Frequently Asked Questions

Please send suggestions and questions for the FAQ to the CactusMaint mailing list.

The Questions:

Configuring and Building
Running
Thorn Writing
General
Documentation
1. How can I build the ThornGuide documentation for single thorns or arrangements?
2. I have a configuration with over ten thorns, but when I make the ThornGuide I only see the first few of them.
I/O
1. I want to run an old parameter file, but none of the I/O parameters are recognised!
2. 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
1. 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

Configuring and Building
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.
2. Compilation of Cactus fails with the error: identifier “DECLARE_CCTK_PARAMETERS” is undefined?
  
  You need to include the header: #include "cctk_Parameters.h”
3. (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.
4. 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
5. 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.
6. 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.
7. (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.
8. How do I compile Cactus in 32 bit mode on a 64 bit irix machine?
  
  gmake <config>-config IRIX_BITS=32
9. 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
10. 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.
11. 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>
12. 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.
13. 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.
14. 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.
15. 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.
16. (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.
17. (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.
18. (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'
  1. 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.
19. (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.
20. (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.
21. (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.
22. (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
23. 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.
24. 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.
25. 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.
26. 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
27. 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.
28. (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).
29. 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.
30. (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.
31. 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).
32. 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..
33. 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.
34. 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.
35. 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.
36. (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
```
37. 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.
38. What can I do about __builtin errors reported by Intel 9.0?
  
  This problem is solved with the Intel 9.1 compilers. The rest of this is for those who are still using Intel 9.0.
  
  The documentation for Intel 9.0 C/C++ claims only that it is compatible with Gcc 3.x; in fact Intel 9.0 is not compatible with Gcc 4.x. It tries to read the Gcc C++ header files, but fails in the case of Gcc 4.x
  
  We have submitted a feature request to Intel, and we hear that they intend to fix the problem in the 9.1 release. Until then, configure with
  
  SYS_INC_DIRS = /opt/intel/compiler90/include/c++ LD = icpc -L/opt/intel/compiler90/lib/ -lcprts -lunwind -lcxa
  
  (where the paths point to your Intel compiler installation, of course). This will cause the compiler to use its own C++ header files, and associated libraries.
Running
1. 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
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. (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.
8. (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.
9. 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".
10. 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.
11. 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.
12. 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
1. 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) 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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
10. 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
11. 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.
12. 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
```
13. 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.
14. 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.
15. 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.
16. 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
17. 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.
18. 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.
19. 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.
20. 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
1. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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
1. 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"
2. 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
1. 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 this mail message
  
  Note that there is a perl script for which can automatically update parameter files for these changes.
  
  FixParametersForBETA13.p
2. 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
1. 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

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