Galacticus on N-body merger trees

[abensonca]

Original report by Io Odderskov (Bitbucket: ioodderskov, GitHub: ioodderskov).

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I have made a minimal installation of Galacticus v0.9.4, and I am now trying to get it to run on merger trees from N-body simulations (calculated with the Consistent Trees code).

In the Galacticus manual (on page 154), it is mentioned that for an example of how to create trees in Galacticus format, one can look at the example in "tests/nBodyMergerTrees", which runs on trees from the Millennium project.

It looks as though the example is deprecated (for example, the file "scripts/aux/Run_Galacticus.pl", which is referred to in the "ReadMe" is not included in Galacticus version 0.9.4), but from line 73 in the script "getMillenniumTrees.pl", I take that the syntax required to create the trees are:

make Simple_Merger_Tree_File_Maker.exe
Simple_Merger_Tree_File_Maker.exe input_trees.csv output_trees.hdf5

However, the make-command fails. The output is:

#!bash




gfortran -c ./work/build/ISO_Varying_String/iso_varying_string.p.F90 -o ./work/build/ISO_Varying_String/iso_varying_string.o -ffree-line-length
-none -frecursive -J./work/build/ -I./work/build/  -fintrinsic-modules-path /usr/local/finclude -fintrinsic-modules-path /usr/local/include/gfo
rtran -fintrinsic-modules-path /usr/local/include -fintrinsic-modules-path /usr/lib/gfortran/modules -fintrinsic-modules-path /usr/include/gfor
tran -fintrinsic-modules-path /usr/include -fintrinsic-modules-path /usr/finclude -fintrinsic-modules-path /usr/lib64/gfortran/modules -pthread
 -Wall -g -fbacktrace -ffpe-trap=invalid,zero,overflow -g -O3 -ffinite-math-only -fno-math-errno -fopenmp
./work/build/ISO_Varying_String/iso_varying_string.p.F90:2648.4:
    class(varying_string), intent(inout) :: string
    1
Error: Unclassifiable statement at (1)
./work/build/ISO_Varying_String/iso_varying_string.p.F90:2650.24:
    if (allocated(string%chars)) deallocate(string%chars)
                        1
Error: Syntax error in argument list at (1)  
./work/build/ISO_Varying_String/iso_varying_string.p.F90:2656.4:
    class(varying_string), intent(inout) :: string
    1
Error: Unclassifiable statement at (1)
./work/build/ISO_Varying_String/iso_varying_string.p.F90:2661.15:
    call string%destroy()
               1
Error: Syntax error in CALL statement at (1)  
./work/build/ISO_Varying_String/iso_varying_string.p.F90:2662.16:
    open(newUnit=iUnit,file=fileName,status='old',access='stream',ioStat=ioErro
                1
Error: Syntax error in OPEN statement at (1)  
./work/build/ISO_Varying_String/iso_varying_string.p.F90:2664.19:
    allocate(string%chars(fileSize))
                   1
Error: Syntax error in ALLOCATE statement at (1)
./work/build/ISO_Varying_String/iso_varying_string.p.F90:2670.10:
          string%chars(iChar)=thisChar
          1
Error: Unclassifiable statement at (1)
./work/build/ISO_Varying_String/iso_varying_string.p.F90:2646.31:
  subroutine destroy_VS (string)
                               1
Error: Symbol 'string' at (1) has no IMPLICIT type
./work/build/ISO_Varying_String/iso_varying_string.p.F90:2654.37:
  subroutine load_from_file_VS(string,fileName)
                                     1
Error: Symbol 'string' at (1) has no IMPLICIT type
./work/build/ISO_Varying_String/iso_varying_string.p.F90:61.14:
     procedure :: destroy => destroy_VS
              1
Error: Argument 'string' of 'destroy_vs' with PASS(string) at (1) must be of the derived-type 'varying_string'
./work/build/ISO_Varying_String/iso_varying_string.p.F90:67.14:
     procedure :: loadFromFile => load_from_file_VS
              1
Error: Argument 'string' of 'load_from_file_vs' with PASS(string) at (1) must be of the derived-type 'varying_string'
scripts/build/preprocess.pl source/utility.command_arguments.F90 ./work/build/utility.command_arguments.p.F90
Can't locate File/Slurp.pm in @INC (@INC contains: ./perl /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at perl/Galacticus/Build/SourceTree.pm line 14.
BEGIN failed--compilation aborted at perl/Galacticus/Build/SourceTree.pm line 14.
Compilation failed in require at scripts/build/preprocess.pl line 12.
make: *** [work/build/utility.command_arguments.p.F90] Error 2

Is this the correct way to use the Simper_Merger_Tree_File_Maker program? And if so, do you have an idea about what goes wrong?

[abensonca]

Original comment by Andrew Benson (Bitbucket: abensonca, GitHub: abensonca).

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Thanks for pointing out the out of date information in the ReadMe - that will get fixed.

The errors when you try to make Simple_Merger_Tree_File_Maker.exe suggest that you're using a gfortran that is too old. If you used the Galacticus installation script to do a minimal install you should have a newer gfortran installed, but it will be in whatever path you told the install script to install to. You'll need to be sure that your PATH environment is set to include the relevant directory containing the new gfortran executable. The install script gives an option to add commands to your .cshrc or .bashrc to do this for you - if you allowed it to do this simply typing "galacticus094" should set the environment variables for you - otherwise you'll need to do this manually.

You can tell which version of gfortran you're using by typing:

gfortran -v

If you have the correct one installed the version should be 6.0 or higher.

[abensonca]

Original comment by Io Odderskov (Bitbucket: ioodderskov, GitHub: ioodderskov).

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Thank you, that seemed to solve the problem.