[FLASH-USERS] CCSN doesn't compile as is?
Sean Couch
smc at flash.uchicago.edu
Fri Jul 29 16:09:46 EDT 2016
Hi Marco,
In your Makefile.h, make sure you have your F90FLAGS such that:
F90FLAGS = -I ${HDF5_PATH}/include -DH5_USE_16_API
and LIB_HDF5 should also include the fortran flag such that:
LIB_HDF5 = -L${HDF5_PATH}/lib -lhdf5_fortran -lhdf5 -lz
Try that and let me know if it compiles! It should… I think… But there has been some significant code drift.
Sean
> On Jul 29, 2016, at 3:20 AM, Marco Limongi <marco.limongi at oa-roma.inaf.it> wrote:
>
> Dear Sean,
>
> I am trying to test the CCSN with FLASH4.3.
> In the following the sequence of operations I am doing:
>
> setup:
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> stars at lucifero:~/discoNAS/FLASH/FLASH4.3$ ./setup CCSN -auto -1d +spherical -objdir ccsn1d -nxb=16 threadBlockList=False +pm4dev threadWithinBlock=False +newMpole +uhdopt
> Processing Shortcut file:
> /home/stars/discoNAS/FLASH/FLASH4.3/bin/setup_shortcuts.txt
>
> ***WARNING*** Ignoring unknown shortcut +uhdopt while expanding .
>
> checking for needed files and directories
> checking sites Aliases file
> site directory for site lucifero not found;
> using prototype Linux
> generating default Units file
> Driver/DriverMain/Split
> Grid/GridBoundaryConditions
> Grid/GridMain/paramesh/interpolation/Paramesh4/prolong
> Grid/GridMain/paramesh/interpolation/prolong
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/headers
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/mpi_source
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/source
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/utilities/multigrid
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/flash_avoid_orrery
> Grid/GridSolvers/Multipole_new
> Grid/localAPI
> IO/IOMain/hdf5/serial/PM
> IO/localAPI
> PhysicalConstants/PhysicalConstantsMain
> RuntimeParameters/RuntimeParametersMain
> Simulation/SimulationMain/CCSN
> flashUtilities/contiguousConversion
> flashUtilities/general
> flashUtilities/interpolation/oneDim
> flashUtilities/nameValueLL
> flashUtilities/sorting/quicksort
> flashUtilities/system/memoryUsage/legacy
> monitors/Logfile/LogfileMain
> monitors/Timers/TimersMain/MPINative
> physics/Eos/EosMain/Nuclear/kernel
> physics/Eos/localAPI
> physics/Gravity/GravityMain/Poisson/Multipole
> physics/Hydro/HydroMain/split/PPM/PPMKernel
> physics/Hydro/localAPI
> physics/RadTrans/RadTransMain/NeutrinoLeakage
> physics/RadTrans/localAPI
> physics/sourceTerms/Deleptonize/DeleptonizeMain
> physics/sourceTerms/Deleptonize/localAPI
> scanning /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/Units file for included
> units
> Driver/DriverMain/Split
> Grid/GridBoundaryConditions
> Grid/GridMain/paramesh/interpolation/Paramesh4/prolong
> Grid/GridMain/paramesh/interpolation/prolong
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/headers
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/mpi_source
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/source
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/PM4_package/utilities/multigrid
> Grid/GridMain/paramesh/paramesh4/Paramesh4dev/flash_avoid_orrery
> Grid/GridSolvers/Multipole_new
> Grid/localAPI
> IO/IOMain/hdf5/serial/PM
> IO/localAPI
> PhysicalConstants/PhysicalConstantsMain
> RuntimeParameters/RuntimeParametersMain
> Simulation/SimulationMain/CCSN
> flashUtilities/contiguousConversion
> flashUtilities/general
> flashUtilities/interpolation/oneDim
> flashUtilities/nameValueLL
> flashUtilities/sorting/quicksort
> flashUtilities/system/memoryUsage/legacy
> monitors/Logfile/LogfileMain
> monitors/Timers/TimersMain/MPINative
> physics/Eos/EosMain/Nuclear/kernel
> physics/Eos/localAPI
> physics/Gravity/GravityMain/Poisson/Multipole
> physics/Hydro/HydroMain/split/PPM/PPMKernel
> physics/Hydro/localAPI
> physics/RadTrans/RadTransMain/NeutrinoLeakage
> physics/RadTrans/localAPI
> physics/sourceTerms/Deleptonize/DeleptonizeMain
> physics/sourceTerms/Deleptonize/localAPI
> Computing default values for options not specified on command line
> Using Makefile.h: /home/stars/discoNAS/FLASH/FLASH4.3/sites/Prototypes/Linux/Makefile.h
> generating Makefile
> SUCCESS
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>
> make:
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> ……
> ……
> /usr/local/mpich//bin/mpif90 -ggdb -c -O2 -fdefault-real-8 -fdefault-double-8 -Wuninitialized -DMAXBLOCKS=1000 -DNXB=16 -DNYB=1 -DNZB=1 -DN_DIM=1 readtable.F90
> readtable.F90:28.6:
>
> use hdf5
> 1
> Fatal Error: Can't open module file 'hdf5.mod' for reading at (1): No such file or directory
> make: *** [readtable.o] Error 1
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> I have installed HDF5 with Fortran (gfortran) binding, in fact I could find hdf5.mod in /usr/local/hdf5/include.
> After copying hdf5.mod from /usr/local/hdf5/include to ccsn1d/ and recompiled again, I got the following linking error:
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:51: undefined reference to `__h5lib_MOD_h5open_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:53: undefined reference to `__h5f_MOD_h5fopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:59: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:60: undefined reference to `__h5d_provisional_MOD_h5dread_integer_scalar'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:61: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:68: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:69: undefined reference to `__h5d_provisional_MOD_h5dread_integer_scalar'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:70: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:77: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:78: undefined reference to `__h5d_provisional_MOD_h5dread_integer_scalar'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:79: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:90: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:91: undefined reference to `__h5_dble_interface_MOD_h5dread_double_1'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:92: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:98: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:99: undefined reference to `__h5_dble_interface_MOD_h5dread_double_1'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:100: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:105: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:106: undefined reference to `__h5_dble_interface_MOD_h5dread_double_1'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:107: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:147: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:148: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:149: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:152: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:153: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:154: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:157: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:158: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:159: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:162: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:163: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:164: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:167: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:168: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:169: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:172: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:173: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:174: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:177: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:178: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:179: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:182: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:183: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:184: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:189: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:190: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:191: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:195: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:196: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:197: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:201: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:202: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:203: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:207: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:208: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:209: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:214: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:215: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:216: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:220: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:221: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:222: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:226: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:227: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:228: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:232: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:233: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:234: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:240: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:241: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:242: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:246: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:247: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:248: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:253: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:254: undefined reference to `__h5_dble_interface_MOD_h5dread_double_3'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:255: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:260: undefined reference to `__h5d_MOD_h5dopen_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:261: undefined reference to `__h5_dble_interface_MOD_h5dread_double_scalar'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:262: undefined reference to `__h5d_MOD_h5dclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:270: undefined reference to `__h5f_MOD_h5fclose_f'
> /home/stars/discoNAS/FLASH/FLASH4.3/ccsn1d/readtable.F90:272: undefined reference to `__h5lib_MOD_h5close_f'
> collect2: error: ld returned 1 exit status
> make: *** [flash4] Error 1
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Can anybody help me?
> Maybe I did not understand exactly what it is meant for HDF5 library with Fortran bindings.
>
> Thank you,
> Marco
>
>
>
>> On Jul 29, 2014, at 8:22 PM, Sean Couch <smc at flash.uchicago.edu <mailto:smc at flash.uchicago.edu>> wrote:
>>
>> Hi Hava,
>>
>> In its current incarnation, the Nuclear EOS on which CCSN depends requires an HDF5 library with the Fortran bindings built in. If you do not need the Nuclear EOS (i.e., you aren't doing actually stellar core collapse simulations) then you can get rid of the Nuclear EOS and it should compile. Or, rebuild your HDF5 library with Fortran bindings.
>>
>> Sean
>>
>>
>> --------------------------------------------------------
>> Sean M. Couch
>> Hubble Fellow
>> Flash Center for Computational Science
>> Department of Astronomy & Astrophysics
>> The University of Chicago
>> 5747 S Ellis Ave, Jo 315
>> Chicago, IL 60637
>> (773) 702-3899
>> www.flash.uchicago.edu/~smc <http://www.flash.uchicago.edu/~smc>
>>
>>
>>
>>>
>>> On Jul 29, 2014, at 1:10 PM, Hava Turkakin <turkakin at ualberta.ca <mailto:turkakin at ualberta.ca>> wrote:
>>>
>>>> Hi
>>>> I am trying to compile CCSN and getting following error? Can anybody
>>>> help me with this?
>>>> *********************************************************************************************************
>>>> readtable.F90(6): error #7013: This module file was not generated by
>>>> any release of this compiler. [HDF5]
>>>> use hdf5
>>>> ------^
>>>> readtable.F90(15): error #6683: A kind type parameter must be a
>>>> compile-time constant. [HID_T]
>>>> integer(HID_T) file_id,dset_id,dspace_id
>>>> ----------^
>>>> readtable.F90(16): error #6683: A kind type parameter must be a
>>>> compile-time constant. [HSIZE_T]
>>>> integer(HSIZE_T) dims1(1), dims3(3)
>>>> ----------^
>>>> readtable.F90(31): error #6404: This name does not have a type, and
>>>> must have an explicit type. [H5F_ACC_RDONLY_F]
>>>> call h5fopen_f (trim(adjustl(eos_filename)), H5F_ACC_RDONLY_F, file_id, error)
>>>> -----------------------------------------------^
>>>> readtable.F90(38): error #6404: This name does not have a type, and
>>>> must have an explicit type. [H5T_NATIVE_INTEGER]
>>>> call h5dread_f(dset_id, H5T_NATIVE_INTEGER, nrho, dims1, error)
>>>> --------------------------^
>>>> readtable.F90(69): error #6404: This name does not have a type, and
>>>> must have an explicit type. [H5T_NATIVE_DOUBLE]
>>>> call h5dread_f(dset_id, H5T_NATIVE_DOUBLE, logrho, dims1, error)
>>>> --------------------------^
>>>> compilation aborted for readtable.F90 (code 1)
>>>> gmake: *** [readtable.o] Error 1
>>>> ***************************************************************************
>>>> Thank you
>>>> --
>>>> Hava Turkakin
>>>> PhD Candidate
>>>> University of Alberta
>>>> Space Physics Research Group
>>>
>>
>
> ******************************************
> Dr. Marco Limongi
> INAF - Osservatorio Astronomico di Roma
> Via Frascati 33, I-00040
> Monteporzio Catone, Rome, Italy
> Tel: 0039-06-94286-443
> Fax: 0039-06-9447-243
> email: marco.limongi at oa-roma.inaf.it <mailto:marco.limongi at oa-roma.inaf.it>
> Skype Internet Phone User : Marco Limongi
> Web Page: http://www.oa-roma.inaf.it/limongi/ <http://www.oa-roma.inaf.it/limongi/>
> ORCID ID: 0000-0003-0636-7834
> ******************************************
>
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