path: root/doc/FAQ

Cactus Code Frequently Asked Questions

$Header: /mnt/data2/cvs2svn/cvs-repositories/Cactus/doc/FAQ,v 1.37 2002-07-30 15:11:25 allen Exp $

Also available at http://www.cactuscode.org/Documentation/FAQ

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1. 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.

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2. Compilation of Cactus fails with the error:
	 identifier "DECLARE_CCTK_PARAMETERS" is undefined?

   You have to include the header: 
	#include "cctk_Parameters.h"

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3. 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 seperate these files, 
   e.g. into bin and lib directories.

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4. 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.

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5. 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 toplevel 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.

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6. 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 

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7. 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.
   
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8. 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.

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9. On my SUN I start a configuration process with gmake, but on the second 
    gmake it wants to set up the configuration again and again .... 
    Why is this ?

    You are using a version of gmake which is too outdated (even though
    this version may pefectly work on other architectures). We found
    that GNU Make version 3.79 works fine.

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10. How do I compile Cactus in 32 bit mode on a 64 bit irix machine?

    gmake <config>-config IRIX_BITS=32

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11. 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

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12. 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. 

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13. 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

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14. 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.

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15. 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.

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16. 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). You should try and remove any single apostrophes in 
    Fortran comments for now, or use gmake twice.

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17. 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.)

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18. 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 at the Release web pages 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

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19a. 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.

19b. 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.
    
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20. Why can'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.

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21. 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>
    
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22. 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.

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23. 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.

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24. 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 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 No. 18.

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25. 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.

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26. 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.

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27. 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.

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28. I can run my non-MPI executable using shared libraries without problems now
    but still get the same error as in FAQ 27 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.

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29. 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.

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30. 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.

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31. Compiling files in Cactus seems to involve three steps, preprocessing,
    compiling, and then postprocessing. What is the postprocessing step
    for? 

    This is for architecture dependent things which come up. For example,
    some machines don't allow using a "-o" flag for naming the resulting
    object file, in which case part of postprocessing would involve
    renaming and moving the file.

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32. 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.

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33. 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)

    Probably ADMBase is 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. 

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34. 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.

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35. 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.

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36. 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.

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