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

[Paul Johnson]

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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