[R-sig-hpc] wrestling to compile sprng as RPM for a Rocks Cluster. Long rambling whining request for help :)

[Hao Yu]

Paul,

rsprng is suggested (not required) in Rmpi. I am using rlecuyer. rlecuyer
can be simply installed in R as
install.packages("rlecuyer")

To use rlecuyer in Rmpi, run mpi.setup.rngstream(). Otherwise use
mpi.setup.sprng() for SRRNG.

Hao


Paul Johnson wrote:
> Anybody have sprng (scalable parallel random number generator) RPM and
> SRPM files for RedHat/Centos with MPI?
>
> There are various posts about troubles compiling it, but I don't find
> details on the fixes.
>
> Many R packages for HPC require Rmpi, Rmpi requires rsprng, which in
> turn requires the C++/Fortran library SPRNG (capitalized? or not?).
>
> SPRNG is here, http://sprng.fsu.edu/. AFAICT, it is now in version 4.
> The source (dated 6/7/2007) is available here:
>
> http://sprng.fsu.edu/Version4.0/sprng4.tar.gz
>
> I've been trying to compile that on Centos so I can build an RPM for a
> Cluster.
>
> There are a number of wrinkles with this compile. It has a standard
> GNU INSTALL file, which is encouraging.  But
>
> 1. The c++ code in the sprng4 package is not consistent with the
> guidelines of the current gcc c++ compiler.  There are quite a few
> little changes to make, like changing
>
> #include <iostream.h>
>
> to
>
> #include <iostream>
>
> I am attaching a patch file which includes the changes  that are, as
> far as I can tell, MINIMALLY necessary to get sprng4 to compile,
> except for the EXAMPLES directory.
>
> In the sprng4 source directory, this patch requires -p2, as in
>
> patch -p2 < sprng-4.patch
>
> 2. The build in the EXAMPLES directory  has some big problems. Even
> after applying that patch, the "make" fails with errors in [1].
>
> The make will complete, however, if we delete the EXAMPLES directory
> from the Makefile in the top level. That is, change:
>
> SUBDIRS = SRC lib check TESTS include EXAMPLES .
>
> to
>
> SUBDIRS = SRC lib check TESTS include .
>
> After applying the sprng-4.patch (attached), running the configure,
> and then making that one change, then the make will finish.
>
> 3. The "make install" step does not copy the include files into the
> install directory. I mean, if you run "ls" in the install folder,
> there is "bin", "lib" and "share", but no "include".
>
>
> I found many hints about the required fixes in the packaging efforts
> of Eugeny A. Rostovtsev (REAL) <real at altlinux.org> in the ALTLINUX
> distribution.  The SRPM file supplies "sprng4.tar.gz", but it is not
> the original source code package from the SPRNG authors.  The
> packaging is a little atypical for the RPM framework, as one is
> supposed to supply the original "pristine" source and a patch.
> Nevertheless, it is very informative. The patch I attach here includes
> the changes incorporated in the ALTLINUX package (after some cleanup).
> Most changes are C++ cleanup.
>
> In the SPEC file that Mr. Rostovtsev uses in ALTLINUX, he deals with
> the "lack of installed include files" problem by copying the *.h files
> "by hand" after running "make install". For your reference, I'm
> attaching that SPEC file so you can see for yourself. The SPEC file
> assumes the MPI implementation has an executable file called
> "mpivars.sh", and there is no such file in OpenMPI 1.3.
>
> In Debian/Ubuntu, I see Dirk Eddelbuettel supplies libsprng-2.  I'm trying
> to see how that compiles. The source code on that one is pretty
> old.  If I can't figure out sprng4, I
> will go back and work more on sprng-2 following Dirk's lead.
>
> I find also Nakama's mention of troubles compiling sprng4 and some
> proposed patches:
>
> http://prs.ism.ac.jp/~nakama/mascagni/
>
> He proposes patches and fixes, but I can't make them compile AT ALL.
> I notice those patches were proposed here about 1.5 years ago.
>
> If you have ideas, I'd be glad to hear them. In the interim, I'm going
> to study how Dirk compiled & installed SPRNG2 to see if I can make an RPM
> that way.
>
> pj
>
> [1]
> mpif77 -Wl,-R/usr/local/libexec/openmpi/lib -DHAVE_CONFIG_H -I. -I.
> -I../.. -I../../include   -I../../include -DSPRNG_MPI -g -O2 -c -o
> sprngf_mpi_tmp-sprngf_mpi.o `test -f 'sprngf_mpi.F' || echo
> './'`sprngf_mpi.F
> mpif77 -Wl,-R/usr/local/libexec/openmpi/lib  -g -O2   -o
> sprngf_mpi.tmp -I/usr/lib/openmpi/include
> -I/usr/lib/openmpi/include/openmpi -pthread
> -Wl,-R/usr/local/libexec/openmpi/lib --showme:link
> sprngf_mpi_tmp-sprngf_mpi.o -L../../lib -lsprng -lm -lstdc++ -lm
> -pthread -Wl,-R/usr/local/libexec/openmpi/lib -g -O2 -o sprngf_mpi.tmp
> -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -pthread
> -Wl,-R/usr/local/libexec/openmpi/lib sprngf_mpi_tmp-sprngf_mpi.o
> -L../../lib -lsprng -lm -lstdc++ -lm -L/usr/lib/openmpi/lib -lmpi_f77
> -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm
> -ldl
> mpif77 -Wl,-R/usr/local/libexec/openmpi/lib -DHAVE_CONFIG_H -I. -I.
> -I../.. -I../../include   -I../../include -DSPRNG_MPI -g -O2 -c -o
> sprngf_simple_mpi_tmp-sprngf-simple_mpi.o `test -f
> 'sprngf-simple_mpi.F' || echo './'`sprngf-simple_mpi.F
> mpif77 -Wl,-R/usr/local/libexec/openmpi/lib  -g -O2   -o
> sprngf-simple_mpi.tmp -I/usr/lib/openmpi/include
> -I/usr/lib/openmpi/include/openmpi -pthread
> -Wl,-R/usr/local/libexec/openmpi/lib --showme:link
> sprngf_simple_mpi_tmp-sprngf-simple_mpi.o -L../../lib -lsprng -lm
> -lstdc++ -lm
> -pthread -Wl,-R/usr/local/libexec/openmpi/lib -g -O2 -o
> sprngf-simple_mpi.tmp -I/usr/lib/openmpi/include
> -I/usr/lib/openmpi/include/openmpi -pthread
> -Wl,-R/usr/local/libexec/openmpi/lib
> sprngf_simple_mpi_tmp-sprngf-simple_mpi.o -L../../lib -lsprng -lm
> -lstdc++ -lm -L/usr/lib/openmpi/lib -lmpi_f77 -lmpi -lopen-rte
> -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
> mv: cannot stat `sprng-simple_mpi.tmp': No such file or directory
> make[4]: *** [sprng_mpi_test] Error 1
> make[4]: Leaving directory
> `/home/pauljohn/LinuxDownloads/src/sprngrpm/sprng-4.0/EXAMPLES/mpisprng'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory
> `/home/pauljohn/LinuxDownloads/src/sprngrpm/sprng-4.0/EXAMPLES/mpisprng'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory
> `/home/pauljohn/LinuxDownloads/src/sprngrpm/sprng-4.0/EXAMPLES'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory
> `/home/pauljohn/LinuxDownloads/src/sprngrpm/sprng-4.0'
> make: *** [all] Error 2
>
>
>
> --
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
> _______________________________________________
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> R-sig-hpc at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>


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