[Rd] Installing Rmpi on 64-bit Linux Athlon
McGehee, Robert
Robert.McGehee at geodecapital.com
Fri Oct 13 20:44:33 CEST 2006
Many thanks for help on this. Using Hin-Tak's (offline) suggestion, I
was able to get Rmpi to compile on R 2.4.0 by manually linking the
offending code using a different shared library (which didn't seem to be
picked up with any of the command-line arguments), and then
re-installing the usual way.
setenv LDFLAGS "-L$prefix/lib -L$prefix/lib64"
R CMD INSTALL ~/code/Rmpi --configure-args="--with-mpi=$prefix
--prefix=$prefix CC=mpicc" -l $R_LIBS
cd ~/code/Rmpi/src
gcc -shared -L$prefix/lib -o Rmpi.so RegQuery.o Rmpi.o conversion.o
internal.o -lmpi -llam -lutil -lpthread
R CMD INSTALL ~/code/Rmpi --configure-args="--with-mpi=$prefix CC=mpicc"
-l $R_LIBS
Once the package was installed, I quickly found out that Rmpi simply
does not work under R 2.4.0 (for me at least), partly because of a
change in the serialize function in R 2.4.0 (affecting bin.nchar()), and
partly for reasons I haven't been able to figure out. (Looks like a
failure in the mpi_allgather function in Rmpi.c, but am not sure). So
for now, I'm retaining R 2.3.1 for parallel processing work.
If anyone succeeds in compiling Rmpi on 2.4.0, please pass along any
necessary changes to the package maintainer.
Best,
Robert
-----Original Message-----
From: Hin-Tak Leung [mailto:hin-tak.leung at cimr.cam.ac.uk]
Sent: Tuesday, October 10, 2006 6:10 AM
To: c.farrow at compserv.gla.ac.uk
Cc: McGehee, Robert; r-devel at stat.math.ethz.ch
Subject: Re: [Rd] Installing Rmpi on 64-bit Linux Athlon
No, both of you are not doing it correctly - you are confused about
linker problem with runtime issue. LD_LIBRARY_PATH is a runtime
flag. You want to set the linker flag to influence the linker behavior:
setenv LDFLAGS="-L$prefix/lib -L$prefix/lib64"
or edit the makefile or Makevars do the equivalent with PKG_LDFLAGS
in the Rmpi package.
BTW, the syntax for using LD_LIBRARY_PATH is also wrong - to use it the
way it is intended, you need:
setenv LD_LIBRARY_PATH "$prefix/lib:$prefix/lib64"
c.farrow at compserv.gla.ac.uk wrote:
> 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
>
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