Re: [R] installing Rmpi on centos 6 with mpich
On Nov 21, 2012, at 11:36 AM, Ricardo Román Brenes wrote:
> i've followed that guide already to no success
That installation guide shows the installation taking place from the CLI
outside of R, using R CMD INSTALL ..., not using install.packages() from within
an R session, which is what you are showing below.
If you have tried that and failed, then I would recommend contacting the
package maintainer for assistance or perhaps posting to R-SIG-HPC:
https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
Marc
>
> On Wed, Nov 21, 2012 at 11:34 AM, Marc Schwartz wrote:
>
> On Nov 21, 2012, at 10:40 AM, Ricardo Román Brenes wrote:
>
> > Hello everyone
> >
> > im trying to install Rmpi library on centos 6. I have already installed
> > mpich2 1.4
> >
> > [root@localhost ~]# R --version
> >> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> >> Copyright (C) 2012 The R Foundation for Statistical Computing
> >> ISBN 3-900051-07-0
> >> Platform: x86_64-redhat-linux-gnu (64-bit)
> >
> >
> >
> > [root@localhost ~]# mpich2version
> >> MPICH2 Version: 1.4.1p1
> >> MPICH2 Release date: Thu Sep 1 13:53:02 CDT 2011
> >> MPICH2 Device: ch3:nemesis
> >> MPICH2 configure:
> >> MPICH2 CC: gcc-O2
> >> MPICH2 CXX: c++ -O2
> >> MPICH2 F77: gfortran -O2
> >> MPICH2 FC: f95 -O2
> >
> >
> >
> >
> > when i issue the install order i get this output:
> >
> >
> >> install.packages("Rmpi")
> >> Installing package(s) into /usr/lib64/R/library
> >> (as lib is unspecified)
> >> trying URL 'http://cran.rstudio.com/src/contrib/Rmpi_0.6-1.tar.gz'
> >> Content type 'application/x-gzip' length 92977 bytes (90 Kb)
> >> opened URL
> >> ==
> >> downloaded 90 Kb
> >> * installing *source* package Rmpi ...
> >> ** package Rmpi successfully unpacked and MD5 sums checked
> >> checking for gcc... gcc -m64 -std=gnu99
> >> checking whether the C compiler works... yes
> >> checking for C compiler default output file name... a.out
> >> checking for suffix of executables...
> >> checking whether we are cross compiling... no
> >> checking for suffix of object files... o
> >> checking whether we are using the GNU C compiler... yes
> >> checking whether gcc -m64 -std=gnu99 accepts -g... yes
> >> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
> >> I am here /usr/local and it is OpenMPI
> >> Trying to find mpi.h ...
> >> Found in /usr/local/include
> >> Trying to find libmpi.so or libmpich.a ...
> >> checking for main in -lmpi... no
> >> libmpi not found. exiting...
> >> ERROR: configuration failed for package Rmpi
> >> * removing /usr/lib64/R/library/Rmpi
> >> The downloaded source packages are in
> >> /tmp/RtmpBvTTqc/downloaded_packages
> >> Updating HTML index of packages in '.Library'
> >> Making packages.html ... done
> >> Warning message:
> >> In install.packages("Rmpi") :
> >> installation of package Rmpi had non-zero exit status
> >
> >
> >
> > I have tried with different configure.args but the result is the same, i
> > cant seem to install it...
> >
> > Is there someone who has been through the same problem? or that knows a
> > guide i can follow or something?
> >
> > Thanks in advance
> >
> > Ricardo
>
>
> There is a page here:
>
> http://www.stats.uwo.ca/faculty/yu/Rmpi/
>
> which is linked from the CRAN page for the package. On the above page, there
> is an Installation for Linux link, which is likely to be helpful.
>
> Regards,
>
> Marc Schwartz
>
>
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] installing Rmpi on centos 6 with mpich
i've followed that guide already to no success
On Wed, Nov 21, 2012 at 11:34 AM, Marc Schwartz wrote:
>
> On Nov 21, 2012, at 10:40 AM, Ricardo Román Brenes
> wrote:
>
> > Hello everyone
> >
> > im trying to install Rmpi library on centos 6. I have already installed
> > mpich2 1.4
> >
> > [root@localhost ~]# R --version
> >> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> >> Copyright (C) 2012 The R Foundation for Statistical Computing
> >> ISBN 3-900051-07-0
> >> Platform: x86_64-redhat-linux-gnu (64-bit)
> >
> >
> >
> > [root@localhost ~]# mpich2version
> >> MPICH2 Version: 1.4.1p1
> >> MPICH2 Release date: Thu Sep 1 13:53:02 CDT 2011
> >> MPICH2 Device: ch3:nemesis
> >> MPICH2 configure:
> >> MPICH2 CC: gcc-O2
> >> MPICH2 CXX: c++ -O2
> >> MPICH2 F77: gfortran -O2
> >> MPICH2 FC: f95 -O2
> >
> >
> >
> >
> > when i issue the install order i get this output:
> >
> >
> >> install.packages("Rmpi")
> >> Installing package(s) into /usr/lib64/R/library
> >> (as lib is unspecified)
> >> trying URL 'http://cran.rstudio.com/src/contrib/Rmpi_0.6-1.tar.gz'
> >> Content type 'application/x-gzip' length 92977 bytes (90 Kb)
> >> opened URL
> >> ==
> >> downloaded 90 Kb
> >> * installing *source* package Rmpi ...
> >> ** package Rmpi successfully unpacked and MD5 sums checked
> >> checking for gcc... gcc -m64 -std=gnu99
> >> checking whether the C compiler works... yes
> >> checking for C compiler default output file name... a.out
> >> checking for suffix of executables...
> >> checking whether we are cross compiling... no
> >> checking for suffix of object files... o
> >> checking whether we are using the GNU C compiler... yes
> >> checking whether gcc -m64 -std=gnu99 accepts -g... yes
> >> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
> >> I am here /usr/local and it is OpenMPI
> >> Trying to find mpi.h ...
> >> Found in /usr/local/include
> >> Trying to find libmpi.so or libmpich.a ...
> >> checking for main in -lmpi... no
> >> libmpi not found. exiting...
> >> ERROR: configuration failed for package Rmpi
> >> * removing /usr/lib64/R/library/Rmpi
> >> The downloaded source packages are in
> >> /tmp/RtmpBvTTqc/downloaded_packages
> >> Updating HTML index of packages in '.Library'
> >> Making packages.html ... done
> >> Warning message:
> >> In install.packages("Rmpi") :
> >> installation of package Rmpi had non-zero exit status
> >
> >
> >
> > I have tried with different configure.args but the result is the same, i
> > cant seem to install it...
> >
> > Is there someone who has been through the same problem? or that knows a
> > guide i can follow or something?
> >
> > Thanks in advance
> >
> > Ricardo
>
>
> There is a page here:
>
> http://www.stats.uwo.ca/faculty/yu/Rmpi/
>
> which is linked from the CRAN page for the package. On the above page,
> there is an Installation for Linux link, which is likely to be helpful.
>
> Regards,
>
> Marc Schwartz
>
>
[[alternative HTML version deleted]]
__
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.
Re: [R] installing Rmpi on centos 6 with mpich
On Nov 21, 2012, at 10:40 AM, Ricardo Román Brenes wrote:
> Hello everyone
>
> im trying to install Rmpi library on centos 6. I have already installed
> mpich2 1.4
>
> [root@localhost ~]# R --version
>> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
>> Copyright (C) 2012 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>
>
>
> [root@localhost ~]# mpich2version
>> MPICH2 Version: 1.4.1p1
>> MPICH2 Release date: Thu Sep 1 13:53:02 CDT 2011
>> MPICH2 Device: ch3:nemesis
>> MPICH2 configure:
>> MPICH2 CC: gcc-O2
>> MPICH2 CXX: c++ -O2
>> MPICH2 F77: gfortran -O2
>> MPICH2 FC: f95 -O2
>
>
>
>
> when i issue the install order i get this output:
>
>
>> install.packages("Rmpi")
>> Installing package(s) into ‘/usr/lib64/R/library’
>> (as ‘lib’ is unspecified)
>> trying URL 'http://cran.rstudio.com/src/contrib/Rmpi_0.6-1.tar.gz'
>> Content type 'application/x-gzip' length 92977 bytes (90 Kb)
>> opened URL
>> ==
>> downloaded 90 Kb
>> * installing *source* package ‘Rmpi’ ...
>> ** package ‘Rmpi’ successfully unpacked and MD5 sums checked
>> checking for gcc... gcc -m64 -std=gnu99
>> checking whether the C compiler works... yes
>> checking for C compiler default output file name... a.out
>> checking for suffix of executables...
>> checking whether we are cross compiling... no
>> checking for suffix of object files... o
>> checking whether we are using the GNU C compiler... yes
>> checking whether gcc -m64 -std=gnu99 accepts -g... yes
>> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
>> I am here /usr/local and it is OpenMPI
>> Trying to find mpi.h ...
>> Found in /usr/local/include
>> Trying to find libmpi.so or libmpich.a ...
>> checking for main in -lmpi... no
>> libmpi not found. exiting...
>> ERROR: configuration failed for package ‘Rmpi’
>> * removing ‘/usr/lib64/R/library/Rmpi’
>> The downloaded source packages are in
>> ‘/tmp/RtmpBvTTqc/downloaded_packages’
>> Updating HTML index of packages in '.Library'
>> Making packages.html ... done
>> Warning message:
>> In install.packages("Rmpi") :
>> installation of package ‘Rmpi’ had non-zero exit status
>
>
>
> I have tried with different configure.args but the result is the same, i
> cant seem to install it...
>
> Is there someone who has been through the same problem? or that knows a
> guide i can follow or something?
>
> Thanks in advance
>
> Ricardo
There is a page here:
http://www.stats.uwo.ca/faculty/yu/Rmpi/
which is linked from the CRAN page for the package. On the above page, there is
an Installation for Linux link, which is likely to be helpful.
Regards,
Marc Schwartz
__
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.
[R] installing Rmpi on centos 6 with mpich
Hello everyone
im trying to install Rmpi library on centos 6. I have already installed
mpich2 1.4
[root@localhost ~]# R --version
> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-redhat-linux-gnu (64-bit)
[root@localhost ~]# mpich2version
> MPICH2 Version: 1.4.1p1
> MPICH2 Release date: Thu Sep 1 13:53:02 CDT 2011
> MPICH2 Device: ch3:nemesis
> MPICH2 configure:
> MPICH2 CC: gcc-O2
> MPICH2 CXX: c++ -O2
> MPICH2 F77: gfortran -O2
> MPICH2 FC: f95 -O2
when i issue the install order i get this output:
> install.packages("Rmpi")
> Installing package(s) into /usr/lib64/R/library
> (as lib is unspecified)
> trying URL 'http://cran.rstudio.com/src/contrib/Rmpi_0.6-1.tar.gz'
> Content type 'application/x-gzip' length 92977 bytes (90 Kb)
> opened URL
> ==
> downloaded 90 Kb
> * installing *source* package Rmpi ...
> ** package Rmpi successfully unpacked and MD5 sums checked
> checking for gcc... gcc -m64 -std=gnu99
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -m64 -std=gnu99 accepts -g... yes
> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
> I am here /usr/local and it is OpenMPI
> Trying to find mpi.h ...
> Found in /usr/local/include
> Trying to find libmpi.so or libmpich.a ...
> checking for main in -lmpi... no
> libmpi not found. exiting...
> ERROR: configuration failed for package Rmpi
> * removing /usr/lib64/R/library/Rmpi
> The downloaded source packages are in
> /tmp/RtmpBvTTqc/downloaded_packages
> Updating HTML index of packages in '.Library'
> Making packages.html ... done
> Warning message:
> In install.packages("Rmpi") :
> installation of package Rmpi had non-zero exit status
I have tried with different configure.args but the result is the same, i
cant seem to install it...
Is there someone who has been through the same problem? or that knows a
guide i can follow or something?
Thanks in advance
Ricardo
[[alternative HTML version deleted]]
__
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.
[R] installing Rmpi on centos 6 with mpich
Hello everyone
im trying to install Rmpi library on centos 6. I have already installed
mpich2 1.4
[root@localhost ~]# R --version
> R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-redhat-linux-gnu (64-bit)
[root@localhost ~]# mpich2version
> MPICH2 Version: 1.4.1p1
> MPICH2 Release date: Thu Sep 1 13:53:02 CDT 2011
> MPICH2 Device: ch3:nemesis
> MPICH2 configure:
> MPICH2 CC: gcc-O2
> MPICH2 CXX: c++ -O2
> MPICH2 F77: gfortran -O2
> MPICH2 FC: f95 -O2
when i issue the install order i get this output:
> install.packages("Rmpi")
> Installing package(s) into /usr/lib64/R/library
> (as lib is unspecified)
> trying URL 'http://cran.rstudio.com/src/contrib/Rmpi_0.6-1.tar.gz'
> Content type 'application/x-gzip' length 92977 bytes (90 Kb)
> opened URL
> ==
> downloaded 90 Kb
> * installing *source* package Rmpi ...
> ** package Rmpi successfully unpacked and MD5 sums checked
> checking for gcc... gcc -m64 -std=gnu99
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -m64 -std=gnu99 accepts -g... yes
> checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
> I am here /usr/local and it is OpenMPI
> Trying to find mpi.h ...
> Found in /usr/local/include
> Trying to find libmpi.so or libmpich.a ...
> checking for main in -lmpi... no
> libmpi not found. exiting...
> ERROR: configuration failed for package Rmpi
> * removing /usr/lib64/R/library/Rmpi
> The downloaded source packages are in
> /tmp/RtmpBvTTqc/downloaded_packages
> Updating HTML index of packages in '.Library'
> Making packages.html ... done
> Warning message:
> In install.packages("Rmpi") :
> installation of package Rmpi had non-zero exit status
I have tried with different configure.args but the result is the same, i
cant seem to install it...
Is there someone who has been through the same problem? or that knows a
guide i can follow or something?
Thanks in advance
Ricardo
[[alternative HTML version deleted]]
__
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.
Re: [R] Installing Rmpi on hpc
On Mon, 14 Mar 2011, Brian Smith wrote:
Hi,
I was trying to install the package Rmpi on a hpc cluster running SGE. The
Which is what? (If Sun Grid Engine, not relevant and it is your
unstated OS that we needed to know. Not just 'Linux', but the
precise distro.))
Please do note the posting guide: your R is several versions old, for
example, and this was an R-devel question (most questions about
installing wrapper packages will be, since they are almost nothing to
do with the R language).
The symptoms you post are those of finding a 32-bit libmpi on a 64-bit
install. Please consult the documentation for Rmpi and set the RMPI*
environment variables appropriately for your installed 64-bit libmpi
(regratably Rmpi does not use the recommended methods and so often
needs to be overridden). Also, most modern OSes use OpenMPI and not
lam, so see if you can use the former.
One guess is that it needs to be told to look in /usr/lib64/lam.
OTOH, for x86_64 Fedora 14 I am using
setenv RMPI_INCLUDE /usr/include/openmpi-x86_64
setenv RMPI_LIB_PATH /usr/lib64/openmpi/lib
setenv RMPI_TYPE OPENMPI
command, and the sessionInfo() is as follows:
===
install.packages("Rmpi",dependencies=TRUE)
also installing the dependency ?rsprng?
trying URL '
http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/rsprng_1.0.tar.gz'
Content type 'application/x-gzip' length 35916 bytes (35 Kb)
opened URL
==
downloaded 35 Kb
trying URL '
http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/Rmpi_0.5-9.tar.gz'
Content type 'application/x-gzip' length 87953 bytes (85 Kb)
opened URL
==
downloaded 85 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 ?/home/bs/R_home/R-2.11.1/library/rsprng?
Well, first you need to install sprng-2.0b
* installing *source* package ?Rmpi? ...
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
I am here /usr/lib/lam and it is LAM
Trying to find mpi.h ...
Found in /usr/lib/lam/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib/lam/lib
Try to find liblam.so ...
Found liblam in /usr/lib/lam/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include-fpic -g -O2 -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include-fpic -g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include-fpic -g -O2 -c conversion.c -o conversion.o
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include-fpic -g -O2 -c internal.c -o internal.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o
conversion.o internal.o -L/usr/lib/lam/lib -lmpi -llam -lutil -lpthread
/usr/bin/ld: skipping incompatible /us
[R] Installing Rmpi on hpc
Hi,
I was trying to install the package Rmpi on a hpc cluster running SGE. The
command, and the sessionInfo() is as follows:
===
> install.packages("Rmpi",dependencies=TRUE)
also installing the dependency rsprng
trying URL '
http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/rsprng_1.0.tar.gz'
Content type 'application/x-gzip' length 35916 bytes (35 Kb)
opened URL
==
downloaded 35 Kb
trying URL '
http://www.ibiblio.org/pub/languages/R/CRAN/src/contrib/Rmpi_0.5-9.tar.gz'
Content type 'application/x-gzip' length 87953 bytes (85 Kb)
opened URL
==
downloaded 85 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 /home/bs/R_home/R-2.11.1/library/rsprng
* installing *source* package Rmpi ...
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
I am here /usr/lib/lam and it is LAM
Trying to find mpi.h ...
Found in /usr/lib/lam/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib/lam/lib
Try to find liblam.so ...
Found liblam in /usr/lib/lam/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include-fpic -g -O2 -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include-fpic -g -O2 -c Rmpi.c -o Rmpi.o
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include-fpic -g -O2 -c conversion.c -o conversion.o
gcc -std=gnu99 -I/home/bs/R_home/R-2.11.1/include -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -I/usr/lib/lam/include -DMPI2 -DLAM
-I/usr/local/include-fpic -g -O2 -c internal.c -o internal.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o Rmpi.o
conversion.o internal.o -L/usr/lib/lam/lib -lmpi -llam -lutil -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.so when searching
for -lmpi
/usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.a when searching
for -lmpi
/usr/bin/ld: cannot find -lmpi
collect2: ld returned 1 exit status
make: *** [Rmpi.so] Error 1
ERROR: compilation failed for package Rmpi
* removing /home/bs/R_home/R-2.11.1/library/Rmpi
The downloaded packages are in
/tmp/RtmpShmM5e/downloaded_packages
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("Rmpi", dependencies = TRUE) :
installation of package 'rsprng' had non-zero exit status
2: In install.packages("Rmpi", dependencies = TRUE) :
installation of package 'Rmpi' had non-zero exit status
>
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base pa
Re: [R] Installing Rmpi on Fedora Linux [was: Re: help installing Rmpi]
For future reference, I put up the instructions here:
http://www.cybaea.net/Blogs/Data/R-tips-Installing-Rmpi-on-Fedora-Linux.html
Allan
On 12/06/09 10:59, Allan Engelhardt wrote:
On 11/06/09 22:46, ALAN SMITH wrote:
Hello R users and developers,
I would like to install Rmpi so that I may take advantage of all of
the CPUs in my computer
Package "multicore" *may* be easier for this.
, but I cannot get it to install [...]
The configuration file for Rmpi is, unfortunately, completely
brain-damaged with hard-coded assumptions about which subdirectories
should contain header and library files and no way of overriding it.
This is what I did:
[...]
#I have tried two different ways to install openMPI in fedora in the
linux shell
In any recent version of Fedora don't do any of what you suggest;
instead do
# yum install openmpi openmpi-devel openmpi-libs
Then *download* the Rmpi package and unpack it using something like
$ tar xvf Rmpi_0.5-7.tar.gz
(version number may be different).
Then go into the Rmpi directory and change configure.ac. If you are
on a x86_64 platform, the following hack should work (for 32 bit try
s/64/32/g):
+++[cut here]+++
Process this file with autoconf to produce a configure script.
AC_INIT(DESCRIPTION)
AC_PROG_CC
MPI_LIBS=`pkg-config --libs openmpi-1.3.1-gcc-64`
MPI_INCLUDE=`pkg-config --cflags openmpi-1.3.1-gcc-64`
MPITYPE="OPENMPI"
MPI_DEPS="-DMPI2"
AC_CHECK_LIB(util, openpty, [ MPI_LIBS="$MPI_LIBS -lutil" ])
AC_CHECK_LIB(pthread, main, [ MPI_LIBS="$MPI_LIBS -lpthread" ])
PKG_LIBS="${MPI_LIBS} -fPIC"
PKG_CPPFLAGS="${MPI_INCLUDE} ${MPI_DEPS} -D${MPITYPE} -fPIC"
AC_SUBST(PKG_LIBS)
AC_SUBST(PKG_CPPFLAGS)
AC_SUBST(DEFS)
AC_OUTPUT(src/Makevars)
---[cut here]---
The number 1.3.1 may change in future updates to Fedora, I guess
Now (still in Rmpi directory) do
$ autoconf
$ cd ..
$ tar zcvf Rmpi-0.5-7-F1.tar.gz Rmpi
$ R CMD INSTALL Rmpi-0.5-7-F1.tar.gz
Which more-or-less works in R:
> library("Rmpi")
> mpi.spawn.Rslaves(nslaves=2)
2 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 3 is running on: server
slave1 (rank 1, comm 1) of size 3 is running on: server
slave2 (rank 2, comm 1) of size 3 is running on: server
> x=c(10,20)
> mpi.apply(x,runif)
[[1]]
[1] 0.25142616 0.93505554 0.03162852 0.71783194 0.35916139 0.85082154
[7] 0.35404191 0.14221315 0.60063773 0.71805190
[[2]]
[1] 0.84157864 0.63481773 0.38217188 0.67839089 0.27827728 0.35429266
[7] 0.04898744 0.96601584 0.25687905 0.77381186 0.69011927 0.37391028
[13] 0.19017369 0.51196594 0.51970563 0.15791524 0.21358237 0.69642478
[19] 0.12690207 0.44177656
>
Hope this helps!
Allan.
__
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.
[R] Installing Rmpi on Fedora Linux [was: Re: help installing Rmpi]
On 11/06/09 22:46, ALAN SMITH wrote:
Hello R users and developers,
I would like to install Rmpi so that I may take advantage of all of
the CPUs in my computer
Package "multicore" *may* be easier for this.
, but I cannot get it to install [...]
The configuration file for Rmpi is, unfortunately, completely
brain-damaged with hard-coded assumptions about which subdirectories
should contain header and library files and no way of overriding it.
This is what I did:
[...]
#I have tried two different ways to install openMPI in fedora in the linux shell
In any recent version of Fedora don't do any of what you suggest; instead do
# yum install openmpi openmpi-devel openmpi-libs
Then *download* the Rmpi package and unpack it using something like
$ tar xvf Rmpi_0.5-7.tar.gz
(version number may be different).
Then go into the Rmpi directory and change configure.ac. If you are on
a x86_64 platform, the following hack should work (for 32 bit try
s/64/32/g):
+++[cut here]+++
Process this file with autoconf to produce a configure script.
AC_INIT(DESCRIPTION)
AC_PROG_CC
MPI_LIBS=`pkg-config --libs openmpi-1.3.1-gcc-64`
MPI_INCLUDE=`pkg-config --cflags openmpi-1.3.1-gcc-64`
MPITYPE="OPENMPI"
MPI_DEPS="-DMPI2"
AC_CHECK_LIB(util, openpty, [ MPI_LIBS="$MPI_LIBS -lutil" ])
AC_CHECK_LIB(pthread, main, [ MPI_LIBS="$MPI_LIBS -lpthread" ])
PKG_LIBS="${MPI_LIBS} -fPIC"
PKG_CPPFLAGS="${MPI_INCLUDE} ${MPI_DEPS} -D${MPITYPE} -fPIC"
AC_SUBST(PKG_LIBS)
AC_SUBST(PKG_CPPFLAGS)
AC_SUBST(DEFS)
AC_OUTPUT(src/Makevars)
---[cut here]---
The number 1.3.1 may change in future updates to Fedora, I guess
Now (still in Rmpi directory) do
$ autoconf
$ cd ..
$ tar zcvf Rmpi-0.5-7-F1.tar.gz Rmpi
$ R CMD INSTALL Rmpi-0.5-7-F1.tar.gz
Which more-or-less works in R:
> library("Rmpi")
> mpi.spawn.Rslaves(nslaves=2)
2 slaves are spawned successfully. 0 failed.
master (rank 0, comm 1) of size 3 is running on: server
slave1 (rank 1, comm 1) of size 3 is running on: server
slave2 (rank 2, comm 1) of size 3 is running on: server
> x=c(10,20)
> mpi.apply(x,runif)
[[1]]
[1] 0.25142616 0.93505554 0.03162852 0.71783194 0.35916139 0.85082154
[7] 0.35404191 0.14221315 0.60063773 0.71805190
[[2]]
[1] 0.84157864 0.63481773 0.38217188 0.67839089 0.27827728 0.35429266
[7] 0.04898744 0.96601584 0.25687905 0.77381186 0.69011927 0.37391028
[13] 0.19017369 0.51196594 0.51970563 0.15791524 0.21358237 0.69642478
[19] 0.12690207 0.44177656
>
Hope this helps!
Allan.
__
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.
[R] Installing Rmpi on Centos 5.2
I am trying to install the R package "Rmpi" which needs libmpi. I've installed openmpi and lam in Centos 5.2: [r...@rab45-1 /]# rpm -qv openmpi openmpi-1.2.5-5.el5 openmpi-1.2.5-5.el5 [r...@rab45-1 /]# rpm -qv lam lam-7.1.2-14.el5 lam-7.1.2-14.el5 I'm using this to install Rmpi: R CMD INSTALL /home/rick/Rmpi_0.5-7.tar.gz --with-mpi=/usr/lib64/lam/include But I get the following error message: /usr/bin/ld: skipping incompatible /usr/lib/lam/lib/libmpi.so when searching for -lmpi I'm not sure what else to install/uninstall to fix this. Rick B. __ 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.
Re: [R] installing Rmpi
On Fri, 5 Oct 2007, Erin Hodgess wrote: > Hi R people: > > I installed R-2.6.0 on a Red Hat Linux system and am now trying > to install the Rmpi package. > > The installation cannot seem to find the mpi.h file, even though it exists. > > Is there a variable that I should be exporting into the process, please? It's tricky, and we may need to know a bit more about your OS. I presume you have the latest Rmpi 0.5-4: if not get it from the CRAN master (it may still be propagating). On the RH systems I have seen the mpi.h file is in /usr/include/lam. So you need to ensure you have that installed, and it is in the lam-devel RPM (which has other dependencies, including lam and lam-libs). If that is installed and this is still failing you need to look at the config.log to see why -- that's not R-help territory and I think you need to find some local expertise to help you: if that is not possible, use R-devel. The problems I usually find are with the next step, finding the libraries. I've seen systems where /usr/lib64/lam was not in the ld.so cache, and others where you needed to link against -lutil as well as -lmpi -llam. Only someone with essentially the same OS on the same cputype will be able to help you find things like this. (For some reaons Rmpi tests for static libraries on 32-bit systems and dynamic ones on 64-bit systems.) Incidentally, the lam RPMs have things in quite different places from a vanilla source install of lam, so you do need to tell us exactly when your MPI libraries came from. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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.
[R] installing Rmpi
Hi R people: I installed R-2.6.0 on a Red Hat Linux system and am now trying to install the Rmpi package. The installation cannot seem to find the mpi.h file, even though it exists. Is there a variable that I should be exporting into the process, please? Thanks in advance, Sincerely, Erin Hodgess mailto: [EMAIL PROTECTED] __ 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.
