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|
Cactus Code Frequently Asked Questions
$Header: /mnt/data2/cvs2svn/cvs-repositories/Cactus/doc/FAQ,v 1.79 2004-05-01 22:06:14 tradke Exp $
Also available at http://www.cactuscode.org/Documentation/FAQ
==============================================================================
The Questions:
------------------------------------------------------------------------------
Background:
A1 How did Cactus start?
A2 Who develops and maintains Cactus?
A3 How can I get involved?
------------------------------------------------------------------------------
Distributions and CVS Checkout:
B1 When doing a cvs update I get 'not enough slashes in ...' .
B2 I want to recreate a Cactus executable from last year, I have a thorn list
but when I try and check it out from the /cactus or /cactusdevcvs
repository I don't get some of the thorns.
B3 How do I checkout an earlier version of Cactus ?
B4 When running GetCactus it tells me it is refusing to update my thorn
because it is installed from a different repository.
B5 Tell me how I can get thorns?
------------------------------------------------------------------------------
Configuring and Building:
C1 The make system says "Checking status of libXXX.a" and then just
sits there. What can I do ?
C2 Compilation of Cactus fails with the error:
identifier "DECLARE_CCTK_PARAMETERS" is undefined?
C3 (Linux) I get 'g77: cannot specify -o with -c or -S and multiple
compilations' when compiling with the Pacific VAST90 compiler.
C4 How do I compile with MPI? Why isn't it automatic like in Cactus 3?
C5 I can't compile because the compiler complains that a routine name has
been previously defined ... but I can't find it repeated?
C6 How can I make sure that one thorn is compiled before another? For example
to make sure that F90 module files from ArrangementA/ThornA are available
for ArrangementB/ThornB.
C7 (Solaris) I start a configuration process with gmake, but on the second
gmake it wants to set up the configuration again and again ....
C8 How do I compile Cactus in 32 bit mode on a 64 bit irix machine?
C9 What can I do if I don't have enough disk space to compile Cactus?
C10 When I compile Cactus I get an error with "unterminated character
constants", but on typing gmake again it proceeds without problem.
C11 Sometimes when I compile in parallel with TJOBS or FJOBS the compilation
stops halfway through.
C12 I get the following error when compiling?
Checking status of libIOJpeg.a
gmake[3]: *** No rule to make target \
`/u1/allen/scratch/Cactus/arrangements/
CactusIO/IOJpeg/src/IOJpeg.h', needed by `JPEG.c.d'. Stop.
gmake[2]: *** [make.checked] Error 2
gmake[1]: *** [/u1/allen/scratch/Cactus/configs/wave/lib/libIOJpeg.a] \
Error 2
gmake: *** [wave] Error 2
C13 Compiling files in Cactus seems to involve three steps, preprocessing,
compiling, and then postprocessing. What are they doing?
C14 When trying to create the Cactus executable I get the error the
error <Unresolved text symbol "SetCartSymVN" -- 1st referenced
by /data2/Cactus/configs/origin/lib/libADMBase.a>
C15 My thorn is calling directly a function from another thorn. Both thorns
are in my ThornList, but on linking I get the error
Startup.c.o(.text+0x4d): undefined reference to `OtherThornsFunction'
C16 (Linux) When trying the new gcc 3.1.1 compiler, I received a lot of
warnings about the compiler flag "-I/usr/local/include".
C17 (OpenBSD) The system linker /usr/bin/ld crashes when linking C++ thorns.
C18 (Linux) When I compile Fortran I get errors because characters
are in the first 5 columns, but I can't see anything wrong in the
source code.
C19 (Linux) I get internal errors using the Pacific-Sierra Fortran 90 compiler
C20 (Linux) I get the linking error "/usr/bin/ld: cannot find -lIEPCF90"
with the Intel Fortran compiler.
C21 (Solaris) Building PUGHReduce under Solaris 2.8 gives several errors
with macro recursion.
C22 (MacOS) Compiling with the Absoft F90 compiler I get error messages
about large "fixups"
C23 How can I see the commands which Cactus is actually using to build
the executable?
C24 My configuration takes forever to build, are there any ways to speed
this up?
C25 On compiling Fortran code I get errors like "dummy argument CCTK_DIM has
not been given a type", but I'm not using CCTK_DIM in the routine?
C26 I'm passing arguments to my scheduled routine using CCTK_ARGUMENTS and
I get the compile error "identifier DECLARE_CCTK_ARGUMENTS is undefined"
C27 I have a code block commented out by '#if 0 ... #endif' in a C/C++
routine which uses the DECLARE_CCTK_ARGUMENTS and/or
DECLARE_CCTK_PARAMETERS macro. The compiler stops with a parsing error
on this piece of code.
C28 (Linux IA64) I get a segmentation violation compiling snprintf.c in
the Cactus flesh?
C29 On linking I get an "unresolved text symbol" for a scheduled function
called from libCactusBindings.a
C30 (Linux) Using the Intel Fortran compiler I get the error "/usr/bin/ld
cannot find -lintrins" on linking.
C31 I just want to check that one thorn compiles correctly, can I test
this without compiling all the thorns which come before it?
C32 What is the Cactus c-preprocessor (Cactus cpp) ?
C33 I'm working on a machine where a compiler problem means that I
need to compile a particular thorn with a lower optimisation level.
Is there an easy way to do this?
C34 How can I make sure that one file is compiled before another? For example
to make sure that an F90 module file "module.F90" is available for other
file "using.F90".
C35 I started building a Cactus configuration and it asked me if
I wanted to edit the thornlist, I pressed 'y' and then 'enter'
but nothing happened?
C36 (Linux) Compiling Cactus with Redhat 8 or 9 it fails in CactusBase/IOUtil
because the system failed to find <sys/stat.h>
C37 Why can't I use different F90 and F77 compilers with Cactus?
------------------------------------------------------------------------------
Running:
D1 I'm trying to run Cactus with MPI using "mpirun", but I just get an error
"Unknown option -np"?
D2 I'm running Cactus on a parallel system with missing C++ libraries on some
nodes. Cactus compiles but it won't run?
D3 I can build a Cactus configuration using some external libraries (e.g.
HDF5, PETSc) but get errors with shared libraries on running the
executable.
D4 I can run my non-MPI executable using shared libraries without problems now
but still get the same error as in FAQ D3 for MPI jobs started with mpirun.
D5 (Irix) I'm using the web server thorn CactusConnect/HTTPD, I compiled with
PTHREADS=yes to get better response, but the executable just hangs.
D6 I get a segmentation fault running Cactus, right after the schedule
tree is printed to screen?
D7 (Linux) I'm using the NaNChecker thorn and seeing very strange results.
D8 (Linux) Testsuites for CactusEinstein/AHFinder and CactusBench/BenchADM
are failing, but the release notices say that they pass.
D9 How do I run Cactus until a given coordinate time instead of to a
given iteration number?
D10 Output to screen using the Info IO method of IOBasic doesn't work.
D11 I get an error saying "CCTK_Equals: First string null".
D12 I have a Cactus executable compiled with MPI. When running it on a single
processor (without using mpirun) I get an error saying "Unable to open
parameter file ...".
------------------------------------------------------------------------------
Thorn Writing:
E1 While implementing some MPI code in Cactus, I came across the problem of
getting an MPI communicator. I basically have the choice between using
MPI_COMM_WORLD, assuming that no processors have been set aside by the
driver, or tying myself to a certain driver, such as PUGH, and using the
driver's internal data structures. Both choices are clearly not
desirable.
E2 How can I communicate the value of a local scalar on one processor to all
processors? There doesn't seem to be an API for this in Cactus.
E3 What about if I only want to send a local scalar to a single processor?
E4 Why shouldn't I make direct calls to MPI from my thorns? Your default
driver uses MPI.
E5 What is the difference between using "const cGH *cctkGH" and "cGH *cctkGH"
for argument declarations? What about "const cGH* const cctkGH"?
E6 On compiling Fortran code I get errors like "dummy argument CCTK_DIM has
not been given a type", but I'm not using CCTK_DIM in the routine?
E7 If I have two grid array groups with identical sizes (and ghost zones,
distributions, etc.), are they guaranteed to be distributed in the same
way? That is, can I count on the fact that their local shapes (lsh)
will be the same? It is true empirically. What if the grid arrays have
different variable types or numbers of time levels?
E8 Is there anyway to only compile certain lines of source code if a
particular thorn is in the compiled ThornList?
E9 How can I find out in make.configuration.defn, whether MPI is being
used or not?
E10 How can I see in source code whether MPI is being used?
E11 The functions CCTK_Exit and CCTK_Abort require cctkGH as an argument.
How can I call these functions deep inside my thorns where this pointer
is not available?
E12 I'm getting weird syntax errors in Fortran code, with an extra
garbage character (often $ or &) stuck in the middle of a CCTK_INFO()
or CCTK_WARN() or CCTK_EQUALS() call after it has been processed.
E13 I want to write the value of a KEYWORD parameter in Fortran code to
a file, but nothing I try works.
E14 I write my thorns with Fortran, do you have any general advice?
E15 In my Fortran thorn the value of a Cactus integer parameter is totally
wrong when I print it, but when I print it from C it is fine.
E16 I write my thorns with C, do you have any general advice?
E17 Why is it that when I schedule more than one routine in the same thorn
at ANALYSIS only the first routine is executed and the second one is
ignored?
E18 Is there a way to synchronize individual grid variables in a group?
E19 Is there a way to synchronize just one time level of a grid variable?
Right now only one time level is synchronized, that is the "current" level.
Other time levels cannot be synchronized and are assumed to be fixed
or read only.
E20 I'm using the CCTK_ParameterSet function to change a parameter, but
after calling it the parameters value doesn't change?
------------------------------------------------------------------------------
General
F1 Why do I have to use e.g. "mpirun -np 1 ./exe/cactus_myconfig -O" to see
the compiled parameters, can't the parameters be output before MPI is
initialised?
F2 Why isn't a BOOLEAN parameter a LOGICAL in Fortran?
F3 Why is there an MPI call in the Flesh (MPI_Init)? I thought that the
Cactus flesh was independent of any parallel protocol, why isn't this
call made from a driver thorn?
F4 Is there any way to tell what CVS version of individual source files
was used to build an executable?
F5 Why is the main routine of Cactus written in C++ (src/main/flesh.cc) when
the rest of the flesh is standard ANSI C? More strangely, why does Cactus
still compile when I have no C++ compiler on my system?
F6 Are there grid scalars of type STRING ?
F7 Why don't you use compilers mpicc, mpiCC etc when they exist on parallel
machines?
F8 How does Cactus manage to so seamlessly call Fortran routines from
C, and vice versa?
F9 The documentation says that Cactus parameters are read-only, but I
can trivially change the value of a parameter in the Fortran source
code of my thorn.
------------------------------------------------------------------------------
Documentation:
G1 How can I build the ThornGuide documentation for single thorns or
arrangements?
G2 I have a configuration with over ten thorns, but when I make the
ThornGuide I only see the first few of them.
------------------------------------------------------------------------------
I/O:
H1 I want to run an old parameter file, but none of the I/O parameters are
recognised!
H2 I would like to use checkpointing for a thorn which has complex grid
arrays. I tried to use the IOFlexIO thorn and received the error:
Unsupported CCTK variable datatype 10. Is there a way to checkpoint
complex variables?
------------------------------------------------------------------------------
Configuration Files:
I1 The size of array parameters is specified by a integer number in the
param.ccl file. Why can't a parameter itself be used here?
==============================================================================
The Answers:
------------------------------------------------------------------------------
Background:
A1 How did Cactus start?
Cactus originated in the Numerical Relativity community to realise
the large scale computing needs and collaborative working practices
required to model objects such as black holes, neutron stars and
and gravitational waves using Einsteins Theory of General Relativity.
In particular, Cactus grew out of codes, experiences, and ideas of
members of the NCSA and AEI numerical relativity groups together with
a number of friends and collaborators. Since the first Beta release
of Cactus 4.0 many suggestions and contributions have also been made
by the users.
A2 Who develops and maintains Cactus?
Cactus is primarily developed and maintained at the Max Planck Institute
for Gravitational Physics (Albert Einstein Institute) in Potsdam, Germany.
The funding for this support is mainly obtained through independent
grants for projects in both computer science and physics which focus
around Cactus.
A3 How can I get involved?
First, if you use Cactus, send bug reports, bug fixes, comments,
suggestions, documentation to cactusmaint@cactuscode.org, or use
the bug tracking/feature request system.
If you have written thorns which could be useful to other people,
make them available for others to use (if you have a web page,
send us the link to put on our page).
To find out about any existing or upcoming research programmer or
student positions associated with Cactus development please contact
Ed Seidel (eseidel@aei.mpg.de).
-------------------------------------------------------------------------------
Distributions and CVS Checkout:
B1 When doing a cvs update I get 'not enough slashes in ...' .
It seems that CVS sometimes gets confused with multiple repositories.
Check that you are using the latest version of CVS, otherwise moving into
the arrangements directory and performing another 'cvs update', followed
by a final one in the top-level directory should complete your update.
There is now a Cactus make target "gmake cvsupdate" which avoids this
problem by updating the flesh and checked out thorns explicitly.
B2 I want to recreate a Cactus executable from last year, I have a thorn list
but when I try and check it out from the /cactus or /cactusdevcvs
repository I don't get some of the thorns.
This is probably because the thorns moved arrangement, or were rewritten.
To checkout the right code, look in doc/ReleaseNotes to decide which
release the thorn was in, and then checkout the thorn from the /cactus
repository, eg. if the thorn "OldThorn" was last in the Beta 7 release use:
cvs -d :pserver:cvs_anon@cvs.cactuscode.org:/cactus co -d OldThorn \
beta7/OldThorn
B3 How do I checkout an earlier version of Cactus ?
Cactus is "tagged" in CVS for each release, so to checkout for example
the flesh for Beta 10 use:
cvs -d :pserver:cvs_anon@cvs.cactuscode.org:/cactus checkout -r \
Cactus_4_0_Beta_10 Cactus
[to see a list of possible tags go to the Cactus home directory
and type "cvs status -v Makefile"]
To checkout from a particular date, for example the 7th July 2000, use
cvs -d :pserver:cvs_anon@cvs.cactuscode.org:/cactus checkout -D \
"7 July 2000"
Also look at FAQ B2.
B4 When running GetCactus it tells me it is refusing to update my thorn
because it is installed from a different repository.
What GetCactus does is look in the thorn's CVS/Root to get the repository
that it was originally installed from. If the repository specified in
your thornlist (using the !REPOSITORY_LOCATION directive) is not the same,
then GetCactus will refuse to update your thorn.
This problem commonly occurs when people interchange repository locations
that actually point to the same place. For example, using cvs.aei.mpg.de
for the initial checkout, and then using cvs.cactuscode.org for an update.
To fix this problem, simply be consistent with repository locations.
B5 Tell me how I can get thorns?
The best way is to use CVS, all the Cactus thorns and most other
public community thorns are distributed this way.
- If you already have the Cactus flesh installed and want to
install a standard Cactus thorn just type
gmake checkout
for a list of thorns you can then download
- If you have a thornlist annotated with CVS information get
hold of the GetCactus script, e.g.
wget http://www.cactuscode.org/Download/GetCactus
and use this with your thornlist, if you already have the flesh
installed it will just checkout the thorns (the script needs to be
run in the directory above your checked out Cactus at the moment)
GetCactus <thornlist>
------------------------------------------------------------------------------
Configuring and Building:
C1 The make system says "Checking status of libXXX.a" and then just
sits there. What can I do ?
The first thing to do whenever a problem arises from the make system
is to run with the "SILENT=no" option.
In this case, though, first check that the clocks on the machine on
which you are editing files and the clock on the machine you are compiling
on are synchronised. If the compilation machine's clock is slow, then the
newly made dependency files will still be `older' than the file you
edited, and the system will loop until this situation changes.
C2 Compilation of Cactus fails with the error:
identifier "DECLARE_CCTK_PARAMETERS" is undefined?
You need to include the header:
#include "cctk_Parameters.h"
C3 (Linux) I get 'g77: cannot specify -o with -c or -S and multiple
compilations' when compiling with the Pacific VAST90 compiler.
If the libvast90.a library is in the same directory as your F90 script,
F90 passes -lvast90 to the underlying G77 compile, which is of course only
a valid switch when linking. The solution is to separate these files,
e.g. into bin and lib directories.
C4 How do I compile with MPI? Why isn't it automatic like in Cactus 3?
The standard MPI driver (PUGH) is in a thorn now (CactusPUGH/PUGH), so
there is now the possibility to add other parallel drivers using
alternative message passing schemes as separate thorns. To compile with
MPI, when you make a configuration, use
gmake <configuration>-config MPI=<MPI_TYPE>
where the allowed values of MPI_TYPE are discussed in the documentation.
For machines where Cactus 3 used to use MPI by default, the correct option
is probably MPI=NATIVE
C5 I can't compile because the compiler complains that a routine name has
been previously defined ... but I can't find it repeated?
If it is a C routine, whose name is either all in capitals or all in
lowercase, and the routine has a Fortran wrapper, then it could be that
the compiler doesn't attach underscores to the Fortran name and there is a
conflict. To remove this possibility always use mixed case names for C
routines with Fortran wrappers.
C6 How can I make sure that one thorn is compiled before another? For example
to make sure that F90 module files from ArrangementA/ThornA are available
for ArrangementB/ThornB.
Add a dependency to a ThornB's make.configuration.deps file, for example
ifneq (,$(findstring ArrangementA/ThornA,$(THORNS)))
$(CCTK_LIBDIR)$(DIRSEP)libThornB.a : $(CCTK_LIBDIR)$(DIRSEP)libThornA.a
endif
we will try to modify the make system to make this more automatic in the
future.
C7 (Solaris) I start a configuration process with gmake, but on the second
gmake it wants to set up the configuration again and again ....
You are using a version of gmake which is too outdated (even though
this version may work perfectly on other architectures). We found
that GNU Make version 3.79 works fine.
C8 How do I compile Cactus in 32 bit mode on a 64 bit irix machine?
gmake <config>-config IRIX_BITS=32
C9 What can I do if I don't have enough disk space to compile Cactus?
If you have access to some scratch space, or temporary space, you can
instruct Cactus to put the "configs" directory there (with all the
object files and intermediate files).
For example, to use the directory /scratch/myconfigs with csh or tcsh,
setenv CACTUS_CONFIGS_DIR /scratch/myconfigs
or with bash
CACTUS_CONFIGS_DIR=/scratch/myconfigs
export CACTUS_CONFIGS_DIR
C10 When I compile Cactus I get an error like
/home/allen/Cactus/arrangements/MineStuff/Test/src/metric.F90:3:
unterminated character constant
make[2]: *** [metric.F90.d] Error 33
But then when I type gmake again the compilation proceeds without problem.
You are probably using Linux, and the C preprocessor is complaining
about single apostrophes in a Fortran comment line when it is creating the
dependency file for metric.F90. Make continues the second time because
the dependency file now exists (although it won't necessarily contain
the right information).
We could remove this problem by removing comments from Fortran files
before using the C preprocessor, but we don't want to add this overhead
at the moment, since we are writing a Cactus preprocessor which won't
have this problem (and will solve a number of other preprocessing
problems).
Your choices for getting past this for now are
- try and remove any single apostrophes in Fortran comments
- use gmake twice and live with possibly bad dependency information
for these files
- if you are using Linux, try using the option "-traditional"
with the GNU cpp which does ignore the apostrophes.
Unfortunately, cpp is broken in Red Hat's version 2.96, and in the
official releases 3.0 up to 3.0.3. The versions 2.95.x and 3.0.4
do work fine.
In order to use a different cpp and to pass the option
"-traditional", use for example
FPP = /home/user/gcc/bin/cpp -traditional
when you configure your application.
C11 Sometimes when I compile in parallel with TJOBS or FJOBS the compilation
stops halfway through.
Compiling in parallel using TJOBS/FJOBS is not always failsafe. Usually
simply issuing your gmake command again will complete the compilation
and produce an executable. Occasionally you may see link errors
in the last stage of compilation, if this happens remove the libraries
rm configs/<config>/lib/*
and issue gmake once more.
Problems with TJOBS/FJOBS can be avoided if your version of gmake
supports parallel make (this happened somewhere between 3.74 and3.78.1),
in which case you can use instead the more robust:
gmake <config> -j <number of processors>
C12 I get the following error when compiling?
Checking status of libIOJpeg.a
gmake[3]: *** No rule to make target \
`/u1/allen/scratch/Cactus/arrangements/
CactusIO/IOJpeg/src/IOJpeg.h', needed by `JPEG.c.d'. Stop.
gmake[2]: *** [make.checked] Error 2
gmake[1]: *** [/u1/allen/scratch/Cactus/configs/wave/lib/libIOJpeg.a] \
Error 2
gmake: *** [wave] Error 2
This is because an include file which was used in your previous compile is
no longer there (in this case the file IOJpeg.h was renamed ioJpeg.h).
To solve this, delete the dependency information by issuing
gmake <config>-cleandeps
before compiling again.
C13 Compiling files in Cactus seems to involve three steps, preprocessing,
compiling, and then postprocessing. What are they doing?
Cactus specific preprocessing is performed for most source files, for
example to expand c-preprocessor macros (e.g. DECLARE_CCTK_PARAMETERS)
in .F, .F90 and .F77 files or to set correct names for calling Fortran
functions in C files. At the end of the preprocessing stage the
resulting source file is placed into the
configs/<config>/build/<thorn>
directory and if ready to be passed to the compiler.
Once a file has been preprocessed, the resulting source file is
compiled, with the working directory set to
configs/<config>/scratch
(which ensures, for example, that all F90 modules can be found by
the compiler).
After the file is compiled, some architectures may require
postprocessing of the object files, for example,some machines
don't allow the use of a "-o" flag for naming the resulting
object file, in which case part of postprocessing would involve
renaming and moving the file.
C14 When trying to create the Cactus executable I get the error
Creating cactus_origin in /data2/convCactus/exe from
CactusBase/IOASCII CactusBase/Boundary CactusPUGH/PUGHInterp
CactusBase/CartGrid3D CactusEinstein/StaticConformal CactusPUGH/PUGHReduce
CactusEinstein/ADMBase CactusBase/Time CactusPUGH/PUGH CactusPUGH/PUGHSlab
CactusBase/IOUtil CactusElliptic/EllBase CactusBase/IOBasic
ld64: ERROR 33 : Unresolved text symbol "SetCartSymVN" -- 1st referenced
by /data2/Cactus/configs/origin/lib/libADMBase.a\
(InitSymBound.c.o)
In this case ADMBase is probably not inheriting from the thorn which
contains the SetCartSymVN function which it is using. When Cactus makes
up the link line order it then doesn't know to list the ADMBase library
before the library containing this function. To test this and/or to get an
executable, find the link line used by issuing
gmake origin SILENT=no
and add the missing library to the end of the link line.
C15 My thorn is calling directly a function from another thorn. Both thorns
are in my ThornList, but on linking I get the error
Startup.c.o(.text+0x4d): undefined reference to `OtherThornsFunction'
Make sure that your thorn inherits from the implementation provided by
the other thorn. If you don't do this, the end link line may not list
the libraries in the right order for linking.
C16 (Linux) When trying the new gcc 3.1.1 compiler, I received a lot of
warnings about the compiler flag "-I/usr/local/include".
This is because HDF5 is installed on this machine in what we
would consider to be a sub-optimal place. HDF5 is preferably
installed in own installation directory with (optionally) sym-links to
the system directories. Cactus configurations should use the HDF5
installation directory itself.
It is a matter of office debate as to whether it would be really be a
good idea or not to check for and remove system directories, we can come
up with pathological examples both if they are left or if they are
removed.
C17 (OpenBSD) The system linker /usr/bin/ld (called by gcc's collect2)
crashes when linking C++ thorns if GNU ar is used to create the
libraries.
collect2: ld terminated with signal 11 [Segmentation fault]
ld: /home/jonathan/cactus/Cactus/configs/test-interp2/lib/ \
libTestInterp2.a(driver.cc.o): unexpected multiple definitions \
of symbol `axis_list::string(void) const', type 0xf
The workaround is to use the system's ar if you have any C++ thorns.
C18 (Linux) When I compile Fortran I get errors because characters
are in the first 5 columns, but I can't see anything wrong in the
source code.
The C preprocessor /lib/cpp distributed with Redhat 7.x causes
problems with Fortran code (Fortran source code is by default
passed through a preprocessor). The C preprocessor can change the
spacings in a file, which is fine for C but can seriously affect
Fortran code. If this is happening, you will see errors such as
************************************************************************
Preprocessing
/Cactus_hydratest/arrangements/CactusPUGH/Interp/src/interp3.F
Compiling
/Cactus_hydratest/arrangements/CactusPUGH/Interp/src/interp3.F
Pacific-Sierra Research vf90 Personal V3.4N5 12:49:17 10/31/01 f90 to f77
subroutine INTERP3_CCTK_REAL
Syntax, line 140: Non-blank characters in columns 1-5 of continuation line
subroutine INTERP3_CCTK_COMPLEX
Syntax, line 319: Non-blank characters in columns 1-5 of continuation line
function LINEAR
function INTERP_QUAD
function CUBIC
gmake[3]: *** [interp3.F.o] Error 16
gmake[2]: *** [make.checked] Error 2
gmake[1]: ***
There are two suggested ways to get around this problem:
1. If you are using Beta 11 or higher, try using the
architecture independent Cactus preprocessor which we are
developing by configuring with
make <config>-config FPP='$${PERL} $${CCTK_HOME}/lib/sbin/cpp.pl'
2. Another way around this problem is to get hold of a copy of
cpp from an earlier RedHat distribution (here is cpp from 6.2)
and either replace the original cpp, or place it somewhere else
and add the option FPP=<location of new cpp> when you configure
Cactus.
C19 (Linux) I get internal errors using the Pacific-Sierra Fortran 90 compiler
The free version of the Pacific Sierra compiler can generate
uncompilable code, this is a problem with the translator. The
error messages look something like:
Compiling
/home/Cactus/arrangements/CactusEinstein/AHFinder/src/AHFinder_pow.F \
Pacific-Sierra Research vf90 Personal V3.4N5 19:44:34 11/20/01 f90 to f77
module F1COM
subroutine POWELL
Warning, line 167:
Too large to translate -- reduce program or loop size (RPNGEN)
Fatal, line 198: Internal error detected -- please report (EXPGET)
Syntax, line 198: Duplicate I/O specifier.
subroutine LINMIN
Warning, line 497:
Too large to translate -- reduce program or loop size (RPNGEN)
function F1DIM
The fix is to either do what the message says and reduce the code
size, or move to a different compiler.
C20 (Linux) I get the linking error "/usr/bin/ld: cannot find -lIEPCF90"
with the Intel Fortran compiler.
If you get the linking error
/usr/bin/ld: cannot find -lIEPCF90
Then you need to append ${IA32ROOT}/lib to your LD_LIBRARY_PATH
environment variable. You can do this directly in your shell setup
file (e.g. .cshrc) or alternatively there is a script
$IA32ROOT/bin/iccvars.csh which does this for you.
C21 (Solaris) Building PUGHReduce under Solaris 2.8 gives several errors
with macro recursion.
Checking status of libPUGHReduce.a
"/home/CCTK/Cactus_beta13/Cactus/arrangements/CactusPUGH/PUGHReduce/src
line 323: CCTK_Cmplx_: macro recursion
This problem occurs only in the dependency generation part of the
Cactus build. The Sun's /lib/cpp preprocessor cannot handle macro
recursion levels of more than 3. Since we are loath to rewrite our
macros just for Solaris, we would rather wait for a better system
preprocessor, or for a fuller version of the Cactus cpp sometime
in the future.
As a solution, you could try using the Cactus preprocessor:
make -config FPP='$${PERL} $${CCTK_HOME}/lib/sbin/cpp.pl'
which has the advantage that it doesn't stop for errors but prints
a warning message. Be wary though, it isn't perfect yet and may
fail for some thorns.
Otherwise, you can keep rerunning your make command to skip past
the problem files (since only the dependency generation is
failing). Of course, dependencies (for just these files), will
then not work.
C22 (MacOS) Compiling with the Absoft F90 compiler I get error messages
about large "fixups"
Compiling /home/Cactus/arrangements/AEIThorns/ADM_BSSN/src/Sources.F
Sources.f:unknown:Fixup of -44148 too large for field width of 16 bits
Sources.f:unknown:Fixup of -42232 too large for field width of 16 bits
Sources.f:unknown:Fixup of -33028 too large for field width of 16 bits
Add the following text to the thorn's make.code.defn file:
ifeq ($(shell uname), Darwin)
F90FLAGS += -N11
endif
C23 How can I see the commands which Cactus is actually using to build
the executable?
Add SILENT=no to the end of the compile command and the actual commands
will be echoed to standard output.
C24 My configuration takes forever to build, are there any ways to speed
this up?
If you are developing and testing, you could build executables without
using optimisation ... but remember that they will run much slower. To
do this configure Cactus with OPTIMISE=no.
C25 On compiling Fortran code I get errors like "dummy argument CCTK_DIM has
not been given a type", but I'm not using CCTK_DIM in the routine?
Look to see if you are passing CCTK_ARGUMENTS into your routine, if so
you need to use DECLARE_CCTK_ARGUMENTS in the declarations for the routine.
C26 I'm passing arguments to my scheduled routine using CCTK_ARGUMENTS and
I get the compile error "identifier DECLARE_CCTK_ARGUMENTS is undefined"
Make sure you have the lines
#include "cctk.h"
#include "cctk_Arguments.h"
at the top of your source file
C27 I have a code block commented out by '#if 0 ... #endif' in a C/C++
routine which uses the DECLARE_CCTK_ARGUMENTS and/or
DECLARE_CCTK_PARAMETERS macro. The compiler stops with a parsing error
on this piece of code.
For C/C++ code, these two macros expand into (a list of) declarations
of local variables, with the same names of the arguments/parameters,
and their initialization statements, plus a single opening curly bracket.
This bracket starts a new block for the statements following the macros.
The matching closing bracket is automatically inserted during the
preprocessing phase by the CST's c_file_preprocessor.pl program at the end
of a routine's body. This is simply determined as the closing bracket
matching the opening bracket of the routine's body.
Because the c_file_preprocessor.pl program is run before $CPP and doesn't
understand $CPP directives itself, it would not correctly detect the end of
the routine's body in the following (legal C code) example:
int bla(void)
{
DECLARE_CCTK_PARAMETERS
#if 0
if (1) {
#endif
return (0);
}
The automatically inserted closing bracket would be added outside of the
routine's body and thus cause a syntax error in the code following.
As a solution, you should make sure that all the statements in your routine
(including those which you have commented out via '#if 0 ... #endif')
are always properly enclosed in blocks of matching curly brackets.
C28 (Linux IA64) I get a segmentation violation compiling snprintf.c in
the Cactus flesh?
Compiling /home/Cactus/src/util//snprintf.c
/home/Cactus/configs/admeccy/build/Cactus/util/snprintf.c
ecc: error: Fatal error in /usr/local/intel/compiler60/ia64/bin/mcpcom,
terminated by segmentation violation
compilation aborted for
/home/Cactus/configs/admeccy/build/Cactus/util/snprintf.c
(code 1)
The Intel C++ compiler (Version 6.0, Build 20020320) has problems
dealing with this file, which needs to be compiled without the -ip
option. Either run gmake with the option SILENT=no then cut and paste
the compile statement to the command line and remove the -ip option
before executing it, and then continue to build the executable as normal.
Alternatively configure with the -O1 option. (Note, so far our benchmarks
have indicated that -O1 actually executes faster than -O3, although this
may be just for our particular benchmarks).
C29 On linking I get an "unresolved text symbol" for a scheduled function
called from libCactusBindings.a
Check the size of the object file which was created for the source
file containing this function in configs/<config>/build/<thorn>.
With some compilers, making object files for complicated source files
can fail because it takes too much memory, and an empty object file
will be created and the make process will fail. If you continue the
make process Cactus will not realise that the object file is empty.
If this is what happened, touch the relevant source file and try
compiling again. It may be that you will need to switch optimisations off
for this file, or split up the troublesome code into smaller components.
C30 (Linux) Using the Intel Fortran compiler I get the error "/usr/bin/ld
cannot find -lintrins" on linking.
Set the environment variable IA32ROOT to point to the location of your
Intel compiler installation (eg /opt/intel/compiler60/ia32). You will
need to reconfigure, and then try building your executable again.
C31 I just want to check that one thorn compiles correctly, can I test
this without compiling all the thorns which come before it?
make <config>-build BUILDLIST="<list of thorns>"
builds thorns in the order they appear in the list. (Note, this does
not link any thorn libraries together).
C32 What is the Cactus preprocessor (Cactus cpp) ?
Part of the pre-processing step for Fortran files involves the use of
a C-preprocessor. On some architectures the native CPP does not
correctly handle spaces in source files, and thus corrupts the
resulting file. On other machines there is no native way to generate
dependency information for files. In an attempt to solve these problems
we have written a replacement of CPP in perl, which you may use for
all Fortran code if you configure with
FPP='$${PERL} $${CCTK_HOME}/lib/sbin/cpp.pl'
or in an options file without the quotes
FPP=$${PERL} $${CCTK_HOME}/lib/sbin/cpp.pl
The Cactus preprocessor may also be used for C files by replacing FPP
with CPP in the above statements.
The Cactus preprocessor is still being developed and improved, known
problems include
- only currently supports #ifdef, #if defined for a single token and
not operations involving more than one token connected by && and ||,
etc
- problems with macros whose overall expansion contains the original
macro name
The Cactus make system does not use the standalone CPP to preprocess C
source files, as the first step of a C compilation involves the use of
a CPP (normally internal). In any case we do not recommend the use of
this perl CPP to process C files, partly due to the above problems, and
partly as the preprocessor does not pre-define certain symbols which
the native preprocessor would..
C33 I'm working on a machine where a compiler problem means that I
need to compile a particular thorn with a lower optimisation level.
Is there an easy way to do this?
Yes, if you want to change the optimisation for one thorn, you can
add to the make.code.defn in the thorn, e.g.
C_OPTIMISE_FLAGS = <new flags>
CXX_OPTIMISE_FLAGS = <new flags>
F77_OPTIMISE_FLAGS = <new flags>
F90_OPTIMISE_FLAGS = <new flags>
These flags will then only apply for the particular thorn. These flags
will be machine/compiler specific, so you only want to add them for
the problematic machine.
C34 How can I make sure that one file is compiled before another? For example
to make sure that an F90 module file "module.F90" is available for other
file "using.F90".
Add dependency declarations to the thorn's make.code.deps file, for example
using.F90.o: module.F90.o
Note that you have to use the source file names and append the suffix ".o".
This convention is different from the default Makefile rules.
C35 I started building a Cactus configuration and it asked me if
I wanted to edit the thornlist, I pressed 'y' and then 'enter'
but nothing happened?
Cactus uses the program defined by the standard EDITOR environment
variable as an editor at this point, check that this variable is
defined and is actually a working editor.
C36 (Linux) Compiling Cactus with Redhat 8 or 9 with Intel compilers my build
fails in CactusBase/IOUtil because configure failed to find <sys/stat.h>
Intel supports their compilers only for RedHat 7.x, and gives no guarantees
for their compilers to work properly with newer releases. On RH 8/9.x there
is a problem with the include order of system header files with the new
glibc (you should see this in your configuration's config.log file) and
some other header needs to be included before <sys/stat.h>. The same
problem occurs with Debian Sarge.
One way to fix this is to ask your sys admin to edit the corresponding
Intel header file, or wait until Intel provides a patch. As a starting
point, here is a diff which worked for one user ...
--- /opt/intel/compiler70/ia32/substitute_headers/sys/stat.h~ 2003-05-09 20:45:49.000000000 +0200
+++ /opt/intel/compiler70/ia32/substitute_headers/sys/stat.h 2003-09-23 23:26:42.000000000 +0200
@@ -27,10 +27,17 @@
#include <bits/types.h> /* For __mode_t and __dev_t. */
-#ifdef __USE_XOPEN
-# define __need_time_t
-# include <time.h> /* For time_t. */
+#if defined __USE_XOPEN || defined __USE_MISC
+# ifdef __USE_XOPEN
+# define __need_time_t
+# endif
+# ifdef __USE_MISC
+# define __need_timespec
+# endif
+# include <time.h> /* For time_t resp. timespec. */
+#endif
+#ifdef __USE_XOPEN
/* The Single Unix specification says that some more types are
available here. */
# ifndef __dev_t_defined
C37 Why can't I use different F90 and F77 compilers with Cactus?
Because Cactus does some automatic name mangling to allow you to call
Fortran routines from C and vice-versa, and different compilers will use
different conventions for the way that they generate routine names in
the object files. This means that you would only be able to use different
compilers for F90 and F77 if they used the same conventions. In
principle we could check to make sure that they are compatible, but for
now we require you to use the same compiler for both F77 and F90 code.
------------------------------------------------------------------------------
Running:
D1 I'm trying to run Cactus with MPI using "mpirun", but I just get an error
"Unknown option -np", what's the problem?
It looks like the MPI implementation on the machine you're using isn't
removing its arguments correctly, so they are being passed to the
Cactus run. You need to use the "-i" command line option for Cactus to
ignore the MPI arguments, e.g.
mpirun ./cactus_foo foobar.par -i -np 8
D2 I'm running Cactus on a parallel system with missing C++ libraries on some
nodes. Cactus compiles but it won't run. Is there anything I can do?
If C++ isn't being used in any thorn, you can compile Cactus without using
C++ using the configure option CXX=none.
D3 I can build a Cactus configuration using some external libraries such as
HDF5 or PETSc without any problems but when I run the executable I get
the following error:
./cactus_WaveDemo: error while loading shared libraries: libhdf5.so.0:
cannot load shared object file: No such file or directory
This is a problem with using shared libraries on your system:
the dynamic loader couldn't locate a shared library on the system
you are trying to run on.
You can set the LD_LIBRARY_PATH environment variable in your shell setup
to point to your local installation of HDF5. For global installations
located in a standard place (such as /usr/local/lib), this should ideally
be done by your system administrator for you.
Another possibility to get around the above problem is to use
static libraries in favor of shared ones. For this you need to remove
the *.so files from your installation directory (leaving the *.a files).
Cactus would then link against the static libraries automatically.
D4 I can run my non-MPI executable using shared libraries without problems now
but still get the same error as in FAQ D3 for MPI jobs started with mpirun.
This indicates a misconfigured mpirun script. When it starts a shell on
other nodes it probably doesn't read in the user's shell setup so that the
LD_LIBRARY_PATH environment is not set properly.
You should contact your system administrator to get this fixed.
D5 I'm using the web server thorn CactusConnect/HTTPD on an Irix machine, I
compiled with PTHREADS=yes to get better response, but the executable
just hangs (even with the httpd::use_pthreads="no" in the parameter file)
SGI/Irix machines with native MPI cannot make use of Pthreads (the native
MPI uses some Irix threads which are incompatible with Pthreads), and the
executable hangs on the first call to a pthread routine.
You could instead use MPICH on your Irix machine instead of native MPI.
Note that native MPI will probably be better optimised for you application
than MPICH though.
D6 I get a segmentation fault running Cactus, right after the schedule
tree is printed to screen?
Check to see if you are passing CCTK_ARGUMENTS into any routines
registered at CCTK_STARTUP, if so these need to be removed and void
used instead. The STARTUP timebin is run before the driver sets up
any grid variables, and the segmentation fault occurs in
CCTK_DECLARE_ARGUMENTS when these undefined variables are accessed.
Parameters can however be used in STARTUP routines.
D7 (Linux) I'm using the NaNChecker thorn and seeing very strange results.
There is a bug in the isnan function with the Fortran Intel
compiler (for IA32 and IA64). This bug means that any thorn using
isnan (for example CactusUtils/NaNChecker) will produce
inconsistent results.
D8 (Linux) The testsuites for CactusEinstein/AHFinder and
CactusBench/BenchADM fail for me, but the release notices say that they
pass.
The Absoft Fortran compiler (Version 6) produces the wrong answers
for CactusEinstein/AHFinder and CactusBench/BenchADM if
optimisation is not used.
D9 How do I run Cactus until a given coordinate time instead of to a
given iteration number?
Instead of setting cactus::cctk_itlast set cactus::cctk_final_time to
the required coordinate time, and also set cactus::terminate = "time".
D10 Output to screen using the Info IO method of IOBasic doesn't work.
I want to watch min/max values for 'wavetoy::phi' during a cactus run
on stdout. For that, I added
IOBasic::outInfo_every = 10
IOBasic::outInfo_vars = "wavetoy::phi"
to my parameter file. Thorn IOBasic is active, but I only get the
iteration number and coordinate time printed to screen.
You need to activate a thorn which implements the min/max reductions,
for example CactusPUGH/PUGHReduce.
D11 I get an error saying "CCTK_Equals: First string null".
The routine CCTK_Equals tries to look at the value of a keyword or
a string parameter. The value "null" indicates that this
parameter has never been set.
The problem could be that Cactus mis-detected the way the Fortran
compiler does its name mangling. The linker then creates two
tables that contain parameter values, where one is set by the
flesh and the other is accessed by Fortran code.
Try to re-configure your application, perform a "make
CONFIG-realclean", and then recompile.
D12 I have a Cactus executable compiled with MPI. When running it on a single
processor (without using mpirun) I get an error saying "Unable to open
parameter file ...".
If you built Cactus with the ch_p4 device of the MPICH distribution
and then execute the program directly (without using mpirun), it will
start in the directory where the executable resides.
If you specified a relative path to your parameter file Cactus would
start searching for it from that directory (rather than the directory
you are currently working in) and then potentially not find it.
The solution is to never run an MPICH ch_p4 executable directly but
always use mpirun. This will make sure that the program will start
in your current working directory.
------------------------------------------------------------------------------
Thorn Writing:
E1 While implementing some MPI code in Cactus, I came across the problem of
getting an MPI communicator. I basically have the choice between using
MPI_COMM_WORLD, assuming that no processors have been set aside by the
driver, or tying myself to a certain driver, such as PUGH, and using the
driver's internal data structures. Both choices are clearly not
desirable.
We are aware of this, and in fact, it is the reason why some of the
I/O thorns are directly dependent on the PUGH driver.
The solution for all this will be the Cactus Communication
Infrastructure (CCI: http://www.cactuscode.org/Development/Specs/CCI.txt)
which will eventually be integrated into the flesh and will provide a
generic function interface for communicating data.
Thus when you plug in different communication drivers, I/O thorns
won't need to be changed if they use the CCI routines.
E2 How can I communicate the value of a local scalar on one processor to all
processors? There doesn't seem to be an API for this in Cactus.
There isn't a general broadcast API in Cactus at the moment, this is
planned as part of a new Cactus Communication Interface (CCI) layer
in the 4.1 release (see the Specs web page for more information about
this).
Until then, the best way to communicate your variable is to use the the
CCTK reduction API. For example, make a call to CCTK_ReduceLocalScalar()
with the "sum" reduction operator, and set your local variable to zero
on all processors except for the one with the value you want to have
communicated.
E3 What about if I only want to send a local scalar to a single processor?
This type of point-to-point communication is not possible with Cactus
APIs right now. Any CCTK_Reduce*() is a global communication so far,
and all processors must take part in that communication.
For doing point-to-point communication you should use the appropriate API
of an underlying communication layer like MPI.
E4 Why shouldn't I make direct calls to MPI from my thorns? Your default
driver uses MPI.
Keeping all MPI calls in the driver thorn keeps the code modular, allowing
for you to use alternate drivers when they become available, for example
using PVM or some other communication layer.
Also, since not all underlying MPI implementations provide the same
Fortran bindings it is best to use a C wrapper for making MPI calls,
and this is automatically done for you if you use the Cactus APIs.
E5 I am writing a thorn, what is the difference between using
"const cGH *cctkGH" and "cGH *cctkGH" for argument declarations?
And what about "const cGH* const cctkGH"?
'cGH *' is a pointer to a cGH structure which can be modified. This is
necessary eg. in routines which initialize a cGH.
'const cGH *' is a pointer to a cGH structure which is marked as
constant (i.e. read-only). The code is not allowed to change the cGH
using such a pointer. The compiler should refuse to compile it otherwise,
or at least print a warning.
Our policy now is to use "const cGH*" for all CCTK_ calls, and it is
recommended that this is also implemented in all thorns. (It is being
implemented in all the released Cactus thorns, but you may still find
some exceptions).
[Note: August 2002: We have still to implement const cGH* in a few
CCTK_ calls, namely
* calls to CCTK_Sync()
* calls to CCTK_Reduce()
* calls to CCTK_Interp() (the old API)
and it is still a matter of debate whether the const qualifier
should be used for CCTK_Sync calls.]
Finally, the additional const qualifier in 'const cGH * const GH' says
that the pointer variable itself cannot be changed (it's just a
one-time-only assignment). For instance, no pointer arithmetic is
allowed on such a pointer. In principle, one could declare all local
variables as const if they aren't changed afterwards. But it's doesn't
have any benefit in writing cleaner code. I think this is just
overkill and using just 'const cGH *' is fine.
E6 On compiling Fortran code I get errors like "dummy argument CCTK_DIM has
not been given a type", but I'm not using CCTK_DIM in the routine?
Check if you have passed CCTK_ARGUMENTS in the argument list for the
routine, is do you must have a line
DECLARE_CCTK_ARGUMENTS
in your declarations section.
E7 If I have two grid array groups with identical sizes (and ghost zones,
distributions, etc.), are they guaranteed to be distributed in the same
way? That is, can I count on the fact that their local shapes (lsh)
will be the same? It is true empirically. What if the grid arrays have
different variable types or numbers of time levels?
Yes to all.
E8 Is there anyway to only compile certain lines of source code if a
particular thorn is in the compiled ThornList?
Yes, but this is not a good idea for a number of reasons
- it adds hidden dependencies between thorns, and can easily lead to
unexpected and hard to track down behaviour when a thorn is compiled
but not active
- it breaks all kinds of modularity infrastructure in Cactus
- the include file you need to use will cause your source code to be
recompiled when other thorns change
But if you insist, and accept the consequences, this is how you do it,
Include the header file cctk_DefineThorn.h
In your code use
#ifdef ARRANGEMENTNAME_THORNNAME
<your source code>
#endif
If appropriate, to give yourself some protection, use the function
CCTK_IsThornActive to only execute the source code if the thorn was
actually activated (and not just compiled in).
Add a comment to your README/Documentation.tex to remind yourself, and
others of what you have done.
E9 How can I find out in make.configuration.defn, whether MPI is being
used or not? The thorn EllPETSc checks whether the makefile variable
MPI_LIBS is empty. This doesn't work on systems where using MPI does
not require any explicitely specified libraries, such as when using the
mpicc script to compile. Is there a better way?
You can grep for MPI in the file
configs/<your_config>/config-data/cctk_Extradefs.h
see for example CactusPUGHIO/IOPanda/src/make.configuration.deps
if test -z "`grep CCTK_MPI $(CONFIG)/cctk_Extradefs.h`" ; then
echo "IOPanda requires MPI"; \
exit 2; \
fi
E10 How can I see in source code whether MPI is being used?
Check whether the preprocessor macro CCTK_MPI exists, for example,
#ifdef CCTK_MPI
/* Only included if MPI is being used */
#else
/* Only included if MPI is *not* being used */
#endif
E11 The functions CCTK_Exit and CCTK_Abort require cctkGH as an argument.
How can I call these functions deep inside my thorns where this pointer
is not available?
These routines are overloaded by a driver, and the reason for passing
in a cctkGH is to allow the driver to tidy up before exiting. If the
particular driver you are using allows a NULL pointer to be passed you
can pass this instead of the cctkGH pointer. (The worst that will happen
should be a segfault if the driver cannot handle NULL). Alternatively,
you need to include a mechanism to obtain the cctkGH deep inside your
thorns code.
E12 I'm getting wierd syntax errors in Fortran code, with an extra
garbage character (often $ or &) stuck in the middle of a CCTK_INFO()
or CCTK_WARN() or CCTK_EQUALS() call after it has been processed.
You have probably used Fortran (either 77 or 90) line continuation
in a macro call
c example of broken Fortran code fragment
if (CCTK_EQUALS(test,"on")) then
test_state = 1
else if (CCTK_EQUALS(test,
$ "off")) then
test_state = 3
end if
The $ is in column 6 is the Fortran 77 standard way of doing
a line continuation. This doesn't work, because CCTK_EQUALS()
is a macro, and macros use C lexical conventions (regardless of
what language your code is written in). To continue a line in a
macro, use the same technique you would in C, i.e. put a backslash
( \ ) at the end of the line to be continued (note there must *not*
be any whitespace after the \ !!). For example, the above code
should be written
c example of valid Fortran code fragment
if (CCTK_EQUALS(test,"on")) then
test_state = 1
else if (CCTK_EQUALS(test, \
"off")) then
test_state = 0
end if
E13 I want to write the value of a KEYWORD parameter in Fortran code to
a file, but nothing I try works.
Cactus KEYWORD and STRING parameters are not stored as Fortran strings
(they are pointers to C strings) so you need to convert them first.
Use the routine CCTK_FortranString to copy them to a locally defined
Fortran string, then you can manipulate them as usual. If you just
want to print the value to the standard output there is also the
routine CCTK_PrintString.
E14 I write my thorns with Fortran, do you have any general advice?
Yes. Read the section "Fortran Thorn Writers" in the Users Guide, and
follow these general recommendations
- use IMPLICIT NONE in your Cactus subroutines and functions, this
will help in finding errors at compile time.
E15 In my Fortran thorn the value of a Cactus integer parameter is totally
wrong when I print it, but when I print it from C it is fine.
Check that you remembered to add DECLARE_CCTK_PARAMETERS to the
declaration area of the subroutine.
E16 I write my thorns with C, do you have any general advice?
Yes, hopefully this list will grow, but for now
- don't use C++ comments (//) in C code this will cause difficulties
on some platforms
E17 Why is it that when I schedule more than one routine in the same thorn
at ANALYSIS only the first routine is executed and the second one is
ignored?
Are you triggering on different variables with the two routines? If
not, it doesn't matter which thorns they come from, only the first
scheduled routine will be called. This is part of the special design of
the ANALYSIS bin.
E18 Is there a way to synchronize individual grid variables in a group?
Not at the moment. This was a design decision partly to be able to
support "compact" groups of variables in the future (that is, groups
where the group members at any grid point are stored contiguously in
memory ... compared to the "normal" way we have now where each group
member is stored as a different array). With compact groups synchronizing
single members would be more computationally expensive. Currently
the infrastructure is mainly built around the concept of groups of
variables, and changing this would involve changes to the driver
interface.
E19 Is there a way to synchronize just one time level of a grid variable?
Right now only one time level is sychronized, that is the "current" level.
Other time levels cannot be synchronized and are assumed to be fixed
or read only.
E20 I'm using the CCTK_ParameterSet function to change a parameter, but
after calling it the parameters value doesn't change?
First make sure that you really want to change a parameters value and
that you really know what you are doing. In general parameters are
fixed thoughout a run, and should only be changed by steering thorns.
If you change a parameter with CCTK_ParameterSet it won't change in
the routine you call it from, because the DECLARE_CCTK_PARAMETERS
macro currently expands to define all a thorns parameters as local
variables with a const qualifier (in C) and sets them to the current
values of the parameters. Thus calling CCTK_ParameterSet will not
affect the value of the local copy.
------------------------------------------------------------------------------
General
F1 Why do I have to use e.g. "mpirun -np 1 ./exe/cactus_myconfig -O" to see
the compiled parameters, can't the parameters be output before MPI is
initialised?
Alas some MPIs add their own command-line options, so we need to do
MPI_Init before parsing the command line, or parse it twice, once before
the MPI_Init and once after, to detect invalid options.
F2 Why isn't a BOOLEAN parameter a LOGICAL in Fortran?
There is no way we can guarantee the way the Fortran logical type is
represented at machine level, and since all Fortran variables need
to be mapped internally to C data structures, we use integers to ensure
portability.
F3 Why is there an MPI call in the Flesh (MPI_Init)? I thought that the
Cactus flesh was independent of any parallel protocol, why isn't this
call made from a driver thorn?
We would love to get rid of the last remaining MPI calls from the flesh,
unfortunately in MPI 1, MPI implementations are allowed to play around
with the argument list, so we need to call MPI_Init before parsing the
command line argument, and this makes it very difficult to have it
called from the driver, since we don't even know what the parameter
file is at that stage, so we don't even know which driver to activate!
MPI 2 allows NULL to be passed to MPI_Init, which gets around the
problem, but the only machines currently with MPI 2 are Japanese
supercomputers.
It is the only MPI call made before the driver is activated, and it
sets a global variable to tell you it's been done, so it isn't a
major problem apart from being extremely ugly. You can even turn
it off with an environment variable, but then if you run with MPICH
you'll find the code complaining about unknown command line arguments
like -p4grp. If we had a precise list of the arguments passed by each
MPI implementation we could guard against them, but that's an even
uglier option.
F4 Is there any way to tell what CVS version of individual source files
was used to build an executable?
Actually there is, just issue the Unix command:
strings cactus_<config> | grep Header
to see all the version information for all source files, and
strings cactus_<config> | grep Header | grep <filename>
to look for a particular file.
(Note that this only works for files using the CCTK_FILEVERSION macro.)
F5 Why is the main routine of Cactus written in C++ (src/main/flesh.cc) when
the rest of the flesh is standard ANSI C? More strangely, why does Cactus
still compile when I have no C++ compiler on my system?
The main routine of the flesh is written in C++, since any static C++
classes need to be initialised before the main routine is called. So if
there is a C++ compiler available we use this for compiling flesh.cc.
Since we use only ANSI C in flesh.cc, if there is no C++ compiler
available on your machine (and so you are not trying to compile any thorns
containing C++), we use the C compiler instead.
F6 Are there grid scalars of type STRING ?
No, there is only a CCTK_CHAR type. You can however define an array
with DISTRIB=CONSTANT with a maximum length.
F7 Why don't you use compilers mpicc, mpiCC etc when they exist on parallel
machines?
The compilers mpicc etc are scripts for compilation which are site
dependent and whose contents can change. The major reason we don't
use these is that in general it is difficult to work out what
underlying compiler is being used, which in turn leads to problems
adding the correct compilation flags.
So far we have found it more convenient and transparent to manually add
libraries and options to the configure system than to rely on
mpicc behaving well on all platforms. At some point we will be
reinvestigating this.
F8 How does Cactus manage to so seamlessly call Fortran routines from
C, and vice versa?
Part of the configuration step on a machine involves automatically
deducing the convention which the fortran compiler uses for its symbols
(for example, upper or lower case and the addition of underscores).
This information is then used to construct the macros which are used
at preprocessing to translate Fortran names to C-callable routines.
We also use macros to facilitate passing strings from Fortran into
C. Strings must always be at the end of argument lists for this
(which is why some of our choices of order in argument lists may
seem strange), and the architecture details of string passing are
maintained in the file src/include/cctk_FortranString.h. At the moment
we have macros for one, two or three strings in an argument list.
F9 The documentation says that Cactus parameters are read-only, but I
can trivially change the value of a parameter in the Fortran source
code of my thorn.
Although changing parameters in Fortran is possible (we haven't thought
of an easy way to enforce read-only parameters) it is not supported and
should not be done!
------------------------------------------------------------------------------
Documentation:
G1 How can I build the ThornGuide documentation for single thorns or
arrangements?
Give the names of the thorns or arrangements on the make line, e.g.
gmake ThornGuide THORNS="CactusBase/Boundary"
gmake ThornGuide ARRANGEMENTS="CactusBase"
G2 I have a configuration with over ten thorns, but when I make the
ThornGuide I only see the first few of them.
It could be that the documentation in one of the thorns is not
following the Cactus ThornGuide coding convention, for example
see the file doc/ThornGuide/template.tex.
------------------------------------------------------------------------------
I/O:
H1 I want to run an old parameter file, but none of the I/O parameters are
recognised!
In Beta 13 the "old" I/O parameter names were finally fully removed in
favour of "new" more consister parameter names across the I/O thorns in
the computational toolkit. A complete list of I/O parameters which
changed is contained in the following mail:
http://www.cactuscode.org/archives_html/users/msg00278.html
Note that there is a perl script for which can automatically update
parameter files for these changes.
http://www.cactuscode.org/Development/Release/FixParametersForBETA13.pl
H2 I would like to use checkpointing for a thorn which has complex grid
arrays. I tried to use the IOFlexIO thorn and received the error:
Unsupported CCTK variable datatype 10. Is there a way to checkpoint
complex variables?
Yes there is: use IOHDF5 instead of IOFlexIO. The FlexIO library doesn't
support a native complex datatype, and we decided not to add extra logic
complex numbers in IOFlexIO. HDF5 does not have this limitation, it
natively supports all Cactus datatypes.
------------------------------------------------------------------------------
Configuration Files:
I1 The size of array parameters is specified by a integer number in the
param.ccl file. Why can't a parameter itself be used here?
The size of the array has to be fixed at compile time to accomodate
the use of parameters in Fortran thorns.
LocalWords: Absoft fixups endif snprintf libCactusBindings lintrins cpp
|