[R-sig-hpc] Unable to install Rmpi under Leopard with MPICH2 installed

[Blanchette, Marco]

Dear list,

I found one of my problem. There was a orphan header file (mpi.h) from lam-mpi left in /usr/include that was breaking ./configure script. Now, after removing the file, I can succesfully build Rmpi from source (see below). It builds in 64bit as seen by the -arch x86_64 flag passed to gcc (see below). However, when I try to load Rmpi in R I still get a library error. Again, your kind help would be appreciated. I would really like to hear whether the problem comes from the MPICH2 library not build in 64 bit.

Thanks

Marco

### Error from R following attempt to load Rmpi
> library(Rmpi)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library '/Users/mab/Library/R/2.8/library/Rmpi/libs/x86_64/Rmpi.so':
  dlopen(/Users/mab/Library/R/2.8/library/Rmpi/libs/x86_64/Rmpi.so, 6): Symbol not found: _MPI_Abort
  Referenced from: /Users/mab/Library/R/2.8/library/Rmpi/libs/x86_64/Rmpi.so
  Expected in: dynamic lookup

Error in library(Rmpi) : .First.lib failed for 'Rmpi'
Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi", .Platform$dynlib.ext,  :
  dynamic/shared library '/Users/mab/Library/R/2.8/library/Rmpi/libs/Rmpi.so' was not loaded


### Output from installing Rmpi
m007344upz:src mab$ R CMD INSTALL Rmpi
* Installing to library '/Users/mab/Library/R/2.8/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
I am here /usr/local
Try to find mpi.h ...
Found in /usr/local/include
Try to find libmpi.so or libmpich.a
Found libmpich in /usr/local/lib
checking whether MPICH2 is declared... yes
checking whether MPICH2 is declared... (cached) yes
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_DECL_MPICH2=1 -DHAVE_DECL_MPICH2=1 -I/usr/local/include -DMPI2 -DMPICH -fPIC -I/usr/local/include    -fPIC  -g -O2 -c RegQuery.c -o RegQuery.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_DECL_MPICH2=1 -DHAVE_DECL_MPICH2=1 -I/usr/local/include -DMPI2 -DMPICH -fPIC -I/usr/local/include    -fPIC  -g -O2 -c Rmpi.c -o Rmpi.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_DECL_MPICH2=1 -DHAVE_DECL_MPICH2=1 -I/usr/local/include -DMPI2 -DMPICH -fPIC -I/usr/local/include    -fPIC  -g -O2 -c conversion.c -o conversion.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_DECL_MPICH2=1 -DHAVE_DECL_MPICH2=1 -I/usr/local/include -DMPI2 -DMPICH -fPIC -I/usr/local/include    -fPIC  -g -O2 -c internal.c -o internal.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/local/lib -lmpich -lutil -lpthread -fPIC   -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld warning: in /usr/local/lib/libmpich.a, file is not of required architecture
** R
** demo
** inst
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'Rmpi'
     Formats: text html latex example
** building package indices ...
* DONE (Rmpi)


On 1/31/09 3:01 PM, "Blanchette, Marco" <MAB at stowers.org> wrote:

Dear list,

Because one of the application we use do not run under lam-mpi, I just migrated from lam-mpi 7.1.2 to MPICH2 1.0.8. I have been struggling to reinstall Rmpi with the new 64 bit R deployment [R 2.8.1 Patched (2009-01-29)] on a Mac Pro running Mac OSX 10.5.5 (leopard). Snow builds and runs correctly, however Rmpi give the following error after installation (either from the repository or from a local install):
> library(Rmpi)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library '/Users/mab/Library/R/2.8/library/Rmpi/libs/x86_64/Rmpi.so':
  dlopen(/Users/mab/Library/R/2.8/library/Rmpi/libs/x86_64/Rmpi.so, 6): Library not loaded: /usr//lib/libmpi.0.dylib
  Referenced from: /Users/mab/Library/R/2.8/library/Rmpi/libs/x86_64/Rmpi.so
  Reason: image not found
Error in library(Rmpi) : .First.lib failed for 'Rmpi'
Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi", .Platform$dynlib.ext,  :
  dynamic/shared library '/Users/mab/Library/R/2.8/library/Rmpi/libs/Rmpi.so' was not loaded

MPICH2 (the mpirun, mpiexec and mpicc) is install under /usr/local/bin and the libaries are under /usr/local/lib. Is the standard R CMD INSTALL Rmpi is suppose to guess the correct configuration? Do I need to have MPICH2 compile in 64bit? I use to be able to run Rmpi with lam-mpi no problem under the 64 bit R 2.8.0.

Your help will be greatly appreciated.

Thanks

Marco
--
Marco Blanchette, Ph.D.
Assistant Investigator
Stowers Institute for Medical Research
1000 East 50th St.

Kansas City, MO 64110

Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018

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--
Marco Blanchette, Ph.D.
Assistant Investigator
Stowers Institute for Medical Research
1000 East 50th St.

Kansas City, MO 64110

Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018