________________________________________
Dr. Kristian Unger
Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology
Group
Abteilung f?r Strahlenzytogenetik / Research Unit of Radiation
Cytogenetics
Tel.: +49-89-3187-3515
Mob.: +49-160-90641879
Am 15.06.11 17:25 schrieb "Hugo Mildenberger" unter
<Hugo.Mildenberger at web.de>:
Kristian,
these are the usual problems with binary distributions.
Regarding
> --with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include
and configure output
> checking for mpi.h... no
... so does "/usr/lib64/mpi/gcc/openmpi/include" really exist? At
least,
that appears to be a very unusual place to look for mpi.h (normally
to be found in "/usr/include" ).
And if you try to compile & link the attached demo program: does
the link phase succeed? Compile & link using
$ mpicc mtest.c -o mtest
Presumably you have already tried to run install.packages("Rmpi").
Kind regards
Hugo
On Wednesday 15 June 2011 16:22:07 Unger, Kristian, Dr. wrote:
Thanks Hugo.
I am pretty sure openmpi is installed:
# zypper se openmpi
Loading repository data...
Reading installed packages...
S | Name | Summary | Type
--+---------------+---------------------------------+-----------
i | openmpi | A powerful implementaion of MPI | package
| openmpi | A powerful implementaion of MPI | srcpackage
i | openmpi-devel | A powerful implementaion of MPI | package
I got the same error message with the latest version available. The
reason
why I took the somewhat older version is that I wanted to make sure
that
it is not related to any libraries used by the newest version.
Best wishes
Kristian
________________________________________
Dr. Kristian Unger
Arbeitsgruppenleiter Integrative Biologie / Head of Integrative
Biology
Group
Abteilung f?r Strahlenzytogenetik / Research Unit of Radiation
Cytogenetics
Tel.: +49-89-3187-3515
Mob.: +49-160-90641879
Am 15.06.11 16:16 schrieb "Hugo Mildenberger" unter
<Hugo.Mildenberger at web.de>:
Kristian,
I just tried that particular command here on a Gentoo system with
openmpi-1.5.3 installed, because I wondered why the Rmpi configure
script tests for "main" function in a shared library ...
But I got a completly different output from configure. While the
linker succeeds here, the package load test does not. However, on
your
system, may be the openmpi installation really is a kinda private
one
of
gcc? I heard gcc makes use of openmpi internally. So is openmpi
really
installed?
I just recognize that you are trying to use Rmpi_0.5-4.tar.gz while
current
version on CRAN is Rmpi_0.5-9.tar.gz.
Best
Hugo
R CMD INSTALL --configure-args="--with-Rmpi-include=/usr/include
--with-Rmpi-libpath=/usr/lib64/openmpi --with-Rmpi-type=OPENMPI"
Rmpi_0.5-9.tar.gz
* installing to library
?/home/hm/R/x86_64-pc-linux-gnu-library/2.13?
* installing *source* package ?Rmpi? ...
checking for openpty in -lutil... no
checking for main in -lpthread... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** libs
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2
-DOPENMPI -I/usr/local/include -fpic -O3 -pipe -march=core2 -
mtune=core2 -ggdb -c RegQuery.c -o RegQuery.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2
-DOPENMPI -I/usr/local/include -fpic -O3 -pipe -march=core2 -
mtune=core2 -ggdb -c Rmpi.c -o Rmpi.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2
-DOPENMPI -I/usr/local/include -fpic -O3 -pipe -march=core2 -
mtune=core2 -ggdb -c conversion.c -o conversion.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -
DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -I/usr/include -DMPI2
-DOPENMPI -I/usr/local/include -fpic -O3 -pipe -march=core2 -
mtune=core2 -ggdb -c internal.c -o internal.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed
-o
Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o
-L/usr/lib64/openmpi
-lmpi
-L/usr/lib64/R/lib -lR
installiert nach
/home/hm/R/x86_64-pc-linux-gnu-library/2.13/Rmpi/libs
[...]
ompi_mpi_init: orte_init failed
--> Returned "Not found" (-13) instead of "Success" (0)
On Wednesday 15 June 2011 15:19:22 Unger, Kristian, Dr. wrote:
Thank you very much Hugo. Using the command as suggested results
exactly
the same error:
# R CMD INSTALL
--configure-args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/includ
e
--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64
--with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
* installing to library ?/usr/local/lib64/R/library?
* installing *source* package ?Rmpi? ...
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 ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/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 mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
Try to find libmpi or libmpich ...
checking for main in -lmpi... no
libmpi not found. exiting...
ERROR: configuration failed for package ?Rmpi?
* removing ?/usr/local/lib64/R/library/Rmpi?
Best wishes
Kristian
________________________________________
Dr. Kristian Unger
Arbeitsgruppenleiter Integrative Biologie / Head of Integrative
Biology
Group
Abteilung f?r Strahlenzytogenetik / Research Unit of Radiation
Cytogenetics
Tel.: +49-89-3187-3515
Mob.: +49-160-90641879
Am 15.06.11 15:12 schrieb "Hugo Mildenberger" unter
<Hugo.Mildenberger at web.de>:
Hmm,
looks like there was a trailing blank after the backslash and
before
end
of line,
resulting in --with-Rmpi-libpath possibly not recognised:
> \--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \
I also doubt there is real need to escape newlines within a
string.
But
another
possible problem source is that according to R CMD INSTALL
--help,
the
parameter
is called "--configure-args", not "configure.args".
$ R CMD INSTALL
--configure-args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/inc
lu
de
--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 --
with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
Best
On Wednesday 15 June 2011 14:25:46 Unger, Kristian, Dr. wrote:
Hi there
I am trying to install Rmpi (version 0.5-4) on our 8-core SUSE
Linux
Enterprise Server 11 SP1. I read all I could find about Rmpi
installation
but still cannot get it working.
Here the last command that I used:
R CMD INSTALL
--configure.args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/in
cl
ud
e
\
--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \
--with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
Resulting in the following:
zytosrv01dmi:/home/unger/R_projects/OS # R CMD INSTALL
--configure-args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/incl
ud
e
\--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \
--with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
* installing to library ?/usr/local/lib64/R/library?
* installing *source* package ?Rmpi? ...
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 ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e...
/usr/bin/grep
checking for egrep... /usr/bin/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 mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
Try to find libmpi or libmpich ...
checking for main in -lmpi... no
libmpi not found. exiting...
ERROR: configuration failed for package ?Rmpi?
* removing ?/usr/local/lib64/R/library/Rmpi?
So obviously libmpi is not found. Doing a locate search for
"libmpi"
(straight after updatedb) shows:
zytosrv01dmi:/home/unger/R_projects/OS # locate libmpi
/opt/mpich/ch-p4/lib64/libmpich.a
/opt/mpich/ch-p4/lib64/libmpichf90.a
/opt/mpich/ch-p4/lib64/libmpichf90nc.a
/opt/mpich/ch-p4/lib64/libmpichfarg.a
/opt/mpich/ch-p4/lib64/libmpichfsup.a
/opt/mpich/ch-p4mpd/lib64/libmpich.a
/opt/mpich/ch-p4mpd/lib64/libmpichf90.a
/opt/mpich/ch-p4mpd/lib64/libmpichf90nc.a
/opt/mpich/ch-p4mpd/lib64/libmpichfarg.a
/opt/mpich/ch-p4mpd/lib64/libmpichfsup.a
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.la
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so.0.0.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.la
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so.0.0.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.la
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so.0.0.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.la
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so.0
/usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so.0.0.0
What lets me assume that the path to libmpi is
/usr/lib64/mpi/gcc/openmpi/lib64 which I already included in
the
options...
How can I get this working?
I would highly appreciate any help on this!
Best wishes
Kristian
________________________________________
Dr. Kristian Unger
Arbeitsgruppenleiter Integrative Biologie / Head of Integrative
Biology
Group
Abteilung f?r Strahlenzytogenetik / Research Unit of Radiation
Cytogenetics
Helmholtz Zentrum M?nchen
Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH)
Ingolst?dter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe
Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum
Registergericht: Amtsgericht M?nchen HRB 6466
USt-IdNr: DE 129521671
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Helmholtz Zentrum M?nchen
Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH)
Ingolst?dter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe
Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum
Registergericht: Amtsgericht M?nchen HRB 6466
USt-IdNr: DE 129521671
Helmholtz Zentrum M?nchen
Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH)
Ingolst?dter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe
Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum
Registergericht: Amtsgericht M?nchen HRB 6466
USt-IdNr: DE 129521671
Helmholtz Zentrum M?nchen
Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH)
Ingolst?dter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe
Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum
Registergericht: Amtsgericht M?nchen HRB 6466
USt-IdNr: DE 129521671