Dear mac folks, I have started porting a large legacy toolset maintained in windows and heavily mpi laden so it can be used across platforms in R... so I am building a package out of it. On this note, I am noticing that almost all of the mpi dependent packages do not compile on the CRAN repositories.... with the basic issue that it appears it can not find mpi installed: configure: error: "Cannot find mpi.h header file" I do not see any chatter about mpi issues in the lists since the inception of mavericks.. and possibly this question should go to Simon.. but in case I missed a discussion, or if anyone has any suggestions on how to proceed, or what might be missing from the Rmpi, npRmpi, etc. packages for compilation on Mavericks, it would be greatly appreciated if you could let me know.. and maybe I can help fix the other packages as well. Thanks for any help or pointers to guide me! dan
mpi.h errors on Mavericks packages
5 messages · Daniel Fuka, Martin Morgan, Simon Urbanek +1 more
On 10/03/2014 04:17 PM, Daniel Fuka wrote:
Dear mac folks, I have started porting a large legacy toolset maintained in windows and heavily mpi laden so it can be used across platforms in R... so I am building a package out of it. On this note, I am noticing that almost all of the mpi dependent packages do not compile on the CRAN repositories.... with the basic issue that it appears it can not find mpi installed: configure: error: "Cannot find mpi.h header file"
Hi Dan -- not a mac folk, or particularly expert on the subject, but have you
looked at section 1.2.1.1 of RShowDoc("R-exts")? The basic idea is
a) check for compiler support via a src/Makevars file that might be like
PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
b) conditionally include mpi header files and execute mpi code with
#ifdef SUPPORT_OPENMP
#include <mpi.h>
#endif
and similarly for #pragma's and other mpi-isms littered through your code?
Likely this gets quite tedious for projects making extensive use of openMP.
Martin
I do not see any chatter about mpi issues in the lists since the inception of mavericks.. and possibly this question should go to Simon.. but in case I missed a discussion, or if anyone has any suggestions on how to proceed, or what might be missing from the Rmpi, npRmpi, etc. packages for compilation on Mavericks, it would be greatly appreciated if you could let me know.. and maybe I can help fix the other packages as well. Thanks for any help or pointers to guide me! dan
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Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
On 10/03/2014 04:58 PM, Martin Morgan wrote:
On 10/03/2014 04:17 PM, Daniel Fuka wrote:
Dear mac folks, I have started porting a large legacy toolset maintained in windows and heavily mpi laden so it can be used across platforms in R... so I am building a package out of it. On this note, I am noticing that almost all of the mpi dependent packages do not compile on the CRAN repositories.... with the basic issue that it appears it can not find mpi installed: configure: error: "Cannot find mpi.h header file"
sorry for the noise! you're after mpi and not openMP. Arrgh Martin
Hi Dan -- not a mac folk, or particularly expert on the subject, but have you
looked at section 1.2.1.1 of RShowDoc("R-exts")? The basic idea is
a) check for compiler support via a src/Makevars file that might be like
PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
b) conditionally include mpi header files and execute mpi code with
#ifdef SUPPORT_OPENMP
#include <mpi.h>
#endif
and similarly for #pragma's and other mpi-isms littered through your code?
Likely this gets quite tedious for projects making extensive use of openMP.
Martin
I do not see any chatter about mpi issues in the lists since the inception of mavericks.. and possibly this question should go to Simon.. but in case I missed a discussion, or if anyone has any suggestions on how to proceed, or what might be missing from the Rmpi, npRmpi, etc. packages for compilation on Mavericks, it would be greatly appreciated if you could let me know.. and maybe I can help fix the other packages as well. Thanks for any help or pointers to guide me! dan
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
Daniel,
On Oct 3, 2014, at 7:17 PM, Daniel Fuka <drf28 at cornell.edu> wrote:
Dear mac folks, I have started porting a large legacy toolset maintained in windows and heavily mpi laden so it can be used across platforms in R... so I am building a package out of it. On this note, I am noticing that almost all of the mpi dependent packages do not compile on the CRAN repositories.... with the basic issue that it appears it can not find mpi installed: configure: error: "Cannot find mpi.h header file" I do not see any chatter about mpi issues in the lists since the inception of mavericks.. and possibly this question should go to Simon.. but in case I missed a discussion, or if anyone has any suggestions on how to proceed, or what might be missing from the Rmpi, npRmpi, etc. packages for compilation on Mavericks, it would be greatly appreciated if you could let me know.. and maybe I can help fix the other packages as well.
Apple has removed MPI from recent OS X versions so it is not available there. So currently, you have to install whatever MPI implementation you prefer from sources since neither the libraries nor the toolchain are available. What Apple used to ship was OpenMPI which still exists, but to my best knowledge there is no official, maintained binary for OS X so on Mavericks we have nothing to build CRAN binaries against, so you have to install everything from sources. Cheers, Simon
FYI https://groups.google.com/forum/#!topic/rbigdataprogramming/k1uZWmzd1L8 or FAQ, Section 8.3, question 10 at https://github.com/snoweye/pbdMPI/blob/master/inst/doc/pbdMPI-guide.pdf?raw=true may be useful. On Fri, Oct 3, 2014 at 9:10 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
Daniel, On Oct 3, 2014, at 7:17 PM, Daniel Fuka <drf28 at cornell.edu> wrote:
Dear mac folks, I have started porting a large legacy toolset maintained in windows and heavily mpi laden so it can be used across platforms in R... so I am building a package out of it. On this note, I am noticing that almost all of the mpi dependent packages do not compile on the CRAN repositories.... with the basic issue that it appears it can not find mpi installed: configure: error: "Cannot find mpi.h header file" I do not see any chatter about mpi issues in the lists since the inception of mavericks.. and possibly this question should go to Simon.. but in case I missed a discussion, or if anyone has any suggestions on how to proceed, or what might be missing from the Rmpi, npRmpi, etc. packages for compilation on Mavericks, it would be greatly appreciated if you could let me know.. and maybe I can help fix the other packages as well.
Apple has removed MPI from recent OS X versions so it is not available there. So currently, you have to install whatever MPI implementation you prefer from sources since neither the libraries nor the toolchain are available. What Apple used to ship was OpenMPI which still exists, but to my best knowledge there is no official, maintained binary for OS X so on Mavericks we have nothing to build CRAN binaries against, so you have to install everything from sources. Cheers, Simon
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