## Running config.status. ##
> ## ---------------------- ##
>
> This file was extended by config.status, which was
> generated by GNU Autoconf 2.59. Invocation command line was
>
> CONFIG_FILES =
> CONFIG_HEADERS =
> CONFIG_LINKS =
> CONFIG_COMMANDS =
> $ ./config.status
>
> on lwtc5.fmr.com
>
> config.status:635: creating src/Makevars
>
> ## ---------------- ##
> ## Cache variables. ##
> ## ---------------- ##
>
> ac_cv_env_CC_set=set
> ac_cv_env_CC_value=mpicc
> ac_cv_env_CFLAGS_set=
> ac_cv_env_CFLAGS_value=
> ac_cv_env_CPPFLAGS_set=
> ac_cv_env_CPPFLAGS_value=
> ac_cv_env_CPP_set=
> ac_cv_env_CPP_value=
> ac_cv_env_LDFLAGS_set=
> ac_cv_env_LDFLAGS_value=
> ac_cv_env_build_alias_set=
> ac_cv_env_build_alias_value=
> ac_cv_env_host_alias_set=
> ac_cv_env_host_alias_value=
> ac_cv_env_target_alias_set=
> ac_cv_env_target_alias_value=
> ac_cv_lib_lam_main=yes
> ac_cv_lib_mpi_main=yes
> ac_cv_lib_pthread_main=yes
> ac_cv_lib_util_openpty=yes
>
> ## ----------------- ##
> ## Output variables. ##
> ## ----------------- ##
>
> CC='mpicc'
> CFLAGS=''
> CPP=''
> CPPFLAGS=''
> DEFS='-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" '
> ECHO_C=''
> ECHO_N='-n'
> ECHO_T=''
> EGREP='grep -E'
> EXEEXT=''
> LDFLAGS=''
> LIBOBJS=''
> LIBS=''
> LTLIBOBJS=''
> OBJEXT=''
> PACKAGE_BUGREPORT=''
> PACKAGE_NAME=''
> PACKAGE_STRING=''
> PACKAGE_TARNAME=''
> PACKAGE_VERSION=''
> PATH_SEPARATOR=':'
> PKG_CPPFLAGS='-I/gcm/home/a347549/local64/include -DMPI2'
> PKG_LIBS='-lmpi -llam -lutil -lpthread'
> SHELL='/bin/sh'
> ac_ct_CC=''
> bindir='${exec_prefix}/bin'
> build_alias=''
> datadir='${prefix}/share'
> exec_prefix='${prefix}'
> host_alias=''
> includedir='${prefix}/include'
> infodir='${prefix}/info'
> libdir='${exec_prefix}/lib'
> libexecdir='${exec_prefix}/libexec'
> localstatedir='${prefix}/var'
> mandir='${prefix}/man'
> oldincludedir='/usr/include'
> prefix='/gcm/home/a347549/local64'
> program_transform_name='s,x,x,'
> sbindir='${exec_prefix}/sbin'
> sharedstatedir='${prefix}/com'
> sysconfdir='${prefix}/etc'
> target_alias=''
>
> ## ----------- ##
> ## confdefs.h. ##
> ## ----------- ##
>
> #define PACKAGE_BUGREPORT ""
> #define PACKAGE_NAME ""
> #define PACKAGE_STRING ""
> #define PACKAGE_TARNAME ""
> #define PACKAGE_VERSION ""
>
> configure: exit 0
>
>
>
> Robert McGehee
> Quantitative Analyst
> Geode Capital Management, LLC
> 53 State Street, 5th Floor | Boston, MA | 02109
> Tel: 617/392-8396 Fax:617/476-6389
> mailto:robert.mcgehee at geodecapital.com
>
>
>
> This e-mail, and any attachments hereto, are intended for us...{{dropped}}
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Colin Farrow
Computing Service, University of Glasgow, Glasgow G12 8QQ
Tel: 0141 330 4862, Email: c.farrow at compserv.gla.ac.uk
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