[FLASH-USERS] flash2.5 in kraken

[John ZuHone]

Hi Diego,

.DS_Store files are files that Mac OS X creates for its HFS+ filesystem. Did you copy over the FLASH directory tree from OS X? If so, you need to delete these files manually because the FLASH 2.5 setup script is not savvy enough to avoid them. 

You will need to load the hdf5 module, and if you are going to run on many processors it should be the hdf5-parallel module:

module load hdf5-parallel

or for serial:

module load hdf5

Depending on what compiler you are using, you may need to load the compiler module as well. I think PGI is the default, but there are also GNU and Intel, I believe. 

Best,

John

On Jul 10, 2012, at 3:56 PM, Diego wrote:

> Hi John, I'ts Diego once more... I am sorry to bother you, but I am new to kraken. 
> 
> I am trying to get flash (version 2.5) running in kraken, but the sedov shock test tube problem is not even able to compile.
> 
> I already have flash2.5 in my home directory and now I want to make sure thet the sedov test tube is working fine. For this I put the Makefile.h in the correspondent sites directory (diego/flash2.5/source/sites/krakenpf9.nics.utk.edu).
> I checked your Makefile.h and its basically the same as what I had before... supposedly leaving the paths blank the wrapper would manage to find the HD5 and mpi. 
> FCOMP   = ftn
> CCOMP   = cc
> CPPCOMP = CC
> LINK    = ftn
> 
> The problem is that when I compile the sedov test tube problem (./setup sedov -auto) I have an error.
> 
> It says:
> --------------------------------------------------------------
> diego at krakenpf1:~/flash2.5> ./setup sedov -autochecking for needed files and directories
>     checking sites Aliases file
>         couldn't open sites Aliases file
>     site directory for site krakenpf1.nics.utk.edu not found;
>     using prototype Linux
> generating default Modules file
>     renaming original to Modules.bak
> removing old links in build directory object
> scanning /nics/b/home/diego/flash2.5/Modules file for included modules
>     database/amr/paramesh2.0
>     driver/time_dep
>     gravity/null
>     hydro/explicit/split/ppm
>     io/amr/hdf5_serial
>     materials/eos/gamma
>     mesh/amr/paramesh2.0/second_order_old
>     util/tools
>     util/wrapping
> checking for default sub-modules in included modules
> checking that no mutually exclusive sub-modules are included together
> looking for paths of non-included modules
> .DS_Store is not a valid directory
> --------------------------------------------------------------
> 
> Can you help me with this problem?
> 
> Or before doing the ./setup sedov -auto do I have to load any module (or modules)?
> 
> Thanks.
> 
> Diego

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