[R-sig-hpc] Patches -> success with sprng2.0b on Ubuntu; Centos/Rocks Cluster still mysterious in Fortran

[Paul Johnson]

Hello, everybody.

I stubbornly persist (for replication purposes) toward the goal of
building sprng on a cluster running Rocks Linux (Centos based) in
order to use Rmpi.


=============Chapter 1: Ubuntu likes me================

My laptop is Ubuntu 8.10, and I have been doing the development there.
 I ended up taking advantage of fixes discovered by Dirk E in his
package for Debian/Ubuntu and the fixes proposed for ALTLinux. And
advice from several others in various email lists.

I have worked with sprng versions 2.0a and 2.0b.  2.0a is used in the
libsprng package in Debian/Ubuntu channels, but it is no longer
available from the FSU website.  From the FSU site, they offer version
2.0b.

I uploaded a series of patches, a copy of the source code (for your
convenience), and output to this directory:
http://pj.freefaculty.org/linux/sprng

sprng2.0b.tar.gz

sprng-01-C-comments-onlyfor2.0a.patch
sprng-02-dirk-misc.patch
sprng-03-makefiles.patch
sprng-04-AllCFixes.patch
sprng-05-fixmenu.patch
sprng-06-openmpi.patch

The first patch is only used if you are working with sprng2.0a.tar.gz,
it is NOT used with 2.0b.  All of the rest apply to both. The last is
strictly optional.

The steps to open the code, apply the patches, and, most importantly,
to demonstrate the full functionality (results of "checksprng" and
"timespring") are in this text files:

Ubuntu-build-check.txt
timesprng.txt

The C and Fortran examples work fine.  As a result, I consider the
question of compiling "cleanly" and "testing" on Ubuntu to be solved.
It works with or without MPI.

That may seem trivial, but it takes some effort.  The Debian/Ubuntu
package libsrpng does not currently conduct the testing phase.  In the
files I uploaded, you can see full functioning versions of checksprng
and testsprng.


==========Chapter 2: Centos hate me ========

The report on my final goal--installing this in a Rocks cluster--is
not so perfect.  The C examples work. The Fortran with pointer
checking examples don't work.  Maybe I don't care??  The libraries do
compile.  Maybe that's good enough for Rmpi?

I put the output from "make" and the check programs in this file:

Centos-build.txt

Even getting this to compile on Centos is a hassle.  The versions of
the compilers, openmpi, and the "echo" program are different. For
example, the fortran compiler on Centos enforces a line length
limitation, so several print statements in Fortran examples cause
compiler failures.  I also learned that, unlike Ubuntu where "echo"
will translate \134 into the "backslash" character, on Centos it is
necessary to add a zero, as in \0134.  After hacking and such, I'm
able to compile sprng2.0b on Centos, and I can run all of the C-based
random generator tests.  The Fortran scripts with pointer checking
fail.

I'm trying to decide if that's important. I don't write Fortran
programs. But I'd hate to release this on an unsuspecting user group
unless I can understand what's going on. If you are a Fortran user,
perhaps you can advise me how to debug this.

Observe the last part of the output:


./checksprng

lfg: Checking Default C interface:

Result:  PASSED


lfg: Checking Simple C interface:

Result:  PASSED


lfg: Checking C interface with pointer checking:

Result:  PASSED


lcg: Checking Default C interface:

Result:  PASSED


lcg: Checking Simple C interface:

Result:  PASSED


lcg: Checking C interface with pointer checking:

Result:  PASSED


lcg64: Checking Default C interface:

Result:  PASSED


lcg64: Checking Simple C interface:

Result:  PASSED


lcg64: Checking C interface with pointer checking:

Result:  PASSED


cmrg: Checking Default C interface:

Result:  PASSED


cmrg: Checking Simple C interface:

Result:  PASSED


cmrg: Checking C interface with pointer checking:

Result:  PASSED


mlfg: Checking Default C interface:

Result:  PASSED


mlfg: Checking Simple C interface:

Result:  PASSED


mlfg: Checking C interface with pointer checking:

Result:  PASSED


pmlcg: Checking Default C interface:

Result:  PASSED


pmlcg: Checking Simple C interface:

Result:  PASSED


pmlcg: Checking C interface with pointer checking:

Result:  PASSED


lfg: Checking Default FORTRAN interface:
./checksprng: line 57:  6879 Segmentation fault      ./check.fsprng <
gen0_lfg.data 2> /dev/null

lfg: Checking Simple FORTRAN interface:
  Expect SPRNG ERROR: packed string invalid.

 Result:  PASSED


lfg: Checking FORTRAN interface with pointer checking:
 FAILED: Integer generator incorrect.
 FAILED: Float generator incorrect.
 FAILED: Double generator incorrect stream.
 FAILED: Generator was unable to spawn.
 FAILED: Generator incorrect after spawning.
 Probable  error in spawning the generators.
 FAILED: Generator was unable to pack.
 FAILED: Incorrect stream after pack/unpack.
 Probable error in (un)packing the generators.
 FAILED: Generator incorrect stream after pack/unpack.
 Probably an error in (un)packing the generators.
 FAILED: Free returns           -1 instead of 6.
 FAILED: Free returns           -1 instead of 0.
 FAILED: Generator does not produce expected stream
    ... when ngens <= 0.
 FAILED: Generator produces more than 1 stream
     ... when ngens = 0.
 FAILED: Spawn returned           0  instead of 1
    ... when nspawned was 0.
 FAILED: Generator wrong when nspawned = -1.
 Expect SPRNG ERROR: packed string invalid

 Result:  FAILED


lcg: Checking Default FORTRAN interface:
./checksprng: line 66:  6882 Segmentation fault      ./check.fsprng <
gen1_lcg.data 2> /dev/null

lcg: Checking Simple FORTRAN interface:
  Expect SPRNG ERROR: packed string invalid.

 Result:  PASSED


lcg: Checking FORTRAN interface with pointer checking:
 FAILED: Integer generator incorrect.
 FAILED: Float generator incorrect.
 FAILED: Double generator incorrect stream.
 FAILED: Generator was unable to spawn.
 FAILED: Generator incorrect after spawning.
 Probable  error in spawning the generators.
 FAILED: Generator was unable to pack.
 FAILED: Incorrect stream after pack/unpack.
 Probable error in (un)packing the generators.
 FAILED: Generator incorrect stream after pack/unpack.
 Probably an error in (un)packing the generators.
 FAILED: Free returns           -1 instead of 6.
 FAILED: Free returns           -1 instead of 0.
 FAILED: Generator does not produce expected stream
    ... when ngens <= 0.
 FAILED: Generator produces more than 1 stream
     ... when ngens = 0.
 FAILED: Spawn returned           0  instead of 1
    ... when nspawned was 0.
 FAILED: Generator wrong when nspawned = -1.
 Expect SPRNG ERROR: packed string invalid

 Result:  FAILED


lcg64: Checking Default FORTRAN interface:
./checksprng: line 75:  6885 Segmentation fault      ./check.fsprng <
gen2_lcg64.data 2> /dev/null

lcg64: Checking Simple FORTRAN interface:
  Expect SPRNG ERROR: packed string invalid.

 Result:  PASSED


lcg64: Checking FORTRAN interface with pointer checking:
 FAILED: Integer generator incorrect.
 FAILED: Float generator incorrect.
 FAILED: Double generator incorrect stream.
 FAILED: Generator was unable to spawn.
 FAILED: Generator incorrect after spawning.
 Probable  error in spawning the generators.
 FAILED: Generator was unable to pack.
 FAILED: Incorrect stream after pack/unpack.
 Probable error in (un)packing the generators.
 FAILED: Generator incorrect stream after pack/unpack.
 Probably an error in (un)packing the generators.
 FAILED: Free returns           -1 instead of 6.
 FAILED: Free returns           -1 instead of 0.
 FAILED: Generator does not produce expected stream
    ... when ngens <= 0.
 FAILED: Generator produces more than 1 stream
     ... when ngens = 0.
 FAILED: Spawn returned           0  instead of 1
    ... when nspawned was 0.
 FAILED: Generator wrong when nspawned = -1.
 Expect SPRNG ERROR: packed string invalid

 Result:  FAILED


cmrg: Checking Default FORTRAN interface:
./checksprng: line 84:  6888 Segmentation fault      ./check.fsprng <
gen3_cmrg.data 2> /dev/null

cmrg: Checking Simple FORTRAN interface:
  Expect SPRNG ERROR: packed string invalid.

 Result:  PASSED


cmrg: Checking FORTRAN interface with pointer checking:
 FAILED: Integer generator incorrect.
 FAILED: Float generator incorrect.
 FAILED: Double generator incorrect stream.
 FAILED: Generator was unable to spawn.
 FAILED: Generator incorrect after spawning.
 Probable  error in spawning the generators.
 FAILED: Generator was unable to pack.
 FAILED: Incorrect stream after pack/unpack.
 Probable error in (un)packing the generators.
 FAILED: Generator incorrect stream after pack/unpack.
 Probably an error in (un)packing the generators.
 FAILED: Free returns           -1 instead of 6.
 FAILED: Free returns           -1 instead of 0.
 FAILED: Generator does not produce expected stream
    ... when ngens <= 0.
 FAILED: Generator produces more than 1 stream
     ... when ngens = 0.
 FAILED: Spawn returned           0  instead of 1
    ... when nspawned was 0.
 FAILED: Generator wrong when nspawned = -1.
 Expect SPRNG ERROR: packed string invalid

 Result:  FAILED


mlfg: Checking Default FORTRAN interface:
./checksprng: line 93:  6891 Segmentation fault      ./check.fsprng <
gen4_mlfg.data 2> /dev/null

mlfg: Checking Simple FORTRAN interface:
  Expect SPRNG ERROR: packed string invalid.

 Result:  PASSED


mlfg: Checking FORTRAN interface with pointer checking:
 FAILED: Integer generator incorrect.
 FAILED: Float generator incorrect.
 FAILED: Double generator incorrect stream.
 FAILED: Generator was unable to spawn.
 FAILED: Generator incorrect after spawning.
 Probable  error in spawning the generators.
 FAILED: Generator was unable to pack.
 FAILED: Incorrect stream after pack/unpack.
 Probable error in (un)packing the generators.
 FAILED: Generator incorrect stream after pack/unpack.
 Probably an error in (un)packing the generators.
 FAILED: Free returns           -1 instead of 6.
 FAILED: Free returns           -1 instead of 0.
 FAILED: Generator does not produce expected stream
    ... when ngens <= 0.
 FAILED: Generator produces more than 1 stream
     ... when ngens = 0.
 FAILED: Spawn returned           0  instead of 1
    ... when nspawned was 0.
 FAILED: Generator wrong when nspawned = -1.
 Expect SPRNG ERROR: packed string invalid

 Result:  FAILED


pmlcg: Checking Default FORTRAN interface:
./checksprng: line 102:  6894 Segmentation fault      ./check.fsprng <
gen5_pmlcg.data 2> /dev/null

pmlcg: Checking Simple FORTRAN interface:
  Expect SPRNG ERROR: packed string invalid.

 Result:  PASSED


pmlcg: Checking FORTRAN interface with pointer checking:
 FAILED: Integer generator incorrect.
 FAILED: Float generator incorrect.
 FAILED: Double generator incorrect stream.
 FAILED: Generator was unable to spawn.
 FAILED: Generator incorrect after spawning.
 Probable  error in spawning the generators.
 FAILED: Generator was unable to pack.
 FAILED: Incorrect stream after pack/unpack.
 Probable error in (un)packing the generators.
 FAILED: Generator incorrect stream after pack/unpack.
 Probably an error in (un)packing the generators.
 FAILED: Free returns           -1 instead of 6.
 FAILED: Free returns           -1 instead of 0.
 FAILED: Generator does not produce expected stream
    ... when ngens <= 0.
 FAILED: Generator produces more than 1 stream
     ... when ngens = 0.
 FAILED: Spawn returned           0  instead of 1
    ... when nspawned was 0.
 FAILED: Generator wrong when nspawned = -1.
 Expect SPRNG ERROR: packed string invalid

-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas