[FLASH-USERS] looking for help

[Zhang Chao]

Dear Dean and all,

Thank you for the advice in the last email.

I really use different users when I run the setup and gmake. Yesterday I 
thought it would be ok. But now, you are right.

The following is the last part of my gmake. There is a “warning”, do you 
think it is ok?

/opt/hdf-1.6.5/lib/libhdf5.a(H5FDstream.o): In function `H5FD_stream_open':
H5FDstream.c:(.text+0x1207): warning: Using 'gethostbyname' in statically 
linked applications requires at runtime the shared libraries from the glibc 
version used for linking
SUCCESS


After the step of gmake, I type “./flash3” in the object/ directory. It 
just tells me that:

[walli at localhost object]$ ./flash3
Segmentation fault

So it is a new problem. I am sorry that I met lots of problems when I use 
the Flash Code.

Can anyone help me about it??


Best wishes,
Zhang Chao


--------------------------------------------------
From: "Dean Townsley" <Dean.M.Townsley at ua.edu>
Sent: Friday, June 17, 2011 1:38 AM
To: "Zhang Chao" <walli1986 at hotmail.com>
Cc: <flash-users at flash.uchicago.edu>
Subject: Re: [FLASH-USERS] looking for help

> Hi Zhang,
>
> I don't think anything in flash (at least in the core modules) uses the
> C++ compiler (mpiCC) so don't worry about that.
>
> The problem you are having now looks like a simple unix permissions
> problem. Did you run the setup as a different user than you are running
> gmake?
>
> You apparently made it past this point before in order to get the
> compiler errors from your previous email.
>
> You might want to save your Makefile.h and start over from a fresh tree
> in case something has gotten messed up.
>
> I hope you can figure it out,
> Dean
>
> On 06/16/2011 02:34 AM, Zhang Chao wrote:
>> Dear Dean and Shravan,
>>
>> Thank you for the help.
>>
>> I would like to thank Dean especially, because I learn a lot from your
>> email.
>> But now I meet a new problem, I follow the User’s guide, create a new
>> folder (named my hostname) in the sites/ directory and create a
>> Makefile.h.
>>
>>
>> This time I want to ask 2 problems.
>> Firstly, in the Makefile.h, there is a path “CPPCOMP =
>> /opt/software/mpich2-gnu/bin/mpiCC”. But I cannot find “mpiCC” in my
>> computer. There are “mpif90”and “mpicc” in the computer.
>>
>> Secondly, when I type “gmake” in the object/ directory, the error
>> comes out.
>> Here is the error:
>>
>> [walli at localhost object]$ gmake
>> Calculating dependencies
>> ./setup_depends.py --generateINTERMEDIATElines -c -O2 -fdefault-real-8
>> -fdefault-double-8 -ffree-line-length-none -I /opt/hdf-1.6.5/include
>> -O2 -c *.f *.f90 *.F90 *.F
>> Traceback (most recent call last):
>> File "./setup_depends.py", line 257, in ?
>> main()
>> File "./setup_depends.py", line 133, in main
>> ofd = file("Makefile.Depend","w")
>> IOError: [Errno 13] Permission denied: 'Makefile.Depend'
>> rm: cannot remove `.success': Permission denied
>> gmake: *** [printflags] Error 1
>>
>>
>>
>> I really don’t know how to deal with this. Could anyone help me about
>> this?
>>
>>
>> Best wish,
>>
>> Zhang Chao
>>
>>
>>
>> The following is my Makefile.h
>> I just change the “HDF5_PATH”, “NCMPI_PATH”, “FCOMP”, “CCOMP”,
>> “CPPCOMP”, “LINK”
>>
>> # FLASH makefile definitions for ix86-64 Linux (gfortran compiler)
>>
>> #----------------------------------------------------------------------------
>>
>> # Set the HDF/HDF5 library paths -- these need to be updated for your
>> system
>> #----------------------------------------------------------------------------
>>
>> HDF4_PATH =
>> HDF5_PATH = /opt/hdf-1.6.5
>>
>> ZLIB_PATH =
>>
>> PAPI_PATH =
>> PAPI_FLAGS =
>>
>> NCMPI_PATH = /opt/software/parallel-netcdf-1.0.2
>> MPE_PATH =
>>
>> #----------------------------------------------------------------------------
>>
>> # Compiler and linker commands
>> #
>> # Use the MPICH wrappers around the compilers -- these will automatically
>> # load the proper libraries and include files. Version of MPICH prior
>> # to 1.2.2 (?) do not recognize .F90 as a valid Fortran file extension.
>> # You need to edit mpif90 and add .F90 to the test of filename
>> extensions,
>> # or upgrade your MPICH.
>> #----------------------------------------------------------------------------
>>
>> FCOMP = /opt/software/mpich2-gnu/bin/mpif90
>> CCOMP = /opt/software/mpich2-gnu/bin/mpicc
>> CPPCOMP = /opt/software/mpich2-gnu/bin/mpiCC
>> LINK = /opt/software/mpich2-gnu/bin/mpif90
>>
>> # pre-processor flag
>> PP = -D
>>
>> #----------------------------------------------------------------------------
>>
>> # Compilation flags
>> #
>> # Three sets of compilation/linking flags are defined: one for optimized
>> # code, one for testing, and one for debugging. The default is to use the
>> # _OPT version. Specifying -debug to setup will pick the _DEBUG version,
>> # these should enable bounds checking. Specifying _TEST is used for
>> # flash_test, and is set for quick code generation, and (sometimes)
>> # profiling. The Makefile generated by setup will assign the generic
>> token
>> # (ex. FFLAGS) to the proper set of flags (ex. FFLAGS_OPT).
>> #----------------------------------------------------------------------------
>>
>>
>> FFLAGS_OPT = -c -O2 -fdefault-real-8 -fdefault-double-8
>> -ffree-line-length-none
>> FFLAGS_DEBUG = -g -c -fdefault-real-8 -fdefault-double-8
>> -ffree-line-length-none
>> FFLAGS_TEST = -c -fdefault-real-8 -fdefault-double-8
>> -ffree-line-length-none
>>
>> F90FLAGS =
>>
>> CFLAGS_OPT = -O2 -c
>> CFLAGS_DEBUG = -g -c
>> CFLAGS_TEST = -c
>>
>> # if we are using HDF5, we need to specify the path to the include files
>> CFLAGS_HDF5 = -I ${HDF5_PATH}/include
>>
>> CFLAGS_NCMPI = -I$(NCMPI_PATH)/include
>>
>> #----------------------------------------------------------------------------
>>
>> # Linker flags
>> #
>> # There is a seperate version of the linker flags for each of the _OPT,
>> # _DEBUG, and _TEST cases.
>> #----------------------------------------------------------------------------
>>
>>
>> LFLAGS_OPT = -static -o
>> LFLAGS_DEBUG = -g -o
>> LFLAGS_TEST = -o
>>
>>
>> #----------------------------------------------------------------------------
>>
>> # Library specific linking
>> #
>> # If a FLASH module has a 'LIBRARY xxx' line in its Config file, we
>> need to
>> # create a macro in this Makefile.h for LIB_xxx, which will be added
>> to the
>> # link line when FLASH is built. This allows us to switch between
>> different
>> # (incompatible) libraries. We also create a _OPT, _DEBUG, and _TEST
>> # library macro to add any performance-minded libraries (like fast math),
>> # depending on how FLASH was setup.
>> #----------------------------------------------------------------------------
>>
>>
>> LIB_OPT =
>> LIB_DEBUG =
>> LIB_TEST =
>>
>> LIB_HDF4 = -lmfhdf -ldf -ljpeg -lz
>> LIB_HDF5 = -L ${HDF5_PATH}/lib -lhdf5 /usr/lib64/libz.a
>>
>> LIB_PAPI =
>> LIB_MATH = -ldfftw -ldrfftw
>>
>> LIB_MPI =
>> LIB_NCMPI = -L $(NCMPI_PATH)/lib -lpnetcdf
>> LIB_MPE =
>>
>> #----------------------------------------------------------------------------
>>
>> # Additional machine-dependent object files
>> #
>> # Add any machine specific files here -- they will be compiled and linked
>> # when FLASH is built.
>> #----------------------------------------------------------------------------
>>
>>
>> MACHOBJ =
>>
>>
>> #----------------------------------------------------------------------------
>>
>> # Additional commands
>> #----------------------------------------------------------------------------
>>
>>
>> MV = mv -f
>> AR = ar -r
>> RM = rm -f
>> CD = cd
>> RL = ranlib
>> ECHO = echo
>>
>>
>>
>> --------------------------------------------------
>> From: "Dean Townsley" <Dean.M.Townsley at ua.edu>
>> Sent: Thursday, June 16, 2011 2:44 AM
>> To: "Zhang Chao" <walli1986 at hotmail.com>
>> Cc: <flash-users at flash.uchicago.edu>
>> Subject: Re: [FLASH-USERS] looking for help
>>
>>> Hi Zhang,
>>>
>>> It looks like your compiler flags are probably not appropriate for your
>>> compiler.
>>>
>>> Assuming that you are using a gnu compiler stack (i.e. gfortran) the
>>> flags I use are:
>>>
>>> FFLAGS_OPT = -c -O3 -fdefault-real-8 -fdefault-double-8
>>> -ffree-line-length-none
>>> FFLAGS_DEBUG = -g -Warray-bounds -c -fdefault-real-8 -fdefault-double-8
>>> -ffree-line-length-non
>>> e
>>> FFLAGS_TEST = -c -fdefault-real-8 -fdefault-double-8
>>> -ffree-line-length-none
>>>
>>> These are basically the same as those in the
>>> sites/Prototypes/Linux/Makefile.h.gfortran file included with the
>>> distribution. If you are using gnu compilers, you should take that as
>>> your starting point for getting a working Makefile.h rather than the
>>> plain sites/Prototypes/Linux/Makefile.h one.
>>>
>>> I hope that helps.
>>>
>>> Dean
>>>
>>> On 06/14/2011 10:14 PM, Zhang Chao wrote:
>>>> Dear all,
>>>> I am new to the flash code. when I follow the user's guide. I met lots
>>>> of questions.
>>>> First, when I type "./setup Sedov -auto", "cd object" and "gmake", the
>>>> error came out
>>>> [walli at localhost object]$ gmake
>>>> rm -f reorder.sh
>>>> /opt/software/mpich2-gnu/bin/mpif90 -c -O2 --tp4 -CcdRR8
>>>> -DMAXBLOCKS=1000 -DNXB=8 -DNYB=8 -DNZB=1 -DN_DIM=2
>>>> ut_interpolationInterface.F90
>>>> gfortran: unrecognized option '-CcdRR8'
>>>> cc1: error: unrecognized command line option "-ftp4"
>>>> gmake: *** [ut_interpolationInterface.o] Error 1
>>>> a part of my Makefile.h is that:
>>>> #----------------------------------------------------------------------------
>>>>
>>>> # Set the HDF/HDF5 library paths -- these need to be updated for your
>>>> system
>>>> #----------------------------------------------------------------------------
>>>>
>>>>
>>>> HDF5path = /opt/hdf-1.6.5
>>>> MPIpath = /opt/software/mpich2-gnu
>>>> PAPI_PATH =
>>>> PAPI_FLAGS =
>>>> ZLIB_PATH =
>>>> NCMPI_PATH = /opt/parallel-netcdf-1.0.2
>>>> MPE_PATH =
>>>> #----------------------------------------------------------------------------
>>>>
>>>> # Compiler and linker commands
>>>> #
>>>> # We use the f90 compiler as the linker, so some C libraries may
>>>> explicitly
>>>> # need to be added into the link line.
>>>> #----------------------------------------------------------------------------
>>>>
>>>> FCOMP = ${MPIpath}/bin/mpif90
>>>> CCOMP = gcc
>>>> CPPCOMP = gcc
>>>> LINK = ${MPIpath}/bin/mpif90
>>>>
>>>> # pre-processor flag
>>>>
>>>> PP = -D
>>>> FFLAGS_OPT = -c -O2 --tp4 -CcdRR8
>>>> FFLAGS_DEBUG = -c -g --trace --trap --chk[aes] -CcdRR8
>>>> FFLAGS_TEST = -c -CcdRR8
>>>> should I change the "FFLAGS_OPT, FFLAGS_DEBUT, FFLAGS_TEST"?
>>>> I really don't know how to do this. Can anybody help me?
>>>> Best wishes,
>>>> Zhang Chao
>>>
>>
>