[Hdf-forum] Best Way to Patch HDF5 1.8.17 to compile with nagfor

Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] matthew.thompson at nasa.gov
Fri Aug 19 08:11:10 CDT 2016


On 08/18/2016 02:35 PM, Scot Breitenfeld wrote:
>
>> On Aug 18, 2016, at 11:01 AM, Thompson, Matt (GSFC-610.1)[SCIENCE
>> SYSTEMS AND APPLICATIONS INC] <matthew.thompson at nasa.gov
>> <mailto:matthew.thompson at nasa.gov>> wrote:
>>
>> On 08/16/2016 02:33 PM, Scot Breitenfeld wrote:
>>> Hi,
>>>
>>> I’ve fixed the issue in 1.8 and the fix will be in the next release of
>>> 1.8, or you can try checking out 1.8 from svn,
>>>
>>> https://svn.hdfgroup.uiuc.edu/hdf5/branches/hdf5_1_8
>>>
>>> Also, we don’t have access to a NAG compiler, so if you can compile 1.8,
>>> run the fortran tests (i.e. in the fortran directory, issue “make
>>> check”), and report back any issues then that would be great.
>>
>> Scot,
>>
>> I downloaded the 1.8 SVN and ran into the same issue:
>
>>
>>> make[4]: Entering directory
>>> `/gpfsm/dswdev/mathomp4/Baselibs/TmpBaselibs/GMAO-Baselibs-5_0_2-NAG/src/hdf5-1.8-svn/fortran/test'
>>>  FC       tf_F03.lo
>>> NAG Fortran Compiler Release 6.0(Hibiya) Build 1064
>>> Error: tf_F03.f90, line 128: Implicit type for SIZEOF in H5_SIZEOF_DP
>>> Error: tf_F03.f90, line 128: Implicit type for SIZEOF in H5_SIZEOF_SP
>>> Error: tf_F03.f90, line 128: Implicit type for SIZEOF in H5_SIZEOF_I
>>> Error: tf_F03.f90, line 128: Implicit type for SIZEOF in H5_SIZEOF_CHR
>>> Error: tf_F03.f90, line 128: Implicit type for SIZEOF in H5_SIZEOF_CMPD
>>> [NAG Fortran Compiler pass 1 error termination, 5 errors]
>>
>> It looks to me like the SVN tf_F03.f90 is identical to that in 1.8.17.
>> So this is expected, I suppose.
>
> I’m sorry, I did not update the Makefile.in, it should now compile
> tf_F08.F90 instead.

I did an 'svn update' and, huzzah!, it built. It still dies in the same 
place in the tests though:

> ============================
> Fortran API: Testing  fortranlib_test_F03
> ============================
> Fortran API:  fortranlib_test_F03  Test Log
> ============================
> Runtime Error: Invalid edit descriptor for integer i/o-list item
> Program terminated by I/O error on internal file
>                         ==============================
>                               FORTRAN 2003 tests
>                         ==============================
>  FORTRANLIB_TEST is linked with HDF5 Library version 1.8 release  18
>
>  Testing 1-D Array of Compound Datatypes Functionality                  PASSED
>  Testing 1-D Array of Compound Array Datatypes Functionality            PASSED
>  Testing 3-D array by dataset, using C_LOC                              PASSED
>  Testing writing/reading enum dataset, using C_LOC                      PASSED
>  Testing enumeration conversions                                        PASSED
>  Testing writing/reading bitfield dataset, using C_LOC                  PASSED
>  Testing writing/reading opaque datatypes, using C_LOC                  PASSED
>  Testing writing/reading object references, using C_LOC                 PASSED
>  Testing writing/reading region references, using C_LOC                 PASSED
>  Testing writing/reading variable-length datatypes, using C_LOC         PASSED
>  Testing writing/reading variable-string datatypes, using C_LOC         PASSED
>  Testing variable-string write/read, using h5dwrite_f/h5dread_f         PASSED
>  Testing writing/reading string datatypes, using C_LOC                  PASSED
> Command terminated by signal 6
> 0.01user 0.01system 0:00.04elapsed 52%CPU (0avgtext+0avgdata 7380maxresident)k
> 0inputs+0outputs (0major+5953minor)pagefaults 0swaps
> make[4]: *** [fortranlib_test_F03.chkexe_] Error 1


****** 1.10 ******

>
> I think I fixed the issue in trunk, can you try it again? If that does
> not work then can you send the config.log file. I would be interested in
> the lines of output from configure:
>
> checking if Fortran compiler supports intrinsic SIZEOF... yes
> checking if Fortran compiler supports intrinsic C_SIZEOF... yes
> checking if Fortran compiler supports intrinsic STORAGE_SIZE... yes
> checking if Fortran compiler supports intrinsic module
> ISO_FORTRAN_ENV... yes
> checking for Fortran INTEGER KINDs... {1,2,4,8,16}
> checking for Fortran REAL KINDs... {4,8,10,16}
> checking for Fortran REALs maximum decimal precision... 33
> checking sizeof of native KINDS...
> checking for Fortran INTEGER KINDs... {1,2,4,8,16}
> checking for Fortran REAL KINDs... {4,8,10,16}
> checking for Fortran REALs maximum decimal precision... 33
> checking sizeof of available INTEGER KINDs... {1,2,4,8,16}
> checking sizeof of available REAL KINDs... {4,8,16,16}
> checking if Fortran compiler supports intrinsic C_LONG_DOUBLE... yes
> checking if Fortran C_LONG_DOUBLE is different from C_DOUBLE... yes
> checking for Fortran interoperable KINDS with C... {4,8,10,16}
> checking whether we are using the GNU C++ compiler… yes

Well, it died again, but slightly differently:

> make[4]: Entering directory `/gpfsm/dswdev/mathomp4/Baselibs/TmpBaselibs/GMAO-Baselibs-5_0_2-NAG/src/hdf5-1.10-trunk/fortran/src'
>   CC       H5match_types.o
> H5match_types.c: In function ‘main’:
> H5match_types.c:163:7: warning: unused variable ‘found_long_double’ [-Wunused-variable]
>    int found_long_double = 0;
>        ^~~~~~~~~~~~~~~~~
>   CCLD     H5match_types
> ./H5match_types
> make  install-am
> make[5]: Entering directory `/gpfsm/dswdev/mathomp4/Baselibs/TmpBaselibs/GMAO-Baselibs-5_0_2-NAG/src/hdf5-1.10-trunk/fortran/src'
>   PPFC     H5fortran_types.lo
> libtool: compile:  mpifort -I. -I../../src -I../../src -I../../fortran/src -fpp -mismatch_all -c H5fortran_types.F90 -o H5fortran_types.o
> NAG Fortran Compiler Release 6.0(Hibiya) Build 1064
> [NAG Fortran Compiler normal termination]
>   PPFC     H5f90global.lo
> libtool: compile:  mpifort -I. -I../../src -I../../src -I../../fortran/src -fpp -mismatch_all -c H5f90global.F90 -o H5f90global.o
> NAG Fortran Compiler Release 6.0(Hibiya) Build 1064
> [NAG Fortran Compiler normal termination]
>   PPFC     H5_ff.lo
> libtool: compile:  mpifort -I. -I../../src -I../../src -I../../fortran/src -fpp -mismatch_all -c H5_ff.F90 -o H5_ff.o
> NAG Fortran Compiler Release 6.0(Hibiya) Build 1064
> Error: H5_ff.F90, line 396: Implicit type for FORTRAN_INTEGER_8
>        detected at FORTRAN_INTEGER_8@)
> Warning: H5_ff.F90, line 424: Symbol FORTRAN_INTEGER_8 referenced but never set
> [NAG Fortran Compiler pass 1 error termination, 1 error, 1 warning]
> make[5]: *** [H5_ff.lo] Error 1

Perhaps this is due to NAG's weirdness (kind(0.0d0) is 2, not 8). Here 
is the bit of the configure run, and find attached the config.log:

> checking if Fortran compiler supports intrinsic SIZEOF... no
> checking if Fortran compiler supports intrinsic C_SIZEOF... no
> checking if Fortran compiler supports intrinsic STORAGE_SIZE... yes
> checking if Fortran compiler supports intrinsic module ISO_FORTRAN_ENV... yes
> checking for Fortran INTEGER KINDs... {1,2,3,4}
> checking for Fortran REAL KINDs... {1,2,3}
> checking for Fortran REALs maximum decimal precision... 31
> checking sizeof of native KINDS...
> checking for Fortran INTEGER KINDs... {1,2,3,4}
> checking for Fortran REAL KINDs... {1,2,3}
> checking for Fortran REALs maximum decimal precision... 31
> checking sizeof of available INTEGER KINDs... {1,2,4,8}
> checking sizeof of available REAL KINDs... {4,8,16}
> checking if Fortran compiler supports intrinsic C_LONG_DOUBLE... no
> checking if Fortran C_LONG_DOUBLE is different from C_DOUBLE... no
> checking for Fortran interoperable KINDS with C... {1,2,3}
> checking whether we are using the GNU C++ compiler... yes


> BTW, you can find a script at
>
> https://github.com/HDFGroup/build_hdf5/blob/master/preinstall_hdf5.sh
>
> which will automatically download and install (locally) all the packages
> needed to successfully run autogen.sh.

Yup. That looks like most of what I got. I actually grabbed the latest 
m4 as well. :)

Matt

-- 
Matt Thompson, SSAI, Sr Scientific Programmer/Analyst
NASA GSFC,    Global Modeling and Assimilation Office
Code 610.1,  8800 Greenbelt Rd,  Greenbelt,  MD 20771
Phone: 301-614-6712                 Fax: 301-614-6246
http://science.gsfc.nasa.gov/sed/bio/matthew.thompson
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