From schnetter at cct.lsu.edu  Sun Feb  3 11:27:29 2008
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Sun, 3 Feb 2008 11:27:29 -0600
Subject: [Users] New thorn CactusBase/InitBase
Message-ID: <123ECD7B-B4AA-44A4-BA06-86BB2F4355D4@cct.lsu.edu>

There is now a new thorn CactusBase/InitBase.  This thorn can help  
avoid uninitialised or multiply-initialised initial data, especially  
when mesh refinement is used.

This thorn InitBase specifis how initial data are to be set up.  It  
does not set up any initial data by itself, nor does it contain any  
routines which are to be called.  It is merely a convenient place to  
remember how initial data are to be set up, so that other thorns can  
check their actions against this thorn.  The "setup method" can e.g.  
be "initialise all time levels at once analytically", or "initialise  
only the current time level", etc.

The decision how to set up initial data is explicitly made by the  
user in the parameter file.  All thorns participating in initial data  
setup can then check their actions against this decision, reporting  
errors if there is an inconsistency.  The driver can also enforce  
that certain time levels are not to be accessed.

There is one parameter, InitBase::initial_data_setup_method, which  
selects the users' decision.  At the moment, nothing will happen yet  
when InitBase is used.  Future changes to the driver or to initial  
data routines will then contain the consistency checks.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/ 
~eschnett/

My email is as private as my paper mail.  I therefore support encrypting
and signing email messages.  Get my PGP key from www.keyserver.net.




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From dlleuz at xmission.com  Thu Feb 14 21:11:17 2008
From: dlleuz at xmission.com (rsoares)
Date: Thu, 14 Feb 2008 20:11:17 -0700
Subject: [Users] Virtual Memory in Inits
Message-ID: <47B502D5.6000602@xmission.com>

Hi,

When I do inits -d  TopGridParameters for AMRCosmologySimulation A2 or 
B2 (sims with large N=512^3 etc) I get message:

forrtl: severe (41): insufficient virtual memory
Image              PC        Routine            Line        
Source            
libifcoremt.so.5   001A9162  Unknown               Unknown  Unknown
libifcoremt.so.5   001A7415  Unknown               Unknown  Unknown
libifcoremt.so.5   001A7389  Unknown               Unknown  Unknown
libifcoremt.so.5   0012E567  Unknown               Unknown  Unknown
libifcoremt.so.5   001601F7  Unknown               Unknown  Unknown
libifcoremt.so.5   00160128  Unknown               Unknown  Unknown
inits              0804A2E3  Unknown               Unknown  Unknown

Stack trace terminated abnormally.
Reading parameter file
Initializing power spectrum
Generating look-up table
GrowthFactor = 0.02157
GrowthFunction: dlog(D+)/dlog(a) = 0.999995
ParticleSubgridLeftEdge  = 0.000000 0.000000 0.000000
ParticleSubgridRightEdge = 1.000000 1.000000 1.000000
NumberOfParticles = 134217728
GenerateRealization: particle dim 0.
filling k-space...
transforming...

No usual runtime files are generated except PowerSpectrum.out and when I 
try to run:
enzo -d AMRCosmologySimulation I get:

MPI_Init: NumberOfProcessors = 1



*********************************************************************
*                                                                   *
*  Enzo is an Eulerian adaptive mesh refinement cosmology code      *
*  developed and maintained by the Laboratory for Computational     *
*  Astrophysics at the University of California at San Diego under  *
*  the direction of Michael L. Norman.                              *
*                                                                   *
*  Enzo was originally written by Greg Bryan at the National Center *
*  for Supercomputing Applications at the University of Illinois in *
*  Urbana-Champaign.  For more inforamtion, see the Enzo website at *
*  http://cosmos.ucsd.edu/enzo/.                                    *
*                                                                   *
*********************************************************************



CosmologySimulation: check CellFlaggingMethod.
InitializeRateData: NumberOfTemperatureBins = 600
WARNING! Setting MetaData.PPMDiffusionParameter = 0
InitializeNew: Starting problem initialization.
InitializeNew: Finished problem initialization.
ExtBndry: BoundaryRank = 3
ExtBndry: GridDimension = 518 518 518
ExtBndry: NumberOfBaryonFields = 12
CosmologySimulation: ReInitializing grid 0
Allocating 12 baryon fields of size 138991832
p0_5297:  p4_error: interrupt SIGx: 6

=============================

The website this is from:
http://lca.ucsd.edu/data/concordance/

Any suggestions welcome.  Thanks for your time.

-R.Soares

From schnetter at cct.lsu.edu  Thu Feb 14 21:50:24 2008
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Thu, 14 Feb 2008 21:50:24 -0600
Subject: [Users] Virtual Memory in Inits
In-Reply-To: <47B502D5.6000602@xmission.com>
References: <47B502D5.6000602@xmission.com>
Message-ID: <E9C69F4C-8FD6-4DA0-B977-8E290A075345@cct.lsu.edu>

On Feb 14, 2008, at 21:11:17, rsoares wrote:

> Hi,
>
> When I do inits -d  TopGridParameters for AMRCosmologySimulation A2 or
> B2 (sims with large N=512^3 etc) I get message:


Dear R. Soares,

you sent this message to the Cactus users' mailing list.  However, the  
error message you are reporting sound like a plain Enzo simulation.   
Are you using Cactus, Enzo, or a combination of both?

The error message itself could be caused by using too much memory.  It  
is likely that you either need to use more processors or a smaller  
grid size.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/

My email is as private as my paper mail.  I therefore support encrypting
and signing email messages.  Get my PGP key from www.keyserver.net.



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From stokes at marshall.edu  Fri Feb 22 11:37:45 2008
From: stokes at marshall.edu (Paul Edward Stokes)
Date: Fri, 22 Feb 2008 12:37:45 -0500 (EST)
Subject: [Users] compiler
Message-ID: <7165605.1203701865131.JavaMail.pduser@MULM3PDWWW01>

I am a new user and am having problems compiling the wavedemo.  I am 
usingLinex Red Hat Enterprise OS and have installed and sourced Intel 
compiler for C++ and fortran, but everytime I try to compile I get this 
error;

Creating cactus_waveDemo in /home/stokes/Desktop/Cactus/exe from 
CactusBase/Boundary CactusBase/CartGrid3D CactusBase/CoordBase 
CactusConnect/HTTPD CactusConnect/HTTPDExtra CactusWave/IDScalarWaveC 
CactusBase/IOASCII CactusBase/IOBasic CactusIO/IOJpeg CactusBase/IOUtil 
CactusPUGHIO/IsoSurfacer CactusBase/LocalReduce CactusPUGH/PUGH 
CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusConnect/Socket 
CactusBase/SymBase CactusBase/Time CactusWave/WaveBinarySource 
CactusWave/WaveToyC CactusExternal/jpeg6b
c++: /opt/intel/fc/10.1.012/lib/icrt.link: No such file or directory


From schnetter at cct.lsu.edu  Sun Feb 24 10:12:24 2008
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Sun, 24 Feb 2008 10:12:24 -0600
Subject: [Users] compiler
In-Reply-To: <7165605.1203701865131.JavaMail.pduser@MULM3PDWWW01>
References: <7165605.1203701865131.JavaMail.pduser@MULM3PDWWW01>
Message-ID: <1BAC73F2-EAC7-4CE6-BAD7-1225BA6A7A3D@cct.lsu.edu>

On Feb 22, 2008, at 11:37:45, Paul Edward Stokes wrote:

> I am a new user and am having problems compiling the wavedemo.  I am
> usingLinex Red Hat Enterprise OS and have installed and sourced Intel
> compiler for C++ and fortran, but everytime I try to compile I get  
> this
> error;
>
> Creating cactus_waveDemo in /home/stokes/Desktop/Cactus/exe from
> CactusBase/Boundary CactusBase/CartGrid3D CactusBase/CoordBase
> CactusConnect/HTTPD CactusConnect/HTTPDExtra CactusWave/IDScalarWaveC
> CactusBase/IOASCII CactusBase/IOBasic CactusIO/IOJpeg CactusBase/ 
> IOUtil
> CactusPUGHIO/IsoSurfacer CactusBase/LocalReduce CactusPUGH/PUGH
> CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusConnect/Socket
> CactusBase/SymBase CactusBase/Time CactusWave/WaveBinarySource
> CactusWave/WaveToyC CactusExternal/jpeg6b
> c++: /opt/intel/fc/10.1.012/lib/icrt.link: No such file or directory


Paul,

we need additional information to see what is going wrong here.  It  
seems that Cactus didn't quite understand where or how your Intel  
compiler is installed.  Can you

(a) run your make command with the option "SILENT=no", as e.g. in

	make waveDemo SILENT=no

(b) send us the file Cactus/configs/waveDemo/config-data/ 
make.config.defn, which should have been created by Cactus when you  
configured?

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/

My email is as private as my paper mail.  I therefore support encrypting
and signing email messages.  Get my PGP key from www.keyserver.net.



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From stokes at marshall.edu  Thu Feb 28 16:57:50 2008
From: stokes at marshall.edu (Paul Stokes)
Date: Thu, 28 Feb 2008 17:57:50 -0500
Subject: [Users] compiler
In-Reply-To: <1BAC73F2-EAC7-4CE6-BAD7-1225BA6A7A3D@cct.lsu.edu>
References: <7165605.1203701865131.JavaMail.pduser@MULM3PDWWW01>
	<1BAC73F2-EAC7-4CE6-BAD7-1225BA6A7A3D@cct.lsu.edu>
Message-ID: <47C73C6E.6030307@marshall.edu>

Erik Schnetter wrote:
> On Feb 22, 2008, at 11:37:45, Paul Edward Stokes wrote:
>
>> I am a new user and am having problems compiling the wavedemo.  I am
>> usingLinex Red Hat Enterprise OS and have installed and sourced Intel
>> compiler for C++ and fortran, but everytime I try to compile I get this
>> error;
>>
>> Creating cactus_waveDemo in /home/stokes/Desktop/Cactus/exe from
>> CactusBase/Boundary CactusBase/CartGrid3D CactusBase/CoordBase
>> CactusConnect/HTTPD CactusConnect/HTTPDExtra CactusWave/IDScalarWaveC
>> CactusBase/IOASCII CactusBase/IOBasic CactusIO/IOJpeg CactusBase/IOUtil
>> CactusPUGHIO/IsoSurfacer CactusBase/LocalReduce CactusPUGH/PUGH
>> CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusConnect/Socket
>> CactusBase/SymBase CactusBase/Time CactusWave/WaveBinarySource
>> CactusWave/WaveToyC CactusExternal/jpeg6b
>> c++: /opt/intel/fc/10.1.012/lib/icrt.link: No such file or directory
>
>
> Paul,
>
> we need additional information to see what is going wrong here.  It 
> seems that Cactus didn't quite understand where or how your Intel 
> compiler is installed.  Can you
>
> (a) run your make command with the option "SILENT=no", as e.g. in
>
>     make waveDemo SILENT=no
>
> (b) send us the file 
> Cactus/configs/waveDemo/config-data/make.config.defn, which should 
> have been created by Cactus when you configured?
>
> -erik
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Users mailing list
> Users at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/users
>   
> ------------------------------------------------------------------------
>
> No virus found in this incoming message.
> Checked by AVG Free Edition. 
> Version: 7.5.516 / Virus Database: 269.21.0/1296 - Release Date: 2/24/2008 12:19 PM
>   
I tried the
make waveDemo SILENT=no
 but it did the same thing.
Here is the file you asked for

# /*@@
#   @file    make.config.defn.in
#   @date    Sun Jan 17 22:33:51 1999
#   @author  Tom Goodale
#   @desc
#            Make definition file for a configuration
#            Defines the compilers, etc.
#
#            Should be run through autoconf to produce make.config.defn
#   @enddesc
#   @version $Header: /cactus/Cactus/lib/make/make.config.defn.in,v 
1.39 2004/05/19 09:53:23 goodale Exp $
# @@*/

# Include stuff defined by optional extra arrangements
include $(TOP)/config-data/make.extra.defn


# Compiler/executable info
SHELL       = /bin/sh
MKDIR       = mkdir
CC          = gcc
CXX         = c++
F90         = ifort
F77         = ifort
CPP         = /lib/cpp
FPP         = /lib/cpp
LD          = c++
AR          = ar
RANLIB      = ranlib
PERL        = perl

CFLAGS      = -pipe
CXXFLAGS    = -pipe
F90FLAGS    = -align -w95
F77FLAGS    = -align -w95
CPPFLAGS    = 
FPPFLAGS    = -traditional

C_LINE_DIRECTIVES = no
F_LINE_DIRECTIVES = no

MKDIRFLAGS  = -p

LDFLAGS     =  -Qy /opt/intel/fc/10.1.012/lib/icrt.link

ARFLAGS     = rucs
RANLIBFLAGS = -cs

# Debug flags
C_DEBUG_FLAGS   = -g
CXX_DEBUG_FLAGS = -g
F90_DEBUG_FLAGS = -g
F77_DEBUG_FLAGS = -g

# Optimisation flags
C_OPTIMISE_FLAGS   = -O3
CXX_OPTIMISE_FLAGS = -O3
F90_OPTIMISE_FLAGS = -O2 -xN -ip
F77_OPTIMISE_FLAGS = -O2 -xN -ip

# Warning flags
C_WARN_FLAGS   = -Wall -W -Wshadow -Wpointer-arith -Wbad-function-cast 
-Wcast-qual -Wcast-align -Wstrict-prototypes -Wmissing-prototypes 
-Wmissing-declarations -Winline
CXX_WARN_FLAGS = -Wall -W -Wshadow -Wpointer-arith -Wcast-qual 
-Wcast-align -Wstrict-prototypes -Wmissing-prototypes -Winline 
-Woverloaded-virtual
F90_WARN_FLAGS = 
F77_WARN_FLAGS = 

# Most compilers use -c -o to compile only, some do something different
CCOMPILEONLY = -c -o
FCOMPILEONLY = -c -o

# Most compilers use -o for naming the executable, alas some don't
CREATEEXE = -o

# On Unix a /
DIRSEP = /

EMPTY_VAR = # Nothing.  Leading space is removed.

# Mostly a single space, sometimes nothing at all
OPTIONSEP = $(EMPTY_VAR) # a single space

# Some architectures need to do something special for linking in 
libraries
LIBNAME_PREFIX = lib# Make sure there is no space at end.
LIBNAME_SUFFIX = .a

CACTUSLIBLINKLINE = -L$(CCTK_LIBDIR) $(addprefix -l, $(ALLCACTUSLIBS))

# Dependency file generation
C_DEPEND             = $(CC) -E -M $(CPPFLAGS)
CXX_DEPEND           = $(CXX) -E -M $(CPPFLAGS)
F77_DEPEND           = $(FPP) -M $(FPPFLAGS)
F_DEPEND             = $(FPP) -M $(FPPFLAGS)
F_DEPEND_MODULES     = $(CCTK_HOME)/lib/sbin/f_depend_modules.pl

C_DEPEND_OUT         =  > $@
CXX_DEPEND_OUT       =  > $@
F77_DEPEND_OUT       =  > $@
F_DEPEND_OUT         =  > $@
F_DEPEND_MODULES_OUT =  >> $@

# Some compilers are very picky about the names of C++ files
CXX_WORKING_NAME = $(notdir $<)

# Some compilers are very picky about the suffix for fortran files
F90_SUFFIX = f90

# How to postprocess object files
C_POSTPROCESSING   = 
CXX_POSTPROCESSING = 
F77_POSTPROCESSING = 
F_POSTPROCESSING   = 
F90_POSTPROCESSING = 

# Do we need to use ranlib ?
USE_RANLIB = no

# Exclude some files from the dependency lists
DEP_EXCLUDE_FILES = 
cctk_Functions\.h|CParameterStructNames\.h|cctk_Arguments\.h|definethist
horn\.h|FParameters.h|CParameters\.h

# Command used to get the working directory
GET_WD = pwd

# Way for Make to transofrm things like include directories
# into a form suitable for the compiler.

TRANSFORM_DIRS = $(1)

# Library info
LIBS    += crypt  ifcore imf svml m
LIBDIRS += /opt/intel/fc/10.1.012/lib

# Command to generate the link line for libraries
GENERAL_LIBRARIES = $(LIBDIRS:%=-L%) $(LIBS:%=-l%)

# System include directories
SYS_INC_DIRS +=  

# Annoying stuff for some file systems.
PERL_BACKUP_NECESSARY = 

# Stuff for the architecture
OS     = linux-gnu
CPU    = x86_64
VENDOR = unknown

# X stuff
X_LIB_DIR  = NONE
X_INC_DIR  = NONE

# GNU stuff
BUILD_GETOPT = no
BUILD_REGEX  = no

# Where the CCTK puts things
PACKAGE_DIR = $(CCTK_HOME)/arrangements
BUILD_DIR   = $(TOP)/build
CCTK_LIBDIR = $(TOP)/lib

# The perl scripts run by the make system
BUILD_ACTIVETHORNS = $(CCTK_HOME)/lib/sbin/BuildActiveThorns.pl
CST = $(CCTK_HOME)/lib/sbin/CST

C_FILE_PROCESSOR = $(CCTK_HOME)/lib/sbin/c_file_processor.pl
F_FILE_PROCESSOR = $(CCTK_HOME)/lib/sbin/f_file_processor.pl

# The directory in which to place the executable
EXEDIR = $(CCTK_HOME)/exe

# The name of the executable
EXE    = cactus_waveDemo


# Is this a debug configuration ?
CCTK_DEBUG_MODE = no

ifeq ($(strip $(CCTK_DEBUG_MODE)),yes)
  CFLAGS   += $(C_DEBUG_FLAGS)
  CXXFLAGS += $(CXX_DEBUG_FLAGS)
  F77FLAGS += $(F77_DEBUG_FLAGS)
  F90FLAGS += $(F90_DEBUG_FLAGS)
endif

# Is this an optimising configuration ?
CCTK_OPTIMISE_MODE = yes

ifeq ($(strip $(CCTK_OPTIMISE_MODE)),yes)
  CFLAGS   += $(C_OPTIMISE_FLAGS)
  CXXFLAGS += $(CXX_OPTIMISE_FLAGS)
  F77FLAGS += $(F77_OPTIMISE_FLAGS)
  F90FLAGS += $(F90_OPTIMISE_FLAGS)
endif

# Are we building with all warnings switched on ?
# This option may be overwritten at compile time.
ifeq ($(WARN),)
  CCTK_WARN_MODE = no
else
  CCTK_WARN_MODE = $(WARN)
endif

ifeq ($(strip $(CCTK_WARN_MODE)),yes)
  CFLAGS   += $(C_WARN_FLAGS)
  CXXFLAGS += $(CXX_WARN_FLAGS)
  F77FLAGS += $(F77_WARN_FLAGS)
  F90FLAGS += $(F90_WARN_FLAGS)
endif

# Stuff specific to an architecture.
include $(TOP)/config-data/make.arch.defn




-- No virus found in this incoming message. Checked by AVG Free Edition. 
Version: 7.5.516 / Virus Database: 269.21.1/1302 - Release Date: 
2/27/2008 4:34 PM




From schnetter at cct.lsu.edu  Thu Feb 28 17:32:28 2008
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Thu, 28 Feb 2008 17:32:28 -0600
Subject: [Users] compiler
In-Reply-To: <47C73C6E.6030307@marshall.edu>
References: <7165605.1203701865131.JavaMail.pduser@MULM3PDWWW01>
	<1BAC73F2-EAC7-4CE6-BAD7-1225BA6A7A3D@cct.lsu.edu>
	<47C73C6E.6030307@marshall.edu>
Message-ID: <C44DB35F-26D9-422F-A511-FB5511F94B75@cct.lsu.edu>

On Feb 28, 2008, at 16:57:50, Paul Stokes wrote:

> I tried the
> make waveDemo SILENT=no
> but it did the same thing.

Yes, but it produced more output.  In fact, it lists all the commands  
which it is going to execute.  Can you show us the last command that  
Cactus was trying to run?  It should begin with "c++".

> Here is the file you asked for

> CC          = gcc
> CXX         = c++
> F90         = ifort
> F77         = ifort

This indicates that you are mixing gcc's C and C++ compilers with  
Intel's Fortran compilers.  That is not bad in itself, but you have to  
be aware that you are not using Intel's C and C++ compilers.

> LDFLAGS     =  -Qy /opt/intel/fc/10.1.012/lib/icrt.link

This is where Cactus picks up the problematic option.  Does this file  
exist?  If not, where is your Intel Fortran compiler installed?  You  
find out by issuing

	which ifort

The remainder looks fine.

> -- No virus found in this incoming message. Checked by AVG Free  
> Edition. 
> Version: 7.5.516 / Virus Database: 269.21.1/1302 - Release Date:
> 2/27/2008 4:34 PM


I'm happy to know that.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/

My email is as private as my paper mail.  I therefore support encrypting
and signing email messages.  Get my PGP key from www.keyserver.net.



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